content stringlengths 4 1.04M | lang stringclasses 358 values | score int64 0 5 | repo_name stringlengths 5 114 | repo_path stringlengths 4 229 | repo_licenses listlengths 1 8 |
|---|---|---|---|---|---|
package {
public class Test {
}
}
/* NOTE: This is not the actual source to this test.
*
* This is just a tribute. The actual source is in test-0 and this file (as
* well as the accompanying FLA) is provided purely for reference only.
*
* The AS3 compiler in modern versions of Adobe Animate does not allow
* generating references to the package-internal specializations of Vector, so
* this code will yield runtime errors if compiled normally.
*
* Instead, compile the test, disassemble the resulting ABC (using rabcasm),
* and open the PackageInternalNs("__AS3__.vec") namespace in each access to
* the Vector$... classes. After reassembling and running the movie you should
* be able to get debug output (at least in Scout).
*/
trace("///Vector$int === Vector.<int>");
trace(Vector$int === Vector.<int>);
trace("///Vector$uint === Vector.<uint>");
trace(Vector$uint === Vector.<uint>);
trace("///Vector$double === Vector.<Number>");
trace(Vector$double === Vector.<Number>);
trace("///Vector$object === Vector.<Object>");
trace(Vector$object === Vector.<Object>);
trace("///Vector$object === Vector.<*>");
trace(Vector$object === Vector.<*>); | ActionScript | 4 | Sprak1/ruffle | tests/tests/swfs/avm2/vector_legacy/Test.as | [
"Apache-2.0",
"Unlicense"
] |
function fibR(n)
{
if (n < 2) return n;
return (fibR(n-2) + fibR(n-1));
}
local function fibI(n)
{
local last = 0;
local cur = 1;
n = n - 1;
while(n)
{
--n;
local tmp = cur;
cur = last + cur;
last = tmp;
}
return cur;
}
loadfile("profile.nut")()
print("fibonacci loop: " + profile_it(20, function() {fibI(6511134)}) + "\n");
print("fibonacci recursive: " + profile_it(20, function() {fibR(31)}) + "\n");
| Squirrel | 3 | profelis/daScript | examples/profile/tests/squirrel/fib.nut | [
"BSD-3-Clause"
] |
create {
source {
git {
repo: "https://r8.googlesource.com/r8"
tag_pattern: "%s-dev"
}
patch_dir: "patches"
}
build {
dep: "chromium/third_party/jdk"
# gradle cannot be executed correctly under docker env
no_docker_env: true
}
}
upload {
pkg_prefix: "chromium/third_party"
universal: true
}
| PureBasic | 3 | zealoussnow/chromium | third_party/r8/3pp/3pp.pb | [
"BSD-3-Clause-No-Nuclear-License-2014",
"BSD-3-Clause"
] |
package com.baeldung.comparison.shiro;
import java.sql.Connection;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authc.AuthenticationInfo;
import org.apache.shiro.authc.AuthenticationToken;
import org.apache.shiro.authc.SimpleAuthenticationInfo;
import org.apache.shiro.authc.UnknownAccountException;
import org.apache.shiro.authc.UsernamePasswordToken;
import org.apache.shiro.authz.AuthorizationInfo;
import org.apache.shiro.authz.SimpleAuthorizationInfo;
import org.apache.shiro.realm.jdbc.JdbcRealm;
import org.apache.shiro.subject.PrincipalCollection;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class CustomRealm extends JdbcRealm {
private Logger logger = LoggerFactory.getLogger(CustomRealm.class);
private Map<String, String> credentials = new HashMap<>();
private Map<String, Set<String>> roles = new HashMap<>();
private Map<String, Set<String>> permissions = new HashMap<>();
{
credentials.put("Tom", "password");
credentials.put("Jerry", "password");
roles.put("Jerry", new HashSet<>(Arrays.asList("ADMIN")));
roles.put("Tom", new HashSet<>(Arrays.asList("USER")));
permissions.put("ADMIN", new HashSet<>(Arrays.asList("READ", "WRITE")));
permissions.put("USER", new HashSet<>(Arrays.asList("READ")));
}
@Override
protected AuthenticationInfo doGetAuthenticationInfo(AuthenticationToken token) throws AuthenticationException {
UsernamePasswordToken userToken = (UsernamePasswordToken) token;
if (userToken.getUsername() == null || userToken.getUsername()
.isEmpty() || !credentials.containsKey(userToken.getUsername())) {
throw new UnknownAccountException("User doesn't exist");
}
return new SimpleAuthenticationInfo(userToken.getUsername(), credentials.get(userToken.getUsername()), getName());
}
@Override
protected AuthorizationInfo doGetAuthorizationInfo(PrincipalCollection principals) {
Set<String> roles = new HashSet<>();
Set<String> permissions = new HashSet<>();
for (Object user : principals) {
try {
roles.addAll(getRoleNamesForUser(null, (String) user));
permissions.addAll(getPermissions(null, null, roles));
} catch (SQLException e) {
logger.error(e.getMessage());
}
}
SimpleAuthorizationInfo authInfo = new SimpleAuthorizationInfo(roles);
authInfo.setStringPermissions(permissions);
return authInfo;
}
@Override
protected Set<String> getRoleNamesForUser(Connection conn, String username) throws SQLException {
if (!roles.containsKey(username)) {
throw new SQLException("User doesn't exist");
}
return roles.get(username);
}
@Override
protected Set<String> getPermissions(Connection conn, String username, Collection<String> roles) throws SQLException {
Set<String> userPermissions = new HashSet<>();
for (String role : roles) {
if (!permissions.containsKey(role)) {
throw new SQLException("Role doesn't exist");
}
userPermissions.addAll(permissions.get(role));
}
return userPermissions;
}
}
| Java | 4 | DBatOWL/tutorials | apache-shiro/src/main/java/com/baeldung/comparison/shiro/CustomRealm.java | [
"MIT"
] |
(defun parse-argv (args)
(flet ((parse-int-value (option value)
(handler-case (parse-integer value)
(error (e)
(error "Invalid value for ~S: ~S~% ~A" option value e)))))
(loop for option = (pop args)
for value = (pop args)
while option
if (not (starts-with option "--"))
do (error "Invalid option: ~S" option)
else
if (equal option "--address")
append (list :address value)
else
if (equal option "--port")
append (list :port (parse-int-value option value))
else
if (equal option "--worker")
append (list :worker-num (parse-int-value option value))
else
do (error "Unknown option: ~S" option))))
| Common Lisp | 4 | xsoheilalizadeh/FrameworkBenchmarks | frameworks/Lisp/woo/helpers/parse-argv.lisp | [
"BSD-3-Clause"
] |
/* Driver for the DS2411 unique ID chip.
*
* @author: Andreas Koepke <koepke@tkn.tu-berlin.de>
* @author: Brad Campbell <bradjc@umich.edu>
*/
#include "ds2411.h"
module Ds2411P {
provides {
interface ReadId48;
}
uses {
interface OneWireReadWrite as OneWire;
interface StdControl as PowerControl;
}
}
implementation {
bool haveId = FALSE;
ds2411_serial_t ds2411id;
// The CRC polynomial is X^8 + X^5 + X^4 + 1,
// code is taken from http://linux.die.net/man/3/_crc_ccitt_update
bool ds2411_check_crc (const ds2411_serial_t *id) {
uint8_t crc = 0;
uint8_t idx;
for (idx = 0; idx < DS2411_DATA_LENGTH; idx++) {
uint8_t i;
crc = crc ^ (*id).data[idx];
for (i = 0; i < 8; i++) {
if (crc & 0x01) {
crc = (crc >> 1) ^ 0x8C;
} else {
crc >>= 1;
}
}
}
return crc == 0;
}
error_t readId () {
error_t e;
e = call PowerControl.start();
if (e != SUCCESS) return FAIL;
e = call OneWire.read(DS2411_READ_ADDR,
ds2411id.data,
DS2411_DATA_LENGTH);
call PowerControl.stop();
if (e == SUCCESS) {
if (ds2411_check_crc(&ds2411id)) {
haveId = TRUE;
} else {
e = EINVAL;
}
}
return e;
}
command error_t ReadId48.read (uint8_t *id) {
error_t e = SUCCESS;
if (!haveId) {
e = readId();
}
if (haveId) {
memcpy(id, ds2411id.serial, DS2411_SERIAL_LENGTH);
}
return e;
}
}
| nesC | 5 | mtaghiza/tinyos-main-1 | tos/chips/ds2411/Ds2411P.nc | [
"BSD-3-Clause"
] |
/* Copyright 2021 The TensorFlow Authors. All Rights Reserved.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
==============================================================================*/
#include "tensorflow/core/profiler/utils/buffer_pool.h"
#include "tensorflow/core/platform/test.h"
namespace tensorflow {
namespace profiler {
namespace {
TEST(BufferPoolTest, GetOrCreateBufferAlloc) {
constexpr size_t kBufferSizeInBytes = 32 * 1024;
BufferPool buffer_pool(kBufferSizeInBytes);
uint8_t* first_buffer = buffer_pool.GetOrCreateBuffer();
EXPECT_NE(first_buffer, nullptr);
// Checks that a second unique buffer is allocated.
uint8_t* second_buffer = buffer_pool.GetOrCreateBuffer();
EXPECT_NE(second_buffer, first_buffer);
for (size_t idx = 0; idx < kBufferSizeInBytes; ++idx) {
// Check that buffer is writable, msan will warn if not.
first_buffer[idx] = 0xAB;
}
// Clean up buffers held by the test.
buffer_pool.ReclaimBuffer(first_buffer);
buffer_pool.ReclaimBuffer(second_buffer);
}
TEST(BufferPoolTest, GetOrCreateBufferReuse) {
constexpr size_t kBufferSizeInBytes = 32 * 1024;
BufferPool buffer_pool(kBufferSizeInBytes);
uint8_t* buffer = buffer_pool.GetOrCreateBuffer();
EXPECT_NE(buffer, nullptr);
// Write a dummy value to the buffer.
buffer[0] = 0xFF;
uint8_t* previous_buffer = buffer;
buffer_pool.ReclaimBuffer(buffer);
// Check that we can retrieved a recently reclaimed buffer.
uint8_t* reused_buffer = buffer_pool.GetOrCreateBuffer();
EXPECT_EQ(reused_buffer, previous_buffer);
for (size_t idx = 0; idx < kBufferSizeInBytes; ++idx) {
// Check that reused buffer is writable, msan will warn if not.
reused_buffer[idx] = 0xCD;
}
// Clean up buffers held by the test.
buffer_pool.ReclaimBuffer(reused_buffer);
}
TEST(BufferPoolTest, DestroyAllBuffers) {
constexpr size_t kBufferSizeInBytes = 32 * 1024;
BufferPool buffer_pool(kBufferSizeInBytes);
uint8_t* first_buffer = buffer_pool.GetOrCreateBuffer();
EXPECT_NE(first_buffer, nullptr);
// Check that first buffer (not reclaimed) is still writable after
// DestroyAllBuffers.
buffer_pool.DestroyAllBuffers();
for (size_t idx = 0; idx < kBufferSizeInBytes; ++idx) {
first_buffer[idx] = 0xEF;
}
uint8_t* second_buffer = buffer_pool.GetOrCreateBuffer();
for (size_t idx = 0; idx < kBufferSizeInBytes; ++idx) {
// Check that second buffer is writable.
second_buffer[idx] = 0xAB;
}
// Clean up buffers held by the test.
buffer_pool.ReclaimBuffer(first_buffer);
buffer_pool.ReclaimBuffer(second_buffer);
}
} // namespace
} // namespace profiler
} // namespace tensorflow
| C++ | 4 | EricRemmerswaal/tensorflow | tensorflow/core/profiler/utils/buffer_pool_test.cc | [
"Apache-2.0"
] |
# -*- coding: utf-8 -*-
from sphinx import addnodes
"""
``local_toctree``: A callable yielding the global TOC tree that contains
list of all the content below the specified page. ``local_toctree`` need
pagename specifying as like as ``{{ local_toctree(pagename) }}`` and
optional keyword arguments are available:
* maxdepth (defaults to the max depth selected in the toctree directive):
the maximum depth of the tree; set it to -1 to allow unlimited depth
"""
def init_local_toctree(app):
def _get_local_toctree(docname, **kwds):
doctree = app.env.get_doctree(docname)
if 'maxdepth' not in kwds:
kwds['maxdepth'] = 0
toctrees = []
for toctreenode in doctree.traverse(addnodes.toctree):
toctree = app.env.resolve_toctree(
docname, app.builder, toctreenode, **kwds)
toctrees.append(toctree)
if not toctrees:
return None
result = toctrees[0]
for toctree in toctrees[1:]:
result.extend(toctree.children)
return app.builder.render_partial(result)['fragment']
ctx = app.env.config['html_context']
if 'local_toctree' not in ctx:
ctx['local_toctree'] = _get_local_toctree
def setup(app):
app.connect('builder-inited', init_local_toctree)
| Python | 5 | gh-oss-contributor/graphql-engine-1 | docs/_ext/local_toctree.py | [
"Apache-2.0",
"MIT"
] |
import * as React from 'react'
export const fromJsx = <div />
| JSX | 3 | bkucera2/cypress | npm/webpack-batteries-included-preprocessor/test/fixtures/file-types/jsx-file.jsx | [
"MIT"
] |
.slide-up-enter
opacity 0
transform translate(0, 50%)
.slide-up-leave-to
opacity 0
transform translate(0, -50%)
.slide-down-enter, .slide-down-leave-to
opacity 0
transform translate(0, -20px)
@keyframes rotate
0%
transform rotate(0deg)
100%
transform rotate(360deg)
@keyframes pulse
0%
opacity 1
50%
opacity .2
100%
opacity 1
| Stylus | 4 | ericnograles/vue-devtools | src/devtools/style/transitions.styl | [
"MIT"
] |
[platform]=1
[LCDDriver]=0
[color]=0
[SizeX]=128
[SizeY]=64
[WindowIndex]=3
[ControlIndex]=5
[Compiler]=2
[FontGraphicFunction]=False
[OnlySmallFont]=True
[Control]=False
[Cursor]=False
[RichStyle]=False
[RedrawInCallback]=True
[NoLCDBuffer]=False
[HaveDesktop]=True
[Icon]=True
[FreeRTOSSupport]=False
[SerialCursorDebug]=False
[HookFunction]=True
[SourceFolder]=..\code
[ProjectName]=example_KS010X
[ProjectFolder]=.\
[DataFile]=example_KS010X.dat
| Ecere Projects | 2 | hyller/GladiatorLibrary | EmbeddedGUI_0.6.2/0.6.2/designer/example_KS010X.epj | [
"Unlicense"
] |
-- Options
OptCaseSensitive=true
-- End of options
F=far.Flags
color = far.AdvControl(F.ACTL_GETCOLOR, far.Colors.COL_EDITORTEXT)
color.ForegroundColor, color.BackgroundColor = color.BackgroundColor, color.ForegroundColor
colorguid=win.Uuid "507CFA2A-3BA3-4f2b-8A80-318F5A831235"
words={}
Macro
area:"Editor"
key:"F5"
description:"Color Word Under Cursor"
action:->
ei=editor.GetInfo!
id=ei.EditorID
if words[id] then words[id]=nil
else
pos=ei.CurPos
line=editor.GetString!.StringText
if pos<=line\len()+1
slab=pos>1 and line\sub(1,pos-1)\match('[%w_]+$') or ""
tail=line\sub(pos)\match('^[%w_]+') or ""
if slab~="" or tail~="" then words[id]=OptCaseSensitive and slab..tail or (slab..tail)\lower!
Event
group:"EditorEvent"
action:(id,event,param)->
if event==F.EE_REDRAW
if words[id]
ei=editor.GetInfo id
start,finish=ei.TopScreenLine,math.min ei.TopScreenLine+ei.WindowSizeY,ei.TotalLines
for ii=start,finish
line,pos=editor.GetString(id,ii).StringText,1
while true
jj,kk,curr=line\cfind("([%w_]+)",pos)
if not jj then break
if not OptCaseSensitive then curr=curr\lower!
if curr==words[id] then editor.AddColor id,ii,jj,kk,F.ECF_AUTODELETE,color,100,colorguid
pos=kk+1
elseif event==F.EE_CLOSE then words[id]=nil
| MoonScript | 5 | MKadaner/FarManager | extra/Addons/Macros/Editor.ColorWord.moon | [
"BSD-3-Clause"
] |
<script>{%- include 'include-script-2.js' -%}</script> | Liquid | 0 | AleksandrHovhannisyan/eleventy | test/stubs-layout-cache/_includes/layout.liquid | [
"MIT"
] |
package com.baeldung.jnosql.artemis;
import de.flapdoodle.embed.mongo.MongodExecutable;
import de.flapdoodle.embed.mongo.MongodProcess;
import de.flapdoodle.embed.mongo.MongodStarter;
import de.flapdoodle.embed.mongo.config.MongodConfigBuilder;
import de.flapdoodle.embed.mongo.config.Net;
import de.flapdoodle.embed.mongo.distribution.Version;
import de.flapdoodle.embed.process.runtime.Network;
import javax.enterprise.context.ApplicationScoped;
import javax.enterprise.context.Destroyed;
import javax.enterprise.context.Initialized;
import javax.enterprise.event.Observes;
import java.io.IOException;
@ApplicationScoped
public class EmbeddedMongoDBSetup {
private static final String MONGODB_HOST = "localhost";
private static final int MONGODB_PORT = 27019;
private static final MongodStarter starter = MongodStarter.getDefaultInstance();
private static MongodExecutable _mongodExe;
private static MongodProcess _mongod;
public void init(@Observes @Initialized(ApplicationScoped.class) Object init) {
try {
System.out.println("Starting Embedded MongoDB");
initdb();
System.out.println("Embedded MongoDB started");
} catch (IOException e) {
System.out.println("Embedded MongoDB starting error !!");
e.printStackTrace();
}
}
private void initdb() throws IOException {
_mongodExe = starter.prepare(new MongodConfigBuilder()
.version(Version.Main.DEVELOPMENT)
.net(new Net(MONGODB_HOST, MONGODB_PORT, Network.localhostIsIPv6()))
.build());
_mongod = _mongodExe.start();
}
public void destroy(@Observes @Destroyed(ApplicationScoped.class) Object init) {
System.out.println("Stopping Embedded MongoDB");
_mongod.stop();
_mongodExe.stop();
System.out.println("Embedded MongoDB stopped !");
}
}
| Java | 4 | scharanreddy/tutorials | jnosql/jnosql-artemis/src/main/java/com/baeldung/jnosql/artemis/EmbeddedMongoDBSetup.java | [
"MIT"
] |
<!--
* Copyright 2019 Google Inc. All Rights Reserved.
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
-->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta http-equiv="X-UA-Compatible" content="ie=edge">
<title>Source maps tester</title>
</head>
<body>
<script>
// Test that source maps work.
//# sourceMappingURL=http://localhost:10200/source-map/script.js.map
</script>
<script>
// Test that source maps work when on a different origin (CORS).
//# sourceMappingURL=http://localhost:10503/source-map/script.js.map
</script>
map time map time! map time map time! 🎉
</body>
</html> | HTML | 3 | martin-maunoury/lighthouse | lighthouse-cli/test/fixtures/source-map/source-map-tester.html | [
"Apache-2.0"
] |
"""
l = [1, 2, 3]
assert((1 == l[0]))
assert((2 == l[1]))
assert(([1, 2] == l[:2]))
assert(([1] == l[0:1]))
assert(([1] == l[:1]))
assert((3 == l[(-1)]))
assert(([2, 3] == l[1:]))
assert(([3, 2, 1] == l[::(-1)]))
assert(([1, 2, 3] == l[:]))
assert(([1, 3] == l[::2]))
"""
l = [1, 2, 3]
assert((1 == l[0]))
assert((2 == l[1]))
assert(([1, 2] == l[:2]))
assert(([1] == l[0:1]))
assert(([1] == l[:1]))
assert((3 == l[(-1)]))
assert(([2, 3] == l[1:]))
assert(([3, 2, 1] == l[::(-1)]))
assert(([1, 2, 3] == l[:]))
assert(([1, 3] == l[::2]))
| Boo | 3 | popcatalin81/boo | tests/testcases/parser/wsa/slicing-1.boo | [
"BSD-3-Clause"
] |
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/geno.owl#"
xml:base="http://purl.obolibrary.org/obo/geno.owl"
xmlns:urigen-plugin="http://urigen-plugin/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:ont="http://www.co-ode.org/ontologies/ont.owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:genotype_model="http://www.lamhdi.org/obo/genotype_model/"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:obi="http://purl.obolibrary.org/obo/obi.owl#"
xmlns:property="http://property/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/geno.owl">
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl"/>
<owl:imports rdf:resource="https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/src/ontology/imports/oboInOwl.owl"/>
<rdfs:comment>GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations.
Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013</rdfs:comment>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/GENO_0000834 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000834">
<obo:IAO_0000115>Used to annotation axioms that define identity criteria for instances of a class.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_identity_criteria</rdfs:label>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000867 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000867">
<rdfs:label xml:lang="en">proabalistic_quantifier</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000905 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000905">
<rdfs:comment>Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models.</rdfs:comment>
<rdfs:label xml:lang="en">mixin</rdfs:label>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000909 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000909">
<rdfs:label xml:lang="en">gene symbol</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_alt_id -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_alt_id"/>
<!-- http://purl.obolibrary.org/obo/IAO_created_by -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_created_by"/>
<!-- http://purl.obolibrary.org/obo/IAO_creation_date -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_creation_date"/>
<!-- http://purl.obolibrary.org/obo/IAO_id -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_id"/>
<!-- http://purl.obolibrary.org/obo/IAO_subset -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_subset"/>
<!-- http://purl.obolibrary.org/obo/IAO_xref -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_xref"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://biohackathon.org/resource/faldo#begin -->
<owl:ObjectProperty rdf:about="http://biohackathon.org/resource/faldo#begin">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000708"/>
<rdfs:label xml:lang="en">begin</rdfs:label>
</owl:ObjectProperty>
<!-- http://biohackathon.org/resource/faldo#end -->
<owl:ObjectProperty rdf:about="http://biohackathon.org/resource/faldo#end">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000708"/>
<rdfs:label xml:lang="en">end</rdfs:label>
</owl:ObjectProperty>
<!-- http://biohackathon.org/resource/faldo#location -->
<owl:ObjectProperty rdf:about="http://biohackathon.org/resource/faldo#location">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000708"/>
<rdfs:label xml:lang="en">location</rdfs:label>
</owl:ObjectProperty>
<!-- http://biohackathon.org/resource/faldo#reference -->
<owl:ObjectProperty rdf:about="http://biohackathon.org/resource/faldo#reference">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000708"/>
<obo:IAO_0000115>The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly.</obo:IAO_0000115>
<rdfs:label>reference</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:label>is part of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:label>has part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000207 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000207">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000701"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000702"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000713"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<obo:IAO_0000115>A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'.</obo:IAO_0000115>
<obo:IAO_0000116>Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants.</obo:IAO_0000116>
<oboInOwl:hasDbXref>http://purl.obolibrary.org/obo/so_has_quality</oboInOwl:hasDbXref>
<rdfs:label>has_sequence_attribute</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000211 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000211">
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0000053"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0000059"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes</obo:IAO_0000115>
<obo:IAO_0000118>materializes</obo:IAO_0000118>
<rdfs:comment>Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence.</rdfs:comment>
<rdfs:label>bears_concretization_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000220 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000220">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000222"/>
<rdfs:label>is_genotype_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000222 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000222">
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000536"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000536"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<obo:IAO_0000115>A relationship that holds between a biological entity and some level of genetic variation present in its genome.</obo:IAO_0000115>
<obo:IAO_0000116>This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype.</obo:IAO_0000116>
<rdfs:comment>The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations.</rdfs:comment>
<rdfs:label>has_genotype</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000231 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000231">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000248"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000115>An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)</obo:IAO_0000115>
<obo:IAO_0000116>No proper part relation anymore in RO/BFO?</obo:IAO_0000116>
<oboInOwl:hasDbXref>http://semanticscience.org/resource/SIO_000053</oboInOwl:hasDbXref>
<rdfs:label>has_proper_part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000239 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000239">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000251"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
<obo:IAO_0000115>A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears.</obo:IAO_0000115>
<obo:IAO_0000118>has_sequence_component</obo:IAO_0000118>
<obo:IAO_0000118>has_state</obo:IAO_0000118>
<oboInOwl:hasDbXref>VMC:state</oboInOwl:hasDbXref>
<rdfs:comment>'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule.</rdfs:comment>
<rdfs:label>has_sequence</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000242 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000242">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000253"/>
<obo:IAO_0000112>A geno:intrinnsic genotype 'specifies' a SO:genome.
A geno:karyotype 'specifies' a geno:karyotype feature collection.</obo:IAO_0000112>
<obo:IAO_0000115>A relationship between an information content entity representing a specification, and the entity it specifies.</obo:IAO_0000115>
<rdfs:label>obsolete_specifies</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000243 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000243">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<obo:IAO_0000116>Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. </obo:IAO_0000116>
<rdfs:label>obsolete_approximates_sequence</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000244 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000244">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<obo:IAO_0000116>Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. </obo:IAO_0000116>
<rdfs:label>obsolete_resolves_to_sequence</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000248 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000248">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<obo:IAO_0000115>An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole.</obo:IAO_0000115>
<oboInOwl:hasDbXref>http://semanticscience.org/resource/SIO_000093</oboInOwl:hasDbXref>
<rdfs:label>is_proper_part_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000251 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000251">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
<rdfs:label>is_sequence_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000252 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000252">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:label>is_subject_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000253 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000253">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<rdfs:label>obsolete_is_specified_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000359 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000359">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0001001"/>
<obo:IAO_0000115>shortcut relation used to link a phenotype directly to a genotype of an organism</obo:IAO_0000115>
<obo:IAO_0000118>is_phenotype_of_organism_with_genotype</obo:IAO_0000118>
<obo:IAO_0000118>is_phenotype_with_genotype</obo:IAO_0000118>
<obo:IAO_0000118>phenotype_has_genotype</obo:IAO_0000118>
<rdfs:comment>Might expand to something like:
phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype)))))))</rdfs:comment>
<rdfs:label>obsolete_is_phenotype_of_genotype</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000368 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000368">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/GENO_0000141"/>
<obo:IAO_0000115>A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next.</obo:IAO_0000115>
<obo:IAO_0000116>Exploratory/temporary property, as we formalize our phenotypic inheritance model.</obo:IAO_0000116>
<rdfs:label>obsolete_participates_in_inheritance_process</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000382 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000382">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000654"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000115>A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_variant_part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000383 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000383">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000655"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:label xml:lang="en">is_variant_part_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000385 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000385">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000654"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000387"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000115>A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant.</obo:IAO_0000115>
<obo:IAO_0000118>has_reference_sequence_part</obo:IAO_0000118>
<rdfs:label>has_reference_part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000387 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000387">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000655"/>
<rdfs:label>is_reference_part_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000408 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000408">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000418"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000413"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
<obo:IAO_0000112>The allele instance <fgf8a^ti282a> is_allele_of the gene class 'danio rerio fgf8a'.
Note that the allele <fgf8a^ti282a> may not be an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the <fgf8a^ti282a> allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It is, however, an instance of the 'danio rerio fgf8a gene allele' class, as being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product.</obo:IAO_0000112>
<obo:IAO_0000115>A relation linking an instance of a variable feature (aka an allele) to a class of genomic feature it is an instance of (typically a gene class).</obo:IAO_0000115>
<obo:IAO_0000116>Domain = allele
Range = punned gene class
In owl models where alleles are instances of gene classes, this relation links an owl:Individual to an owl:Class, and thus 'puns' the gene class IRI.</obo:IAO_0000116>
<obo:IAO_0000118>is_sequence_variant_of</obo:IAO_0000118>
<rdfs:label>is_allele_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000410 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000410">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000411"/>
<obo:IAO_0000115>A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level).</obo:IAO_0000115>
<obo:IAO_0000118>is_variant_instance_of</obo:IAO_0000118>
<obo:IAO_0000231>formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)</obo:IAO_0000231>
<rdfs:comment>Domain = genomic feature instance
Range = punned gene class IRI</rdfs:comment>
<rdfs:label>obsolete_is_genetic_variant_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000411 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000411">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<obo:IAO_0000115>A relation linking a gene class to a sequence-varaint or expression-variant of the gene.</obo:IAO_0000115>
<obo:IAO_0000118>has_variant_instance</obo:IAO_0000118>
<obo:IAO_0000231>formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)</obo:IAO_0000231>
<rdfs:comment>Domain = punned gene class
Range = genomic feature</rdfs:comment>
<rdfs:label>obsolete_has_genetic_variant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000413 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000413">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000445"/>
<obo:IAO_0000115>A relation linking a gene class to one of its sequence-variant alleles.</obo:IAO_0000115>
<obo:IAO_0000116>Domain = punned gene class
Range = allele</obo:IAO_0000116>
<obo:IAO_0000118>has_sequence_variant</obo:IAO_0000118>
<rdfs:label>has_allele</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000414 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000414">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000418"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000447"/>
<obo:IAO_0000115>A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets.</obo:IAO_0000115>
<rdfs:comment>This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets.</rdfs:comment>
<rdfs:label>targets_gene</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000418 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000418">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000445"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000382"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000418"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000418"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation that holds between an instance of a genotype or variant sequence feature or collection, and a genomic feature class (typically a gene) that is affected in its sequence or expression.</obo:IAO_0000115>
<rdfs:comment>This is an organizational grouping class to collect all relations used to link instances of sequence features or qualified sequence features to genomic feature classes. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset.</rdfs:comment>
<rdfs:label>has_affected_feature</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000443 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000443">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000418"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000449"/>
<obo:IAO_0000115>A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents.</obo:IAO_0000115>
<obo:IAO_0000116>Domain = expression variant feature.
Range = punned gene class</obo:IAO_0000116>
<rdfs:comment>This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class.</rdfs:comment>
<rdfs:label>is_expression_variant_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000445 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000445">
<obo:IAO_0000115>A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature.</obo:IAO_0000115>
<obo:IAO_0000118>class_to_feature_relation</obo:IAO_0000118>
<rdfs:comment>This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases)</rdfs:comment>
<rdfs:label>is_feature_affected_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000447 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000447">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000445"/>
<obo:IAO_0000115>A relation between a gene class and a gene targeting reagent that targets it.</obo:IAO_0000115>
<obo:IAO_0000118>is_target_of</obo:IAO_0000118>
<rdfs:comment>Domain = punned gene class
Range = gene knockdown reagent</rdfs:comment>
<rdfs:label>is_gene_target_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000449 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000449">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000445"/>
<obo:IAO_0000115>A relation linking a gene class to one of an expression-variant of that gene..</obo:IAO_0000115>
<obo:IAO_0000116>Domain = punned gene class
Range = expression variant feature</obo:IAO_0000116>
<obo:IAO_0000118>has_expression_variant_instance</obo:IAO_0000118>
<rdfs:label>has_expression_variant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000486 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000486">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<obo:IAO_0000115>A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression.</obo:IAO_0000115>
<obo:IAO_0000231>Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property.</obo:IAO_0000231>
<rdfs:comment>This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of.</rdfs:comment>
<rdfs:label xml:lang="en">obsolete_is_variant_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000488 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000488">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<obo:IAO_0000115>A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways).</obo:IAO_0000115>
<rdfs:label xml:lang="en">obsolete_is_expression_variant_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000580 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000580">
<obo:IAO_0000115>A relation used to describe a context or conditions that define and/or identify an entity.</obo:IAO_0000115>
<obo:IAO_0000116>Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association.
Used in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features.</obo:IAO_0000116>
<obo:IAO_0000118>has_qualifying_context</obo:IAO_0000118>
<rdfs:label>has_qualifier</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000608 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000608">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GENO_0000516"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/GENO_0000133"/>
<obo:IAO_0000115>a relation to link a single locus complement to its zygosity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_zygosity</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000610 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000610">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000408"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GENO_0000036"/>
<obo:IAO_0000115>A relationship between a reference locus/allele and the gene class it is an allele of.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_reference_allele_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000626 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000626">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<obo:IAO_0000116>Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_color_value</obo:IAO_0000118>
<rdfs:comment>Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized.</rdfs:comment>
<rdfs:label>has_staining_intensity</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000634 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000634">
<obo:IAO_0000112>Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant.</obo:IAO_0000112>
<obo:IAO_0000115>relation between an molecular agent and its molecular target</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_targeted_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000639 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000639">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000639"/>
</owl:propertyChainAxiom>
<obo:IAO_0000112>1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance.
2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds.
3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)</obo:IAO_0000112>
<obo:IAO_0000115>Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence.</obo:IAO_0000115>
<rdfs:label xml:lang="en">sequence_derives_from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000641 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000641">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000408"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GENO_0000002"/>
<obo:IAO_0000115>A relationship between a variant allele and the gene class it is an allele of.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_variant_allele_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000650 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000650">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000654"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000661"/>
<obo:IAO_0000116>Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases.</obo:IAO_0000116>
<rdfs:label xml:lang="en">has_sex_agnostic_part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000651 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000651">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000641"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GENO_0000491"/>
<rdfs:comment>A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of.</rdfs:comment>
<rdfs:label xml:lang="en">is_mutant_allele_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000652 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000652">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000641"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GENO_0000497"/>
<obo:IAO_0000115>A relationship between a polymorphic allele and the gene class it is an allele of.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_polymorphic_allele_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000653 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000653">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000408"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GENO_0000501"/>
<obo:IAO_0000115>A relationship between a wild-type allele and the gene class it is an allele of.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_wild_type_allele_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000654 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000654">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000655"/>
<obo:IAO_0000115>An organizational class to hold relations of parthood between sequences/features.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_sequence_part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000655 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000655">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<rdfs:label xml:lang="en">is_sequence_part_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000661 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000661">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000655"/>
<obo:IAO_0000115>Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_sex_agnostic_part_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000683 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000683">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<obo:IAO_0000115>A relation between two sequence features at a particular genomic locus that vary in their sequence (in whole or in part).</obo:IAO_0000115>
<rdfs:comment>This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)</rdfs:comment>
<rdfs:label xml:lang="en">varies_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000708 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000708">
<rdfs:comment>organizational property to hold imports from faldo.</rdfs:comment>
<rdfs:label xml:lang="en">faldo properties</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000726 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000726">
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000714"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000715"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<obo:IAO_0000115>A relation linking a qualified sequence feature to its component sequence feature.</obo:IAO_0000115>
<obo:IAO_0000118>has_sequence_feature_component</obo:IAO_0000118>
<rdfs:comment>In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism.</rdfs:comment>
<rdfs:label xml:lang="en">has_sequence_feature</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000740 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000740">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002200"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000382"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000413"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000413"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000449"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000449"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:propertyChainAxiom>
<rdfs:label xml:lang="en">has_inferred_phenotype</rdfs:label>
</owl:ObjectProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000740"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000382"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000740"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred phenotype associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000740"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000740"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000413"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred phenotype associations from an intrinsic genotype component (e.g. a (sequence-)variant locus instance) to a gene class.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000740"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000413"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus).</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000740"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000449"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred phenotype associations from an extrinnsic genotype component (e.g. a expression-variant gene instance) to a gene class.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000740"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000449"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene).</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000740"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000743"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)</rdfs:comment>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/GENO_0000741 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000741">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<rdfs:comment>Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes.</rdfs:comment>
<rdfs:label xml:lang="en">obsolete_has_regulatory_part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000742 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000742">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000408"/>
</owl:propertyChainAxiom>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A relation linking a sequence_alteration to the gene it alters.</obo:IAO_0000115>
<obo:IAO_0000118>is_within_allele_of</obo:IAO_0000118>
<rdfs:label xml:lang="en">obsolete_is_alteration_within</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000743 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000743">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002200"/>
<rdfs:label xml:lang="en">has_asserted_phenotype</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000761 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000761">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000655"/>
<obo:IAO_0000116>Proposal for a property linking regulatory elements to larger features of which they are a part.</obo:IAO_0000116>
<rdfs:label xml:lang="en">is_regulatory_part_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000767 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000767">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<obo:IAO_0000115>A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances.</obo:IAO_0000115>
<obo:IAO_0000116>For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them.</obo:IAO_0000116>
<rdfs:label xml:lang="en">obsolete_has_position_component</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000783 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000783">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000654"/>
<obo:IAO_0000115>A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_sequence_unit</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000784 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000784">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000683"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<obo:IAO_0000115>A relation between two seqeunces or features that are considered variant with each other along their entire extents.</obo:IAO_0000115>
<rdfs:label xml:lang="en">completely_varies_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000790 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000790">
<rdfs:label xml:lang="en">related_condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000791 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000791">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000790"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000382"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000382"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000413"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000413"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000445"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000382"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000445"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000445"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:propertyChainAxiom>
<obo:IAO_0000116>Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene)</obo:IAO_0000116>
<obo:IAO_0000116>The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains.
Below are the different kinds/paths of propagation we desire:
1. Propagation 'down' a genotype (from larger components to smaller ones)
2. Propagation 'up' a genotype (from smaller components to larger ones)
3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype).
4. From an effective genotype to its intrinsic and extrinsic components.
5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele).
6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this.
Note that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha<tbx392>/shha<tbx392> [AB] to shha<tbx392>/shha<tbx392> [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition')</obo:IAO_0000116>
<rdfs:label xml:lang="en">inferred_to_cause_condition</rdfs:label>
</owl:ObjectProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000382"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>This is a case of inter-gneotype phenotype propagation, requiring propagation down oen genotype and then up another. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to have this chain.
This property chain propagates a phenotype asserted on a sex-qualified intrinsic genotype, down to its sex-agnostic genotype part, and then up to a parent effective genotype that has it as a variant part. I think this is OK in all cases, so we can implement this as the one case where we can have inter-genotype pheno propagation. But as noted, there will likely be no data that actually meets criteria to use this chain, so we can probably leave it out.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000382"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, to the coompnent variant parts of this sex-agnostic genotype.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to move past the sex-agnostic genotype and down to its parts.
The following shorter chain would also suffice here:
is_variant_part_of o inferred_to_cause_condition</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000413"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, through the coompnent variant parts of this sex-agnostic genotype, and to the affected gene.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000413"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to propagate to genes.
The shorter chain below would also suffice for this propagation:
has_allele o inferred_to_cause_condition</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000445"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000382"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations from an sequence alteration through the variant locus to a gene class. (separate chains are needed to propagate from the variant locus to the gene class, and another to propagate from a genotype, GVC, or VSLC to the gene class).
NOTE that i dont need this property chain if I have a property chain to infer a has_affected_locus link from a sequence alteration to a gene when the link is asserted from the variant locus to the gene:
is_variant_part_of o has_affected_locus --> has_affected_locus</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000445"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Obsolete comment: Property chain to propagate inferred condition associations from an intrinsic genotype, GC, or VLSC to a gene class. (a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class).
The following, shorter chain, would also suffice here:
has_allele o inferred_to_cause_condition -> inferred_to_cause_condition</rdfs:comment>
<rdfs:comment>Property chain to propagate inferred condition associations from an intrinsic genotype, GVC, or VLSC to an affected gene class, or from an extrinsic gneotype or component to an affected gene class.
The following, shorter chain, would also suffice here:
has_affected_locus o inferred_to_cause_condition -> inferred_to_cause_condition
Note that a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class in cases where the link to gene is through the variant locus rather than the seq alteration).</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000445"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele).</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000383"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype to a sex-agnostic intrinsic genotype.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000791"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000661"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0003303"/>
</owl:annotatedTarget>
<rdfs:comment>Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)</rdfs:comment>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/GENO_0000793 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000793">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000790"/>
<rdfs:label xml:lang="en">inferred_to_contribute_to_condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000794 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000794">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000790"/>
<rdfs:label xml:lang="en">inferred_to_correlate_with_condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000840 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000840">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0003303"/>
<oboInOwl:hasDbXref>LOINC:LA6668-3</oboInOwl:hasDbXref>
<rdfs:label xml:lang="en">pathogenic_for_condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000841 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000841">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0003303"/>
<oboInOwl:hasDbXref>LOINC:LA26332-9</oboInOwl:hasDbXref>
<rdfs:label xml:lang="en">likely_pathogenic_for_condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000842 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000842">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000790"/>
<obo:IAO_0000115>Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to.</obo:IAO_0000115>
<rdfs:label xml:lang="en">non-causal_for_condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000843 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000843">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000842"/>
<oboInOwl:hasDbXref>LOINC:LA6675-8</oboInOwl:hasDbXref>
<rdfs:label xml:lang="en">benign_for_condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000844 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000844">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000842"/>
<oboInOwl:hasDbXref>LOINC:LA26334-5</oboInOwl:hasDbXref>
<rdfs:label xml:lang="en">likely_benign_for_condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000845 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000845">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000790"/>
<oboInOwl:hasDbXref>LOINC:LA26333-7</oboInOwl:hasDbXref>
<rdfs:label xml:lang="en">has_uncertain_significance_for_condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000846 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000846">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000580"/>
<obo:IAO_0000115>A relation used to describe a process contextualizing the identity of an entity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_qualifying_process</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000847 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000847">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000580"/>
<obo:IAO_0000115>A relation used to describe an environment contextualizing the identity of an entity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_qualifying_environment</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000849 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000849">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000790"/>
<rdfs:label xml:lang="en">is_candidate_variant_for</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000903 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000903">
<obo:IAO_0000115>A relation linking a sequence feature to the location it occupies on some reference sequence.</obo:IAO_0000115>
<obo:IAO_0000118>occupies</obo:IAO_0000118>
<rdfs:label xml:lang="en">has_location</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000906 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000906">
<rdfs:comment>Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from.</rdfs:comment>
<rdfs:label xml:lang="en">on strand</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000136 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000136">
<obo:IAO_0000115>is_about is a (currently) primitive relation that relates an information artifact to an entity.</obo:IAO_0000115>
<rdfs:label>is about</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000219 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000219">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<obo:IAO_0000115>Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically</obo:IAO_0000115>
<obo:IAO_0000116>Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of.</obo:IAO_0000116>
<rdfs:label>denotes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000293 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000293">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002233"/>
<obo:IAO_0000115>A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.</obo:IAO_0000115>
<rdfs:label>has_specified_input</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000299 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000299">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002234"/>
<obo:IAO_0000115>A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
<rdfs:label>has_specified_output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000052 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000052">
<obo:IAO_0000115>a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence</obo:IAO_0000115>
<rdfs:label>inheres_in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000053 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000053">
<obo:IAO_0000115>a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence</obo:IAO_0000115>
<rdfs:label xml:lang="en">bearer of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000056 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000056">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<obo:IAO_0000115>a relation between a continuant and a process, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<rdfs:label>participates in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000057 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000057">
<obo:IAO_0000115>a relation between a process and a continuant, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<rdfs:label>has participant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000059 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
<obo:IAO_0000112>A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
<obo:IAO_0000115>A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.</obo:IAO_0000115>
<rdfs:label xml:lang="en">concretizes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000086 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000086">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<obo:IAO_0000115>a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence</obo:IAO_0000115>
<rdfs:label>has quality</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000087 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000087">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<rdfs:label>has_role</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000091 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000091">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<obo:IAO_0000115>a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence</obo:IAO_0000115>
<rdfs:label>has disposition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001000 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001000">
<rdfs:label>derives from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002091 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002091">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<rdfs:label>starts during</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002093 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002093">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<rdfs:label>ends during</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002131 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002131">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<obo:IAO_0000115>x overlaps y if and only if there exists some z such that x has part z and z part of y</obo:IAO_0000115>
<rdfs:label xml:lang="en">overlaps</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002162 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002162">
<obo:IAO_0000115>x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.</obo:IAO_0000115>
<rdfs:label xml:lang="en">in taxon</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002200 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002200">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002201"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0001001"/>
<obo:IAO_0000115>A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).</obo:IAO_0000115>
<rdfs:label>has phenotype</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002201 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002201">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0001001"/>
<rdfs:label xml:lang="en">phenotype of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002222 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002222">
<rdfs:label xml:lang="en">temporally related to</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002233 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002233">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<obo:IAO_0000115>p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has input</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002234 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002234">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002353"/>
<obo:IAO_0000115>p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002350 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002350">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
<rdfs:label>is member of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002351 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002351">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<obo:IAO_0000112>Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes
Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component</obo:IAO_0000112>
<obo:IAO_0000115>has member is a mereological relation between a collection and an item.</obo:IAO_0000115>
<rdfs:label>has member</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002352 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002352">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:label xml:lang="en">input of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002353 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002353">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:label xml:lang="en">output of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002354 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002354">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<rdfs:label xml:lang="en">obsolete_formed as result of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_000244 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_000244">
<obo:IAO_0000115>Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b</obo:IAO_0000115>
<rdfs:label xml:lang="en">molecularly controls</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002524 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002524">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000654"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002525"/>
<obo:IAO_0000115>x has subsequence y iff all of the sequence parts of x are sequence parts of y</obo:IAO_0000115>
<rdfs:label xml:lang="en">has subsequence</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002525 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002525">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000655"/>
<rdfs:label xml:lang="en">is subsequence of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002528 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002528">
<obo:IAO_0000115>inverse of downstream of sequence of</obo:IAO_0000115>
<rdfs:label xml:lang="en">is upstream of sequence of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002529 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002529">
<obo:IAO_0000115>x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is downstream of sequence of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0003301 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0003301">
<obo:IAO_0000115>Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.</obo:IAO_0000115>
<obo:IAO_0000116>To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?</obo:IAO_0000116>
<obo:IAO_0000117>Matthew Brush</obo:IAO_0000117>
<rdfs:comment>The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.</rdfs:comment>
<rdfs:label xml:lang="en">is model of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0003302 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0003302">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000790"/>
<obo:IAO_0000112>The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.
An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.</obo:IAO_0000112>
<obo:IAO_0000115>A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition.</obo:IAO_0000115>
<obo:IAO_0000116>Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.</obo:IAO_0000116>
<rdfs:comment>Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.
Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.</rdfs:comment>
<rdfs:label xml:lang="en">causes or contributes to condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0003303 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0003303">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0003302"/>
<obo:IAO_0000115>A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition.</obo:IAO_0000115>
<rdfs:label xml:lang="en">causes condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0003304 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0003304">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0003302"/>
<obo:IAO_0000115>A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition.</obo:IAO_0000115>
<rdfs:label xml:lang="en">contributes to condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0003305 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0003305">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0003304"/>
<obo:IAO_0000115>A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual.</obo:IAO_0000115>
<obo:IAO_0000118>contributes to expressivity of condition</obo:IAO_0000118>
<rdfs:label xml:lang="en">contributes to severity of condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0003306 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0003306">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0003304"/>
<obo:IAO_0000115>A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population.</obo:IAO_0000115>
<obo:IAO_0000118>contributes to penetrance of condition</obo:IAO_0000118>
<rdfs:label xml:lang="en">contributes to frequency of condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0003307 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0003307">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000790"/>
<obo:IAO_0000115>A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition.</obo:IAO_0000115>
<rdfs:comment>Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.
Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.</rdfs:comment>
<rdfs:label xml:lang="en">is preventative for condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0003308 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0003308">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000790"/>
<obo:IAO_0000115>A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.</obo:IAO_0000115>
<rdfs:label xml:lang="en">correlated with condition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/oban/association_has_object -->
<owl:ObjectProperty rdf:about="http://purl.org/oban/association_has_object">
<rdfs:label xml:lang="en">association has object</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/oban/association_has_predicate -->
<owl:ObjectProperty rdf:about="http://purl.org/oban/association_has_predicate">
<rdfs:label xml:lang="en">association has predicate</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.org/oban/association_has_subject -->
<owl:ObjectProperty rdf:about="http://purl.org/oban/association_has_subject">
<rdfs:label xml:lang="en">association has subject</rdfs:label>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://biohackathon.org/resource/faldo#position -->
<owl:DatatypeProperty rdf:about="http://biohackathon.org/resource/faldo#position">
<rdfs:comment>The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is.</rdfs:comment>
<rdfs:label xml:lang="en">position</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000678 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000678">
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
<obo:IAO_0000115>Property linking a sequence or sequence feature to an integer representing its length iin terms of the number of units in the sequence.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_extent</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000703 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000703">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
<obo:IAO_0000115>Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg').</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_sequence_string</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000712 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000712">
<rdfs:label xml:lang="en">ObsoleteDataProperty</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000866 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000866">
<obo:IAO_0000112>The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene.</obo:IAO_0000112>
<obo:IAO_0000115>Property to link an assertion or association with some value quantifying its relevance or ranking.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_quantifier</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000894 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000894">
<obo:IAO_0000115>The starting position of a sequence region in 0-based coordinates.</obo:IAO_0000115>
<obo:IAO_0000119>ClinGen Allele Model (http://datamodel.clinicalgenome.org/allele/)</obo:IAO_0000119>
<rdfs:label>start_position</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000895 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000895">
<obo:IAO_0000115>The ending position of a sequence region in 0-based coordinates.</obo:IAO_0000115>
<obo:IAO_0000119>ClinGen Allele Model (http://datamodel.clinicalgenome.org/allele/)</obo:IAO_0000119>
<rdfs:label>end_position</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/GENO_0000896 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/GENO_0000896">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
<obo:IAO_0000115>Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg').</obo:IAO_0000115>
<rdfs:label>has_string</rdfs:label>
</owl:DatatypeProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://biohackathon.org/resource/faldo#BothStrandsPosition -->
<owl:Class rdf:about="http://biohackathon.org/resource/faldo#BothStrandsPosition">
<rdfs:subClassOf rdf:resource="http://biohackathon.org/resource/faldo#StrandedPosition"/>
<rdfs:label xml:lang="en">Both strands</rdfs:label>
</owl:Class>
<!-- http://biohackathon.org/resource/faldo#ExactPosition -->
<owl:Class rdf:about="http://biohackathon.org/resource/faldo#ExactPosition">
<rdfs:subClassOf rdf:resource="http://biohackathon.org/resource/faldo#Position"/>
<obo:IAO_0000115>A position that is exactly known.</obo:IAO_0000115>
<rdfs:label xml:lang="en">Exact position</rdfs:label>
</owl:Class>
<!-- http://biohackathon.org/resource/faldo#ForwardStrandPosition -->
<owl:Class rdf:about="http://biohackathon.org/resource/faldo#ForwardStrandPosition">
<rdfs:subClassOf rdf:resource="http://biohackathon.org/resource/faldo#StrandedPosition"/>
<rdfs:label xml:lang="en">Positive strand</rdfs:label>
</owl:Class>
<!-- http://biohackathon.org/resource/faldo#Position -->
<owl:Class rdf:about="http://biohackathon.org/resource/faldo#Position">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000902"/>
<obo:IAO_0000115>Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.</obo:IAO_0000115>
<obo:IAO_0000116>Placing the FALDO:Position class under GENO:genomic locus, as it represents a type of genomic location with the same start and end coordinates (i.e. a single position as opposed to a location spanning a longer region)</obo:IAO_0000116>
<rdfs:label xml:lang="en">Position</rdfs:label>
</owl:Class>
<!-- http://biohackathon.org/resource/faldo#Region -->
<owl:Class rdf:about="http://biohackathon.org/resource/faldo#Region">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://biohackathon.org/resource/faldo#begin"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://biohackathon.org/resource/faldo#Position"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://biohackathon.org/resource/faldo#end"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://biohackathon.org/resource/faldo#Position"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000115>A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene.</obo:IAO_0000115>
<obo:IAO_0000116>From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence.</obo:IAO_0000116>
<rdfs:label xml:lang="en">Region</rdfs:label>
</owl:Class>
<!-- http://biohackathon.org/resource/faldo#ReverseStrandPosition -->
<owl:Class rdf:about="http://biohackathon.org/resource/faldo#ReverseStrandPosition">
<rdfs:subClassOf rdf:resource="http://biohackathon.org/resource/faldo#StrandedPosition"/>
<rdfs:label xml:lang="en">Negative strand</rdfs:label>
</owl:Class>
<!-- http://biohackathon.org/resource/faldo#StrandedPosition -->
<owl:Class rdf:about="http://biohackathon.org/resource/faldo#StrandedPosition">
<rdfs:subClassOf rdf:resource="http://biohackathon.org/resource/faldo#Position"/>
<rdfs:comment>Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'.</rdfs:comment>
<rdfs:label xml:lang="en">Stranded position</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
<obo:IAO_0000112 xml:lang="en">Julius Caesar</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">Verdi’s Requiem</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the Second World War</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">your body mass index</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>continuant</rdfs:label>
<rdfs:label xml:lang="en">continuant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.</obo:IAO_0000116>
<obo:IAO_0000116>Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>occurrent</rdfs:label>
<rdfs:label xml:lang="en">occurrent</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000004">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000112 xml:lang="en">a chair</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a heart</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a leg</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a molecule</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a spatial region</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an atom</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an orchestra.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an organism</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the bottom right portion of a human torso</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the interior of your mouth</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])</obo:IAO_0000115>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>independent continuant</rdfs:label>
<rdfs:label xml:lang="en">independent continuant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000112 xml:lang="en">a process of cell-division, \ a beating of the heart</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a process of meiosis</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a process of sleeping</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the course of a disease</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the flight of a bird</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the life of an organism</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">your process of aging.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)</obo:IAO_0000116>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>process</rdfs:label>
<rdfs:label xml:lang="en">process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000112 xml:lang="en">an atom of element X has the disposition to decay to an atom of element Y</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">certain people have a predisposition to colon cancer</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">children are innately disposed to categorize objects in certain ways.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the cell wall is disposed to filter chemicals in endocitosis and exocitosis</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>disposition</rdfs:label>
<rdfs:label xml:lang="en">disposition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000112 xml:lang="en">the disposition of this piece of metal to conduct electricity.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the disposition of your blood to coagulate</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of your reproductive organs</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of being a doctor</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of this boundary to delineate where Utah and Colorado meet</obo:IAO_0000112>
<obo:IAO_0000600 xml:lang="en">To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>realizable entity</rdfs:label>
<rdfs:label xml:lang="en">realizable entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:IAO_0000112 xml:lang="en">the ambient temperature of this portion of air</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the color of a tomato</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the length of the circumference of your waist</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mass of this piece of gold.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the shape of your nose</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the shape of your nostril</obo:IAO_0000112>
<obo:IAO_0000600 xml:lang="en">a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>quality</rdfs:label>
<rdfs:label xml:lang="en">quality</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000112 xml:lang="en">Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">of one-sided specifically dependent continuants: the mass of this tomato</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the disposition of this fish to decay</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of this heart: to pump blood</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mutual dependence of proton donors and acceptors in chemical reactions [79</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the pink color of a medium rare piece of grilled filet mignon at its center</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of being a doctor</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the shape of this hole.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the smell of this portion of mozzarella</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.</obo:IAO_0000116>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>specifically dependent continuant</rdfs:label>
<rdfs:label xml:lang="en">specifically dependent continuant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<obo:IAO_0000112 xml:lang="en">John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the priest role</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of a boundary to demarcate two neighboring administrative territories</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of a building in serving as a military target</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of a stone in marking a property boundary</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of subject in a clinical trial</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the student role</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>role</rdfs:label>
<rdfs:label xml:lang="en">role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000112 xml:lang="en">The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the pdf file on your laptop, the pdf file that is a copy thereof on my laptop</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])</obo:IAO_0000115>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>generically dependent continuant</rdfs:label>
<rdfs:label xml:lang="en">generically dependent continuant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<obo:IAO_0000112 xml:lang="en">the function of a hammer to drive in nails</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of a heart pacemaker to regulate the beating of a heart through electricity</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of amylase in saliva to break down starch into sugar</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<obo:IAO_0000112 xml:lang="en">a flame</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a forest fire</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a human being</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a hurricane</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a photon</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a puff of smoke</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a sea wave</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a tornado</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an aggregate of human beings.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an energy wave</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an epidemic</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the undetached arm of a human being</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.</obo:IAO_0000116>
<obo:IAO_0000600 xml:lang="en">A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label>material entity</rdfs:label>
<rdfs:label xml:lang="en">material entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_23367 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_23367">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000116>Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology.</obo:IAO_0000116>
<rdfs:label>molecular entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33696 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33696">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_23367"/>
<rdfs:label>nucleic acid</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CLO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CLO_0000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001000"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).</obo:IAO_0000115>
<rdfs:label xml:lang="en">cell line</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CL_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001062"/>
<rdfs:comment>Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies.</rdfs:comment>
<rdfs:label>cell</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ENVO_01000254 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_01000254">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000116>1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.
2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity).</obo:IAO_0000116>
<rdfs:comment>In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.</rdfs:comment>
<rdfs:label>environmental system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000007 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ERO_0000007">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000115>A technique is a planned process used to accomplish a specific activity or task.</obo:IAO_0000115>
<rdfs:label xml:lang="en">technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0002002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ERO_0002002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0002003"/>
<obo:IAO_0000115>A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo.</obo:IAO_0000115>
<rdfs:label xml:lang="en">embryonic stem cell line</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0002003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ERO_0002003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CLO_0000031"/>
<obo:IAO_0000115>A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.</obo:IAO_0000115>
<rdfs:label xml:lang="en">stem cell line</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000899"/>
<obo:IAO_0000112>Example zebrafish intrinsic genotype:
Genotype = fgf8a<ti282a/+>; shha<tb392/tb392> (AB)
reference component (genomic background) = AB
variant component ('genomic variation complement') = fgf8a<ti282a/+>; shha<tb392/tb392>
. . . and within this variant component, there are two 'variant single locus complements' represented:
allele complement 1 = fgf8a<ti282a/+>
allele complement 2 = shha<tb392/tb392>
and within each of these 'variant single locus complements' there is one or more variant gene locus member:
in complement 1: fgf8a<ti282a>
in complement 2: shha<ttb392></obo:IAO_0000112>
<obo:IAO_0000115>A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement)</obo:IAO_0000115>
<obo:IAO_0000116>This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).
Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype.</obo:IAO_0000116>
<obo:IAO_0000118>genotype</obo:IAO_0000118>
<obo:IAO_0000118>organismal genotype</obo:IAO_0000118>
<obo:IAO_0000118>sex-agnostic intrinsic genotype</obo:IAO_0000118>
<rdfs:comment>In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances).</rdfs:comment>
<rdfs:label>genomic genotype (sex-agnostic)</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000002">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000512"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000683"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000036"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0001059"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002524"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000115>An allele that varies in it sequence from what is considered the reference or canonical sequence at that locus. Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation.</obo:IAO_0000115>
<obo:IAO_0000116>The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles.</obo:IAO_0000116>
<obo:IAO_0000118>alterante allele</obo:IAO_0000118>
<obo:IAO_0000118>sequence-variant feature</obo:IAO_0000118>
<obo:IAO_0000118>variant feature</obo:IAO_0000118>
<rdfs:comment>1. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another.
GENO classifies a feature as 'variant' only in cases where we can be confident that the feature will *always* be considered to be variant with a reference feature. For example, exerimentally induced/generated varaitions in model organism genes that are created expressly to vary from an esablished reference.
2. A variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence.</rdfs:comment>
<rdfs:label>variant allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000009 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000009">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000660"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000382"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000030"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A sequence collection comprised of all 'variant single locus complements' in a single genome, which together constitute the variant component of an intrinsic genotype.</obo:IAO_0000115>
<rdfs:comment>1. Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases.
2. Most genotypes have only one altered locus (ie only one 'single-locus variant complement') that distinguish it from some reference background. For example, the genotype instance 'fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes vary at more than one locus (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)).</rdfs:comment>
<rdfs:label>genomic variation complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000010">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000914"/>
<obo:IAO_0000112>The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)</obo:IAO_0000112>
<obo:IAO_0000115>A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).</obo:IAO_0000115>
<obo:IAO_0000116>Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it.</obo:IAO_0000116>
<obo:IAO_0000118>genomic background</obo:IAO_0000118>
<oboInOwl:hasDbXref>OBI:genetic population background information</oboInOwl:hasDbXref>
<rdfs:label>background genome</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000014 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000014">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000915"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000683"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000704"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000408"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000704"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The "mn004Gt" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome.
http://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722
http://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8</obo:IAO_0000112>
<obo:IAO_0000115>A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene)</obo:IAO_0000115>
<obo:IAO_0000116>Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).
This design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not.</obo:IAO_0000116>
<oboInOwl:hasDbXref>http://purl.obolibrary.org/obo/SO_0001023 ! allele</oboInOwl:hasDbXref>
<rdfs:comment>In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion.
A genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene.</rdfs:comment>
<rdfs:label>gene allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000017">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000702"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000152"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A sequence that serves as a standard against which other sequences at the same location are compared.</obo:IAO_0000115>
<obo:IAO_0000116>The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant.</obo:IAO_0000116>
<obo:IAO_0000118>reference sequence</obo:IAO_0000118>
<rdfs:comment>A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence.</rdfs:comment>
<rdfs:label>reference sequence</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000019">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<obo:IAO_0000115>a collection more than one sequence features (ie a collection of discontinuous sequence features)</obo:IAO_0000115>
<oboInOwl:hasDbXref>perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one)</oboInOwl:hasDbXref>
<rdfs:comment>1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions.</rdfs:comment>
<rdfs:label>obsolete_sequence feature collection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000022">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A sequence feature collection comprised of discontiguous sequences from a single genome</obo:IAO_0000115>
<obo:IAO_0000116>Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system.</obo:IAO_0000116>
<obo:IAO_0000118>genomic feature collection</obo:IAO_0000118>
<rdfs:comment>Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection.</rdfs:comment>
<rdfs:label>obsolete_genomic feature collection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000029 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000029">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A single locus complement that serves as a standard against which 'variant' sequences are compared</obo:IAO_0000115>
<obo:IAO_0000118>reference allelic complement</obo:IAO_0000118>
<obo:IAO_0000118>reference single locus feature complement</obo:IAO_0000118>
<obo:IAO_0000231>Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.
Eq Class axiom:
'single locus complement'
and (has_sequence_attribute some reference)
SC axioms:
'has member' exactly 0 'variant allele'
'has member' only 'reference genomic feature'
'has member' some 'reference genomic feature'</obo:IAO_0000231>
<rdfs:label>obsolete_reference single locus complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000030">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000516"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000382"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000002"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13).</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">variant allelic complement</obo:IAO_0000118>
<obo:IAO_0000118>variant single locus feature complement</obo:IAO_0000118>
<rdfs:comment>Instances of this class are collections comprised of all versions of some defined feature present in a genome (e.g. alleles of a specific gene), where at least one member is variant (non-reference). In diploid genomes this complement is typically the two alleles at the same locus on homologous chromosomes.
This class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant.</rdfs:comment>
<rdfs:label>variant single locus complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000033 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000033">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0001026"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000683"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000914"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000382"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A genome that varies at one or more loci from the sequence of some reference genome.</obo:IAO_0000115>
<oboInOwl:hasDbXref>http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here)</oboInOwl:hasDbXref>
<rdfs:label>variant genome</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000036 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000036">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000512"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000152"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome.</obo:IAO_0000115>
<rdfs:comment>Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.
In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared.</rdfs:comment>
<rdfs:label>reference allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000037 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000037">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus).</obo:IAO_0000115>
<obo:IAO_0000116>Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '.</obo:IAO_0000116>
<obo:IAO_0000231>Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.
Eq Class def: 'genomic feature'
and (has_sequence_attribute some unspecified)</obo:IAO_0000231>
<rdfs:comment>An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele).</rdfs:comment>
<rdfs:label>obsolete_unspecified feature</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000042 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000042">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature.</obo:IAO_0000115>
<obo:IAO_0000118>hemizygous reference junction</obo:IAO_0000118>
<obo:IAO_0000231>Eliminating unecessary defined/organizational classes. Former logical def:
junction
and (has_sequence_attribute some reference)
Subclass axiom:
is_variant_with some insertion</obo:IAO_0000231>
<rdfs:comment>In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.
The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation.</rdfs:comment>
<rdfs:label>obsolete_reference junction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000047 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000047">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0000704"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7955"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A gene that originates from the genome of a danio rerio.</obo:IAO_0000115>
<rdfs:label>danio rerio gene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000054 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000054">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0000704"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A gene that originates from the genome of a homo sapiens.</obo:IAO_0000115>
<rdfs:label>homo sapiens gene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000057 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000057">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0000704"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A gene that originates from the genome of a mus musculus.</obo:IAO_0000115>
<rdfs:label>mus musculus gene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000060 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000060">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000112>A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.
http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690
Note that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469</obo:IAO_0000112>
<obo:IAO_0000115>A version/allele of a gene that serves as a standard against which variant genes are compared.</obo:IAO_0000115>
<obo:IAO_0000118>reference gene</obo:IAO_0000118>
<obo:IAO_0000231>Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.
Eq Class axiom:
'gene allele'
and (has_sequence_attribute some reference)
SC axioms:
is_variant_with some 'gene allele'
is_reference_allele_of some gene</obo:IAO_0000231>
<rdfs:comment>Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.
In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared.</rdfs:comment>
<rdfs:label>obsolete_reference gene allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000091 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000091">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<rdfs:label>obsolete_experimental insertion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000092 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000092">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000667"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002353"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000172"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>gene trap insertion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000093 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000093">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000902"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001218"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A transgene that has been integrated into a chrromosome in the host genome.</obo:IAO_0000115>
<rdfs:comment>An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion.
An 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome.</rdfs:comment>
<rdfs:label>integrated transgene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000106 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000106">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000482"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000108"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000248"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000091"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000139"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny.</obo:IAO_0000115>
<obo:IAO_0000116>1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.
2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way.</obo:IAO_0000116>
<rdfs:comment>1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.
2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms.</rdfs:comment>
<rdfs:label>genomic material</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000108 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000108">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000115>A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion.</obo:IAO_0000115>
<obo:IAO_0000118>physical genome</obo:IAO_0000118>
<rdfs:comment>A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements.
Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome.</rdfs:comment>
<rdfs:label>material genome</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000111 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000111">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
<obo:IAO_0000115>a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)</obo:IAO_0000115>
<obo:IAO_0000116>Consider http://semanticscience.org/resource/SIO_001062 ! human population ("A human population refers to a collection of human beings").</obo:IAO_0000116>
<obo:IAO_0000118>homo sapiens population</obo:IAO_0000118>
<rdfs:label>human population</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000112 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000112">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000113"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical.</obo:IAO_0000115>
<obo:IAO_0000118>organism strain or breed</obo:IAO_0000118>
<rdfs:comment>Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)</rdfs:comment>
<rdfs:label>strain or breed</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000113 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000113">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000000"/>
<obo:IAO_0000116>A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon)</obo:IAO_0000116>
<rdfs:label>taxonomic group</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000118 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000118">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000112"/>
<rdfs:label>mus musculus strain</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000119 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000119">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000112"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7955"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7955"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>danio rerio strain</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000125 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000125">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>sequence attribute that can inhere only in a collection of more than one sequence features</obo:IAO_0000115>
<rdfs:label>obsolete_sequence feature collection attribute</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000131 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000131">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000886"/>
<obo:IAO_0000115>A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes).</obo:IAO_0000115>
<rdfs:label>in cis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000132 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000132">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000886"/>
<obo:IAO_0000115>A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes).</obo:IAO_0000115>
<rdfs:label>in trans</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000133 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000133">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000875"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000516"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An allelic state that describes the degree of similarity of features at a particular locus in the genome (i.e. whether the alleles or haplotypes are the same or different).</obo:IAO_0000115>
<obo:IAO_0000118>allelic state</obo:IAO_0000118>
<obo:IAO_0000119>derived from https://en.wikipedia.org/wiki/Zygosity</obo:IAO_0000119>
<oboInOwl:hasDbXref>http://semanticscience.org/resource/SIO_001263</oboInOwl:hasDbXref>
<rdfs:label>zygosity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000134 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000134">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000391"/>
<rdfs:label>hemizygous</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000135 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000135">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000391"/>
<rdfs:label>heterozygous</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000136 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000136">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000391"/>
<rdfs:label>homozygous</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000137 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000137">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000133"/>
<obo:IAO_0000118>indeterminite zygosity</obo:IAO_0000118>
<obo:IAO_0000118>no-call zygosity</obo:IAO_0000118>
<obo:IAO_0000118>unknown zygosity</obo:IAO_0000118>
<rdfs:label>unspecified zygosity</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000137"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
<owl:annotatedTarget>indeterminite zygosity</owl:annotatedTarget>
<rdfs:comment>MGI uses this term when zygosity is not known.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000137"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
<owl:annotatedTarget>no-call zygosity</owl:annotatedTarget>
<rdfs:comment>(this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples)</rdfs:comment>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/GENO_0000138 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000138">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<obo:IAO_0000115>The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event.</obo:IAO_0000115>
<rdfs:comment>We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells).
We can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms.</rdfs:comment>
<rdfs:label>heritabililty</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000139 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000139">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000138"/>
<rdfs:label>heritable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000140 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000140">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000138"/>
<rdfs:label>non-heritable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000141 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000141">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<obo:IAO_0000115>The disposition of a genetic variant to cause a particular phenotype or disease based on its allelic state (e.g. heterozygous vs homozygous)</obo:IAO_0000115>
<obo:IAO_0000116>Considering alternate definitions:
- a disposition related to the phenotypic effect of a particular allele based on its inherited allelic state (i.e., the complement of alleles present at a particular locus)
- the disposition of an allele in a particular allelic state (e.g. heterozygouse vs homozygous) to cause a particular phenotype.</obo:IAO_0000116>
<obo:IAO_0000118>phenotypic heritability</obo:IAO_0000118>
<obo:IAO_0000118>phenotypic inheritance pattern</obo:IAO_0000118>
<rdfs:label>condition inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000142 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000142">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000141"/>
<obo:IAO_0000115>disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes</obo:IAO_0000115>
<rdfs:label>dominant inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000143 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000143">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000142"/>
<obo:IAO_0000115>A mode of inheritance whereby a heterozygous individual expresses distinct traits or conditions associated with both alleles (e.g. an individual with an AB blood type).</obo:IAO_0000115>
<rdfs:comment>Alt: A disposition inhering in a variant of a genetic locus that is realized in an inheritance pattern whereby two different variants are phenotypically expressed in a heterozygous individual (e.g. an individual with an AB blood type)</rdfs:comment>
<rdfs:label>co-dominant inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000144 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000144">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000142"/>
<obo:IAO_0000118>pure dominant inheritance</obo:IAO_0000118>
<rdfs:label>complete dominant inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000145 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000145">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000142"/>
<obo:IAO_0000115>disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that it's associated phenotype is partially expressed in heterozygotes (ie the observed phenotype is intermediate between that of the two distinct loci)</obo:IAO_0000115>
<obo:IAO_0000118>incomplete dominant inheritance</obo:IAO_0000118>
<rdfs:label>semi-dominant inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000146 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000146">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000144"/>
<obo:IAO_0000118>X-linked dominant inheritance</obo:IAO_0000118>
<rdfs:label>allosomal dominant inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000147 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000147">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000144"/>
<rdfs:label>autosomal dominant iniheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000148 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000148">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000141"/>
<obo:IAO_0000115>disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that no variant-associated phenotype is apparent in heterozygotes</obo:IAO_0000115>
<rdfs:label>recessive inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000149 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000149">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000148"/>
<obo:IAO_0000118>X-linked recessive inheritance</obo:IAO_0000118>
<rdfs:label>allosomal recessive inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000150 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000150">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000148"/>
<rdfs:label>autosomal recessive inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000152 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000152">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000773"/>
<obo:IAO_0000115>An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same locus are compared.</obo:IAO_0000115>
<rdfs:comment>Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another.</rdfs:comment>
<rdfs:label>reference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000160 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000160">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000105"/>
<rdfs:label>unspecified life cycle stage</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000164 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000164">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600043"/>
<rdfs:comment>objective is to insert some specified sequence into the genome of a cell or virus</rdfs:comment>
<rdfs:label>genetic insertion technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000165 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000165">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600043"/>
<rdfs:label>mutagen treatment technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000166 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000166">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600043"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000515"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping).</obo:IAO_0000115>
<rdfs:comment>This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created.</rdfs:comment>
<rdfs:label>targeted gene mutation technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000169 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000169">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000164"/>
<rdfs:comment>Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination.</rdfs:comment>
<rdfs:label>random genetic insertion technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000170 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000170">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000164"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000515"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>targeted genetic insertion technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000171 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000171">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000170"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000515"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>enhancer trapping technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000172 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000172">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000170"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000515"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>gene trapping technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000173 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000173">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000170"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000515"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>promoter trapping technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000174 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000174">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000170"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000515"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>targeted knock-in technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000175 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000175">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000169"/>
<rdfs:label>random transgene insertion technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000324 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000324">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome</obo:IAO_0000115>
<rdfs:label>obsolete_chromosome complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000338 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000338">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000346"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000685"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation</obo:IAO_0000115>
<obo:IAO_0000118>duplicate chromosome</obo:IAO_0000118>
<rdfs:comment>This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome.</rdfs:comment>
<rdfs:label>gained aneusomic chromosome</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000339 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000339">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000346"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000678"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</owl:hasValue>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation.</obo:IAO_0000115>
<obo:IAO_0000116>This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as "the point at which one or more contiguous nucleotides were excised".</obo:IAO_0000116>
<obo:IAO_0000118>absent aneusomic chromosome</obo:IAO_0000118>
<rdfs:label>lost aneusomic chromosome</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000343 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000343">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000513"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000248"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000340"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation.</obo:IAO_0000115>
<obo:IAO_0000116>Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism.</obo:IAO_0000116>
<obo:IAO_0000118>aneuploid chromosomal segment</obo:IAO_0000118>
<obo:IAO_0000118>aneusomic chromosomal subregion/segment</obo:IAO_0000118>
<obo:IAO_0000118>partial aneusomic chromosomal element</obo:IAO_0000118>
<rdfs:comment>Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome."</rdfs:comment>
<rdfs:label>aneusomic chromosomal part</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000344 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000344">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000343"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event.</obo:IAO_0000115>
<obo:IAO_0000118>duplicate partial aneuploid chromosomal element</obo:IAO_0000118>
<obo:IAO_0000118>translocated duplicate chromosomal element</obo:IAO_0000118>
<obo:IAO_0000118>translocated duplicate chromosomal segment</obo:IAO_0000118>
<rdfs:comment>Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus.</rdfs:comment>
<rdfs:label>gained aneusomic chromosomal segment</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000345 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000345">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000343"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000678"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</owl:hasValue>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome.</obo:IAO_0000115>
<obo:IAO_0000116>In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement</obo:IAO_0000116>
<obo:IAO_0000118>dropped partial anneuploid chromosomal element</obo:IAO_0000118>
<obo:IAO_0000118>translocated absent chromosomal segment</obo:IAO_0000118>
<obo:IAO_0000118>truncated chromosome terminus</obo:IAO_0000118>
<rdfs:comment>This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome.
Loss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus.</rdfs:comment>
<rdfs:label>lost aneusomic chromosomal segment</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000346 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000346">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000340"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000513"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation</obo:IAO_0000115>
<obo:IAO_0000118>complete aneusomic chromosome</obo:IAO_0000118>
<rdfs:comment>Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism.
Similarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication.</rdfs:comment>
<rdfs:label>aneusomic chromosome</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000351 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000351">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000116>Stub class to serve as root of hierarchy for imports of biological processes from GO-BP.</obo:IAO_0000116>
<rdfs:label>biological process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000391 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000391">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000133"/>
<rdfs:label>disomic zygosity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000392 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000392">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000133"/>
<rdfs:label>aneusomic zygosity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000393 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000393">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000392"/>
<rdfs:label>trisomic homozygous</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000394 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000394">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000392"/>
<rdfs:label>trisomic heterozygous</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000402 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000402">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000135"/>
<obo:IAO_0000115>A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a<ti282a>/fgf8a<x15>)</obo:IAO_0000115>
<obo:IAO_0000118>trans-heterozygous</obo:IAO_0000118>
<rdfs:label>compound heterozygous</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000415 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000415">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)</obo:IAO_0000115>
<obo:IAO_0000116>replaced with SO:engineered_region</obo:IAO_0000116>
<obo:IAO_0000118>extra-genomic sequence</obo:IAO_0000118>
<rdfs:label>obsolete_reagent sequence feature</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000458 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000458">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000135"/>
<rdfs:comment>a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>)</rdfs:comment>
<rdfs:label>simple heterozygous</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000460 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000460">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000666"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002525"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000902"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)</obo:IAO_0000115>
<rdfs:label>transgene part</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000476 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000476">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000773"/>
<obo:IAO_0000115>An attribute inhering in a locus that varies from some designated reference in virtue of alterations in its sequence or expression level</obo:IAO_0000115>
<rdfs:label xml:lang="en">variant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000477 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000477">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000773"/>
<obo:IAO_0000115>An attribute inhereing in a locus for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant.</obo:IAO_0000115>
<rdfs:label xml:lang="en">polymorphic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000480 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000480">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000773"/>
<obo:IAO_0000115>An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence.</obo:IAO_0000115>
<rdfs:label xml:lang="en">mutant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000481 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000481">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0000110"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001026"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000903"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000902"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A sequence feature (continuous extent of located biological sequence) that is located in the heritable genome of a cell or organism.</obo:IAO_0000115>
<obo:IAO_0000116>This class was created largely as a modeling cnvenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology.</obo:IAO_0000116>
<rdfs:comment>1. A genomic feature is a continuous extent of sequence at a particular location in a genome, which can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero).
2. A feature being 'located in' a genome here means only that the abstract sequence they contain can be positioned in the genome of some organism by alignment with some reference genomic sequence. In this way, we can distinguish features that can be associated with a particular taxa and assigned genomic coordinates.
3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome.</rdfs:comment>
<rdfs:label xml:lang="en">genomic feature</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000482 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000482">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33696"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion).</obo:IAO_0000115>
<rdfs:comment>This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material.</rdfs:comment>
<rdfs:label xml:lang="en">genetic material</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000491 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000491">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain.</obo:IAO_0000115>
<obo:IAO_0000119>Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines</obo:IAO_0000119>
<obo:IAO_0000231>Not required for any specific use case at this point so removed for simplicity.
Formely asserted as allele and inferred as varaint allele.
Eq class definition:
allele
and (mutation or ('has subsequence' some mutation))</obo:IAO_0000231>
<rdfs:comment>'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line.</rdfs:comment>
<rdfs:label>obsolete_mutant allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000492 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000492">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000683"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000501"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain.</obo:IAO_0000115>
<rdfs:label xml:lang="en">mutation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000494 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000494">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000481"/>
<owl:Class>
<owl:complementOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000248"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000340"/>
</owl:Restriction>
</owl:complementOf>
</owl:Class>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000139"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon)</obo:IAO_0000115>
<obo:IAO_0000116>Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element</obo:IAO_0000116>
<obo:IAO_0000118>episomal replicon</obo:IAO_0000118>
<obo:IAO_0000231>Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'.</obo:IAO_0000231>
<rdfs:label xml:lang="en">extrachromosomal replicon</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000495 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000495">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000856"/>
<obo:IAO_0000118>expression construct feature</obo:IAO_0000118>
<rdfs:label xml:lang="en">expression construct</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000497 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000497">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000512"/>
<obo:IAO_0000115>An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population.</obo:IAO_0000115>
<obo:IAO_0000119>PMID: 25741868 ACMG Guidelines</obo:IAO_0000119>
<rdfs:comment>Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%).</rdfs:comment>
<rdfs:label>polymorphic allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000498 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000498">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000497"/>
<obo:IAO_0000115>A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same locus.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">major allele</obo:IAO_0000118>
<rdfs:label>major polymorphic allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000499 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000499">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000497"/>
<obo:IAO_0000115>A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given locus).</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">minor allele</obo:IAO_0000118>
<rdfs:label>minor polymorphic allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000500 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000500">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000497"/>
<obo:IAO_0000115>A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">ancestral allele</obo:IAO_0000118>
<rdfs:label>ancestral polymorphic allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000501 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000501">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000512"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000683"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared.</obo:IAO_0000115>
<obo:IAO_0000118>wild-type allele</obo:IAO_0000118>
<rdfs:comment>'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain.
The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis.</rdfs:comment>
<rdfs:label>wild-type allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000502 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000502">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000501"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000704"/>
<obo:IAO_0000118 xml:lang="en">wild-type gene allele</obo:IAO_0000118>
<rdfs:comment>A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation.</rdfs:comment>
<rdfs:label>wild-type gene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000504 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000504">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000529"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000231"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000534"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000447"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000533"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.</obo:IAO_0000115>
<rdfs:comment>The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position.</rdfs:comment>
<rdfs:label xml:lang="en">reagent targeted gene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000506 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000506">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000529"/>
<obo:IAO_0000115>A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome).</obo:IAO_0000115>
<obo:IAO_0000118>experimentally-expressed transgene</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">extrinsic transgene</obo:IAO_0000118>
<rdfs:label>transiently-expressed transgene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000511 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000511">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000773"/>
<obo:IAO_0000115>An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared.</obo:IAO_0000115>
<rdfs:label xml:lang="en">wild-type</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000512 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000512">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000481"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000683"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>One of a set of sequence features that exist at a particular genomic locus.</obo:IAO_0000115>
<obo:IAO_0000116>The notion of an 'allele' defined here is distinct from that of a genetic 'variant' - as 'allele' includes features considered to be the 'reference' at a particular locus. The notion of an 'allele' captures the state of the sequence found at a genetic locus, be it variant or reference. The notion of a 'variant' implies a state that differs from some 'reference' sequence at that location. What is considered the 'reference' state at a particular locus may vary, depending on the context/goal of a particular analysis.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">variable feature</obo:IAO_0000118>
<rdfs:comment>An allele is a continuous extent of genomic sequence that spans a locus where variation is known to occur (i.e. where >1 version is known to exist). The minimal extent of an allele is the variable sequence itself (i.e. a 'sequence alteration'), but the notion of an allele includes larger regions that contain as proper parts one or more such alterations (e.g. a 'haplotype').
Our landsacpe analysis found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11]. where such variations don't neccessarily impact a gene.
To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, GENO allows for alleles that do not. But we do define the subtype 'gene allele' that refers more specifically to a particular version of a gene.
[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17)
[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17)
[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17)
[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17)
[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17)
[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17)
[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17)
[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17)
[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17)
[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17)
[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)</rdfs:comment>
<rdfs:label>allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000513 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000513">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000773"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation.</obo:IAO_0000115>
<rdfs:label xml:lang="en">aneusomic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000515 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000515">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000014"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000683"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000036"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000382"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000641"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000704"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An allele of a gene that contains some sequence alteration.</obo:IAO_0000115>
<rdfs:comment>A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset.</rdfs:comment>
<rdfs:label>variant gene allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000516 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000516">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000660"/>
<obo:IAO_0000112>The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>.
The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome.</obo:IAO_0000112>
<obo:IAO_0000115>The set of all sequence features occupying a particular genomic location across all homologous chromosomes in a genome.</obo:IAO_0000115>
<obo:IAO_0000116>TO DO: show a VCF representation of this example.</obo:IAO_0000116>
<obo:IAO_0000118>allelic complement</obo:IAO_0000118>
<obo:IAO_0000118>single locus feature complement</obo:IAO_0000118>
<rdfs:comment>- A genomic feature is any located feature in the genome, be it a junction, a single nucleotide, a gene, or an entire chromosome.
- The notion of a "complement" describes the collection of all elements in some defined set.
- The notion of "homologous" genomic features describes those that occupy the same locus on homologous chromosomes.
- Therefore, we use the term "single locus complement" to describe the set of all homologous features present at a particular genomic locus.
- This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes.</rdfs:comment>
<rdfs:label>single locus complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000524 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000524">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000536"/>
<obo:IAO_0000112>In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as:
shha<MO1-1ng/ul>; shhb<pFLAG-mmusShhb>
This notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct.</obo:IAO_0000112>
<obo:IAO_0000115>A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state.</obo:IAO_0000115>
<obo:IAO_0000116>We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes.
Our rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome.
Finally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment."</obo:IAO_0000116>
<obo:IAO_0000118>experimental genotype</obo:IAO_0000118>
<obo:IAO_0000118>expression genotype</obo:IAO_0000118>
<rdfs:comment>An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.
The 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations.</rdfs:comment>
<rdfs:label xml:lang="en">extrinsic genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000525 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000525">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000536"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000524"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000719"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs).</obo:IAO_0000115>
<obo:IAO_0000116>Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment."</obo:IAO_0000116>
<rdfs:comment>An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment.</rdfs:comment>
<rdfs:label xml:lang="en">effective genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000527 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000527">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000715"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000504"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A set of all targeted genes in a single genome in the context of a given experiment (e.g. both copies of the WT shha gene in a zebrafish exposed to shha-targeting morpholinos)</obo:IAO_0000115>
<obo:IAO_0000118>reagent-targeted gene complement</obo:IAO_0000118>
<rdfs:label xml:lang="en">reagent-targeted gene complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000528 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000528">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000715"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000382"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000506"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>The set of all transgenes trransiently expressed in a biological system in the context of a given experiment.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">experimental transgene complement</obo:IAO_0000118>
<rdfs:label>transiently-expressed transgene complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000529 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000529">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000737"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000443"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000704"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes).</obo:IAO_0000112>
<obo:IAO_0000115>A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism).</obo:IAO_0000115>
<obo:IAO_0000116>See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself.</obo:IAO_0000116>
<obo:IAO_0000118>expression allele</obo:IAO_0000118>
<rdfs:comment>Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism).
The identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system.</rdfs:comment>
<rdfs:label xml:lang="en">expression-variant gene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000533 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000533">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000804"/>
<obo:IAO_0000118>gene targeting reagent</obo:IAO_0000118>
<obo:IAO_0000118>sequence targeting reagent</obo:IAO_0000118>
<rdfs:label xml:lang="en">gene knockdown reagent</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000534 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000534">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000737"/>
<obo:IAO_0000115>A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">targeted gene segment</obo:IAO_0000118>
<rdfs:label>reagent-targeted gene subregion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000536 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000536">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000660"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000715"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference.</obo:IAO_0000115>
<obo:IAO_0000116>As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh<tbx292>, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above.</obo:IAO_0000116>
<obo:IAO_0000119>Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09).
Note however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO.</obo:IAO_0000119>
<rdfs:comment>1. Scope of 'Genetic State':
'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular locus ofr loci in a genome (i.e. across all homologous chromosomes containing this locus). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.
2. Genotype Subtypes:
In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed.
Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic locus; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.
3. The Genotype Partonomy:
'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements:
- GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome)
- Genomic Background: AB (the reference against which the GVC is variant)
- VSLC1: fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus)
- VSLC2: fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus)
- Allele 1: fgf8a<ti282a> (variant version of the fgf8a gene, present in two copies)
- Allele 2: fgf3<t24149> (variant version of the fgf3 gene, present in one copy)
- Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy)
- Sequence Alteration1: <ti282a> (the specific mutation within the fgf8a gene that makes it variant)
- Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant)
A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md
One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data.</rdfs:comment>
<rdfs:label xml:lang="en">genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000575 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000575">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0001001"/>
<rdfs:comment>ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl
This ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes.</rdfs:comment>
<rdfs:label>zebrafish phenotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000602 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000602">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000875"/>
<obo:IAO_0000115>an allelic state where a single allele exists at a particular locus in the organellar genome (mitochondrial or plastid) of a cell/organism.</obo:IAO_0000115>
<rdfs:label xml:lang="en">homoplasmic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000603 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000603">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000875"/>
<obo:IAO_0000115>an allelic state where more than one type of allele exists at a particular locus in the organellar genome (mitochondrial or plastid) of a cell/organism.</obo:IAO_0000115>
<rdfs:label xml:lang="en">heteroplasmic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000604 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000604">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000134"/>
<rdfs:label xml:lang="en">hemizygous X-linked</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000605 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000605">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000134"/>
<rdfs:label xml:lang="en">hemizygous Y-linked</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000606 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000606">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000134"/>
<rdfs:label xml:lang="en">hemizygous insertion-linked</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000611 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000611">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000899"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000152"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000010"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).</obo:IAO_0000115>
<obo:IAO_0000116>Being a 'background genotype' implies the derivation of some variant from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it.</obo:IAO_0000116>
<obo:IAO_0000118>reference genotype</obo:IAO_0000118>
<rdfs:label xml:lang="en">background genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000614 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000614">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000830"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000105"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three".</obo:IAO_0000112>
<obo:IAO_0000115>An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.</obo:IAO_0000115>
<obo:IAO_0000116>New term request for SO.</obo:IAO_0000116>
<obo:IAO_0000119>http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:
chromosome > arm > region > band > sub-band
Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):
chromosome > arm > band > sub-band > sub-sub-band</obo:IAO_0000119>
<rdfs:label xml:lang="en">chromosomal region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000616 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000616">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000830"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000341"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000618"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three".</obo:IAO_0000112>
<obo:IAO_0000119>http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:
chromosome > arm > region > band > sub-band
Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):
chromosome > arm > band > sub-band > sub-sub-band</obo:IAO_0000119>
<rdfs:label xml:lang="en">chromosome sub-band</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000618 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000618">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000788"/>
<obo:IAO_0000118>chromosomal band brightness</obo:IAO_0000118>
<rdfs:label xml:lang="en">chromosomal band intensity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000619 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000619">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000618"/>
<rdfs:label xml:lang="en">gpos</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000620 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000620">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000618"/>
<rdfs:label xml:lang="en">gneg</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000621 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000621">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000618"/>
<rdfs:label xml:lang="en">gvar</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000622 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000622">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000619"/>
<rdfs:label xml:lang="en">gpos100</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000623 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000623">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000619"/>
<rdfs:label xml:lang="en">gpos75</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000624 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000624">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000619"/>
<rdfs:label xml:lang="en">gpos50</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000625 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000625">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000619"/>
<rdfs:label xml:lang="en">gpos25</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000628 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000628">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000105"/>
<obo:IAO_0000115>A chromosome arm that is the shorter of the two arms of a given chromosome.</obo:IAO_0000115>
<obo:IAO_0000118>p-arm</obo:IAO_0000118>
<obo:IAO_0000118>stalk</obo:IAO_0000118>
<rdfs:label xml:lang="en">short chromosome arm</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000629 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000629">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000105"/>
<obo:IAO_0000115>A chromosome arm that is the longer of the two arms of a given chromosome.</obo:IAO_0000115>
<obo:IAO_0000118>q-arm</obo:IAO_0000118>
<rdfs:label xml:lang="en">long chromosome arm</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000632 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000632">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000619"/>
<rdfs:label>gpos66</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000633 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000633">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000619"/>
<rdfs:label>gpos33</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000637 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000637">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0005836"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002525"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000902"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed.</obo:IAO_0000115>
<rdfs:label xml:lang="en">regulatory transgene region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000638 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000638">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000460"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002525"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000902"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A transgene part whose sequence is expressed in a gene product through transcription and/or translation.</obo:IAO_0000115>
<obo:IAO_0000118>coding transgene feature</obo:IAO_0000118>
<rdfs:label xml:lang="en">expressed transgene region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000640 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000640">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000638"/>
<rdfs:label xml:lang="en">reporter region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000642 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000642">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0000902"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000911"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000783"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A transgene whose product is used as a selectable marker.</obo:IAO_0000115>
<rdfs:label xml:lang="en">selectable marker transgene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000644 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000644">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000899"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryootic cell.</obo:IAO_0000115>
<obo:IAO_0000119>Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)</obo:IAO_0000119>
<rdfs:comment>Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations).
A base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation).</rdfs:comment>
<rdfs:label xml:lang="en">karyotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000645 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000645">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000899"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000650"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000000"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A genomic genotype where the genomic background specifies a male or female sex chromosome complement.</obo:IAO_0000115>
<obo:IAO_0000116>This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).
In the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former.</obo:IAO_0000116>
<obo:IAO_0000118>intrinsic genotype (sex-specific)</obo:IAO_0000118>
<obo:IAO_0000118>sex-qualified genotype</obo:IAO_0000118>
<obo:IAO_0000118>sex-qualified intrinsic genotype</obo:IAO_0000118>
<rdfs:comment>We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances.
Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome.</rdfs:comment>
<rdfs:label xml:lang="en">genomic genotype (sex-qualified)</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000646 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000646">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000645"/>
<obo:IAO_0000115>A genomic genotype here the genomic background specifies a male sex chromosome complement.</obo:IAO_0000115>
<rdfs:label xml:lang="en">male intrinsic genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000647 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000647">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000645"/>
<obo:IAO_0000115>A genomic genotype here the genomic background specifies a female sex chromosome complement.</obo:IAO_0000115>
<rdfs:label xml:lang="en">female intrinsic genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000649 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000649">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000611"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000772"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A background genotype whose sequence or identity is not known or specified.</obo:IAO_0000115>
<rdfs:label xml:lang="en">unspecified background genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000659 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000659">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000701"/>
<obo:IAO_0000115>An exhaustive collection of all genetic entities of a specified type present as part of some larger genetic entity (e.g. all chromosomes in a genome, all variant alleles in a genome, all copies of a particular gene or allele in a genome, all allleles defined in a haplotype).</obo:IAO_0000115>
<rdfs:comment>Not all sequence feature complements will be collections - i.e. in some cases the complement of all features of type X will consist of a single feature. For example, a 'single locus complement' for an X-linked locus in a XY male.</rdfs:comment>
<rdfs:label xml:lang="en">sequence feature complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000660 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000660">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000659"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An exhaustive collection of all features of a specified type in a single genome (e.g. all chromosomes in a genome, all variant features in a genome, all copies of a given gene or allele in a genome).</obo:IAO_0000115>
<obo:IAO_0000116>In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member.</obo:IAO_0000116>
<obo:IAO_0000118>genomic locus complement</obo:IAO_0000118>
<rdfs:comment>A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. A complement is the collection of all elements in a set (i.e. "the full number of things in a set"). Here, a 'genomic feature complement' is here the set of all features in a single genome of a specified type (according to some defined inclusion criteria).</rdfs:comment>
<rdfs:label xml:lang="en">genomic feature complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000666 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000666">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000481"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002525"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000014"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc).</obo:IAO_0000115>
<obo:IAO_0000118>defined gene part</obo:IAO_0000118>
<rdfs:label>gene part</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000667 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000667">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0000902"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000910"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000640"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000783"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A transgene that codes for a product used as a reporter of gene expression or activity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">reporter transgene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000680 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000680">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000112>A junction between bases, a deletion variant, a terminus at the end of a chromosome.</obo:IAO_0000112>
<obo:IAO_0000115>A genomic feature that has an extent of zero.</obo:IAO_0000115>
<obo:IAO_0000116>Former logical def:
'genomic feature'
and (has_extent value 0)</obo:IAO_0000116>
<rdfs:label xml:lang="en">obsolete_null feature</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000681 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000681">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000684"/>
<rdfs:subClassOf>
<owl:Class>
<owl:complementOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000248"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000340"/>
</owl:Restriction>
</owl:complementOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000139"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000685"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found.</obo:IAO_0000115>
<obo:IAO_0000118>aberrant extrachromosomal replicon</obo:IAO_0000118>
<obo:IAO_0000118>exogenous extrachromosomal replicon</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">transgenic extrachromosomal replicon</obo:IAO_0000118>
<rdfs:comment>Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'variant locus' and a 'sequence alteration'.</rdfs:comment>
<rdfs:label>novel extrachromosomal replicon</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000684 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000684">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000685"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome.</obo:IAO_0000115>
<obo:IAO_0000116>This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature.</obo:IAO_0000116>
<rdfs:comment>Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles.</rdfs:comment>
<rdfs:label xml:lang="en">novel replicon</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000685 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000685">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000773"/>
<obo:IAO_0000115>An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome.</obo:IAO_0000115>
<rdfs:label xml:lang="en">novel</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000688 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000688">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<obo:IAO_0000115>A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide).</obo:IAO_0000115>
<rdfs:label xml:lang="en">terminus</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000701 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000701">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000701"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0000110"/>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<obo:IAO_0000115>An extent of biological sequence, or a collection of such extents, whose identity is dependent on both its sequence and its position.</obo:IAO_0000115>
<rdfs:comment>GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.
1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.
2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).
3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.</rdfs:comment>
<rdfs:label xml:lang="en">sequence feature or collection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000702 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000702">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000896"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An ordered collection units representing successive monomers of a biological macromolecule.</obo:IAO_0000115>
<obo:IAO_0000116>GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.
1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.
2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).
3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.</obo:IAO_0000116>
<obo:IAO_0000118>biomacromolecular sequence</obo:IAO_0000118>
<obo:IAO_0000118>state</obo:IAO_0000118>
<oboInOwl:hasDbXref>VMC:State</oboInOwl:hasDbXref>
<rdfs:comment>'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome.</rdfs:comment>
<rdfs:label xml:lang="en">biological sequence</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000896"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:Restriction>
</owl:annotatedTarget>
<obo:GENO_0000834 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000834>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
<owl:annotatedTarget>state</owl:annotatedTarget>
<obo:IAO_0000116>In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele.</obo:IAO_0000116>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/GENO_0000713 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000713">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<obo:IAO_0000115>A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.</obo:IAO_0000115>
<rdfs:comment>GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.
1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.
2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).
3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.</rdfs:comment>
<rdfs:label xml:lang="en">qualified sequence feature or collection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000714 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000714">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000713"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000580"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000726"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes).</obo:IAO_0000112>
<obo:IAO_0000115>A sequence feature whose identity is dependent on the context or state of its material bearer (in addition to its sequence and position). This context describes factors external to its inherent sequence and position. Examples include the context of being targeted by gene-knockdown reagents, or the context of being the target of an epigenetic modification.</obo:IAO_0000115>
<rdfs:comment>GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.
1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.
2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).
3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.
Modeling sequence entities at this 'qualified' level useful when it is important to distinguish features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, a situation where the shha gene is targeted by two different morpholinos and phenotypes assessed for each. This is analogous to two different alleles of the shha gene at the sequence feature level, and similarly worthy of being distinguished when considering how the resulting alteration in gene expression impacts the measured phenotypes of the host zebrafish.</rdfs:comment>
<rdfs:label xml:lang="en">qualified genomic feature</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000714"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000580"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
</owl:Restriction>
</owl:annotatedTarget>
<obo:GENO_0000834 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000834>
<rdfs:comment>This axiom is an initial attempt to formalize the identity criteria of an extrinnsic context that separates qualified sequence features from sequence features (i.e. the context of its material bearer). As we further develop our efforts here this will get refined and more precise.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000714"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000726"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
</owl:Restriction>
</owl:annotatedTarget>
<obo:GENO_0000834 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000834>
<rdfs:comment>Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position).</rdfs:comment>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/GENO_0000715 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000715">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000713"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000714"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000726"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000660"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A set of all qualified sequence features of a specified type in a single genome.</obo:IAO_0000115>
<obo:IAO_0000116>In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'qualified genomic feature' as a member.</obo:IAO_0000116>
<rdfs:label xml:lang="en">qualified genomic feature complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000719 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000719">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000536"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000516"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0001026"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.</obo:IAO_0000115>
<obo:IAO_0000116>Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome.</obo:IAO_0000116>
<rdfs:comment>1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.
2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons.</rdfs:comment>
<rdfs:label xml:lang="en">intrinsic genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000720 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000720">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000783"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000780"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label xml:lang="en">DNA sequence</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000721 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000721">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000783"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000781"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label xml:lang="en">RNA sequence</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000722 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000722">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000783"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000782"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label xml:lang="en">amino acid sequence</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000724 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000724">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<rdfs:label xml:lang="en">obsolete_biological sequence or collection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000725 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000725">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000724"/>
<rdfs:label xml:lang="en">obsolete_biological sequence collection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000736 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000736">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000714"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature.</obo:IAO_0000115>
<rdfs:comment>As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell).</rdfs:comment>
<rdfs:label xml:lang="en">location-qualified sequence feature</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000737 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000737">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000714"/>
<obo:IAO_0000115>A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct)</obo:IAO_0000115>
<rdfs:label xml:lang="en">expression-qualified sequence feature</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000768 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000768">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence.</obo:IAO_0000115>
<obo:IAO_0000116>This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">genomic coordinates</obo:IAO_0000118>
<obo:IAO_0000231>remodeling notion of sequence feature position around the idea of a 'genomic locus'</obo:IAO_0000231>
<rdfs:label>obsolete_genomic position</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000770 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000770">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000351"/>
<rdfs:label xml:lang="en">phenotypic inheritance process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000772 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000772">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000788"/>
<obo:IAO_0000115>A sequence attribute inhering in a feature whose identity is not specified.</obo:IAO_0000115>
<rdfs:label xml:lang="en">unspecified</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000773 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000773">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000788"/>
<obo:IAO_0000115>An attribute describing a type of variation inhering in a sequence feature or collection.</obo:IAO_0000115>
<obo:IAO_0000118>allele attribute</obo:IAO_0000118>
<rdfs:label xml:lang="en">variation attribute</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000777 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000777">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000899"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000033"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>An intrinsic genotype that specifies variation from a reference or background.</obo:IAO_0000115>
<rdfs:label xml:lang="en">variant genomic genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000778 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000778">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities.</obo:IAO_0000115>
<obo:IAO_0000231>eliminating classes that are not necessary or add uneeded complexity.</obo:IAO_0000231>
<rdfs:label xml:lang="en">obsolete_sequence information entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000779 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000779">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
<obo:IAO_0000118>biological sequence residue</obo:IAO_0000118>
<obo:IAO_0000118>monomeric residue</obo:IAO_0000118>
<rdfs:label xml:lang="en">biological sequence unit</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000780 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000780">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000779"/>
<obo:IAO_0000118>deoxyribonucleic acid residue</obo:IAO_0000118>
<rdfs:label xml:lang="en">DNA residue</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000781 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000781">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000779"/>
<obo:IAO_0000118>ribonucleic acid residue</obo:IAO_0000118>
<rdfs:label xml:lang="en">RNA residue</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000782 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000782">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000779"/>
<rdfs:label xml:lang="en">amino acid residue</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000788 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000788">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:IAO_0000115>An attribute, quality, or state of a sequence or sequence feature.</obo:IAO_0000115>
<obo:IAO_0000116>Sequence feature attributes can be based on qualities of the material bearers of the feature, for example, the staining intensity of a chromosomal band feature.</obo:IAO_0000116>
<oboInOwl:hasDbXref>http://purl.obolibrary.org/obo/SO_0000400</oboInOwl:hasDbXref>
<rdfs:label>sequence feature attribute</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000815 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000815">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000115>The location of a sequence feature as defined by its start and end position on some reference coordinate system.</obo:IAO_0000115>
<rdfs:comment>1. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a location is distinct from a sequence feature that occupies it. A more concrete analogy can be drawn to the distinction between a street address (the location) and the building that occupies it (the sequence feature).
2. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, defined by a alignment to some reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2.</rdfs:comment>
<rdfs:label xml:lang="en">sequence feature location</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000818 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000818">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000714"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature)</obo:IAO_0000115>
<rdfs:label xml:lang="en">modification-qualified sequence feature</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000823 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000823">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000719"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000516"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000112>1. The zebrafish "fgf8a<ti282a>/fgf8a<+>" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state).
2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308.
##fileformat=VCFv4.2
##FORMAT=<ID=GT, Description="Genotype, 0=REF, 1=ALT">
#CHROM POS REF ALT FILTER FORMAT SAMP001
20 2300608 C T PASS GT 0/1
20 2301308 T G PASS GT 1/1
(derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html)
3. Some allelic genotype formats encode the genotype as a single string - e.g. "GRCh38 Chr12:258635(A;T)" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12.</obo:IAO_0000112>
<obo:IAO_0000115>A genotype that specifies the 'allelic state' at a particular locus in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes.</obo:IAO_0000115>
<obo:IAO_0000118>single locus genotype</obo:IAO_0000118>
<rdfs:comment>An 'allelic genotype' describes the set of alleles present at a particular locus ('allelic genotype') in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location.
This contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background.</rdfs:comment>
<rdfs:label xml:lang="en">allelic genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000833 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000833">
<rdfs:subClassOf rdf:resource="http://purl.org/oban/association"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000580"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ENVO_01000254"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000580"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0032502"/>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002091"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000105"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002093"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000105"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/oban/association_has_object"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0001001"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/oban/association_has_subject"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000536"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000536"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000116>Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each.</obo:IAO_0000116>
<rdfs:label xml:lang="en">genotype-phenotype association</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000833"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000580"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ENVO_01000254"/>
</owl:Restriction>
</owl:annotatedTarget>
<obo:GENO_0000834 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000834>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000833"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000580"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0032502"/>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002091"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000105"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002093"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000105"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:annotatedTarget>
<obo:GENO_0000834 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000834>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000833"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/oban/association_has_object"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0001001"/>
</owl:Restriction>
</owl:annotatedTarget>
<obo:GENO_0000834 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000834>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GENO_0000833"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/oban/association_has_subject"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000536"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000536"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:annotatedTarget>
<obo:GENO_0000834 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000834>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/GENO_0000839 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000839">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000527"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000382"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000504"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label xml:lang="en">knockdown reagent targeted gene complement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000848 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000848">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000484"/>
<obo:IAO_0000115>A sequence alteration within the coding sequence of a gene.</obo:IAO_0000115>
<obo:IAO_0000231>Not required at this poitn, so marked exploratory and obsoleted.
Asserted under sequence_alteration.</obo:IAO_0000231>
<rdfs:label xml:lang="en">obsolete_coding sequence alteration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000850 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000850">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000856"/>
<obo:IAO_0000115>A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome.</obo:IAO_0000115>
<rdfs:label xml:lang="en">P-element construct</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000856 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000856">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000804"/>
<obo:IAO_0000115>An engineered region that is used to transfer foreign genetic material into a host cell.</obo:IAO_0000115>
<obo:IAO_0000118>engineered_genetic_vector</obo:IAO_0000118>
<rdfs:comment>Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells.
Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors.</rdfs:comment>
<rdfs:label xml:lang="en">engineered genetic construct</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000861 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000861">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000902"/>
<obo:IAO_0000115>A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct.</obo:IAO_0000115>
<obo:IAO_0000118>non-integrated transgene</obo:IAO_0000118>
<rdfs:label xml:lang="en">extra-chromosomal transgene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000870 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000870">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A collection of more than one sequence feature.</obo:IAO_0000115>
<oboInOwl:hasDbXref>http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection</oboInOwl:hasDbXref>
<rdfs:label xml:lang="en">obsolete_sequence feature collection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000871 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000871">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A set of genetically-linked alleles, that reside at different locations on the same chromosomal strand and are typically inherited/transmitted together.</obo:IAO_0000115>
<obo:IAO_0000231>reconsiderd defintion of haplotype to better align with SO and GA4GH/VMC definitions.
Former SC axiom: has_member some allele.</obo:IAO_0000231>
<terms:source>Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype.</terms:source>
<rdfs:comment>Haplotypes are 'complements' in that they include the set of all alleles in a defined region of the genome. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. Haplotypes are located within 'haplotype blocks' - regions of DNA where no recombination occurs between alleles on the same chromosomal strand. The 'haplotype' within a 'haplotype block' may be comprised of any number of distinct alleles.
As described at https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is commonly used to describe three specific cases of genetically-linked alleles within a haplotype block:
1. The first is a set of linked 'gene alleles' - specific versions of entire genes that reside in tightly linked clusters on a single chromosome.
2. The second is a set of linked 'single nucleotide polymorphism' (SNP) alleles that tend to occur together (i.e. be statistically associated).
3. A third and less common use is describing individual collections of specific mutations within a given genetic segment - typically short tandem repeats.
Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.
The GENO definition is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked and thus tend to be co-inherited across successive generations.</rdfs:comment>
<rdfs:label xml:lang="en">obsolete_haplotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000872 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000872">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000876"/>
<obo:IAO_0000115>A attribute describing the number of copies of a feature present in a genome.</obo:IAO_0000115>
<rdfs:label xml:lang="en">copy number</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000873 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000873">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000874"/>
<obo:IAO_0000115>A relation used to describe an environment contextualizing the identity of an entity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">microsatellite alteration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000874 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000874">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<obo:IAO_0000115>A relation used to describe a process contextualizing the identity of an entity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">repeat region alteration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000875 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000875">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000876"/>
<obo:IAO_0000115>A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism</obo:IAO_0000115>
<rdfs:label xml:lang="en">allelic state</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000876 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000876">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000788"/>
<obo:IAO_0000118>allelic dosage</obo:IAO_0000118>
<obo:IAO_0000118>an attribute inhering in a feature based on the total number or relative stoichiometry of copies present in a particular genome.</obo:IAO_0000118>
<obo:IAO_0000118>gene dosage</obo:IAO_0000118>
<rdfs:label xml:lang="en">genetic dosage</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000877 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000877">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000788"/>
<obo:IAO_0000115>A quality inhering in an allele based on its source/origin - typically the parent from which it was inherited.</obo:IAO_0000115>
<rdfs:label xml:lang="en">allele origin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000878 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000878">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000888"/>
<obo:IAO_0000115>a quality of an allele in virtue of its having been inherited from a female parent.</obo:IAO_0000115>
<rdfs:label xml:lang="en">maternal allele origin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000879 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000879">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000888"/>
<obo:IAO_0000115>a quality of an allele in virtue of its having been inherited from a male parent.</obo:IAO_0000115>
<rdfs:label xml:lang="en">paternal allele origin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000880 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000880">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000877"/>
<obo:IAO_0000115>a quality of an allele in virtue of its having occurred through a de novo mutaiton, rather than inherited from a parent..</obo:IAO_0000115>
<rdfs:label xml:lang="en">de novo allele origin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000881 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000881">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000877"/>
<obo:IAO_0000115>a quality of an allele in virtue of its origin not being known.</obo:IAO_0000115>
<rdfs:label xml:lang="en">unknown allele origin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000882 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000882">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000901"/>
<obo:IAO_0000115>A quality inhering in a particular allele in virtue of its presence only in the genome of non-germ cells in an organism, and therefore not inherited by subsequent generations.</obo:IAO_0000115>
<rdfs:label xml:lang="en">somatic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000883 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000883">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells).</obo:IAO_0000115>
<obo:IAO_0000118>germ-line</obo:IAO_0000118>
<obo:IAO_0000231>replaced by GENO:0000900 ! 'germline'</obo:IAO_0000231>
<rdfs:label xml:lang="en">obsolete_gametic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000885 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000885">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000823"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000516"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/GENO_0000512"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>An allelic genotype specifying the set of two alleles present at a locus in a diploid genome (i.e., a diploid 'single locus complement')
Alt: A sequence feature complement comprised of two haplotypes at a particular locus on paired homologous chromosomes in a diploid genome.</obo:IAO_0000115>
<rdfs:comment>"Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes."
From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/</rdfs:comment>
<rdfs:label xml:lang="en">diplotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000886 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000886">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000788"/>
<obo:IAO_0000115>A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes.</obo:IAO_0000115>
<rdfs:label>allelic phase</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000887 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000887">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000112"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_8090"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_8090"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>oryzias latipes strain</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000888 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000888">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000877"/>
<obo:IAO_0000115>a quality of an allele in virtue of its having been inherited from either parent.</obo:IAO_0000115>
<rdfs:label>parental allele origin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000889 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000889">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000141"/>
<rdfs:label>unknown inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000890 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000890">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000701"/>
<obo:IAO_0000112>The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”.</obo:IAO_0000112>
<obo:IAO_0000115>One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model></obo:IAO_0000115>
<obo:IAO_0000116>The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://datamodel.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model.</obo:IAO_0000116>
<obo:IAO_0000119>http://datamodel.clinicalgenome.org/allele/resource/canonical_allele/</obo:IAO_0000119>
<terms:source>ClinGen Allele Model (http://datamodel.clinicalgenome.org/allele/)</terms:source>
<rdfs:comment>As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.
In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references)</rdfs:comment>
<rdfs:label>canonical allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000891 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000891">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000890"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence.</obo:IAO_0000115>
<obo:IAO_0000116>The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://datamodel.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model.</obo:IAO_0000116>
<obo:IAO_0000119>http://datamodel.clinicalgenome.org/allele/resource/contextual_allele/</obo:IAO_0000119>
<terms:source>ClinGen Allele Model (http://datamodel.clinicalgenome.org/allele/)</terms:source>
<rdfs:comment>The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene.</rdfs:comment>
<rdfs:label>contextual allele</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000892 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000892">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000141"/>
<obo:IAO_0000115>A mode of inheritance whereby manifestation of a trait or condition occurs only when both affected and unaffected mitochondria are inherited (i.e. some mitochondria that do and some that do not contain the causative allele).</obo:IAO_0000115>
<rdfs:label>heteroplasmic mitochondrial inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000893 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000893">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000141"/>
<obo:IAO_0000115>A mode of inheritance whereby manifestation of a trait or condition occurs only when affected mitochondria are inherited (i.e. mitochondria containing the causative allele)</obo:IAO_0000115>
<rdfs:label>homoplasmic mitochondrial inheritance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000897 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000897">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000481"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000726"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000481"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000660"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000481"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000660"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000715"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:GENO_0000905 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000905>
<obo:IAO_0000115>An generically dependent continuant that carries biological sequence that is part of or derived from a genome.</obo:IAO_0000115>
<obo:IAO_0000116>An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities.</obo:IAO_0000116>
<rdfs:label xml:lang="en">genomic entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000898 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000898">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations.</obo:IAO_0000115>
<obo:IAO_0000116>Consider http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block. And consider whether, as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele.</obo:IAO_0000116>
<obo:IAO_0000119>From DOI: 10.1126/science.1069424</obo:IAO_0000119>
<obo:IAO_0000231>reconsiderd defintion of haplotype to better align with SO and GA4GH/VMC definitions.
Former SC axiom: has_part some haplotype</obo:IAO_0000231>
<rdfs:comment>A 'haplotype block' is a continuous region of sequence that contains 'haplotypes' - sets of discontinuous, genetically-linked sequence alterations on the same chromosomal strand that are typically co-inherited within this haplotype block. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span one sequence alteration or several, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.</rdfs:comment>
<rdfs:label xml:lang="en">obsolete_haplotype block</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000899 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000899">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000719"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001026"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000385"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000611"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.</obo:IAO_0000115>
<obo:IAO_0000116>'Genomic Genotype' vs 'Genome' in GENO:
A genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome.</obo:IAO_0000116>
<rdfs:comment>1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.
2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons.</rdfs:comment>
<rdfs:label xml:lang="en">genomic genotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000900 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000900">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000901"/>
<obo:IAO_0000118>gametic</obo:IAO_0000118>
<rdfs:comment>A quality inhering in a particular allele in virtue of its presence in the genome of germ cells in an organism, and therefore having the potential to be inherited by subsequent generations.</rdfs:comment>
<rdfs:label xml:lang="en">germline</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000901 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000901">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000788"/>
<obo:IAO_0000115>A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)</obo:IAO_0000115>
<rdfs:comment>Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others.</rdfs:comment>
<rdfs:label>allele cellular context</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000902 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000902">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000815"/>
<obo:IAO_0000115>The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system</obo:IAO_0000115>
<obo:IAO_0000116>In GENO, the notion of a Genomic Locus plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological semantics FALDO:Region class are not clear, nor is how it fits into the GENO model. We will work to resolve these questions and ideally converge these concepts in the future.
We don't link a Genomic Locus to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given locus is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences.</obo:IAO_0000116>
<obo:IAO_0000116>In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we would have a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed.
For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus).</obo:IAO_0000116>
<obo:IAO_0000118>genomic location</obo:IAO_0000118>
<oboInOwl:hasDbXref>VMC:Location</oboInOwl:hasDbXref>
<rdfs:comment>1. A genomic locus is defined by its begin and end coordinates on a reference genome, but it is not identified by a particular sequence that may reside there. In GENO, we say that a genomic locus is *occupied_by* a sequence feature. This sequence feature is identified by its sequence and its position in the genome (i.e. the locus it occupies). So the ATG sequence beginning the ORF of the human Shh gene shares the same sequence as the ATG beginning the ORF of the human Akt gene. But these are distinct sequence features because they occupy different loci in the genome. We call sequence features that are located in a genome 'genomic features'.
2. A particular locus (e.g. the human Shh gene locus) may be occupied by different sequence features (e.g. different 'alleles' of the Shh gene). Within the genome of a single (diploid) organism, there is potential for two sequence features to exit at such a locus (i.e. two different Shh alleles). Across the genomes of all cells comprising members of a species, many more alleles of the Shh gene may exist. These alleles occupy the same genomic locus with different sequences (or no sequence at all in the case of a complete Shh deletion).
3. The notion of a genomic locus in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic locus is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. A more concrete analogy can be drawn to the distinction between a street address (the locus) and the building that occupies it (the sequence feature).</rdfs:comment>
<rdfs:label xml:lang="en">genomic locus</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000904 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000904">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001000"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:GENO_0000905 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000905>
<obo:IAO_0000115>A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc).</obo:IAO_0000115>
<obo:IAO_0000116>useful organizational term to collect entities that have genomes/genotypes.</obo:IAO_0000116>
<rdfs:label xml:lang="en">organismal entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000907 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000907">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<obo:IAO_0000115>The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)</obo:IAO_0000115>
<rdfs:label xml:lang="en">gene product</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000910 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000910">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000086"/>
<rdfs:label xml:lang="en">reporter role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000911 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000911">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000086"/>
<rdfs:label xml:lang="en">selectable marker role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000912 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000912">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000638"/>
<rdfs:label xml:lang="en">selectable marker region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000914 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000914">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001026"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000239"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001505"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A genome whose sequence is identical to that of a genome sequence considered to be the reference.</obo:IAO_0000115>
<rdfs:label xml:lang="en">reference genome</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000915 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000915">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000512"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000408"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000916"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it.</obo:IAO_0000115>
<obo:IAO_0000119>Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype.</obo:IAO_0000119>
<rdfs:comment>1. Haplotypes typically contain 'genetically-linked' sequence alterations that are likely to be co-inherited and survive descent across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where theis term refers to sequence containing two or more alterations that are beleived to be 'in cis' on the same chromosomal strand. GENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to represent a haplotype, if there is an expectation of low recombination frequency within the allele. For example, a 'gene allele' is a particular version of a gene that contains one or more sequence alterations, and represents a haplotype that spans the extent of a gene.
2. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene' - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (if it is the case that there is a lack of historic recombination within the extent of the gene)
3. As described at https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is commonly used to describe three specific cases of genetically-linked alleles within a haplotype block:
a. The first is a set of linked 'gene alleles' - specific versions of entire genes that reside in tightly linked clusters on a single chromosome.
b. The second is a region containing linked 'single nucleotide polymorphism' (SNP) alleles that tend to occur together on a chromosomal strand (i.e. be statistically associated).
c. A third and less common use is describing individual collections of specific mutations within a given genetic segment - typically short tandem repeats.
Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.
The GENO definition of haplotype is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked and thus tend to be co-inherited across successive generations. This typically covers the case of a 'gene allele' (a particular version of a gene) - as most genes span regions of a size that there is little chance of recombination events moving cis alterations onto separate chromosomes.</rdfs:comment>
<rdfs:label xml:lang="en">haplotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GENO_0000916 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000916">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
<obo:IAO_0000115>A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations.</obo:IAO_0000115>
<obo:IAO_0000119>Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block.</obo:IAO_0000119>
<rdfs:comment>A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene' - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.
The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span one sequence alteration or several, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.</rdfs:comment>
<rdfs:label xml:lang="en">haplotype block</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0003674 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003674">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<rdfs:label>molecular function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0032502 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0032502">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000351"/>
<obo:IAO_0000115>A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]</obo:IAO_0000115>
<rdfs:label xml:lang="en">developmental process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/HP_0000118 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0000118">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0001001"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pulling in HP 'phenotypic abnormality' root here</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">human phenotypic abnormality</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/HsapDv_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/HsapDv_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000351"/>
<obo:IAO_0000116>Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology.</obo:IAO_0000116>
<obo:IAO_0000119>A spatiotemporal region encompassing some part of the life cycle of an organism.</obo:IAO_0000119>
<rdfs:label xml:lang="en">human life cycle stage</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<obo:IAO_0000111 xml:lang="en">information content entity</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Examples of information content entites include journal articles, data, graphical layouts, and graphs.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000142</obo:IAO_0000119>
<rdfs:label>information content entity</rdfs:label>
<rdfs:label xml:lang="en">information content entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000102 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000118>ontology metadata</obo:IAO_0000118>
<rdfs:label>data about an ontology part</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MP_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MP_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0001001"/>
<rdfs:comment>where to place this depends on if we take the organismal view or the quality centric view.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mammalian phenotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_10090 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10090">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdfs:label>Mus musculus</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_10239 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdfs:comment>Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies.</rdfs:comment>
<rdfs:label>Viruses</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_7955 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7955">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdfs:label>Danio rerio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_8090 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_8090">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdfs:label>Oryzias latipes</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_9606 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdfs:label>Homo sapiens</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000011 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>A processual entity that realizes a plan which is the concretization of a plan specification.</obo:IAO_0000115>
<obo:IAO_0000116>Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO.</obo:IAO_0000116>
<rdfs:label>planned process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000086 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000086">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<rdfs:label xml:lang="en">reagent role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000181 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000181">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000113"/>
<obo:IAO_0000115>a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area</obo:IAO_0000115>
<rdfs:label xml:lang="en">population</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000435 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000435">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000007"/>
<obo:IAO_0000115>An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.</obo:IAO_0000115>
<rdfs:label>genotyping assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001148 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001148">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000166"/>
<obo:IAO_0000115>A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.</obo:IAO_0000115>
<rdfs:comment>A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.</rdfs:comment>
<rdfs:label>targeted gene knock-out technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001149 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001149">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000166"/>
<rdfs:label xml:lang="en">targeted gene knock-in technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0100026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100026">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000116>Stub class to serve as root of hierarchy for imports from NCBI Taxonomy.</obo:IAO_0000116>
<rdfs:label>organism</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0600043 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600043">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000007"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000106"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000211"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000002"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>the introduction. alteration or integration of genetic material into a cell or organism</obo:IAO_0000115>
<rdfs:label>genetic modification technique</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PATO_0000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000016">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000116>'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html</obo:IAO_0000116>
<obo:IAO_0000116>Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute.</obo:IAO_0000116>
<obo:IAO_0000118>color value</obo:IAO_0000118>
<rdfs:label xml:lang="en">obsolete_color brightness</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PATO_0000383 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000383">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001894"/>
<rdfs:label>female</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PATO_0000384 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000384">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001894"/>
<rdfs:label>male</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PATO_0001894 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0001894">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<rdfs:label xml:lang="en">phenotypic sex</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002351"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A material entity that consists of two or more organisms, viruses, or viroids.</obo:IAO_0000115>
<rdfs:comment>A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role).</rdfs:comment>
<rdfs:label>collection of organisms</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000000"/>
<obo:IAO_0000115>A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.</obo:IAO_0000115>
<rdfs:label>family</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000533"/>
<obo:IAO_0000115>Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.</obo:IAO_0000115>
<rdfs:label>morpholino_oligo</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000105 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000105">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000830"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000830"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three".</obo:IAO_0000112>
<obo:IAO_0000115>A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.</obo:IAO_0000115>
<obo:IAO_0000116>Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term.</obo:IAO_0000116>
<obo:IAO_0000119>http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:
chromosome > arm > region > band > sub-band
Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):
chromosome > arm > band > sub-band > sub-sub-band</obo:IAO_0000119>
<rdfs:label xml:lang="en">chromosome arm</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000110 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000110">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000701"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000239"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000903"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000815"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Any extent of continuous biological sequence.</obo:IAO_0000115>
<obo:IAO_0000116>GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.
1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.
2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).
3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.</obo:IAO_0000116>
<rdfs:comment>A sequence feature is an extent of biological sequence. An instance of a sequence feature is identified by both its sequence (inherent ordering of units representing nucleic acid or animo acid monomers) and its position (start and stop coordinates based on alignment with some reference feature). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome.</rdfs:comment>
<rdfs:label>sequence_feature</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000239"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000702"/>
</owl:Restriction>
</owl:annotatedTarget>
<obo:GENO_0000834 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000834>
<rdfs:comment>Formalizes the first identity criteria for a sequence feature of its sequence.</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000903"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000815"/>
</owl:Restriction>
</owl:annotatedTarget>
<obo:GENO_0000834 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:GENO_0000834>
<rdfs:comment>Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property).</rdfs:comment>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/SO_0000143 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000143">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001410"/>
<obo:IAO_0000115>A region of known length which may be used to manufacture a longer region.</obo:IAO_0000115>
<rdfs:label xml:lang="en">assembly_component</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000149 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000149">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000143"/>
<obo:IAO_0000115>A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.</obo:IAO_0000115>
<rdfs:label xml:lang="en">contig</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000159 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000159">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000678"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</owl:hasValue>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The point at which one or more contiguous nucleotides were excised.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">deleted_sequence</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleotide deletion</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleotide_deletion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_alt_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000033</obo:IAO_alt_id>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0000159</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<obo:IAO_xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Nucleotide_deletion</obo:IAO_xref>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">deletion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000165 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000165">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0005836"/>
<rdfs:label>enhancer</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000167 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000167">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0005836"/>
<obo:IAO_0000115>A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.</obo:IAO_0000115>
<rdfs:label>promoter</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000199 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000199">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A region of nucleotide sequence that has translocated to a new position.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transchr</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">translocated sequence</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0000199</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DBVAR</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">translocation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000207 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000207">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000248"/>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SSLP</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">simple sequence length polymorphism</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">simple sequence length variation</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0000207</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">simple_sequence_length_variation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000248 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000248">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000002"/>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sequence length variation</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0000248</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sequence_length_variation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000281 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000281">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000704"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000783"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000116>See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25.
Includes things like loxP sites, inducible promoters, ires elements, etc.</obo:IAO_0000116>
<rdfs:label>engineered_foreign_gene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000289 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000289">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
<obo:IAO_0000115>A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.</obo:IAO_0000115>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29</obo:IAO_0000119>
<rdfs:comment>A defined feature that includes any type of VNTR or SSLP locus.</rdfs:comment>
<rdfs:label>microsatellite</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000337 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000337">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000533"/>
<rdfs:label xml:lang="en">RNAi_reagent</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000340 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000340">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
<obo:IAO_0000115>Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.</obo:IAO_0000115>
<rdfs:comment>A complete chromosome sequence.</rdfs:comment>
<rdfs:label>chromosome</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000341 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000341">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000830"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000614"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000618"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three".</obo:IAO_0000112>
<obo:IAO_0000115>A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.</obo:IAO_0000115>
<obo:IAO_0000119>http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:
chromosome > arm > region > band > sub-band
Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):
chromosome > arm > band > sub-band > sub-sub-band
</obo:IAO_0000119>
<rdfs:comment>"Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.</rdfs:comment>
<rdfs:label xml:lang="en">chromosome band</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000577 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000577">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000830"/>
<rdfs:label xml:lang="en">centromere</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000637 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000637">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000116>Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct.</obo:IAO_0000116>
<rdfs:label xml:lang="en">obsolete_engineered_plasmid</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000667 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000667">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">insertion</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleotide insertion</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleotide_insertion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_alt_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000034</obo:IAO_alt_id>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0000667</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DBVAR</obo:IAO_subset>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">insertion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000694 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000694">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001483"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">single nucleotide polymorphism</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0000694</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SNP</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000699 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000699">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<rdfs:comment>A junction is a boundary between regions. A boundary has an extent of zero.</rdfs:comment>
<rdfs:label xml:lang="en">junction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000704 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000704">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
<obo:IAO_0000115>A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.</obo:IAO_0000115>
<obo:IAO_0000116>Regarding the distinction between a 'gene' and a 'gene allele':
Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).</obo:IAO_0000116>
<rdfs:comment>A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion.</rdfs:comment>
<rdfs:label>gene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000771 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000771">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
<obo:IAO_0000115>A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.</obo:IAO_0000115>
<obo:IAO_0000118>quantitative trait locus</obo:IAO_0000118>
<rdfs:label>QTL</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000783 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000783">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000788"/>
<obo:IAO_0000115>An attribute to describe a region that was modified in vitro.</obo:IAO_0000115>
<rdfs:label>engineered</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000804 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000804">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0000110"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000207"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000783"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000118>construct</obo:IAO_0000118>
<rdfs:label xml:lang="en">engineered_region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000830 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000830">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000481"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000248"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000340"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'.</obo:IAO_0000115>
<obo:IAO_0000118>chromosomal feature</obo:IAO_0000118>
<obo:IAO_0000118>gross chromosomal part</obo:IAO_0000118>
<rdfs:label>chromosome part</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000902 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000902">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000704"/>
<obo:IAO_0000115>A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome).</obo:IAO_0000115>
<rdfs:comment>Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism).
Note that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome.</rdfs:comment>
<rdfs:label xml:lang="en">transgene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001013 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001013">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000002"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">multiple nucleotide polymorphism</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001013</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MNP</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A variation that increases or decreases the copy number of a given region.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CNP</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CNV</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">copy number polymorphism</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">copy number variation</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001019</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<obo:IAO_xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Copy_number_variation</obo:IAO_xref>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">copy_number_variation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001026">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000660"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)</obo:IAO_0000115>
<obo:IAO_0000116>Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'referrence genome' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence.</obo:IAO_0000116>
<obo:IAO_0000118>'genome sequence'</obo:IAO_0000118>
<rdfs:comment>A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of chromosomes, but in some organisms (e.g. bacteria) it may be a single chromosomal entity. For this reason 'genome' classifies under 'sequence feature complement' rather than 'sequence feature collection'.</rdfs:comment>
<rdfs:label>genome</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001059 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001059">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GENO_0000512"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/GENO_0000784"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000112>A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele':
1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871.
2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112.
3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112.</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sequence variation</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_alt_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000004</obo:IAO_alt_id>
<obo:IAO_alt_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000007</obo:IAO_alt_id>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001059</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<rdfs:comment>1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion.
Alleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part.
2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'.
For a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference.
3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sequence_alteration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001218 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001218">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000667"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000093"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An insertion that derives from another organism, via the use of recombinant DNA technology.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transgenic insertion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001218</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transgenic_insertion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001410 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001410">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000110"/>
<obo:IAO_0000115>A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.</obo:IAO_0000115>
<rdfs:label xml:lang="en">experimental_feature</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001477 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001477">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000856"/>
<obo:IAO_0000115>A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.</obo:IAO_0000115>
<rdfs:label xml:lang="en">gene_trap_construct</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001478 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001478">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000856"/>
<obo:IAO_0000115>A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.</obo:IAO_0000115>
<rdfs:label xml:lang="en">promoter_trap_construct</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001479 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001479">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000856"/>
<obo:IAO_0000115>A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.</obo:IAO_0000115>
<rdfs:label xml:lang="en">enhancer_trap_construct</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001483 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001483">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000002"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">single nucleotide variant</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">kareneilbeck</obo:IAO_created_by>
<obo:IAO_creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Thu Oct 08 11:37:49 PDT 2009</obo:IAO_creation_date>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001483</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SNV</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001500 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001500">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000481"/>
<obo:IAO_0000115>A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.</obo:IAO_0000115>
<rdfs:label xml:lang="en">heritable_phenotypic_marker</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001505 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001505">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000017"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GENO_0000152"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>'GRCh37.p10' (a human reference genome build)</obo:IAO_0000112>
<obo:IAO_0000115>A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced.</obo:IAO_0000115>
<rdfs:label>reference genome sequence</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001742 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001742">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001019"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">copy number gain</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">gain</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">kareneilbeck</obo:IAO_created_by>
<obo:IAO_creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mon Feb 28 01:54:09 PST 2011</obo:IAO_creation_date>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001742</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DBVAR</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">copy_number_gain</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001743 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001743">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001019"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A sequence alteration whereby the copy number of a given region is less than the reference sequence.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">copy number loss</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">loss</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">kareneilbeck</obo:IAO_created_by>
<obo:IAO_creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mon Feb 28 01:55:02 PST 2011</obo:IAO_creation_date>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001743</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DBVAR</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">copy_number_loss</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001744 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001744">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UPD</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uniparental disomy</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">kareneilbeck</obo:IAO_created_by>
<obo:IAO_creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mon Feb 28 02:01:05 PST 2011</obo:IAO_creation_date>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001744</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DBVAR</obo:IAO_subset>
<obo:IAO_xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http:http\://en.wikipedia.org/wiki/Uniparental_disomy</obo:IAO_xref>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UPD</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001745 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001745">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001744"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">maternal uniparental disomy</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">kareneilbeck</obo:IAO_created_by>
<obo:IAO_creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mon Feb 28 02:03:01 PST 2011</obo:IAO_creation_date>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001745</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">maternal_uniparental_disomy</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001746 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001746">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001744"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paternal uniparental disomy</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">kareneilbeck</obo:IAO_created_by>
<obo:IAO_creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mon Feb 28 02:03:30 PST 2011</obo:IAO_creation_date>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001746</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paternal_uniparental_disomy</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001784 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001784">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001785"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A structural sequence alteration where there are multiple equally plausible explanations for the change.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">complex</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">kareneilbeck</obo:IAO_created_by>
<obo:IAO_creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wed Mar 23 03:21:19 PDT 2011</obo:IAO_creation_date>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001784</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DBVAR</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">complex_structural_alteration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0001785 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0001785">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">kareneilbeck</obo:IAO_created_by>
<obo:IAO_creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fri Mar 25 02:27:41 PDT 2011</obo:IAO_creation_date>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0001785</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DBVAR</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">structural_alteration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0005836 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0005836">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000666"/>
<obo:IAO_0000116>Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term.</obo:IAO_0000116>
<obo:IAO_0000118>regulatory element</obo:IAO_0000118>
<obo:IAO_0000118>regulatory gene region</obo:IAO_0000118>
<rdfs:label>regulatory_region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Any change in genomic DNA caused by a single event.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000002</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">substitution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000005">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000002"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">complex substitution</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000005</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">complex_substitution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000008 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000008">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001483"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">point mutation</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000008</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<obo:IAO_xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Point_mutation</obo:IAO_xref>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">point_mutation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000009 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000009">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001483"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000009</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000010">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000009"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A substitution of a pyrimidine, C or T, for another pyrimidine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pyrimidine transition</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000010</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pyrimidine_transition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000011 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000011">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000010"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transition of a cytidine to a thymine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C to T transition</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000011</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C_to_T_transition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000012 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000012">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000011"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C to T transition at pCpG site</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000012</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C_to_T_transition_at_pCpG_site</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000013 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000013">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000010"/>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">T to C transition</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000013</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">T_to_C_transition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000014 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000014">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000009"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A substitution of a purine, A or G, for another purine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">purine transition</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000014</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">purine_transition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000014"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transition of an adenine to a guanine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A to G transition</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000015</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A_to_G_transition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000014"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transition of a guanine to an adenine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">G to A transition</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000016</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">G_to_A_transition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000017">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001483"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000017</obo:IAO_id>
<obo:IAO_xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Transversion</obo:IAO_xref>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000018 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000018">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000017"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pyrimidine to purine transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000018</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pyrimidine_to_purine_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000018"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transversion from cytidine to adenine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C to A transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000019</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C_to_A_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000018"/>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C to G transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000020</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C_to_G_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000021 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000021">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000018"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transversion from T to A.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">T to A transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000021</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">T_to_A_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000022">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000018"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transversion from T to G.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">T to G transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000022</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">T_to_G_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000023">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000017"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">purine to pyrimidine transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000023</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">purine_to_pyrimidine_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000024 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000024">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000023"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transversion from adenine to cytidine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A to C transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000024</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A_to_C_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000025 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000025">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000023"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transversion from adenine to thymine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A to T transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000025</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A_to_T_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000026">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000023"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transversion from guanine to cytidine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">G to C transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000026</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">G_to_C_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000027 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000027">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000023"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A transversion from guanine to thymine.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">G to T transversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000027</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">G_to_T_transversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000032 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000032">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000032</obo:IAO_id>
<obo:IAO_xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Indel</obo:IAO_xref>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Indels can have a different number of bases than the corresponding reference sequence.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">indel</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000035 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000035">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000667"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleotide duplication</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleotide_duplication</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000035</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">duplication</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000036 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000036">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A continuous nucleotide sequence is inverted in the same position.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">inversion</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000036</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DBVAR</obo:IAO_subset>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOFA</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">inversion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000039 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000039">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000173"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A tandem duplication where the individual regions are in the same orientation.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">direct tandem duplication</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000039</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">direct_tandem_duplication</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000040">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000173"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A tandem duplication where the individual regions are not in the same orientation.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">inverted tandem duplication</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mirror duplication</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000040</obo:IAO_id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">inverted_tandem_duplication</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_1000173 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_1000173">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_1000035"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A duplication consisting of 2 identical adjacent regions.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">erverted</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tandem duplication</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<obo:IAO_id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:1000173</obo:IAO_id>
<obo:IAO_subset rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DBVAR</obo:IAO_subset>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tandem_duplication</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/UBERON_0000105 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000105">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000351"/>
<obo:IAO_0000116>Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms)</obo:IAO_0000116>
<rdfs:label>life cycle stage</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/UBERON_0001062 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001062">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001000"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000116>Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies.</obo:IAO_0000116>
<oboInOwl:hasDbXref>http://purl.obolibrary.org/obo/CARO_0000000</oboInOwl:hasDbXref>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/UPHENO_0001001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UPHENO_0001001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:IAO_0000116>Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework.</obo:IAO_0000116>
<rdfs:comment>1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition)
2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment</rdfs:comment>
<rdfs:label>Phenotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/WBPhenotype_0000886 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/WBPhenotype_0000886">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0001001"/>
<obo:IAO_0000115>Animals exhibit variations compared to a given control.</obo:IAO_0000115>
<obo:IAO_0000116>'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes.</obo:IAO_0000116>
<obo:IAO_0000118>Variant</obo:IAO_0000118>
<obo:IAO_0000118>c. elegans phenotype</obo:IAO_0000118>
<rdfs:label xml:lang="en">worm phenotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ZP_0000199 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ZP_0000199">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000575"/>
<rdfs:label xml:lang="en">abnormal(ly) malformed endocardium cell</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ZP_0000386 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ZP_0000386">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000575"/>
<rdfs:label xml:lang="en">abnormal(ly) absent dorso-rostral cluster</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ZP_0000755 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ZP_0000755">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000575"/>
<rdfs:label xml:lang="en">abnormal(ly) disrupted diencephalon development</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ZP_0005531 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ZP_0005531">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000575"/>
<rdfs:label xml:lang="en">abnormal(ly) disrupted neutrophil aggregation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ZP_0005692 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ZP_0005692">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000575"/>
<rdfs:label>abnormal(ly) absent adaxial cell</rdfs:label>
</owl:Class>
<!-- http://purl.org/oban/association -->
<owl:Class rdf:about="http://purl.org/oban/association">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:label xml:lang="en">association</rdfs:label>
</owl:Class>
<!-- http://www.ncbi.nlm.nih.gov/gene/20423 -->
<owl:Class rdf:about="http://www.ncbi.nlm.nih.gov/gene/20423">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000057"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000514"/>
<rdfs:comment>Equivalent to: http://www.informatics.jax.org/marker/MGI:98297</rdfs:comment>
<rdfs:label>mus musculus shh gene</rdfs:label>
</owl:Class>
<!-- http://www.ncbi.nlm.nih.gov/gene/30269 -->
<owl:Class rdf:about="http://www.ncbi.nlm.nih.gov/gene/30269">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000047"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000514"/>
<oboInOwl:hasDbXref>http://zfin.org/ZDB-GENE-980526-166</oboInOwl:hasDbXref>
<rdfs:label>danio rerio shha gene</rdfs:label>
</owl:Class>
<!-- http://www.ncbi.nlm.nih.gov/gene/399483 -->
<owl:Class rdf:about="http://www.ncbi.nlm.nih.gov/gene/399483">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000047"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000514"/>
<oboInOwl:hasDbXref>http://zfin.org/ZDB-GENE-040123-1</oboInOwl:hasDbXref>
<rdfs:label>danio rerio cdkn1ca gene</rdfs:label>
</owl:Class>
<!-- http://www.ncbi.nlm.nih.gov/gene/6469 -->
<owl:Class rdf:about="http://www.ncbi.nlm.nih.gov/gene/6469">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GENO_0000054"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/GENO_0000514"/>
<rdfs:comment>Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690
Codes for: http://www.uniprot.org/uniprot/Q15465</rdfs:comment>
<rdfs:label xml:lang="en">homo sapiens SHH gene</rdfs:label>
</owl:Class>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Individuals
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/GENO_0000484 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/GENO_0000484">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
<rdfs:label xml:lang="en">exploratory term</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/GENO_0000514 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/GENO_0000514">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
<rdfs:label xml:lang="en">exemplar term</rdfs:label>
</owl:NamedIndividual>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// General axioms
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<owl:Axiom>
<owl:annotatedSource>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
</owl:Restriction>
</owl:annotatedSource>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/SO_0001059"/>
<rdfs:comment>Initially created such that integrated transgene infers as child of sequence_alteration.</rdfs:comment>
</owl:Axiom>
</rdf:RDF>
<!-- Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi -->
| Web Ontology Language | 5 | cthoyt/HumanDiseaseOntology | src/ontology/imports/geno_full.owl | [
"CC0-1.0"
] |
## Block (object)
+ blockNumber: 11109 (number, required),
+ newStateRoot: `0x61684c1bd4ac3f7843b6a20d4270d58dc4139d546ea4249424bc6c2ce0a48f92` (string, required),
+ blockSize: 110 (number, required),
+ commitTxHash: `0xc2541cf68c6f41a6bc55f9d6ba24816c79431942ca3762514f448540cfa475` (string, required, nullable),
+ verifyTxHash: `0x5e188571f82171b0dc313d9ff5433f10d03153a573e6c2ae5b4fbf683dd2a3` (string, required, nullable),
+ committedAt: `2020-10-12T12:05:03.123416742` (string, required)
+ finalizedAt: `2020-10-12T12:10:03.123416742` (string, required, nullable)
+ status: `committed` (string, required)
| API Blueprint | 3 | smishraIOV/ri-aggregation | infrastructure/api-docs/blueprint/types/blocks.apib | [
"Apache-2.0",
"MIT"
] |
Procedure /// 関数
Function /// 関数
| Ragel in Ruby Host | 0 | saurabhacellere/sakura | installer/sinst_src/keyword/uwsc.rl | [
"Zlib"
] |
#!/bin/sh
echo "error: something bad happened" >&2
echo /path/to/sdk
false
| Shell | 3 | lwhsu/swift | test/Driver/Inputs/xcrun-bad.sh | [
"Apache-2.0"
] |
(kicad_pcb (version 20171130) (host pcbnew "(5.1.6)-1")
(general
(thickness 1.6)
(drawings 15)
(tracks 75)
(zones 0)
(modules 26)
(nets 25)
)
(page A4)
(title_block
(title "KCORES CSPS to ATX Converter")
(date 2021-03-17)
(rev 1.0)
(company KCORES)
(comment 1 "Author: AlphaArea")
(comment 4 "License: KCORES Open Source License")
)
(layers
(0 F.Cu signal)
(31 B.Cu signal)
(32 B.Adhes user)
(33 F.Adhes user)
(34 B.Paste user)
(35 F.Paste user)
(36 B.SilkS user)
(37 F.SilkS user)
(38 B.Mask user)
(39 F.Mask user)
(40 Dwgs.User user)
(41 Cmts.User user)
(42 Eco1.User user)
(43 Eco2.User user)
(44 Edge.Cuts user)
(45 Margin user)
(46 B.CrtYd user)
(47 F.CrtYd user)
(48 B.Fab user)
(49 F.Fab user)
)
(setup
(last_trace_width 0.254)
(user_trace_width 0.1524)
(user_trace_width 0.254)
(user_trace_width 0.508)
(user_trace_width 1.5)
(user_trace_width 3)
(trace_clearance 0.1524)
(zone_clearance 0.254)
(zone_45_only no)
(trace_min 0.1524)
(via_size 0.5)
(via_drill 0.3)
(via_min_size 0.5)
(via_min_drill 0.3)
(uvia_size 0.3)
(uvia_drill 0.1)
(uvias_allowed no)
(uvia_min_size 0.2)
(uvia_min_drill 0.1)
(edge_width 0.05)
(segment_width 0.2)
(pcb_text_width 0.3)
(pcb_text_size 1.5 1.5)
(mod_edge_width 0.12)
(mod_text_size 1 1)
(mod_text_width 0.15)
(pad_size 1.524 1.524)
(pad_drill 0.762)
(pad_to_mask_clearance 0.05)
(aux_axis_origin 0 0)
(grid_origin 172.2 79.8)
(visible_elements 7FFFFFFF)
(pcbplotparams
(layerselection 0x010f0_ffffffff)
(usegerberextensions true)
(usegerberattributes true)
(usegerberadvancedattributes true)
(creategerberjobfile true)
(excludeedgelayer true)
(linewidth 0.100000)
(plotframeref false)
(viasonmask false)
(mode 1)
(useauxorigin false)
(hpglpennumber 1)
(hpglpenspeed 20)
(hpglpendiameter 15.000000)
(psnegative false)
(psa4output false)
(plotreference true)
(plotvalue true)
(plotinvisibletext false)
(padsonsilk false)
(subtractmaskfromsilk false)
(outputformat 1)
(mirror false)
(drillshape 0)
(scaleselection 1)
(outputdirectory "Gerber/20210317/"))
)
(net 0 "")
(net 1 GND)
(net 2 +5V)
(net 3 +3V3)
(net 4 /+5VSB)
(net 5 /~ATX_PSON)
(net 6 "Net-(C5-Pad1)")
(net 7 +12V)
(net 8 /SCL)
(net 9 /SDA)
(net 10 "Net-(J1-Pad29)")
(net 11 "Net-(J1-Pad28)")
(net 12 "Net-(J1-Pad27)")
(net 13 "Net-(J1-Pad38)")
(net 14 /+12VSB)
(net 15 /~PRESENT)
(net 16 /CSPS_PSOK)
(net 17 "Net-(J1-Pad34)")
(net 18 /~CSPS_PSON)
(net 19 "Net-(J8-Pad4)")
(net 20 "Net-(J9-Pad15)")
(net 21 "Net-(J9-Pad19)")
(net 22 /ATX_PWOK)
(net 23 /~FPO)
(net 24 "Net-(R2-Pad1)")
(net_class Default "This is the default net class."
(clearance 0.1524)
(trace_width 0.254)
(via_dia 0.5)
(via_drill 0.3)
(uvia_dia 0.3)
(uvia_drill 0.1)
(add_net +12V)
(add_net +3V3)
(add_net +5V)
(add_net /+12VSB)
(add_net /+5VSB)
(add_net /ATX_PWOK)
(add_net /CSPS_PSOK)
(add_net /SCL)
(add_net /SDA)
(add_net /~ATX_PSON)
(add_net /~CSPS_PSON)
(add_net /~FPO)
(add_net /~PRESENT)
(add_net GND)
(add_net "Net-(C5-Pad1)")
(add_net "Net-(J1-Pad27)")
(add_net "Net-(J1-Pad28)")
(add_net "Net-(J1-Pad29)")
(add_net "Net-(J1-Pad34)")
(add_net "Net-(J1-Pad38)")
(add_net "Net-(J8-Pad4)")
(add_net "Net-(J9-Pad15)")
(add_net "Net-(J9-Pad19)")
(add_net "Net-(R2-Pad1)")
)
(module Connector_PinHeader_2.54mm:PinHeader_1x04_P2.54mm_Vertical (layer F.Cu) (tedit 59FED5CC) (tstamp 604FCC50)
(at 124.63 153.74 270)
(descr "Through hole straight pin header, 1x04, 2.54mm pitch, single row")
(tags "Through hole pin header THT 1x04 2.54mm single row")
(path /604FC3D4)
(fp_text reference J2 (at 0 -2.33 90) (layer F.SilkS) hide
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value PMBUS (at 0 9.95 90) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 0 3.81) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start -0.635 -1.27) (end 1.27 -1.27) (layer F.Fab) (width 0.1))
(fp_line (start 1.27 -1.27) (end 1.27 8.89) (layer F.Fab) (width 0.1))
(fp_line (start 1.27 8.89) (end -1.27 8.89) (layer F.Fab) (width 0.1))
(fp_line (start -1.27 8.89) (end -1.27 -0.635) (layer F.Fab) (width 0.1))
(fp_line (start -1.27 -0.635) (end -0.635 -1.27) (layer F.Fab) (width 0.1))
(fp_line (start -1.33 8.95) (end 1.33 8.95) (layer F.SilkS) (width 0.12))
(fp_line (start -1.33 1.27) (end -1.33 8.95) (layer F.SilkS) (width 0.12))
(fp_line (start 1.33 1.27) (end 1.33 8.95) (layer F.SilkS) (width 0.12))
(fp_line (start -1.33 1.27) (end 1.33 1.27) (layer F.SilkS) (width 0.12))
(fp_line (start -1.33 0) (end -1.33 -1.33) (layer F.SilkS) (width 0.12))
(fp_line (start -1.33 -1.33) (end 0 -1.33) (layer F.SilkS) (width 0.12))
(fp_line (start -1.8 -1.8) (end -1.8 9.4) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.8 9.4) (end 1.8 9.4) (layer F.CrtYd) (width 0.05))
(fp_line (start 1.8 9.4) (end 1.8 -1.8) (layer F.CrtYd) (width 0.05))
(fp_line (start 1.8 -1.8) (end -1.8 -1.8) (layer F.CrtYd) (width 0.05))
(pad 4 thru_hole oval (at 0 7.62 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 9 /SDA))
(pad 3 thru_hole oval (at 0 5.08 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 8 /SCL))
(pad 2 thru_hole oval (at 0 2.54 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 1 thru_hole rect (at 0 0 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 18 /~CSPS_PSON))
(model ${KISYS3DMOD}/Connector_PinHeader_2.54mm.3dshapes/PinHeader_1x04_P2.54mm_Vertical.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module KCORES_Connector_CSPS:CSPS_64P_2.54mm (layer F.Cu) (tedit 60520119) (tstamp 604FCC03)
(at 92.4 119.7 270)
(descr 10053363-201LF)
(path /604F599D)
(zone_connect 2)
(fp_text reference J1 (at 0 -8.128 90) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value CSPS (at 0 1.016 90) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user "Card Edge" (at 0 -1.016 90) (layer Cmts.User)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user FCI (at 43.815 -17.145 90) (layer Dwgs.User)
(effects (font (size 1 1) (thickness 0.15)) (justify right))
)
(fp_text user FCI (at 43.815 -17.145 90) (layer Dwgs.User)
(effects (font (size 1 1) (thickness 0.15)) (justify right))
)
(fp_text user WingTAT (at 43.815 -15.24 90) (layer Dwgs.User)
(effects (font (size 1 1) (thickness 0.15)) (justify right))
)
(fp_text user WingTAT (at 43.815 -15.24 90) (layer Dwgs.User)
(effects (font (size 1 1) (thickness 0.15)) (justify right))
)
(fp_line (start -43.41 -21.844) (end 43.41 -21.844) (layer F.CrtYd) (width 0.12))
(fp_line (start -43.41 0) (end 43.41 0) (layer F.CrtYd) (width 0.12))
(fp_line (start 43.41 -21.844) (end 43.41 0) (layer F.CrtYd) (width 0.12))
(fp_line (start -43.41 0) (end -43.41 -21.844) (layer F.CrtYd) (width 0.12))
(fp_line (start 43.41 -21.844) (end 43.41 0) (layer F.SilkS) (width 0.12))
(fp_line (start -43.41 0) (end -43.41 -21.844) (layer F.SilkS) (width 0.12))
(pad 64 thru_hole oval (at -39.37 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 63 thru_hole oval (at -36.83 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 62 thru_hole oval (at -34.29 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 61 thru_hole oval (at -31.75 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 60 thru_hole oval (at -29.21 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 59 thru_hole oval (at -26.67 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 58 thru_hole oval (at -24.13 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 57 thru_hole oval (at -21.59 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 56 thru_hole oval (at -19.05 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 55 thru_hole oval (at -16.51 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 54 thru_hole oval (at -13.97 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 53 thru_hole oval (at -11.43 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 52 thru_hole oval (at -8.89 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 51 thru_hole oval (at -6.35 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 50 thru_hole oval (at -3.81 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 49 thru_hole oval (at -1.27 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 48 thru_hole oval (at 1.27 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 47 thru_hole oval (at 3.81 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 46 thru_hole oval (at 6.35 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 45 thru_hole oval (at 8.89 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 44 thru_hole oval (at 11.43 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 43 thru_hole oval (at 13.97 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 42 thru_hole oval (at 16.51 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 41 thru_hole oval (at 19.05 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 40 thru_hole oval (at 21.59 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 39 thru_hole oval (at 24.13 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 38 thru_hole oval (at 26.67 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 13 "Net-(J1-Pad38)") (zone_connect 2))
(pad 37 thru_hole oval (at 29.21 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 14 /+12VSB) (zone_connect 2))
(pad 36 thru_hole oval (at 31.75 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 15 /~PRESENT) (zone_connect 2))
(pad 35 thru_hole oval (at 34.29 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 16 /CSPS_PSOK) (zone_connect 2))
(pad 34 thru_hole oval (at 36.83 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 17 "Net-(J1-Pad34)") (zone_connect 2))
(pad 33 thru_hole oval (at 39.37 -20.67 270) (size 1.7 2.08) (drill oval 1.1 1.48) (layers *.Cu *.Mask)
(net 18 /~CSPS_PSON) (zone_connect 2))
(pad 32 thru_hole circle (at 39.37 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 8 /SCL) (zone_connect 2))
(pad 31 thru_hole circle (at 36.83 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 9 /SDA) (zone_connect 2))
(pad 30 thru_hole circle (at 34.29 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 29 thru_hole circle (at 31.75 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 10 "Net-(J1-Pad29)") (zone_connect 2))
(pad 28 thru_hole circle (at 29.21 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 11 "Net-(J1-Pad28)") (zone_connect 2))
(pad 27 thru_hole circle (at 26.67 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 12 "Net-(J1-Pad27)") (zone_connect 2))
(pad 26 thru_hole circle (at 24.13 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 25 thru_hole circle (at 21.59 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 24 thru_hole circle (at 19.05 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 23 thru_hole circle (at 16.51 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 22 thru_hole circle (at 13.97 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 21 thru_hole circle (at 11.43 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 20 thru_hole circle (at 8.89 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 19 thru_hole circle (at 6.35 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 18 thru_hole circle (at 3.81 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 17 thru_hole circle (at 1.27 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 16 thru_hole circle (at -1.27 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 15 thru_hole circle (at -3.81 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 14 thru_hole circle (at -6.35 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND) (zone_connect 2))
(pad 13 thru_hole circle (at -8.89 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 12 thru_hole circle (at -11.43 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 11 thru_hole circle (at -13.97 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 10 thru_hole circle (at -16.51 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 9 thru_hole circle (at -19.05 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 8 thru_hole circle (at -21.59 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V) (zone_connect 2))
(pad 7 thru_hole circle (at -24.13 -15.4 270) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
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(offset (xyz 6.3 -1.9 13.6))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 180))
)
)
(module KCORES_Connector_ATX_Power:ATX_8Pin_P4.20mm_Vertical_4.20mm (layer F.Cu) (tedit 6050AB0D) (tstamp 604FCD3A)
(at 155.4 84 180)
(descr "ATX CPU Power Connector 实心针")
(tags "connector Molex Mini-Fit_Jr side entry ATX CPU")
(path /60B44341)
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)
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)
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)
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(net 7 +12V))
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(net 7 +12V))
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(net 7 +12V))
(pad 2 thru_hole oval (at 4.2 0 180) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
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(model ${KIPRJMOD}/Packages3D/KCORES_Connector_ATX_Power/Molex_46207-1008.stp
(offset (xyz 6.3 -1.9 13.6))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 180))
)
)
(module KCORES_Connector_ATX_Power:ATX_8Pin_P4.20mm_Vertical_4.20mm (layer F.Cu) (tedit 6050AB0D) (tstamp 604FCCEC)
(at 119.7 94.5)
(descr "ATX CPU Power Connector 实心针")
(tags "connector Molex Mini-Fit_Jr side entry ATX CPU")
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)
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)
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)
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(net 7 +12V))
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(net 7 +12V))
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(model ${KIPRJMOD}/Packages3D/KCORES_Connector_ATX_Power/Molex_46207-1008.stp
(offset (xyz 6.3 -1.9 13.6))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 180))
)
)
(module KCORES_Connector_ATX_Power:ATX_8Pin_P4.20mm_Vertical_4.20mm (layer F.Cu) (tedit 6050AB0D) (tstamp 604FCC9E)
(at 132.3 84 180)
(descr "ATX CPU Power Connector 实心针")
(tags "connector Molex Mini-Fit_Jr side entry ATX CPU")
(path /60B0B1E3)
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)
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)
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(net 5 /~ATX_PSON))
(pad 19 thru_hole oval (at 25.2 4.2 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 21 "Net-(J9-Pad19)"))
(pad 18 thru_hole oval (at 21 4.2 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 4 /+5VSB))
(pad 17 thru_hole oval (at 16.8 4.2 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 3 +3V3))
(pad 16 thru_hole oval (at 12.6 4.2 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 3 +3V3))
(pad 15 thru_hole oval (at 8.4 4.2 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 20 "Net-(J9-Pad15)"))
(pad 14 thru_hole oval (at 4.2 4.2 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 2 +5V))
(pad 13 thru_hole oval (at 0 4.2 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 2 +5V))
(pad 12 thru_hole oval (at 46.2 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 7 +12V))
(pad 11 thru_hole oval (at 42 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 1 GND))
(pad 10 thru_hole oval (at 37.8 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 1 GND))
(pad 9 thru_hole oval (at 33.6 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 1 GND))
(pad 8 thru_hole oval (at 29.4 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 1 GND))
(pad 7 thru_hole oval (at 25.2 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 1 GND))
(pad 6 thru_hole oval (at 21 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 1 GND))
(pad 5 thru_hole oval (at 16.8 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 3 +3V3))
(pad 4 thru_hole oval (at 12.6 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 3 +3V3))
(pad 3 thru_hole oval (at 8.4 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 2 +5V))
(pad 1 thru_hole roundrect (at 0 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask) (roundrect_rratio 0.09300000000000001)
(net 2 +5V))
(pad 2 thru_hole oval (at 4.2 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 2 +5V))
(model ${KIPRJMOD}/Packages3D/KCORES_Connector_ATX_Power/Molex_46207-1024.stp
(offset (xyz 23.1 -1.9 13.6))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 180))
)
)
(module KCORES_Connector_ATX_Power:ATX_4Pin_P4.20mm_Vertical_4.20mm (layer F.Cu) (tedit 60522651) (tstamp 604FCDF7)
(at 172.2 100.8 270)
(descr "Molex Mini-Fit Jr. Power Connectors, Row Spacing 4.20mm")
(tags "connector Molex Mini-Fit_Jr side entry")
(path /604FF852)
(fp_text reference J8 (at 2.1 -3.45 90) (layer F.SilkS) hide
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value IDE/SATA (at 2.1 -4.2 90) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 2.1 -1.55 90) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start -2.7 -2.9) (end -2.7 6.7) (layer F.Fab) (width 0.1))
(fp_line (start -2.7 6.7) (end 6.9 6.7) (layer F.Fab) (width 0.1))
(fp_line (start 6.9 6.7) (end 6.9 -2.9) (layer F.Fab) (width 0.1))
(fp_line (start 6.9 -2.9) (end -2.7 -2.9) (layer F.Fab) (width 0.1))
(fp_line (start 0.4 6.7) (end 0.4 8.1) (layer F.Fab) (width 0.1))
(fp_line (start 0.4 8.1) (end 3.8 8.1) (layer F.Fab) (width 0.1))
(fp_line (start 3.8 8.1) (end 3.8 6.7) (layer F.Fab) (width 0.1))
(fp_line (start -1.65 -1.65) (end -1.65 1.65) (layer F.Fab) (width 0.1))
(fp_line (start -1.65 1.65) (end 1.65 1.65) (layer F.Fab) (width 0.1))
(fp_line (start 1.65 1.65) (end 1.65 -1.65) (layer F.Fab) (width 0.1))
(fp_line (start 1.65 -1.65) (end -1.65 -1.65) (layer F.Fab) (width 0.1))
(fp_line (start -1.65 5.85) (end -1.65 3.375) (layer F.Fab) (width 0.1))
(fp_line (start -1.65 3.375) (end -0.825 2.55) (layer F.Fab) (width 0.1))
(fp_line (start -0.825 2.55) (end 0.825 2.55) (layer F.Fab) (width 0.1))
(fp_line (start 0.825 2.55) (end 1.65 3.375) (layer F.Fab) (width 0.1))
(fp_line (start 1.65 3.375) (end 1.65 5.85) (layer F.Fab) (width 0.1))
(fp_line (start 1.65 5.85) (end -1.65 5.85) (layer F.Fab) (width 0.1))
(fp_line (start 2.55 2.55) (end 2.55 5.85) (layer F.Fab) (width 0.1))
(fp_line (start 2.55 5.85) (end 5.85 5.85) (layer F.Fab) (width 0.1))
(fp_line (start 5.85 5.85) (end 5.85 2.55) (layer F.Fab) (width 0.1))
(fp_line (start 5.85 2.55) (end 2.55 2.55) (layer F.Fab) (width 0.1))
(fp_line (start 2.55 1.65) (end 2.55 -0.825) (layer F.Fab) (width 0.1))
(fp_line (start 2.55 -0.825) (end 3.375 -1.65) (layer F.Fab) (width 0.1))
(fp_line (start 3.375 -1.65) (end 5.025 -1.65) (layer F.Fab) (width 0.1))
(fp_line (start 5.025 -1.65) (end 5.85 -0.825) (layer F.Fab) (width 0.1))
(fp_line (start 5.85 -0.825) (end 5.85 1.65) (layer F.Fab) (width 0.1))
(fp_line (start 5.85 1.65) (end 2.55 1.65) (layer F.Fab) (width 0.1))
(fp_line (start 2.1 -3.01) (end -2.81 -3.01) (layer F.SilkS) (width 0.12))
(fp_line (start -2.81 -3.01) (end -2.81 6.81) (layer F.SilkS) (width 0.12))
(fp_line (start -2.81 6.81) (end 0.29 6.81) (layer F.SilkS) (width 0.12))
(fp_line (start 0.29 6.81) (end 0.29 8.21) (layer F.SilkS) (width 0.12))
(fp_line (start 0.29 8.21) (end 2.1 8.21) (layer F.SilkS) (width 0.12))
(fp_line (start 2.1 -3.01) (end 7.01 -3.01) (layer F.SilkS) (width 0.12))
(fp_line (start 7.01 -3.01) (end 7.01 6.81) (layer F.SilkS) (width 0.12))
(fp_line (start 7.01 6.81) (end 3.91 6.81) (layer F.SilkS) (width 0.12))
(fp_line (start 3.91 6.81) (end 3.91 8.21) (layer F.SilkS) (width 0.12))
(fp_line (start 3.91 8.21) (end 2.1 8.21) (layer F.SilkS) (width 0.12))
(fp_line (start -0.2 -3.25) (end -3.05 -3.25) (layer F.SilkS) (width 0.12))
(fp_line (start -3.05 -3.25) (end -3.05 -0.4) (layer F.SilkS) (width 0.12))
(fp_line (start -0.2 -3.25) (end -3.05 -3.25) (layer F.Fab) (width 0.1))
(fp_line (start -3.05 -3.25) (end -3.05 -0.4) (layer F.Fab) (width 0.1))
(fp_line (start -3.2 -3.4) (end -3.2 8.6) (layer F.CrtYd) (width 0.05))
(fp_line (start -3.2 8.6) (end 7.4 8.6) (layer F.CrtYd) (width 0.05))
(fp_line (start 7.4 8.6) (end 7.4 -3.4) (layer F.CrtYd) (width 0.05))
(fp_line (start 7.4 -3.4) (end -3.2 -3.4) (layer F.CrtYd) (width 0.05))
(pad 1 thru_hole roundrect (at 0 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask) (roundrect_rratio 0.09300000000000001)
(net 1 GND))
(pad 2 thru_hole oval (at 4.2 0 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 7 +12V))
(pad 3 thru_hole oval (at 0 4.2 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 2 +5V))
(pad 4 thru_hole oval (at 4.2 4.2 270) (size 2.7 3.7) (drill 1.8) (layers *.Cu *.Mask)
(net 19 "Net-(J8-Pad4)"))
(model ${KIPRJMOD}/Packages3D/KCORES_Connector_ATX_Power/Molex_46207-1004.stp
(offset (xyz 2.1 -1.9 13.6))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 180))
)
)
(module Resistor_THT:R_Axial_DIN0207_L6.3mm_D2.5mm_P7.62mm_Horizontal (layer F.Cu) (tedit 5AE5139B) (tstamp 604FCECB)
(at 161.46 149.93 270)
(descr "Resistor, Axial_DIN0207 series, Axial, Horizontal, pin pitch=7.62mm, 0.25W = 1/4W, length*diameter=6.3*2.5mm^2, http://cdn-reichelt.de/documents/datenblatt/B400/1_4W%23YAG.pdf")
(tags "Resistor Axial_DIN0207 series Axial Horizontal pin pitch 7.62mm 0.25W = 1/4W length 6.3mm diameter 2.5mm")
(path /605A4702)
(fp_text reference R4 (at 3.81 0 90) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 3.3K (at 3.81 2.37 90) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 3.81 0 90) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 0.66 -1.25) (end 0.66 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 0.66 1.25) (end 6.96 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 6.96 1.25) (end 6.96 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 6.96 -1.25) (end 0.66 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 0 0) (end 0.66 0) (layer F.Fab) (width 0.1))
(fp_line (start 7.62 0) (end 6.96 0) (layer F.Fab) (width 0.1))
(fp_line (start 0.54 -1.04) (end 0.54 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 -1.37) (end 7.08 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 7.08 -1.37) (end 7.08 -1.04) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 1.04) (end 0.54 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 1.37) (end 7.08 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 7.08 1.37) (end 7.08 1.04) (layer F.SilkS) (width 0.12))
(fp_line (start -1.05 -1.5) (end -1.05 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.05 1.5) (end 8.67 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.67 1.5) (end 8.67 -1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.67 -1.5) (end -1.05 -1.5) (layer F.CrtYd) (width 0.05))
(pad 2 thru_hole oval (at 7.62 0 270) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 2 +5V))
(pad 1 thru_hole circle (at 0 0 270) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 22 /ATX_PWOK))
(model ${KISYS3DMOD}/Resistor_THT.3dshapes/R_Axial_DIN0207_L6.3mm_D2.5mm_P7.62mm_Horizontal.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Package_DIP:DIP-8_W7.62mm (layer F.Cu) (tedit 5A02E8C5) (tstamp 604FCF3C)
(at 138.6 151.2)
(descr "8-lead though-hole mounted DIP package, row spacing 7.62 mm (300 mils)")
(tags "THT DIP DIL PDIP 2.54mm 7.62mm 300mil")
(path /60500D91)
(fp_text reference U4 (at 3.81 3.81) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value TPS3511 (at 3.81 9.95) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 3.81 3.81) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_arc (start 3.81 -1.33) (end 2.81 -1.33) (angle -180) (layer F.SilkS) (width 0.12))
(fp_line (start 1.635 -1.27) (end 6.985 -1.27) (layer F.Fab) (width 0.1))
(fp_line (start 6.985 -1.27) (end 6.985 8.89) (layer F.Fab) (width 0.1))
(fp_line (start 6.985 8.89) (end 0.635 8.89) (layer F.Fab) (width 0.1))
(fp_line (start 0.635 8.89) (end 0.635 -0.27) (layer F.Fab) (width 0.1))
(fp_line (start 0.635 -0.27) (end 1.635 -1.27) (layer F.Fab) (width 0.1))
(fp_line (start 2.81 -1.33) (end 1.16 -1.33) (layer F.SilkS) (width 0.12))
(fp_line (start 1.16 -1.33) (end 1.16 8.95) (layer F.SilkS) (width 0.12))
(fp_line (start 1.16 8.95) (end 6.46 8.95) (layer F.SilkS) (width 0.12))
(fp_line (start 6.46 8.95) (end 6.46 -1.33) (layer F.SilkS) (width 0.12))
(fp_line (start 6.46 -1.33) (end 4.81 -1.33) (layer F.SilkS) (width 0.12))
(fp_line (start -1.1 -1.55) (end -1.1 9.15) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.1 9.15) (end 8.7 9.15) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.7 9.15) (end 8.7 -1.55) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.7 -1.55) (end -1.1 -1.55) (layer F.CrtYd) (width 0.05))
(pad 8 thru_hole oval (at 7.62 0) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 22 /ATX_PWOK))
(pad 4 thru_hole oval (at 0 7.62) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 5 /~ATX_PSON))
(pad 7 thru_hole oval (at 7.62 2.54) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 6 "Net-(C5-Pad1)"))
(pad 3 thru_hole oval (at 0 5.08) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 23 /~FPO))
(pad 6 thru_hole oval (at 7.62 5.08) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 2 +5V))
(pad 2 thru_hole oval (at 0 2.54) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 1 GND))
(pad 5 thru_hole oval (at 7.62 7.62) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 3 +3V3))
(pad 1 thru_hole rect (at 0 0) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 24 "Net-(R2-Pad1)"))
(model ${KISYS3DMOD}/Package_DIP.3dshapes/DIP-8_W7.62mm.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module KCORES_Converter_DCDC:Converter_DCDC_Mini_560 (layer F.Cu) (tedit 5FF15A64) (tstamp 604FCF22)
(at 137.55 136.26)
(path /604FD8F9)
(fp_text reference U3 (at 0 10.16) (layer F.SilkS) hide
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value "Mini560 5V" (at 0 -8) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user + (at 11 -6) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user + (at 11 -6) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 5 0) (end 3 2) (layer F.SilkS) (width 0.5))
(fp_line (start 5 0) (end 3 -2) (layer F.SilkS) (width 0.5))
(fp_line (start -5 0) (end 5 0) (layer F.SilkS) (width 0.5))
(fp_line (start -15 9) (end 15 9) (layer F.CrtYd) (width 0.12))
(fp_line (start 15 9) (end 15 -9) (layer F.CrtYd) (width 0.12))
(fp_line (start 15 -9) (end -15 -9) (layer F.CrtYd) (width 0.12))
(fp_line (start -15 -9) (end -15 9) (layer F.CrtYd) (width 0.12))
(fp_line (start -15 9) (end 15 9) (layer F.SilkS) (width 0.12))
(fp_line (start -15 -9) (end -15 9) (layer F.SilkS) (width 0.12))
(fp_line (start 15 9) (end 15 -9) (layer F.SilkS) (width 0.12))
(fp_line (start 15 -9) (end -15 -9) (layer F.SilkS) (width 0.12))
(pad 1 thru_hole circle (at -13 -6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 14 /+12VSB))
(pad 1 thru_hole circle (at -13 -4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 14 /+12VSB))
(pad 2 thru_hole circle (at -13 6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 2 thru_hole circle (at -13 4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 3 thru_hole circle (at 13 -6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 4 /+5VSB))
(pad 2 thru_hole circle (at 13 4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 3 thru_hole circle (at 13 -4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 4 /+5VSB))
(pad 2 thru_hole circle (at 13 6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 1 smd roundrect (at -14.27 -5.715) (size 5.08 5.08) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.25)
(net 14 /+12VSB))
(pad 3 smd roundrect (at 14.27 -5.715) (size 5.08 5.08) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.25)
(net 4 /+5VSB))
(pad 2 smd roundrect (at 14.27 5.715) (size 5.08 5.08) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.25)
(net 1 GND))
(pad 2 smd roundrect (at -14.27 5.715) (size 5.08 5.08) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.25)
(net 1 GND))
)
(module KCORES_Converter_DCDC:Converter_DCDC_Mini_560 (layer B.Cu) (tedit 5FF15A64) (tstamp 604FCF05)
(at 137.55 119.115)
(path /604FD7A4)
(fp_text reference U2 (at 0 -10.16) (layer B.SilkS) hide
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_text value "Mini560 3.3V" (at 0 8) (layer B.SilkS)
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_text user + (at 11 6) (layer B.SilkS)
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_text user + (at 11 6) (layer B.SilkS)
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_line (start 5 0) (end 3 -2) (layer B.SilkS) (width 0.5))
(fp_line (start 5 0) (end 3 2) (layer B.SilkS) (width 0.5))
(fp_line (start -5 0) (end 5 0) (layer B.SilkS) (width 0.5))
(fp_line (start -15 -9) (end 15 -9) (layer B.CrtYd) (width 0.12))
(fp_line (start 15 -9) (end 15 9) (layer B.CrtYd) (width 0.12))
(fp_line (start 15 9) (end -15 9) (layer B.CrtYd) (width 0.12))
(fp_line (start -15 9) (end -15 -9) (layer B.CrtYd) (width 0.12))
(fp_line (start -15 -9) (end 15 -9) (layer B.SilkS) (width 0.12))
(fp_line (start -15 9) (end -15 -9) (layer B.SilkS) (width 0.12))
(fp_line (start 15 -9) (end 15 9) (layer B.SilkS) (width 0.12))
(fp_line (start 15 9) (end -15 9) (layer B.SilkS) (width 0.12))
(pad 1 thru_hole circle (at -13 6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V))
(pad 1 thru_hole circle (at -13 4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V))
(pad 2 thru_hole circle (at -13 -6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 2 thru_hole circle (at -13 -4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 3 thru_hole circle (at 13 6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 3 +3V3))
(pad 2 thru_hole circle (at 13 -4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 3 thru_hole circle (at 13 4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 3 +3V3))
(pad 2 thru_hole circle (at 13 -6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 1 smd roundrect (at -14.27 5.715) (size 5.08 5.08) (layers B.Cu B.Paste B.Mask) (roundrect_rratio 0.25)
(net 7 +12V))
(pad 3 smd roundrect (at 14.27 5.715) (size 5.08 5.08) (layers B.Cu B.Paste B.Mask) (roundrect_rratio 0.25)
(net 3 +3V3))
(pad 2 smd roundrect (at 14.27 -5.715) (size 5.08 5.08) (layers B.Cu B.Paste B.Mask) (roundrect_rratio 0.25)
(net 1 GND))
(pad 2 smd roundrect (at -14.27 -5.715) (size 5.08 5.08) (layers B.Cu B.Paste B.Mask) (roundrect_rratio 0.25)
(net 1 GND))
)
(module KCORES_Converter_DCDC:Converter_DCDC_Mini_560 (layer F.Cu) (tedit 5FF15A64) (tstamp 604FCEE8)
(at 137.55 113.4)
(path /604FD40C)
(fp_text reference U1 (at 0 10.16) (layer F.SilkS) hide
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value "Mini560 5V" (at 0 -8) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user + (at 11 -6) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user + (at 11 -6) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 5 0) (end 3 2) (layer F.SilkS) (width 0.5))
(fp_line (start 5 0) (end 3 -2) (layer F.SilkS) (width 0.5))
(fp_line (start -5 0) (end 5 0) (layer F.SilkS) (width 0.5))
(fp_line (start -15 9) (end 15 9) (layer F.CrtYd) (width 0.12))
(fp_line (start 15 9) (end 15 -9) (layer F.CrtYd) (width 0.12))
(fp_line (start 15 -9) (end -15 -9) (layer F.CrtYd) (width 0.12))
(fp_line (start -15 -9) (end -15 9) (layer F.CrtYd) (width 0.12))
(fp_line (start -15 9) (end 15 9) (layer F.SilkS) (width 0.12))
(fp_line (start -15 -9) (end -15 9) (layer F.SilkS) (width 0.12))
(fp_line (start 15 9) (end 15 -9) (layer F.SilkS) (width 0.12))
(fp_line (start 15 -9) (end -15 -9) (layer F.SilkS) (width 0.12))
(pad 1 thru_hole circle (at -13 -6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V))
(pad 1 thru_hole circle (at -13 -4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 7 +12V))
(pad 2 thru_hole circle (at -13 6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 2 thru_hole circle (at -13 4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 3 thru_hole circle (at 13 -6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 2 +5V))
(pad 2 thru_hole circle (at 13 4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 3 thru_hole circle (at 13 -4.445) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 2 +5V))
(pad 2 thru_hole circle (at 13 6.985) (size 1.7 1.7) (drill 1) (layers *.Cu *.Mask)
(net 1 GND))
(pad 1 smd roundrect (at -14.27 -5.715) (size 5.08 5.08) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.25)
(net 7 +12V))
(pad 3 smd roundrect (at 14.27 -5.715) (size 5.08 5.08) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.25)
(net 2 +5V))
(pad 2 smd roundrect (at 14.27 5.715) (size 5.08 5.08) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.25)
(net 1 GND))
(pad 2 smd roundrect (at -14.27 5.715) (size 5.08 5.08) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.25)
(net 1 GND))
)
(module Resistor_THT:R_Axial_DIN0207_L6.3mm_D2.5mm_P7.62mm_Horizontal (layer F.Cu) (tedit 5AE5139B) (tstamp 604FCEB4)
(at 128.44 154.375)
(descr "Resistor, Axial_DIN0207 series, Axial, Horizontal, pin pitch=7.62mm, 0.25W = 1/4W, length*diameter=6.3*2.5mm^2, http://cdn-reichelt.de/documents/datenblatt/B400/1_4W%23YAG.pdf")
(tags "Resistor Axial_DIN0207 series Axial Horizontal pin pitch 7.62mm 0.25W = 1/4W length 6.3mm diameter 2.5mm")
(path /6066F22D)
(fp_text reference R3 (at 3.81 0) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 3.3K (at 3.81 2.37) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 3.81 0) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 0.66 -1.25) (end 0.66 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 0.66 1.25) (end 6.96 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 6.96 1.25) (end 6.96 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 6.96 -1.25) (end 0.66 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 0 0) (end 0.66 0) (layer F.Fab) (width 0.1))
(fp_line (start 7.62 0) (end 6.96 0) (layer F.Fab) (width 0.1))
(fp_line (start 0.54 -1.04) (end 0.54 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 -1.37) (end 7.08 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 7.08 -1.37) (end 7.08 -1.04) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 1.04) (end 0.54 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 1.37) (end 7.08 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 7.08 1.37) (end 7.08 1.04) (layer F.SilkS) (width 0.12))
(fp_line (start -1.05 -1.5) (end -1.05 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.05 1.5) (end 8.67 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.67 1.5) (end 8.67 -1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.67 -1.5) (end -1.05 -1.5) (layer F.CrtYd) (width 0.05))
(pad 2 thru_hole oval (at 7.62 0) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 24 "Net-(R2-Pad1)"))
(pad 1 thru_hole circle (at 0 0) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 1 GND))
(model ${KISYS3DMOD}/Resistor_THT.3dshapes/R_Axial_DIN0207_L6.3mm_D2.5mm_P7.62mm_Horizontal.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Resistor_THT:R_Axial_DIN0207_L6.3mm_D2.5mm_P7.62mm_Horizontal (layer F.Cu) (tedit 5AE5139B) (tstamp 604FCE9D)
(at 136.06 151.2 180)
(descr "Resistor, Axial_DIN0207 series, Axial, Horizontal, pin pitch=7.62mm, 0.25W = 1/4W, length*diameter=6.3*2.5mm^2, http://cdn-reichelt.de/documents/datenblatt/B400/1_4W%23YAG.pdf")
(tags "Resistor Axial_DIN0207 series Axial Horizontal pin pitch 7.62mm 0.25W = 1/4W length 6.3mm diameter 2.5mm")
(path /60683652)
(fp_text reference R2 (at 3.81 0) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 22K (at 3.81 2.37) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 3.81 0) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 0.66 -1.25) (end 0.66 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 0.66 1.25) (end 6.96 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 6.96 1.25) (end 6.96 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 6.96 -1.25) (end 0.66 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 0 0) (end 0.66 0) (layer F.Fab) (width 0.1))
(fp_line (start 7.62 0) (end 6.96 0) (layer F.Fab) (width 0.1))
(fp_line (start 0.54 -1.04) (end 0.54 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 -1.37) (end 7.08 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 7.08 -1.37) (end 7.08 -1.04) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 1.04) (end 0.54 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 1.37) (end 7.08 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 7.08 1.37) (end 7.08 1.04) (layer F.SilkS) (width 0.12))
(fp_line (start -1.05 -1.5) (end -1.05 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.05 1.5) (end 8.67 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.67 1.5) (end 8.67 -1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.67 -1.5) (end -1.05 -1.5) (layer F.CrtYd) (width 0.05))
(pad 2 thru_hole oval (at 7.62 0 180) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 7 +12V))
(pad 1 thru_hole circle (at 0 0 180) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 24 "Net-(R2-Pad1)"))
(model ${KISYS3DMOD}/Resistor_THT.3dshapes/R_Axial_DIN0207_L6.3mm_D2.5mm_P7.62mm_Horizontal.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Resistor_THT:R_Axial_DIN0207_L6.3mm_D2.5mm_P7.62mm_Horizontal (layer F.Cu) (tedit 5AE5139B) (tstamp 604FCE86)
(at 124.63 148.91 180)
(descr "Resistor, Axial_DIN0207 series, Axial, Horizontal, pin pitch=7.62mm, 0.25W = 1/4W, length*diameter=6.3*2.5mm^2, http://cdn-reichelt.de/documents/datenblatt/B400/1_4W%23YAG.pdf")
(tags "Resistor Axial_DIN0207 series Axial Horizontal pin pitch 7.62mm 0.25W = 1/4W length 6.3mm diameter 2.5mm")
(path /604FBE3B)
(fp_text reference R1 (at 3.81 0) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 22K (at 3.81 2.37) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 3.81 0) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 0.66 -1.25) (end 0.66 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 0.66 1.25) (end 6.96 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 6.96 1.25) (end 6.96 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 6.96 -1.25) (end 0.66 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 0 0) (end 0.66 0) (layer F.Fab) (width 0.1))
(fp_line (start 7.62 0) (end 6.96 0) (layer F.Fab) (width 0.1))
(fp_line (start 0.54 -1.04) (end 0.54 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 -1.37) (end 7.08 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 7.08 -1.37) (end 7.08 -1.04) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 1.04) (end 0.54 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 0.54 1.37) (end 7.08 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 7.08 1.37) (end 7.08 1.04) (layer F.SilkS) (width 0.12))
(fp_line (start -1.05 -1.5) (end -1.05 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.05 1.5) (end 8.67 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.67 1.5) (end 8.67 -1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.67 -1.5) (end -1.05 -1.5) (layer F.CrtYd) (width 0.05))
(pad 2 thru_hole oval (at 7.62 0 180) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 14 /+12VSB))
(pad 1 thru_hole circle (at 0 0 180) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 15 /~PRESENT))
(model ${KISYS3DMOD}/Resistor_THT.3dshapes/R_Axial_DIN0207_L6.3mm_D2.5mm_P7.62mm_Horizontal.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Jumper:SolderJumper-2_P1.3mm_Open_RoundedPad1.0x1.5mm (layer B.Cu) (tedit 5B391E66) (tstamp 604FCE6F)
(at 120.82 159.455)
(descr "SMD Solder Jumper, 1x1.5mm, rounded Pads, 0.3mm gap, open")
(tags "solder jumper open")
(path /6069FF35)
(attr virtual)
(fp_text reference JP2 (at 0 1.905) (layer B.SilkS)
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_text value ATX_PSON-CSPS_PSON (at 0 -1.9) (layer B.Fab) hide
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_arc (start -0.7 0.3) (end -0.7 1) (angle 90) (layer B.SilkS) (width 0.12))
(fp_arc (start -0.7 -0.3) (end -1.4 -0.3) (angle 90) (layer B.SilkS) (width 0.12))
(fp_arc (start 0.7 -0.3) (end 0.7 -1) (angle 90) (layer B.SilkS) (width 0.12))
(fp_arc (start 0.7 0.3) (end 1.4 0.3) (angle 90) (layer B.SilkS) (width 0.12))
(fp_line (start -1.4 -0.3) (end -1.4 0.3) (layer B.SilkS) (width 0.12))
(fp_line (start 0.7 -1) (end -0.7 -1) (layer B.SilkS) (width 0.12))
(fp_line (start 1.4 0.3) (end 1.4 -0.3) (layer B.SilkS) (width 0.12))
(fp_line (start -0.7 1) (end 0.7 1) (layer B.SilkS) (width 0.12))
(fp_line (start -1.65 1.25) (end 1.65 1.25) (layer B.CrtYd) (width 0.05))
(fp_line (start -1.65 1.25) (end -1.65 -1.25) (layer B.CrtYd) (width 0.05))
(fp_line (start 1.65 -1.25) (end 1.65 1.25) (layer B.CrtYd) (width 0.05))
(fp_line (start 1.65 -1.25) (end -1.65 -1.25) (layer B.CrtYd) (width 0.05))
(pad 2 smd custom (at 0.65 0) (size 1 0.5) (layers B.Cu B.Mask)
(net 5 /~ATX_PSON) (zone_connect 2)
(options (clearance outline) (anchor rect))
(primitives
(gr_circle (center 0 -0.25) (end 0.5 -0.25) (width 0))
(gr_circle (center 0 0.25) (end 0.5 0.25) (width 0))
(gr_poly (pts
(xy 0 0.75) (xy -0.5 0.75) (xy -0.5 -0.75) (xy 0 -0.75)) (width 0))
))
(pad 1 smd custom (at -0.65 0) (size 1 0.5) (layers B.Cu B.Mask)
(net 18 /~CSPS_PSON) (zone_connect 2)
(options (clearance outline) (anchor rect))
(primitives
(gr_circle (center 0 -0.25) (end 0.5 -0.25) (width 0))
(gr_circle (center 0 0.25) (end 0.5 0.25) (width 0))
(gr_poly (pts
(xy 0 0.75) (xy 0.5 0.75) (xy 0.5 -0.75) (xy 0 -0.75)) (width 0))
))
)
(module Jumper:SolderJumper-2_P1.3mm_Bridged_RoundedPad1.0x1.5mm (layer B.Cu) (tedit 5C745284) (tstamp 604FCE5D)
(at 120.82 156.915)
(descr "SMD Solder Jumper, 1x1.5mm, rounded Pads, 0.3mm gap, bridged with 1 copper strip")
(tags "solder jumper open")
(path /6069F524)
(attr virtual)
(fp_text reference JP1 (at 0 -1.905) (layer B.SilkS)
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_text value FPO-CSPS_PSON (at 0 -1.9) (layer B.Fab) hide
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_arc (start -0.7 0.3) (end -0.7 1) (angle 90) (layer B.SilkS) (width 0.12))
(fp_arc (start -0.7 -0.3) (end -1.4 -0.3) (angle 90) (layer B.SilkS) (width 0.12))
(fp_arc (start 0.7 -0.3) (end 0.7 -1) (angle 90) (layer B.SilkS) (width 0.12))
(fp_arc (start 0.7 0.3) (end 1.4 0.3) (angle 90) (layer B.SilkS) (width 0.12))
(fp_line (start -1.4 -0.3) (end -1.4 0.3) (layer B.SilkS) (width 0.12))
(fp_line (start 0.7 -1) (end -0.7 -1) (layer B.SilkS) (width 0.12))
(fp_line (start 1.4 0.3) (end 1.4 -0.3) (layer B.SilkS) (width 0.12))
(fp_line (start -0.7 1) (end 0.7 1) (layer B.SilkS) (width 0.12))
(fp_line (start -1.65 1.25) (end 1.65 1.25) (layer B.CrtYd) (width 0.05))
(fp_line (start -1.65 1.25) (end -1.65 -1.25) (layer B.CrtYd) (width 0.05))
(fp_line (start 1.65 -1.25) (end 1.65 1.25) (layer B.CrtYd) (width 0.05))
(fp_line (start 1.65 -1.25) (end -1.65 -1.25) (layer B.CrtYd) (width 0.05))
(fp_poly (pts (xy 0.25 0.3) (xy -0.25 0.3) (xy -0.25 -0.3) (xy 0.25 -0.3)) (layer B.Cu) (width 0))
(pad 1 smd custom (at -0.65 0) (size 1 0.5) (layers B.Cu B.Mask)
(net 18 /~CSPS_PSON) (zone_connect 2)
(options (clearance outline) (anchor rect))
(primitives
(gr_circle (center 0 -0.25) (end 0.5 -0.25) (width 0))
(gr_circle (center 0 0.25) (end 0.5 0.25) (width 0))
(gr_poly (pts
(xy 0 0.75) (xy 0.5 0.75) (xy 0.5 -0.75) (xy 0 -0.75)) (width 0))
))
(pad 2 smd custom (at 0.65 0) (size 1 0.5) (layers B.Cu B.Mask)
(net 23 /~FPO) (zone_connect 2)
(options (clearance outline) (anchor rect))
(primitives
(gr_circle (center 0 -0.25) (end 0.5 -0.25) (width 0))
(gr_circle (center 0 0.25) (end 0.5 0.25) (width 0))
(gr_poly (pts
(xy 0 0.75) (xy -0.5 0.75) (xy -0.5 -0.75) (xy 0 -0.75)) (width 0))
))
)
(module Diode_THT:D_DO-41_SOD81_P7.62mm_Horizontal (layer F.Cu) (tedit 5AE50CD5) (tstamp 604FCB72)
(at 150.03 154.375)
(descr "Diode, DO-41_SOD81 series, Axial, Horizontal, pin pitch=7.62mm, , length*diameter=5.2*2.7mm^2, , http://www.diodes.com/_files/packages/DO-41%20(Plastic).pdf")
(tags "Diode DO-41_SOD81 series Axial Horizontal pin pitch 7.62mm length 5.2mm diameter 2.7mm")
(path /605A4DEC)
(fp_text reference D2 (at 3.81 0) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 1N4001 (at 3.81 2.47) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user K (at 0 -2.1) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user K (at 0 -2.1) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 4.2 0) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 1.21 -1.35) (end 1.21 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 1.21 1.35) (end 6.41 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 6.41 1.35) (end 6.41 -1.35) (layer F.Fab) (width 0.1))
(fp_line (start 6.41 -1.35) (end 1.21 -1.35) (layer F.Fab) (width 0.1))
(fp_line (start 0 0) (end 1.21 0) (layer F.Fab) (width 0.1))
(fp_line (start 7.62 0) (end 6.41 0) (layer F.Fab) (width 0.1))
(fp_line (start 1.99 -1.35) (end 1.99 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 2.09 -1.35) (end 2.09 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 1.89 -1.35) (end 1.89 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 1.09 -1.34) (end 1.09 -1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 1.09 -1.47) (end 6.53 -1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 6.53 -1.47) (end 6.53 -1.34) (layer F.SilkS) (width 0.12))
(fp_line (start 1.09 1.34) (end 1.09 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 1.09 1.47) (end 6.53 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 6.53 1.47) (end 6.53 1.34) (layer F.SilkS) (width 0.12))
(fp_line (start 1.99 -1.47) (end 1.99 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 2.11 -1.47) (end 2.11 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 1.87 -1.47) (end 1.87 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start -1.35 -1.6) (end -1.35 1.6) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.35 1.6) (end 8.97 1.6) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.97 1.6) (end 8.97 -1.6) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.97 -1.6) (end -1.35 -1.6) (layer F.CrtYd) (width 0.05))
(pad 2 thru_hole oval (at 7.62 0) (size 2.2 2.2) (drill 1.1) (layers *.Cu *.Mask)
(net 7 +12V))
(pad 1 thru_hole rect (at 0 0) (size 2.2 2.2) (drill 1.1) (layers *.Cu *.Mask)
(net 6 "Net-(C5-Pad1)"))
(model ${KISYS3DMOD}/Diode_THT.3dshapes/D_DO-41_SOD81_P7.62mm_Horizontal.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Diode_THT:D_DO-41_SOD81_P7.62mm_Horizontal (layer F.Cu) (tedit 5AE50CD5) (tstamp 604FCB53)
(at 150.03 151.2)
(descr "Diode, DO-41_SOD81 series, Axial, Horizontal, pin pitch=7.62mm, , length*diameter=5.2*2.7mm^2, , http://www.diodes.com/_files/packages/DO-41%20(Plastic).pdf")
(tags "Diode DO-41_SOD81 series Axial Horizontal pin pitch 7.62mm length 5.2mm diameter 2.7mm")
(path /606076DC)
(fp_text reference D1 (at 3.81 0) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 1N4001 (at 3.81 2.47) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user K (at 0 -2.1) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user K (at 0 -2.1) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 4.2 0) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 1.21 -1.35) (end 1.21 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 1.21 1.35) (end 6.41 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 6.41 1.35) (end 6.41 -1.35) (layer F.Fab) (width 0.1))
(fp_line (start 6.41 -1.35) (end 1.21 -1.35) (layer F.Fab) (width 0.1))
(fp_line (start 0 0) (end 1.21 0) (layer F.Fab) (width 0.1))
(fp_line (start 7.62 0) (end 6.41 0) (layer F.Fab) (width 0.1))
(fp_line (start 1.99 -1.35) (end 1.99 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 2.09 -1.35) (end 2.09 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 1.89 -1.35) (end 1.89 1.35) (layer F.Fab) (width 0.1))
(fp_line (start 1.09 -1.34) (end 1.09 -1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 1.09 -1.47) (end 6.53 -1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 6.53 -1.47) (end 6.53 -1.34) (layer F.SilkS) (width 0.12))
(fp_line (start 1.09 1.34) (end 1.09 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 1.09 1.47) (end 6.53 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 6.53 1.47) (end 6.53 1.34) (layer F.SilkS) (width 0.12))
(fp_line (start 1.99 -1.47) (end 1.99 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 2.11 -1.47) (end 2.11 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start 1.87 -1.47) (end 1.87 1.47) (layer F.SilkS) (width 0.12))
(fp_line (start -1.35 -1.6) (end -1.35 1.6) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.35 1.6) (end 8.97 1.6) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.97 1.6) (end 8.97 -1.6) (layer F.CrtYd) (width 0.05))
(fp_line (start 8.97 -1.6) (end -1.35 -1.6) (layer F.CrtYd) (width 0.05))
(pad 2 thru_hole oval (at 7.62 0) (size 2.2 2.2) (drill 1.1) (layers *.Cu *.Mask)
(net 4 /+5VSB))
(pad 1 thru_hole rect (at 0 0) (size 2.2 2.2) (drill 1.1) (layers *.Cu *.Mask)
(net 6 "Net-(C5-Pad1)"))
(model ${KISYS3DMOD}/Diode_THT.3dshapes/D_DO-41_SOD81_P7.62mm_Horizontal.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Capacitor_THT:C_Disc_D5.0mm_W2.5mm_P2.50mm (layer F.Cu) (tedit 5AE50EF0) (tstamp 604FCB34)
(at 150.03 157.55)
(descr "C, Disc series, Radial, pin pitch=2.50mm, , diameter*width=5*2.5mm^2, Capacitor, http://cdn-reichelt.de/documents/datenblatt/B300/DS_KERKO_TC.pdf")
(tags "C Disc series Radial pin pitch 2.50mm diameter 5mm width 2.5mm Capacitor")
(path /60648D9C)
(fp_text reference C5 (at 1.27 2.54) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 100nF (at 1.25 2.5) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 1.25 0) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start -1.25 -1.25) (end -1.25 1.25) (layer F.Fab) (width 0.1))
(fp_line (start -1.25 1.25) (end 3.75 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 3.75 1.25) (end 3.75 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 3.75 -1.25) (end -1.25 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start -1.37 -1.37) (end 3.87 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start -1.37 1.37) (end 3.87 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start -1.37 -1.37) (end -1.37 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 3.87 -1.37) (end 3.87 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start -1.5 -1.5) (end -1.5 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.5 1.5) (end 4 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 4 1.5) (end 4 -1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 4 -1.5) (end -1.5 -1.5) (layer F.CrtYd) (width 0.05))
(pad 2 thru_hole circle (at 2.5 0) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 1 GND))
(pad 1 thru_hole circle (at 0 0) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 6 "Net-(C5-Pad1)"))
(model ${KISYS3DMOD}/Capacitor_THT.3dshapes/C_Disc_D5.0mm_W2.5mm_P2.50mm.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Capacitor_THT:C_Disc_D5.0mm_W2.5mm_P2.50mm (layer F.Cu) (tedit 5AE50EF0) (tstamp 604FCB21)
(at 132.925 157.55)
(descr "C, Disc series, Radial, pin pitch=2.50mm, , diameter*width=5*2.5mm^2, Capacitor, http://cdn-reichelt.de/documents/datenblatt/B300/DS_KERKO_TC.pdf")
(tags "C Disc series Radial pin pitch 2.50mm diameter 5mm width 2.5mm Capacitor")
(path /605A40C1)
(fp_text reference C4 (at 1.25 2.54) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 100nF (at 1.25 2.5) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 1.25 0) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start -1.25 -1.25) (end -1.25 1.25) (layer F.Fab) (width 0.1))
(fp_line (start -1.25 1.25) (end 3.75 1.25) (layer F.Fab) (width 0.1))
(fp_line (start 3.75 1.25) (end 3.75 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start 3.75 -1.25) (end -1.25 -1.25) (layer F.Fab) (width 0.1))
(fp_line (start -1.37 -1.37) (end 3.87 -1.37) (layer F.SilkS) (width 0.12))
(fp_line (start -1.37 1.37) (end 3.87 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start -1.37 -1.37) (end -1.37 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start 3.87 -1.37) (end 3.87 1.37) (layer F.SilkS) (width 0.12))
(fp_line (start -1.5 -1.5) (end -1.5 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start -1.5 1.5) (end 4 1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 4 1.5) (end 4 -1.5) (layer F.CrtYd) (width 0.05))
(fp_line (start 4 -1.5) (end -1.5 -1.5) (layer F.CrtYd) (width 0.05))
(pad 2 thru_hole circle (at 2.5 0) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 5 /~ATX_PSON))
(pad 1 thru_hole circle (at 0 0) (size 1.6 1.6) (drill 0.8) (layers *.Cu *.Mask)
(net 1 GND))
(model ${KISYS3DMOD}/Capacitor_THT.3dshapes/C_Disc_D5.0mm_W2.5mm_P2.50mm.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Capacitor_Tantalum_SMD:CP_EIA-7343-31_Kemet-D_Pad2.25x2.55mm_HandSolder (layer F.Cu) (tedit 5B301BBE) (tstamp 604FCB0E)
(at 159.6 137.55 270)
(descr "Tantalum Capacitor SMD Kemet-D (7343-31 Metric), IPC_7351 nominal, (Body size from: http://www.kemet.com/Lists/ProductCatalog/Attachments/253/KEM_TC101_STD.pdf), generated with kicad-footprint-generator")
(tags "capacitor tantalum")
(path /604FE5A5)
(attr smd)
(fp_text reference C3 (at 0 0.045 90) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 100uF (at 0 3.1 90) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 0 0 90) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 3.65 -2.15) (end -2.65 -2.15) (layer F.Fab) (width 0.1))
(fp_line (start -2.65 -2.15) (end -3.65 -1.15) (layer F.Fab) (width 0.1))
(fp_line (start -3.65 -1.15) (end -3.65 2.15) (layer F.Fab) (width 0.1))
(fp_line (start -3.65 2.15) (end 3.65 2.15) (layer F.Fab) (width 0.1))
(fp_line (start 3.65 2.15) (end 3.65 -2.15) (layer F.Fab) (width 0.1))
(fp_line (start 3.65 -2.26) (end -4.585 -2.26) (layer F.SilkS) (width 0.12))
(fp_line (start -4.585 -2.26) (end -4.585 2.26) (layer F.SilkS) (width 0.12))
(fp_line (start -4.585 2.26) (end 3.65 2.26) (layer F.SilkS) (width 0.12))
(fp_line (start -4.58 2.4) (end -4.58 -2.4) (layer F.CrtYd) (width 0.05))
(fp_line (start -4.58 -2.4) (end 4.58 -2.4) (layer F.CrtYd) (width 0.05))
(fp_line (start 4.58 -2.4) (end 4.58 2.4) (layer F.CrtYd) (width 0.05))
(fp_line (start 4.58 2.4) (end -4.58 2.4) (layer F.CrtYd) (width 0.05))
(pad 2 smd roundrect (at 3.2 0 270) (size 2.25 2.55) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.111111)
(net 1 GND))
(pad 1 smd roundrect (at -3.2 0 270) (size 2.25 2.55) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.111111)
(net 4 /+5VSB))
(model ${KISYS3DMOD}/Capacitor_Tantalum_SMD.3dshapes/CP_EIA-7343-31_Kemet-D.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Capacitor_Tantalum_SMD:CP_EIA-7343-31_Kemet-D_Pad2.25x2.55mm_HandSolder (layer B.Cu) (tedit 5B301BBE) (tstamp 604FCAFB)
(at 159.6 130.2 270)
(descr "Tantalum Capacitor SMD Kemet-D (7343-31 Metric), IPC_7351 nominal, (Body size from: http://www.kemet.com/Lists/ProductCatalog/Attachments/253/KEM_TC101_STD.pdf), generated with kicad-footprint-generator")
(tags "capacitor tantalum")
(path /604FE29A)
(attr smd)
(fp_text reference C2 (at 0 0.045 270) (layer B.SilkS)
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_text value 100uF (at 0 -3.1 270) (layer B.Fab)
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_text user %R (at 0 0 270) (layer B.Fab)
(effects (font (size 1 1) (thickness 0.15)) (justify mirror))
)
(fp_line (start 3.65 2.15) (end -2.65 2.15) (layer B.Fab) (width 0.1))
(fp_line (start -2.65 2.15) (end -3.65 1.15) (layer B.Fab) (width 0.1))
(fp_line (start -3.65 1.15) (end -3.65 -2.15) (layer B.Fab) (width 0.1))
(fp_line (start -3.65 -2.15) (end 3.65 -2.15) (layer B.Fab) (width 0.1))
(fp_line (start 3.65 -2.15) (end 3.65 2.15) (layer B.Fab) (width 0.1))
(fp_line (start 3.65 2.26) (end -4.585 2.26) (layer B.SilkS) (width 0.12))
(fp_line (start -4.585 2.26) (end -4.585 -2.26) (layer B.SilkS) (width 0.12))
(fp_line (start -4.585 -2.26) (end 3.65 -2.26) (layer B.SilkS) (width 0.12))
(fp_line (start -4.58 -2.4) (end -4.58 2.4) (layer B.CrtYd) (width 0.05))
(fp_line (start -4.58 2.4) (end 4.58 2.4) (layer B.CrtYd) (width 0.05))
(fp_line (start 4.58 2.4) (end 4.58 -2.4) (layer B.CrtYd) (width 0.05))
(fp_line (start 4.58 -2.4) (end -4.58 -2.4) (layer B.CrtYd) (width 0.05))
(pad 2 smd roundrect (at 3.2 0 270) (size 2.25 2.55) (layers B.Cu B.Paste B.Mask) (roundrect_rratio 0.111111)
(net 1 GND))
(pad 1 smd roundrect (at -3.2 0 270) (size 2.25 2.55) (layers B.Cu B.Paste B.Mask) (roundrect_rratio 0.111111)
(net 3 +3V3))
(model ${KISYS3DMOD}/Capacitor_Tantalum_SMD.3dshapes/CP_EIA-7343-31_Kemet-D.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(module Capacitor_Tantalum_SMD:CP_EIA-7343-31_Kemet-D_Pad2.25x2.55mm_HandSolder (layer F.Cu) (tedit 5B301BBE) (tstamp 604FCAE8)
(at 159.6 116.55 270)
(descr "Tantalum Capacitor SMD Kemet-D (7343-31 Metric), IPC_7351 nominal, (Body size from: http://www.kemet.com/Lists/ProductCatalog/Attachments/253/KEM_TC101_STD.pdf), generated with kicad-footprint-generator")
(tags "capacitor tantalum")
(path /6055B507)
(attr smd)
(fp_text reference C1 (at 0 0.045 90) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text value 100uF (at 0 3.1 90) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_text user %R (at 0 0 90) (layer F.Fab)
(effects (font (size 1 1) (thickness 0.15)))
)
(fp_line (start 3.65 -2.15) (end -2.65 -2.15) (layer F.Fab) (width 0.1))
(fp_line (start -2.65 -2.15) (end -3.65 -1.15) (layer F.Fab) (width 0.1))
(fp_line (start -3.65 -1.15) (end -3.65 2.15) (layer F.Fab) (width 0.1))
(fp_line (start -3.65 2.15) (end 3.65 2.15) (layer F.Fab) (width 0.1))
(fp_line (start 3.65 2.15) (end 3.65 -2.15) (layer F.Fab) (width 0.1))
(fp_line (start 3.65 -2.26) (end -4.585 -2.26) (layer F.SilkS) (width 0.12))
(fp_line (start -4.585 -2.26) (end -4.585 2.26) (layer F.SilkS) (width 0.12))
(fp_line (start -4.585 2.26) (end 3.65 2.26) (layer F.SilkS) (width 0.12))
(fp_line (start -4.58 2.4) (end -4.58 -2.4) (layer F.CrtYd) (width 0.05))
(fp_line (start -4.58 -2.4) (end 4.58 -2.4) (layer F.CrtYd) (width 0.05))
(fp_line (start 4.58 -2.4) (end 4.58 2.4) (layer F.CrtYd) (width 0.05))
(fp_line (start 4.58 2.4) (end -4.58 2.4) (layer F.CrtYd) (width 0.05))
(pad 2 smd roundrect (at 3.2 0 270) (size 2.25 2.55) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.111111)
(net 1 GND))
(pad 1 smd roundrect (at -3.2 0 270) (size 2.25 2.55) (layers F.Cu F.Paste F.Mask) (roundrect_rratio 0.111111)
(net 2 +5V))
(model ${KISYS3DMOD}/Capacitor_Tantalum_SMD.3dshapes/CP_EIA-7343-31_Kemet-D.wrl
(at (xyz 0 0 0))
(scale (xyz 1 1 1))
(rotate (xyz 0 0 0))
)
)
(gr_text ~ON (at 124.63 156.28) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(gr_text - (at 122.09 156.28) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(gr_text C (at 119.55 156.28) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(gr_text "Contributor:\nAlphaArea\nUbiq" (at 143.85 137.55) (layer B.Mask)
(effects (font (size 1.5 1.5) (thickness 0.2)) (justify left mirror))
)
(gr_text "20210317 v1.0" (at 176.4 161.7 90) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)) (justify left))
)
(gr_text "CSPS to ATX Converter" (at 119.07 123.9 90) (layer F.Mask)
(effects (font (size 1 1) (thickness 0.15)))
)
(gr_text KCORES (at 116.55 123.9 90) (layer F.Mask)
(effects (font (size 2.5 2.5) (thickness 0.3)))
)
(gr_text D (at 117.01 156.28) (layer F.SilkS)
(effects (font (size 1 1) (thickness 0.15)))
)
(gr_line (start 164.85 96.6) (end 176.4 96.6) (layer F.Mask) (width 4.2))
(gr_line (start 157.5 89.25) (end 164.85 96.6) (layer F.Mask) (width 4.2))
(gr_line (start 92.4 162.75) (end 92.4 76.65) (layer Edge.Cuts) (width 0.05) (tstamp 605209ED))
(gr_line (start 178.5 76.65) (end 92.4 76.65) (layer Edge.Cuts) (width 0.05))
(gr_line (start 178.5 162.75) (end 178.5 76.65) (layer Edge.Cuts) (width 0.05))
(gr_line (start 178.5 162.75) (end 92.4 162.75) (layer Edge.Cuts) (width 0.05))
(gr_line (start 108.15 89.25) (end 157.5 89.25) (layer F.Mask) (width 4.2))
(segment (start 107.8 153.99) (end 109.45 153.99) (width 1.5) (layer F.Cu) (net 1))
(segment (start 164.85 100.8) (end 168 100.8) (width 1.5) (layer F.Cu) (net 2))
(segment (start 150.55 106.415) (end 159.235 106.415) (width 1.5) (layer F.Cu) (net 2))
(segment (start 159.235 106.415) (end 164.85 100.8) (width 1.5) (layer F.Cu) (net 2))
(segment (start 160.19 156.28) (end 161.46 157.55) (width 0.254) (layer B.Cu) (net 2))
(segment (start 146.22 156.28) (end 160.19 156.28) (width 0.254) (layer B.Cu) (net 2))
(segment (start 146.22 156.28) (end 144.315 154.375) (width 0.254) (layer F.Cu) (net 2))
(segment (start 144.315 115.19) (end 150.55 108.955) (width 0.254) (layer F.Cu) (net 2))
(segment (start 144.315 154.375) (end 144.315 115.19) (width 0.254) (layer F.Cu) (net 2))
(via (at 143.68 126.1) (size 0.5) (drill 0.3) (layers F.Cu B.Cu) (net 3))
(segment (start 146.22 158.82) (end 143.68 156.28) (width 0.254) (layer F.Cu) (net 3))
(segment (start 143.68 156.28) (end 143.68 132.15) (width 0.254) (layer F.Cu) (net 3))
(segment (start 149.73 126.1) (end 150.55 126.1) (width 0.254) (layer B.Cu) (net 3))
(segment (start 143.68 132.15) (end 143.68 126.1) (width 0.254) (layer F.Cu) (net 3))
(segment (start 143.68 126.1) (end 150.55 126.1) (width 0.254) (layer B.Cu) (net 3))
(segment (start 155.675 134.4) (end 168 134.4) (width 1.5) (layer F.Cu) (net 4))
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(xy 117.842 79.208724) (xy 92.933 79.208724) (xy 92.933 77.183) (xy 177.967001 77.183)
)
)
)
)
| KiCad | 5 | Indexyz/KCORES-CSPS-to-ATX-Converter | Electrical/KCORES CSPS to ATX Converter/KCORES CSPS to ATX Converter.kicad_pcb | [
"RSA-MD"
] |
ruleset io.picolabs.schedule {
meta {
shares getLog, listScheduled
}
global {
getLog = function(){
ent:log;
}
listScheduled = function(){
schedule:list();
}
}
rule clear_log {
select when schedule clear_log
send_directive("clear_log");
fired {
ent:log := []
}
}
rule push_log {
select when schedule push_log
send_directive("push_log");
fired {
ent:log := ent:log.append(event:attrs)
}
}
rule in_5min {
select when schedule in_5min
send_directive("in_5min");
fired {
schedule schedule event "push_log"
at time:add(time:now(), {"minutes": 5})
attributes {
"from": "in_5min",
"name": event:attrs{"name"}
}
setting(foo);
ent:log := ent:log.append({"scheduled in_5min": foo})
}
}
rule every_1min {
select when schedule every_1min
send_directive("every_1min");
fired {
schedule schedule event "push_log"
repeat "* */1 * * * *"
attributes {
"from": "every_1min",
"name": event:attrs{"name"}
}
setting(foo);
ent:log := ent:log.append({"scheduled every_1min": foo})
}
}
rule rm_from_schedule {
select when schedule rm_from_schedule
schedule:remove(event:attrs{"id"});
}
rule dynamic_at {
select when schedule dynamic_at
fired {
schedule event event:attrs{"dn"}
at event:attrs{"at"}
attributes {
"from": "dynamic_at",
"name": event:attrs{"name"}
}
setting(foo);
ent:log := ent:log.append({"scheduled dynamic_at": foo})
}
}
rule dynamic_repeat {
select when schedule dynamic_repeat
fired {
schedule event event:attrs{"dn"}
repeat event:attrs{"timespec"}
attributes {
"from": "dynamic_repeat",
"name": event:attrs{"name"}
}
setting(foo);
ent:log := ent:log.append({"scheduled dynamic_repeat": foo})
}
}
}
| KRL | 4 | CambodianCoder/pico-engine | test-rulesets/schedule.krl | [
"MIT"
] |
# flake8: noqa
# There's no way to ignore "F401 '...' imported but unused" warnings in this
# module, but to preserve other warnings. So, don't check this module at all.
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from typing import TYPE_CHECKING
from ...file_utils import (
_LazyModule,
is_sentencepiece_available,
is_tf_available,
is_tokenizers_available,
is_torch_available,
)
_import_structure = {
"configuration_camembert": ["CAMEMBERT_PRETRAINED_CONFIG_ARCHIVE_MAP", "CamembertConfig"],
}
if is_sentencepiece_available():
_import_structure["tokenization_camembert"] = ["CamembertTokenizer"]
if is_tokenizers_available():
_import_structure["tokenization_camembert_fast"] = ["CamembertTokenizerFast"]
if is_torch_available():
_import_structure["modeling_camembert"] = [
"CAMEMBERT_PRETRAINED_MODEL_ARCHIVE_LIST",
"CamembertForCausalLM",
"CamembertForMaskedLM",
"CamembertForMultipleChoice",
"CamembertForQuestionAnswering",
"CamembertForSequenceClassification",
"CamembertForTokenClassification",
"CamembertModel",
]
if is_tf_available():
_import_structure["modeling_tf_camembert"] = [
"TF_CAMEMBERT_PRETRAINED_MODEL_ARCHIVE_LIST",
"TFCamembertForMaskedLM",
"TFCamembertForMultipleChoice",
"TFCamembertForQuestionAnswering",
"TFCamembertForSequenceClassification",
"TFCamembertForTokenClassification",
"TFCamembertModel",
]
if TYPE_CHECKING:
from .configuration_camembert import CAMEMBERT_PRETRAINED_CONFIG_ARCHIVE_MAP, CamembertConfig
if is_sentencepiece_available():
from .tokenization_camembert import CamembertTokenizer
if is_tokenizers_available():
from .tokenization_camembert_fast import CamembertTokenizerFast
if is_torch_available():
from .modeling_camembert import (
CAMEMBERT_PRETRAINED_MODEL_ARCHIVE_LIST,
CamembertForCausalLM,
CamembertForMaskedLM,
CamembertForMultipleChoice,
CamembertForQuestionAnswering,
CamembertForSequenceClassification,
CamembertForTokenClassification,
CamembertModel,
)
if is_tf_available():
from .modeling_tf_camembert import (
TF_CAMEMBERT_PRETRAINED_MODEL_ARCHIVE_LIST,
TFCamembertForMaskedLM,
TFCamembertForMultipleChoice,
TFCamembertForQuestionAnswering,
TFCamembertForSequenceClassification,
TFCamembertForTokenClassification,
TFCamembertModel,
)
else:
import sys
sys.modules[__name__] = _LazyModule(__name__, globals()["__file__"], _import_structure)
| Python | 4 | arunraja-hub/transformers | src/transformers/models/camembert/__init__.py | [
"Apache-2.0"
] |
/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.hadoop.hdfs;
import java.util.ArrayList;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.test.system.DaemonProtocol;
import org.apache.hadoop.hdfs.test.system.DNProtocol;
import org.apache.hadoop.hdfs.test.system.NNProtocol;
import org.apache.hadoop.security.authorize.Service;
import org.apache.hadoop.security.authorize.ServiceAuthorizationManager;
/**
* This aspect adds two HDFS Herriot specific protocols tp the list of 'authorized'
* Herriot protocols.
* Protocol descriptors i.e. 'security.nn.protocol.acl' have to be added to
* <code>hadoop-policy.xml</code> if present
*/
public privileged aspect HDFSPolicyProviderAspect {
private static final Log LOG = LogFactory
.getLog(HDFSPolicyProviderAspect.class);
ArrayList<Service> herriotHDFSServices = null;
pointcut updateHDFSServices() :
execution (public Service[] HDFSPolicyProvider.getServices());
Service[] around() : updateHDFSServices () {
herriotHDFSServices = new ArrayList<Service>();
for (Service s : HDFSPolicyProvider.hdfsServices) {
LOG.debug("Copying configured protocol to "
+ s.getProtocol().getCanonicalName());
herriotHDFSServices.add(s);
}
herriotHDFSServices.add(new Service("security.daemon.protocol.acl",
DaemonProtocol.class));
herriotHDFSServices.add(new Service("security.nn.protocol.acl",
NNProtocol.class));
herriotHDFSServices.add(new Service("security.dn.protocol.acl",
DNProtocol.class));
final Service[] retArray = herriotHDFSServices
.toArray(new Service[herriotHDFSServices.size()]);
LOG.debug("Number of configured protocols to return: " + retArray.length);
return retArray;
}
}
| AspectJ | 4 | hoppinghippo/HadoopMapReduce | src/test/system/aop/org/apache/hadoop/hdfs/HDFSPolicyProviderAspect.aj | [
"Apache-2.0"
] |
libflightplan(3) "github.com/mitchellh/libflightplan" "Library Functions Manual"
# NAME
libflightplan - library used to read and write aviation flight plans
# DESCRIPTION
*libflightplan* is a library for reading and writing flight plans in
various formats. Flight plans are used in aviation to save properties of
one or more flights such as route (waypoints), altitude, source and departure
airport, etc.
This library is available as a native C library as well as Zig. The man pages
focus on the C API currently.
# API NOTES
- fpl_cleanup(3) should be called when all users of the library are done.
This cleans up any global state associatd with the library.
- The library may allocate global state on the heap to store error
information (accessible via fpl_last_error(3)).
- The library is not threadsafe. Global error state is stored in thread local
variables.
# EXAMPLE
The example below shows how the C API can be used to parse a ForeFlight
flight plan and read route information about it.
```
#include <stddef.h>
#include <stdio.h>
#include <flightplan.h>
int main() {
// Parse our flight plan from an FPL file out of ForeFlight.
flightplan *fpl = fpl_parse_garmin("./test/basic.fpl");
if (fpl == NULL) {
// We can get a more detailed error.
flightplan_error *err = fpl_last_error();
printf("error: %s\n", fpl_error_message(err));
fpl_cleanup();
return 1;
}
// Iterate and output the full ordered route.
int max = fpl_route_points_count(fpl);
printf("\nroute: \"%s\" (points: %d)\n", fpl_route_name(fpl), max);
for (int i = 0; i < max; i++) {
flightplan_route_point *point = fpl_route_points_get(fpl, i);
printf(" %s\n", fpl_route_point_identifier(point));
}
fpl_free(fpl);
fpl_cleanup();
return 0;
}
```
# AUTHORS
Mitchell Hashimoto (xmitchx@gmail.com) and any open source contributors.
See <https://github.com/mitchellh/libflightplan>.
| SuperCollider | 4 | 06kellyjac/libflightplan | doc/libflightplan.3.scd | [
"MIT"
] |
from typing import List
from fastapi import FastAPI
from fastapi.testclient import TestClient
from pydantic import BaseModel
app = FastAPI()
class RecursiveItem(BaseModel):
sub_items: List["RecursiveItem"] = []
name: str
RecursiveItem.update_forward_refs()
class RecursiveSubitemInSubmodel(BaseModel):
sub_items2: List["RecursiveItemViaSubmodel"] = []
name: str
class RecursiveItemViaSubmodel(BaseModel):
sub_items1: List[RecursiveSubitemInSubmodel] = []
name: str
RecursiveSubitemInSubmodel.update_forward_refs()
@app.get("/items/recursive", response_model=RecursiveItem)
def get_recursive():
return {"name": "item", "sub_items": [{"name": "subitem", "sub_items": []}]}
@app.get("/items/recursive-submodel", response_model=RecursiveItemViaSubmodel)
def get_recursive_submodel():
return {
"name": "item",
"sub_items1": [
{
"name": "subitem",
"sub_items2": [
{
"name": "subsubitem",
"sub_items1": [{"name": "subsubsubitem", "sub_items2": []}],
}
],
}
],
}
client = TestClient(app)
def test_recursive():
response = client.get("/items/recursive")
assert response.status_code == 200, response.text
assert response.json() == {
"sub_items": [{"name": "subitem", "sub_items": []}],
"name": "item",
}
response = client.get("/items/recursive-submodel")
assert response.status_code == 200, response.text
assert response.json() == {
"name": "item",
"sub_items1": [
{
"name": "subitem",
"sub_items2": [
{
"name": "subsubitem",
"sub_items1": [{"name": "subsubsubitem", "sub_items2": []}],
}
],
}
],
}
| Python | 4 | Aryabhata-Rootspring/fastapi | tests/test_validate_response_recursive.py | [
"MIT"
] |
P
Y
####T####
# H #
# O #
####N #
# #
#########
| Mask | 0 | kai-pischke/python-constraint | examples/crosswords/python.mask | [
"BSD-2-Clause"
] |
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[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;166;226;46mis_a[0m[38;2;248;248;242m [0m[3;38;2;253;151;31mc[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m
[38;2;248;248;242m [0m[38;2;249;38;114mif[0m[38;2;248;248;242m c [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;190;132;255m'a'[0m[38;2;248;248;242m [0m[38;2;249;38;114mthen[0m[38;2;248;248;242m [0m[38;2;190;132;255mtrue[0m
[38;2;248;248;242m [0m[38;2;249;38;114melse[0m[38;2;248;248;242m [0m[38;2;190;132;255mfalse[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m _ [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;248;248;242mPrintf.[0m[38;2;248;248;242mprintf [0m[38;2;230;219;116m"[0m[38;2;230;219;116m%s[0m[38;2;230;219;116m"[0m[38;2;248;248;242m [0m[38;2;230;219;116m"[0m[38;2;230;219;116mhello[0m[38;2;230;219;116m"[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;190;132;255m([0m[38;2;190;132;255m)[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;248;248;242mPrintf.[0m[38;2;248;248;242mprintf [0m[38;2;230;219;116m"[0m[38;2;230;219;116m%s[0m[38;2;190;132;255m\n[0m[38;2;230;219;116m"[0m[38;2;248;248;242m [0m[38;2;230;219;116m"[0m[38;2;230;219;116mworld[0m[38;2;230;219;116m"[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;255;255;255mx[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;249;38;114mref[0m[38;2;248;248;242m [0m[38;2;190;132;255m0[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m _ [0m[38;2;249;38;114m=[0m[38;2;248;248;242m x [0m[38;2;249;38;114m:=[0m[38;2;248;248;242m [0m[38;2;190;132;255m1[0m
[38;2;249;38;114mtype[0m[38;2;248;248;242m [0m[3;38;2;102;217;239mmy_bool [0m[38;2;248;248;242m=[0m[38;2;248;248;242m [0m[38;2;166;226;46mTrue[0m[38;2;248;248;242m [0m[38;2;248;248;242m|[0m[38;2;248;248;242m [0m[38;2;166;226;46mFalse[0m
[38;2;249;38;114mtype[0m[38;2;248;248;242m [0m[3;38;2;102;217;239mshape [0m[38;2;248;248;242m=[0m[38;2;248;248;242m [0m[38;2;166;226;46mCircle[0m[38;2;248;248;242m [0m[38;2;249;38;114mof[0m[38;2;248;248;242m [0m[3;38;2;102;217;239mfloat[0m[38;2;248;248;242m [0m[38;2;248;248;242m|[0m[38;2;248;248;242m [0m[38;2;166;226;46mSquare[0m[38;2;248;248;242m [0m[38;2;249;38;114mof[0m[38;2;248;248;242m [0m[3;38;2;102;217;239mfloat[0m[38;2;248;248;242m [0m[38;2;248;248;242m|[0m[38;2;248;248;242m [0m[38;2;166;226;46mRectangle[0m[38;2;248;248;242m [0m[38;2;249;38;114mof[0m[38;2;248;248;242m [0m[38;2;248;248;242m([0m[3;38;2;102;217;239mfloat[0m[38;2;248;248;242m [0m[38;2;249;38;114m*[0m[38;2;248;248;242m [0m[3;38;2;102;217;239mfloat[0m[38;2;248;248;242m)[0m
[38;2;249;38;114mtype[0m[38;2;248;248;242m [0m[3;38;2;102;217;239muser [0m[38;2;248;248;242m=[0m[38;2;248;248;242m [0m[38;2;248;248;242m{[0m
[38;2;248;248;242m [0m[38;2;248;248;242mlogin[0m[38;2;248;248;242m [0m[38;2;248;248;242m:[0m[38;2;248;248;242m [0m[3;38;2;102;217;239mstring[0m[38;2;249;38;114m;[0m
[38;2;248;248;242m [0m[38;2;248;248;242mpassword[0m[38;2;248;248;242m [0m[38;2;248;248;242m:[0m[38;2;248;248;242m [0m[3;38;2;102;217;239mstring[0m[38;2;249;38;114m;[0m
[38;2;248;248;242m}[0m
[38;2;249;38;114mtype[0m[38;2;248;248;242m [0m[3;38;2;102;217;239m'a my_ref [0m[38;2;248;248;242m=[0m[38;2;248;248;242m [0m[38;2;248;248;242m{[0m[38;2;248;248;242m [0m[38;2;249;38;114mmutable [0m[38;2;248;248;242mref_value[0m[38;2;248;248;242m [0m[38;2;248;248;242m:[0m[38;2;248;248;242m [0m[3;38;2;102;217;239m'a[0m[38;2;248;248;242m [0m[38;2;248;248;242m}[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;166;226;46m(:=)[0m[38;2;248;248;242m [0m[3;38;2;253;151;31mr[0m[38;2;248;248;242m [0m[3;38;2;253;151;31mv[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m r.ref_value [0m[38;2;249;38;114m<[0m[38;2;249;38;114m-[0m[38;2;248;248;242m v[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;166;226;46m(+)[0m[38;2;248;248;242m [0m[38;2;190;132;255m2[0m[38;2;248;248;242m [0m[38;2;190;132;255m2[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;190;132;255m5[0m
[38;2;249;38;114mexception[0m[38;2;248;248;242m [0m[38;2;166;226;46mBad_value[0m[38;2;248;248;242m of [0m[3;38;2;102;217;239mstring[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;166;226;46mbad_value_error[0m[38;2;248;248;242m [0m[3;38;2;253;151;31m()[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m raise [0m[38;2;248;248;242m([0m[38;2;166;226;46mBad_value[0m[38;2;248;248;242m [0m[38;2;230;219;116m"[0m[38;2;230;219;116myour value is bad and you should feel bad[0m[38;2;230;219;116m"[0m[38;2;248;248;242m)[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;190;132;255m([0m[38;2;190;132;255m)[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m
[38;2;248;248;242m [0m[38;2;249;38;114mtry[0m[38;2;248;248;242m bad_value_error [0m[38;2;190;132;255m([0m[38;2;190;132;255m)[0m
[38;2;248;248;242m [0m[38;2;249;38;114mwith[0m[38;2;248;248;242m [0m[38;2;166;226;46mBad_value[0m[38;2;248;248;242m [0m[38;2;190;132;255m_[0m[38;2;248;248;242m [0m[38;2;248;248;242m->[0m[38;2;248;248;242m [0m[38;2;190;132;255m([0m[38;2;190;132;255m)[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;190;132;255m([0m[38;2;190;132;255m)[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m
[38;2;248;248;242m [0m[38;2;249;38;114mtry[0m[38;2;248;248;242m bad_value_error [0m[38;2;190;132;255m([0m[38;2;190;132;255m)[0m
[38;2;248;248;242m [0m[38;2;249;38;114mwith[0m
[38;2;248;248;242m [0m[38;2;249;38;114m|[0m[38;2;248;248;242m [0m[38;2;166;226;46mBad_value[0m[38;2;248;248;242m [0m[38;2;190;132;255m_[0m[38;2;248;248;242m [0m[38;2;248;248;242m->[0m[38;2;248;248;242m [0m[38;2;190;132;255m([0m[38;2;190;132;255m)[0m
[38;2;248;248;242m [0m[38;2;249;38;114m|[0m[38;2;248;248;242m [0m[38;2;166;226;46mNot_found[0m[38;2;248;248;242m [0m[38;2;248;248;242m->[0m[38;2;248;248;242m [0m[38;2;190;132;255m([0m[38;2;190;132;255m)[0m
[38;2;249;38;114mmodule type [0m[38;2;166;226;46mFOO[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;249;38;114msig[0m
[38;2;248;248;242m [0m[38;2;249;38;114mval[0m[38;2;248;248;242m [0m[38;2;166;226;46mfoo[0m[38;2;248;248;242m [0m[38;2;248;248;242m:[0m[38;2;248;248;242m [0m[3;38;2;102;217;239m'a[0m[38;2;248;248;242m [0m[38;2;248;248;242m->[0m[38;2;248;248;242m [0m[3;38;2;102;217;239m'a[0m
[38;2;249;38;114mend[0m
[38;2;249;38;114mmodule[0m[38;2;248;248;242m [0m[38;2;166;226;46mFoo[0m[38;2;248;248;242m [0m[38;2;248;248;242m:[0m[38;2;248;248;242m [0m[38;2;166;226;46mFOO[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;249;38;114mstruct[0m
[38;2;248;248;242m [0m[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;166;226;46mfoo[0m[38;2;248;248;242m [0m[3;38;2;253;151;31mx[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m x[0m
[38;2;249;38;114mend[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;255;255;255mgreeter[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;249;38;114mobject[0m
[38;2;248;248;242m val greeting [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;230;219;116m"[0m[38;2;230;219;116mHello[0m[38;2;230;219;116m"[0m
[38;2;248;248;242m [0m[38;2;249;38;114mmethod[0m[38;2;248;248;242m [0m[38;2;166;226;46mgreet[0m[38;2;248;248;242m [0m[3;38;2;253;151;31mname[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;248;248;242mPrintf.[0m[38;2;248;248;242msprintf [0m[38;2;230;219;116m"[0m[38;2;230;219;116m%s, %s![0m[38;2;230;219;116m"[0m[38;2;248;248;242m greeting name [0m
[38;2;249;38;114mend[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;255;255;255mgreeting[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m greeter[0m[38;2;248;248;242m#[0m[38;2;248;248;242mgreet[0m[38;2;248;248;242m [0m[38;2;230;219;116m"[0m[38;2;230;219;116mworld[0m[38;2;230;219;116m"[0m
[38;2;249;38;114mclass[0m[38;2;248;248;242m [0m[38;2;166;226;46mgreeter_factory[0m[38;2;248;248;242m [0m[3;38;2;253;151;31mgreeting_text[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;249;38;114mobject[0m[38;2;248;248;242m [0m[38;2;248;248;242m([0m[38;2;166;226;46mself[0m[38;2;248;248;242m)[0m
[38;2;248;248;242m val greeting [0m[38;2;249;38;114m=[0m[38;2;248;248;242m greeting_text[0m
[38;2;248;248;242m [0m[38;2;249;38;114mmethod[0m[38;2;248;248;242m [0m[38;2;166;226;46mgreet[0m[38;2;248;248;242m [0m[3;38;2;253;151;31mname[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;248;248;242mPrintf.[0m[38;2;248;248;242msprintf [0m[38;2;230;219;116m"[0m[38;2;230;219;116m%s, %s![0m[38;2;230;219;116m"[0m[38;2;248;248;242m greeting name[0m
[38;2;248;248;242m [0m[38;2;249;38;114minitializer[0m[38;2;248;248;242m [0m[38;2;248;248;242mPrintf.[0m[38;2;248;248;242mprintf [0m[38;2;230;219;116m"[0m[38;2;230;219;116mObjects will greet the user with [0m[38;2;190;132;255m\"[0m[38;2;230;219;116m%s[0m[38;2;190;132;255m\"[0m[38;2;190;132;255m\n[0m[38;2;230;219;116m"[0m[38;2;248;248;242m greeting[0m
[38;2;249;38;114mend[0m
[38;2;249;38;114mlet[0m[38;2;248;248;242m [0m[38;2;255;255;255mg[0m[38;2;248;248;242m [0m[38;2;249;38;114m=[0m[38;2;248;248;242m [0m[38;2;249;38;114mnew[0m[38;2;248;248;242m greeter_factory [0m[38;2;230;219;116m"[0m[38;2;230;219;116mHi[0m[38;2;230;219;116m"[0m
| OCaml | 5 | JesseVermeulen123/bat | tests/syntax-tests/highlighted/OCaml/syntax-test.ml | [
"Apache-2.0",
"MIT"
] |
scriptname _Frost_ExposureMeterInterfaceHandler extends CommonMeterInterfaceHandler
import CampUtil
function RegisterForEvents()
if !GetSKSELoaded()
return
endif
RegisterForModEvent("Frostfall_ForceExposureMeterDisplay", "ForceMeterDisplay")
RegisterForModEvent("Frostfall_RemoveExposureMeter", "RemoveMeter")
RegisterForModEvent("Frostfall_UpdateExposureMeter", "UpdateMeterDelegate")
RegisterForModEvent("Frostfall_CheckMeterRequirements", "CheckMeterRequirements")
; Special Frostfall indicator element
RegisterForModEvent("Frostfall_UpdateExposureMeterIndicator", "UpdateMeterIndicator")
; Special Frostfall glow
RegisterForModEvent("Frostfall_SetExposureMeterGlow", "SetExposureMeterGlow")
endFunction
Event UpdateMeterIndicator(float percent)
(Meter as _Frost_Meter).SetIndicatorPercent(percent)
endEvent
Event SetExposureMeterGlow(float percent)
(Meter as _Frost_Meter).SetGlow(percent)
endEvent | Papyrus | 4 | chesko256/Campfire | Scripts/Source/_Frost_ExposureMeterInterfaceHandler.psc | [
"MIT"
] |
CREATE TABLE `tb_epubreeayc` (
`col_embnqthyuu` double NOT NULL,
`col_shqnxczemy` binary(149) DEFAULT NULL,
`col_gyjfdfpemu` longtext CHARACTER SET utf8,
PRIMARY KEY (`col_embnqthyuu`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;
CREATE TABLE `tb_uafierhjhg` (
`col_rvdpillohr` smallint(51) unsigned NOT NULL,
`col_wjvgjpqbgz` smallint(5) unsigned zerofill DEFAULT NULL,
PRIMARY KEY (`col_rvdpillohr`),
UNIQUE KEY `uk_aqetlmillq` (`col_wjvgjpqbgz`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
| SQL | 3 | yuanweikang2020/canal | parse/src/test/resources/ddl/alter/mysql_55.sql | [
"Apache-2.0"
] |
; CLW file contains information for the MFC ClassWizard
[General Info]
Version=1
LastClass=CD4dTestDlg
LastTemplate=CDialog
NewFileInclude1=#include "stdafx.h"
NewFileInclude2=#include "D4dTest.h"
ClassCount=3
Class1=CD4dTestApp
Class2=CD4dTestDlg
Class3=CAboutDlg
ResourceCount=5
Resource1=IDD_ABOUTBOX
Resource2=IDR_MAINFRAME
Resource3=IDD_D4DTEST_DIALOG
Resource4=IDD_ABOUTBOX (English (U.S.))
Resource5=IDD_D4DTEST_DIALOG (English (U.S.))
[CLS:CD4dTestApp]
Type=0
HeaderFile=D4dTest.h
ImplementationFile=D4dTest.cpp
Filter=N
[CLS:CD4dTestDlg]
Type=0
HeaderFile=D4dTestDlg.h
ImplementationFile=D4dTestDlg.cpp
Filter=D
BaseClass=CDialog
VirtualFilter=dWC
LastObject=CD4dTestDlg
[CLS:CAboutDlg]
Type=0
HeaderFile=D4dTestDlg.h
ImplementationFile=D4dTestDlg.cpp
Filter=D
[DLG:IDD_ABOUTBOX]
Type=1
ControlCount=4
Control1=IDC_STATIC,static,1342177283
Control2=IDC_STATIC,static,1342308352
Control3=IDC_STATIC,static,1342308352
Control4=IDOK,button,1342373889
Class=CAboutDlg
[DLG:IDD_D4DTEST_DIALOG]
Type=1
ControlCount=3
Control1=IDOK,button,1342242817
Control2=IDCANCEL,button,1342242816
Control3=IDC_STATIC,static,1342308352
Class=CD4dTestDlg
[DLG:IDD_D4DTEST_DIALOG (English (U.S.))]
Type=1
Class=CD4dTestDlg
ControlCount=9
Control1=IDCANCEL,button,1342242816
Control2=IDC_LIST_INFO,listbox,1352728833
Control3=IDB_ASSIGN,button,1342242816
Control4=IDC_EDIT_INTEGER,edit,1350631552
Control5=IDB_TRACE,button,1342242816
Control6=IDB_STACKTRACE,button,1342242816
Control7=IDB_COPY,button,1342242816
Control8=IDB_CLEAR,button,1342242816
Control9=IDB_FAST_TRACE,button,1342242816
[DLG:IDD_ABOUTBOX (English (U.S.))]
Type=1
Class=?
ControlCount=4
Control1=IDC_STATIC,static,1342177283
Control2=IDC_STATIC,static,1342308480
Control3=IDC_STATIC,static,1342308352
Control4=IDOK,button,1342373889
| Clarion | 3 | oudream/ccxx | test/dump/swdbgbk_src/chap27/D4D/D4dTest/D4dTest.clw | [
"MIT"
] |
#!/bin/bash
set -e -u
echo "Publishing Javadoc and JDiff..."
cd $HOME
git clone -q -b gh-pages "https://x-access-token:${GITHUB_TOKEN}@github.com/google/guava.git" gh-pages > /dev/null
cd gh-pages
git config --global user.name "$GITHUB_ACTOR"
git config --global user.email "$GITHUB_ACTOR@users.noreply.github.com"
./updaterelease.sh snapshot
git push -fq origin gh-pages > /dev/null
echo "Javadoc and JDiff published to gh-pages."
| Shell | 4 | ksodhi2/guava | util/update_snapshot_docs.sh | [
"Apache-2.0"
] |
/*
* ESP32S2 ROM address table
* Generated for ROM with MD5sum: 0a2c7ec5109c17884606d23b47045796
*/
PROVIDE (ets_update_cpu_frequency = 0x4000d8a4);
PROVIDE (MD5Final = 0x4000530c);
PROVIDE (MD5Init = 0x4000526c);
PROVIDE (MD5Update = 0x4000528c);
/* bootloader will use following functions from xtensa hal library */
xthal_get_ccount = 0x4001aa90;
xthal_get_ccompare = 0x4001aabc;
xthal_set_ccompare = 0x4001aa98;
| Linker Script | 3 | DCNick3/esp-idf | components/bootloader/subproject/main/ld/esp32s2/bootloader.rom.ld | [
"Apache-2.0"
] |
module CompletionSpec where
exampleValue :: Int
exampleValue = 42
exampleFunction :: Int -> Int
exampleFunction _ = 1
exampleInferredString = ""
infixl 5 exampleFunction as \°/
data ExampleTypeConstructor a b = ExampleTypeConstructor a b
infixl 5 type ExampleTypeConstructor as \°/
class ExampleClass where
exampleMember :: Int
| PureScript | 3 | andys8/purescript | tests/support/pscide/src/CompletionSpec.purs | [
"BSD-3-Clause"
] |
static const uint32_t in_val_decim[1980] = {
0x3d9aeafc, 0x3f800000, 0xbf1bcebc, 0x3d288e27,
0xbf800000, 0xbe63a3ff, 0xbe6f74f1, 0x3f800000,
0x3f002294, 0xbf800000, 0x3f40d559, 0x3d7a1587,
0xbf800000, 0xbe538644, 0x3e3bd6b3, 0xbf4b0178,
0x3f800000, 0x3f3d911e, 0x3d8caa90, 0x3e705d9e,
0x3f800000, 0x3e0724d1, 0xbca52a4b, 0xbf065f5f,
0x3f1c89fb, 0x3efe135f, 0x3e162b52, 0xbe927bd0,
0x3f800000, 0x3f1271bb, 0x3f3ba3cc, 0x3f098db1,
0x3e064429, 0xbf40bd64, 0x3f66ad5b, 0xbe7961df,
0x3e74de85, 0xbf0400c9, 0xbf2c4e2d, 0xbf061416,
0xbe610e9e, 0x3f800000, 0xbe101e01, 0x3d0f114c,
0xbe802694, 0xbe4c6010, 0x3f299ea7, 0x3e51656e,
0xbe5ab3ec, 0x3f800000, 0xbd3ab888, 0xbd558484,
0x3ee2d9b7, 0xbdea06f1, 0xbddb5aa8, 0xbed18c18,
0xbeef3841, 0xbf800000, 0x3f3c6900, 0xbf6c73ae,
0x3d9a8d22, 0x3ef39448, 0xbf800000, 0xbd16c2b4,
0x3e947029, 0xbd7fce40, 0xbf800000, 0xbebfb8fd,
0xbe2e8b3c, 0x3f0767e1, 0x3ec2ef01, 0xbe73ddd7,
0x3f00229a, 0x3ed73812, 0xbdee9c9a, 0x3da02d3c,
0xbe809e2a, 0xbe39ce59, 0x3e0fa22c, 0xbf10003b,
0x3bc28bfe, 0xbe84827b, 0xbeca08c5, 0x3f5a1e79,
0xbeb2ee78, 0x3e438e8c, 0xbe96407a, 0x3f800000,
0xbf800000, 0xbd5d0e1b, 0xbe950cc8, 0x3a92100a,
0x3d893ac0, 0x3f434c20, 0xbed102ec, 0x3cec74e5,
0x3e17fb76, 0x3e22a494, 0xbe53cf97, 0xbc11e7ac,
0x3f6b0a9b, 0x3f800000, 0xbe28f639, 0xbd41e0da,
0xbe9e50bc, 0x3e4d370e, 0x3f1e74b7, 0xbe6428a1,
0xbf186938, 0x3f038d93, 0xbf4fe3d8, 0x3dbe8fb0,
0x3f3a8a44, 0x3f800000, 0x3cf68aa1, 0xbecf3f3b,
0xbe88be59, 0x3f637e89, 0x3e3c40ce, 0xbdf0a33a,
0x3e7145ef, 0x3b982713, 0x3de43f73, 0xbf0f23b6,
0x3c53dff7, 0xbe83ab74, 0xbf6753e8, 0xbee8734d,
0xbf10a5c4, 0xbdcdafda, 0xbf800000, 0xbeb471f1,
0x3f43daae, 0xbf1f844f, 0xbcef123f, 0xbefc4ce2,
0xbf077673, 0xbf800000, 0xbf800000, 0x3f4465ac,
0xbee48948, 0x3cf0cc07, 0x3f2901d2, 0xbecdf851,
0x3e496a3c, 0xbf800000, 0x3f17c6d1, 0x3da5562b,
0xbf41b167, 0x3f005ced, 0xbedf5ce2, 0xbf0560ba,
0xbf046e97, 0xbf800000, 0x3db8f83e, 0xbe226e7e,
0xbe5e2abe, 0xbf3ce3dc, 0x3e6e000f, 0x3da956cf,
0x3e825a90, 0x3f800000, 0x3f16f98e, 0xbebd491a,
0x3f800000, 0x3ed0bc7a, 0xbdbcd94c, 0x3dbef1c8,
0xbd5415e2, 0x3dffbd3a, 0x3f66714e, 0x3ee69a51,
0x3e626fc5, 0xbf800000, 0xbec9437e, 0x3c7d7ff5,
0x3ee0a4fb, 0xbe52e1d2, 0x3e4b0e0c, 0x3e6bd5b7,
0xbe047b0f, 0x3da6abd5, 0xbd54c6b8, 0xbe97e9bf,
0xbe64a77c, 0xbe742405, 0xbe0672ce, 0xbeba8060,
0xbe1e1bb1, 0xbeba9ba4, 0xbe75100b, 0xbf7fc74f,
0x3f5aa9f3, 0xbdd7b3d6, 0x3f460a5c, 0x3e85bf74,
0x3ef0d7a8, 0xbf800000, 0xbf4a3815, 0x3e8bf866,
0xbef9d1b5, 0xbf3edd9f, 0x3ebe217e, 0x3f012626,
0x3f2171c9, 0x3f30a7f9, 0x3f0cd82a, 0xbf0a6c07,
0xbf089ec5, 0x3ed14430, 0x3f800000, 0x3e80dd0c,
0x3cb613aa, 0xbc62cf5a, 0x3e5a3796, 0x3f290ef3,
0xbf1c3462, 0xbf0781bc, 0xbdd71c71, 0x3f800000,
0x3f48d1b8, 0xbf10aa61, 0x3f4d7c82, 0xbe1f087a,
0x3eb0283e, 0x3f2bf09f, 0x3e6e71de, 0xbf64d4b1,
0xbe2d09a9, 0x3e905224, 0x3eb17c90, 0xbea14b46,
0xbe957d5c, 0x3f5b6623, 0x3dbc587d, 0xbee9f6fd,
0xbea17e1e, 0xbf800000, 0x3f17893e, 0x3e78394c,
0xbf147c77, 0x3ef576f1, 0x3f4f634b, 0x3efff38e,
0x3dbd0995, 0x3f0e2643, 0xbea2ecc2, 0x3eb211a6,
0x3ee31b23, 0x3f800000, 0xbeed64d9, 0xbe875891,
0xbe8109a0, 0x3ef9850e, 0xbf329842, 0x3ea0ddb0,
0xbf3fd673, 0xbe9dd12e, 0x3f3840ae, 0x3eda740c,
0xbf27967c, 0xbf32a9a6, 0xbd4af668, 0x3f6902f4,
0xbf1aab6d, 0xbf18e055, 0xbec0e769, 0x3f06e823,
0xbe8f4b22, 0xbe84baed, 0x3edb8b47, 0x3f00b01e,
0x3e9eea21, 0xbc6199e9, 0xbc993e39, 0x3e88831a,
0x3b6a6c84, 0xbf800000, 0x3ec0f628, 0xbee94be9,
0xbe80886e, 0x3d5135c1, 0xbe081611, 0xbbde1f71,
0x3e95462e, 0xbf638a5b, 0x3e6a4622, 0x3e3bae2f,
0xbf10eec1, 0x3e9acb53, 0x3e2b9f65, 0x3e996741,
0x3eecd359, 0xbe793ecf, 0xbebfc649, 0xbf110cf9,
0x3ed0f21f, 0x3d646e55, 0xbf15d211, 0xbe6be701,
0x3ee87297, 0x3d8f1aa4, 0x3ef321d2, 0x3f800000,
0xbef86140, 0x3f2b05a2, 0x3f42c95d, 0xbe50c4f2,
0x3f2cb4b0, 0x3c09bcdc, 0xbe72bb0b, 0xbca9084c,
0xbd8d095b, 0x3e0a2739, 0xbdf82e6a, 0xbedcd03a,
0x3adbfbda, 0x3c6375e8, 0x3ea1fe67, 0xbf800000,
0x3e01d22c, 0xbe57530e, 0x3d8c042d, 0x3e097701,
0xbe22d0ae, 0x3dd28b86, 0x3e77c774, 0xbe596573,
0x3ecc05ce, 0x3e1e297b, 0xbf2a452d, 0xbed97301,
0xbf36e2ab, 0xbea24e79, 0x3ef6cf3d, 0xbf1d2450,
0x3f3c4e0b, 0x3e87dfbb, 0x3eb7d4fe, 0x3df3670c,
0x3dd61ab6, 0x3f1952dc, 0xbed25ced, 0xbd06fa2c,
0x3f24bd66, 0x3e80c704, 0x3ef1c4a2, 0x3e17690e,
0xbf800000, 0x3ee4ae14, 0xbdff0a29, 0xbe36ff1e,
0xbf5013fb, 0x3e107cce, 0xbf2e9144, 0x3ed2c13a,
0xbed3c76e, 0x3f4d7913, 0xbeb1f014, 0x3f1f16b4,
0xbf32238d, 0xbf48e3fd, 0x3f48a160, 0xbf23d361,
0xbe91b43d, 0xbe915296, 0xbf1d952a, 0xbd47803e,
0x3e536c16, 0x3e2b8b26, 0xbf39495b, 0x3f800000,
0x3e641cb4, 0x3f231672, 0xbe1c3c4a, 0x3ec7456f,
0x3e6bf4ac, 0xbf0a3de9, 0x3e911276, 0xbf019535,
0xbeab4fa1, 0xbe4db21b, 0x3eb346d6, 0xbd221e4a,
0x3f2007e2, 0x3eb15429, 0x3d27e5eb, 0x3e468564,
0xbf01af45, 0x3ea06503, 0xbf299233, 0xbe8b6ab6,
0xbf800000, 0x3e4cc71f, 0x3ce4cb0e, 0x3eb0c12c,
0x3f13436e, 0x3e756ca8, 0x3eed299f, 0xbf2a6c30,
0xbe1bf45a, 0x3f800000, 0xbe1f5a8a, 0x3f703363,
0x3d8995aa, 0xbf3fbebc, 0x3ec36b35, 0xbf5189de,
0xbed63d54, 0xbf4b9c08, 0x3dfc59aa, 0xbf800000,
0x3db3f4a1, 0xbe80e58c, 0xbe7389e0, 0x3f035e9a,
0x3e9a30c4, 0xbe9342ac, 0xbed82f26, 0xbc8526ec,
0xbf10d3af, 0xbe789fd5, 0x3f2c7331, 0x3ece7cc7,
0x3f27912c, 0xbf2779ba, 0x3f7d6374, 0xbf800000,
0x3e8b7c39, 0xbe7d2bec, 0x3f1e5004, 0x3f6d4c5b,
0x3f800000, 0xbecffbaf, 0xbef7457e, 0x3dadda13,
0xbf484d6a, 0x3f5e244c, 0xbde9e672, 0x3f155caf,
0x3d824847, 0x3f0f23eb, 0x3f3e6e2e, 0x3d5a79ca,
0xbee58a3b, 0xbf800000, 0xbf5d5eb0, 0xbd5812f3,
0x3ca61aec, 0x3f28aa44, 0xbdb4ad97, 0x3ecbab58,
0x3e37026a, 0x3ce1d543, 0xbec2c193, 0xbe46b0a1,
0xbf50098c, 0xbd3803b8, 0x3efa7a69, 0xbd45a3c0,
0x3f800000, 0x3ed2f731, 0x3f553abf, 0x3edb4c05,
0x3cfcf83c, 0x3e263c30, 0xbf523c82, 0x3ed49e06,
0xbe88969f, 0xbf0413bd, 0x3e1dc97f, 0x3e2d3cdc,
0xbf11ee35, 0xbe339340, 0x3ddf6856, 0xbe37743f,
0xbe0b7c1f, 0xbeb64008, 0xbf7fd4c9, 0xbe1678e3,
0x3deaba8c, 0x3ebe0237, 0x3dd6b83a, 0xbe20f781,
0xbee27fbb, 0x3e55186e, 0x3ecfa254, 0xbe61ebc0,
0x3f800000, 0xbeacb8bf, 0x3ee36ec8, 0xbf54fdef,
0x3e9a7054, 0xbe98fa11, 0x3f26f7ef, 0xbe6c45fb,
0x3eafcb7b, 0x3ebb5010, 0x3ed9938a, 0x3e3a68a1,
0x3d16d519, 0xbcbfc3c6, 0xbeeba502, 0x3f1180f7,
0x3df76099, 0xbc658c37, 0x3e0fc3e5, 0xbe8845c6,
0x3f0f086c, 0x3f786535, 0x3eadafb2, 0xbd9fb56d,
0x3f2f56ea, 0xbe69f921, 0x3e5da08a, 0x3f23c30b,
0xbdfaa05f, 0x3ee7489e, 0xbf0e63a3, 0x3ec73fd4,
0x3ddcb8d1, 0xbe80c68b, 0x3f20880e, 0xbe988ec1,
0x3e194950, 0xbe5b2d95, 0x3e93ad72, 0xbee20114,
0x3f800000, 0x3eb9123a, 0xbeae6615, 0x3e3c72b9,
0xbe999fa9, 0x3f22de35, 0x3ed93aad, 0x3ec6c3d8,
0xbf095f25, 0x3e446b3f, 0x3c81d249, 0xbbb94d97,
0x3ebd3fbd, 0xbe1bbbd7, 0x3e4b52cd, 0xbf800000,
0xbe1d10dd, 0x3e3bed8b, 0xbe990dcf, 0x3f37274b,
0xbe5c15c9, 0xbf30e052, 0x3f49ecd2, 0xbe51d5e9,
0xbf232b8e, 0x3e02b1ee, 0xbf263fc6, 0x3e9d9bf4,
0x3df639ad, 0xbf6a0262, 0x3edc352c, 0xbd39bc04,
0xbf09ffd1, 0xbe94af07, 0x3f37d207, 0xbdd70dd3,
0x3e26dfa5, 0xbea96b6f, 0xbeb2f4fe, 0x3f5df03a,
0xbed082a7, 0xbe6ac9f0, 0x3de726da, 0xbf800000,
0x3da6ef8d, 0xbe98afa9, 0xbe214760, 0x3f3b4c0b,
0x3e3425d6, 0xbe82d225, 0x3ed96686, 0x3efdc759,
0x3b9cd7e3, 0x3f259f82, 0xbf08d8c5, 0xbb189dcb,
0x3ef4c867, 0x3eb56309, 0xbf370146, 0xbf79b033,
0xbdb3c392, 0xbe0984b1, 0x3daaac07, 0x3eb581aa,
0xbe0feb84, 0x3e6d4f86, 0x3ed98d00, 0xbd909c42,
0xbd9efd0a, 0xbf800000, 0x3ee3e231, 0x3f48988e,
0xbe854b0b, 0x3ebf158b, 0x3dc8ebe7, 0xbeed2980,
0x3d9b327c, 0xbe1a24bc, 0xbe9454c4, 0xbe5e8928,
0xbe65c304, 0xbf2a7ce8, 0xbf5c4fb7, 0x3ebdf7ff,
0xbd0648bd, 0x3f65ac28, 0x3f09c587, 0xbeb65751,
0x3d642c79, 0x3d0dbecf, 0x3e1c033c, 0x3e777363,
0x3ec0d180, 0xbf7f147d, 0x3dcf2046, 0x3ed1ce6c,
0x3e215134, 0xbd97ead7, 0x3e819e0d, 0xbf09754d,
0x3e6ca9c8, 0xbd3423d2, 0xbd1571e9, 0x3d24f8e3,
0x3ebc8578, 0xbe8bc361, 0x3ed3cc7f, 0xbec612ea,
0x3e369adf, 0xbebaa638, 0xbdca0c29, 0xbe76efd8,
0xbf04ee9b, 0x3f0b90dc, 0x3de3f5e1, 0x3d4253c5,
0xbe7ca45c, 0xbf800000, 0xbe35004b, 0x3e18d074,
0xbda55913, 0xbd101d69, 0xbd93c0a7, 0xbdd5b112,
0x3e985e4f, 0xbe1a053a, 0x3ebadb45, 0xbef7b4ae,
0xbe685e4e, 0xbef8b25d, 0x3ef6d0ae, 0xbd8c19ed,
0xbb02e749, 0x3e8ad8e5, 0xbf037329, 0xbea17713,
0xbe3dc677, 0xbf1bf1e4, 0x3dfb597e, 0x3ee45dd8,
0x3f800000, 0x3e8a90ab, 0x3e66e45c, 0x3e8d6d35,
0x3eabde4b, 0x3ef2586f, 0xbf469304, 0x3f19a7e3,
0xbdd30286, 0x3e71cabe, 0x3f239c52, 0xbe686ea0,
0x3f029293, 0x3ef5377a, 0x3daf6315, 0x3f322a18,
0x3f005f12, 0x3d6386a2, 0xbe827137, 0x3e8cb844,
0x3f0cf9b1, 0xbef8a868, 0x3dd98e4b, 0x3f06a2b3,
0xbb1607ff, 0xbeab47bc, 0xbda44e87, 0x3d08d0cf,
0xbb195031, 0x3ec97065, 0x3ec8cc2e, 0xbdc08c4b,
0xbeb6478e, 0xbf3db0bd, 0xbdd9bc4e, 0x3de900f1,
0x3f1ba486, 0x3ea595ae, 0xbd2d167c, 0x3ea9f0d5,
0x3ed75949, 0xbf034cb1, 0xbed02747, 0xbe28f8d4,
0x3e8fb68f, 0x3f1199a4, 0x3eef13ff, 0xbf6f5dcb,
0x3e0eae76, 0xbde0e770, 0x3ee880b3, 0xbdaf80ed,
0x3e3db76e, 0xbe182515, 0x3ecf9e64, 0x3e3325a2,
0xbe03dca6, 0x3e114ea3, 0x3d3f9e3a, 0xbe6419c2,
0x3f800000, 0x3f17dbb1, 0x3dc5c212, 0x3dd375ef,
0x3dad21e6, 0x3f30c4ae, 0x3ea4db29, 0xbf21ca14,
0x3e35d5b8, 0x3ce8f023, 0x3f03ac8e, 0xbe966c5e,
0x3f2a0142, 0x3e976834, 0x3f1cf7ee, 0xbdf32756,
0xbd9413c2, 0xbd9b0850, 0x3eb05fd0, 0x3ec17acb,
0x3f0adda3, 0xbecb1c2d, 0xbf05da2a, 0x3cf002d8,
0xbe7bc287, 0x3e920c76, 0xbded0954, 0xbeae3379,
0xbe5e1b04, 0xbd3a2d45, 0xbdff1c6d, 0xbe3ba409,
0x3ede378c, 0x3e223aba, 0xbe4f4931, 0x3e98286c,
0x3d008e33, 0x3e8293a1, 0xbe0eb219, 0xbe32879f,
0x3e6dfb97, 0xbf13c3d7, 0x3df45028, 0x3e8148cf,
0x3f229250, 0xbf3fa0d8, 0xbe4c7f3f, 0xbe8af169,
0x3ccd54a9, 0xbde97c54, 0xbee06c1e, 0xbf57b3ad,
0x3e72b64e, 0x3e4689e3, 0xbe1ee093, 0xbf0b6c5b,
0xbecedbe7, 0x3ef37205, 0x3c92ccd9, 0xbe9b9995,
0xbdc9a77c, 0xbf800000, 0xbdf9b1a7, 0xbe1e2094,
0x3e62464e, 0x3ebeee87, 0x3d1f099e, 0x3e4b6170,
0xbda888b2, 0x3f283ebc, 0x3f511a60, 0xbd56b475,
0x3ef55bde, 0x3da15fb7, 0x3ee7afcf, 0x3dcf401f,
0xbd20801d, 0xbf786ebf, 0x3ed985c6, 0x3ed39204,
0x3d596463, 0xbe12f50f, 0x3f2d7ecb, 0x3d9e9138,
0x3e969288, 0x3d0ebe61, 0x3f7c682c, 0x3e294963,
0x3e9214e3, 0xbe30ad9d, 0x3b73c4c8, 0x3e47e04f,
0xbf362580, 0x3f15a564, 0xbe19bc64, 0xbeea8d84,
0xbf5cab13, 0xbd6b18b6, 0xbf800000, 0x3eb04ab7,
0xbef4c81f, 0xbf50b8f8, 0xbe732507, 0x3f2453f3,
0x3f7d3a38, 0x38e1b101, 0x3f217b61, 0x3ea02d93,
0xbe6c7eb0, 0x3ea5e499, 0x3ea6ca3b, 0x3dcba9eb,
0x3e080151, 0xbf01ff50, 0xbf14dc41, 0x3f29bfc1,
0xbecb7235, 0x3f800000, 0x3e06a60d, 0x3e886e27,
0xbf609099, 0x3ee788a6, 0xbec1de02, 0x3ed75f47,
0xbef2804f, 0xbf3112e3, 0x3e971f77, 0xbd379480,
0xbe87dfd5, 0xbe78b2ef, 0xbeae163a, 0x3f44ce7c,
0xbf2d58e5, 0x3ed6e503, 0xbf290128, 0x3f168023,
0xbebfc292, 0xbe877d58, 0x3f110ff9, 0xbdd8032a,
0x3efb4b65, 0xbde5b7ef, 0x3ee35371, 0xbdca97a2,
0x3d5d8602, 0xbea9ec06, 0xbe120707, 0x3e871c50,
0xbf04b4ac, 0x3b1abdcf, 0xbe466ec8, 0x3ccbfbf7,
0x3e0b7d36, 0xbe957ef1, 0x3eb5eef3, 0xbe8b7aef,
0x3d22be08, 0x3e47d030, 0xbe784dbe, 0x3e65e7d9,
0xbe887074, 0xbd95de9d, 0xbe38d9b2, 0xbd8408d7,
0xbe2dbdf8, 0xbef5506b, 0x3d3f5eb9, 0xbdb605fb,
0xbebc29ab, 0xbe3e03bd, 0x3e792fb6, 0x3e96e4c1,
0x3e5fcc29, 0x3dfdf44a, 0x3ebcf7e5, 0x3f800000,
0xbf20f3a7, 0xbe08a1bf, 0xbed981c0, 0xbe1f629c,
0x3ea0e335, 0x3eaa4e89, 0xbb5ed9ab, 0xbd87724a,
0x3e52c452, 0xbd893420, 0xbe288cf8, 0x3e8fcab0,
0x3e0f29f2, 0x3e646d29, 0x3c52982f, 0xbebb361c,
0x3ed4bf74, 0x3dcdf6c6, 0x3eb3ab78, 0x3f35fde5,
0x3e04ef07, 0x3eb0e616, 0x3df39ed8, 0xbe7179a0,
0xbe67904a, 0x3cf74673, 0xbf058ae4, 0x3e83c12e,
0x3e6a64c5, 0x3f1b17c7, 0x3eead084, 0x3ed3e85e,
0x3f498206, 0x3e82b655, 0x3dd59a9a, 0xbe6bfa16,
0x3ef58827, 0xbf800000, 0xbee70318, 0x3f1ce358,
0xbe57d631, 0x3d0d4db1, 0x3eab6d89, 0x3e9b4fbf,
0xbef3c109, 0x3dbe766e, 0xbc816c98, 0xbeee9a60,
0xbe827392, 0xbe4acddf, 0x3f466add, 0xbf3917fe,
0xbe5af06d, 0xbe779dc9, 0xbce79225, 0x3ca29f07,
0xbf800000, 0xbec07726, 0xbf1711e7, 0xbe4a37b3,
0xbe098318, 0x3f5c1b57, 0x3e9d1c8d, 0x3ea7ca1d,
0xbf5781b3, 0x3e1402bb, 0x3e57349d, 0x3dab7751,
0x3efac01a, 0xbf7c1bb3, 0xbf51f279, 0x3d9002ae,
0xbd45e888, 0x3ef06685, 0xbf4d340c, 0xbedb03ae,
0xbc32a78d, 0xbf69c782, 0x3e127e2c, 0xbf800000,
0xbed5a087, 0x3e2fb460, 0xbcab7c09, 0xbf72ea83,
0x3e7fc281, 0x3ed16956, 0x3df1b0af, 0xbe9b75de,
0xbe5558b1, 0xbed9283b, 0xbed4f8df, 0xbf19d131,
0xbe59442d, 0xbee7f62b, 0xbe6cd0d5, 0x3e141956,
0xbd956d39, 0x3b55c23a, 0xbd3eaf8e, 0x3e5d9d7b,
0x3e76c644, 0x3ea2e1fb, 0xbf4eb01b, 0x3ec7776e,
0xbe9efb2c, 0xbee1b35e, 0xbe981818, 0x3e6771ec,
0xbeeb74d2, 0xbe1d75c0, 0x3ef46ab4, 0xbf800000,
0x3e693373, 0xbdc6ad0f, 0xbe8cd2e0, 0xbe359031,
0x3eac29a8, 0x3d58fc2f, 0xbf800000, 0xbd2f51c2,
0xbd81f94f, 0x3db7c1ea, 0xbcf5162b, 0xbf04db11,
0x3ea563d0, 0xbe61ff4c, 0xbdc81ee4, 0xbf2a75cf,
0x3ea441b2, 0x3eafd3e7, 0x3d9cd757, 0xbe3482e8,
0xbe9c397b, 0x3ece940d, 0xbe4742a5, 0x3d6426b0,
0x3e8e97b0, 0x3e437dfe, 0xbe14172d, 0xbe2c6456,
0x3da97a30, 0xbf1a1701, 0xbe690d20, 0x3e4ba434,
0xbe6b37f9, 0x3dc74fb4, 0xbe3b508e, 0xbdbff130,
0xbe9624dc, 0x3e805247, 0xbeeb6231, 0xbf800000,
0xbe3b4d14, 0x3edcada5, 0xbe747535, 0xbe1ec954,
0xbf2ab415, 0x3e4a3ffa, 0xbe0e6515, 0x3f3f8d3e,
0x3e5e863b, 0x3f66c0a8, 0x3dc5bff6, 0x3e789a6e,
0x3e22a59a, 0x3f611652, 0xbe8ef0c5, 0xbe933ac7,
0xbf5391fc, 0x3f075dcd, 0xbe16acd3, 0xbf3d26cb,
0xbf356adb, 0x3f3d2194, 0x3f2088c2, 0x3e085be2,
0x3e866cbf, 0xbf400229, 0xbf588bbc, 0x3f800000,
0x3e95d89a, 0x3e71eb78, 0xbf28f3e3, 0xbeabbf26,
0xbe66924d, 0x3ed7c2e1, 0x3c8ee709, 0x3e46ab39,
0x3e860ddd, 0xbed2d95f, 0xbe8a62c9, 0x3f26ca64,
0x3e26adcf, 0xbe4f0043, 0xbf66a2be, 0xbec59e1f,
0xbdee80bc, 0xbdfd4ca3, 0x3e7c5cf9, 0xbf105c21,
0xbe40e1c7, 0x3ec4a263, 0xbf256b53, 0x3da15d57,
0xbf212135, 0xbe2eaf70, 0x3f1f39d9, 0xbd05e236,
0x3e3a113a, 0xbeff8b9d, 0x3ec9043f, 0xbf565c36,
0xbdb67a32, 0x3dd61560, 0x3da1e25d, 0xbda3f534,
0x3e021a61, 0x3ea1cd59, 0xbf269b3e, 0xbe50eb78,
0xbe59bccf, 0xbe3bb501, 0xbf59e049, 0x3c840fdb,
0xbbec697d, 0x3eeb2431, 0x3f131532, 0xbf0e1914,
0x3e504e41, 0x3d080f1f, 0xbd15fb18, 0xbcc2b9f7,
0x3e6e3e1f, 0xbbad58d7, 0x3eaee8cc, 0xbeebf0d3,
0xbef5022b, 0x3ca1d00f, 0x3efdd25e, 0x3f148434,
0xbf800000, 0x3de4eee7, 0x3eae057d, 0x3cf85922,
0x3eb375b7, 0xbf07967f, 0x3c8db33a, 0xbd6bb439,
0xbe7aabf0, 0xbf405085, 0xbefd6742, 0xbccee33c,
0x3ef1d692, 0xbe6f2276, 0x3d0f9dbf, 0x3dcc0c28,
0x3eb59202, 0x3c205808, 0x3ce3c09c, 0x3ebd670c,
0xbec21dbe, 0x3eecc344, 0x3e759785, 0xbf00093c,
0xbc8e7eea, 0xbece9d2a, 0xbe655a8b, 0xbe135669,
0x3d907aad, 0xbe66eca8, 0x3ead16fa, 0x3e49dd11,
0x3ce0523c, 0x3f024e09, 0xbddebe0e, 0x3ba69170,
0xbd2f1add, 0xbe473569, 0xbf3d1ff9, 0x3db8f029,
0x3eee4029, 0xbe6508b3, 0xbe59aa26, 0xbc135c06,
0x3d84eba8, 0xbf0423d1, 0x3edeb7f4, 0xbf049db5,
0x3e1d88cb, 0xbe76f4b8, 0x3e8b2d84, 0x3f222e16,
0x3dfdbaa3, 0xbe335a78, 0xbd90c38b, 0x3ef789b3,
0xbe1b7e53, 0x3eeef3d9, 0xbf483781, 0xbe2c8f04,
0x3e17c774, 0xbf3a5e4d, 0x3d5a251a, 0xbf5c005a,
0xbf418f93, 0x3dfd73e8, 0xbd7b561e, 0xbf179d88,
0xbecedd4e, 0xbf77f6db, 0xbf1428e7, 0x3f5673fb,
0x3e80078a, 0xbe9b922b, 0xbdbfc2e8, 0x3e935e15,
0xbdc8b52c, 0xbd7dfe08, 0xbf0387e4, 0xbf6bd7a7,
0xbececfac, 0xbe8de9a7, 0x3f800000, 0xbe951a7a,
0x3e937c97, 0xbc056d36, 0xbeb6a924, 0x3f0ee341,
0xbdecfb2e, 0xbe168e89, 0x3e44b84e, 0x3e5bc17e,
0x3f1792d0, 0xbf2f3086, 0xbedc8caf, 0x3ea264e1,
0x3da79e37, 0xbc82019d, 0x3efe8ea5, 0x3e43882b,
0x3e5ae78b, 0xbf548208, 0xbeed32a9, 0x3ecbf12c,
0x3e80e091, 0x3ed2fe00, 0xbe5fc425, 0xbf6bdeda,
0xbb43450a, 0xbcfe965f, 0x3df02554, 0x3f1bc24c,
0x3eded785, 0x3edae27c, 0x3d6fe100, 0xbea64619,
0x3e03814c, 0x3ed982c3, 0xbf217f18, 0x3d862719,
0xbdc20573, 0xbe319f2c, 0x3f800000, 0x3e27dfc9,
0x3d6be241, 0xbe325e58, 0x3ce8491b, 0xbf32966a,
0xbc984647, 0x3e82095b, 0x3ecfa302, 0xbe1e586f,
0x3ef19b1b, 0x3f0ac3f0, 0xbe50539f, 0xbeb71cbb,
0x3ef568d8, 0xbedc08b0, 0xbe96763c, 0x3e0d1960,
0x3ecb08d8, 0x3f5b6c69, 0xbdec3e67, 0xbdaaeeb0,
0xbe2eaf4f, 0x3ebc913a, 0x3d9b9728, 0xbf0bf764,
0x3e1d7f0c, 0x3d9218f8, 0x3f2ff927, 0xbed229a1,
0xbf44578b, 0xbe5c3803, 0x3e51132e, 0xbe765d3b,
0xbf4e9ece, 0x3ecb83f8, 0xbe4292e2, 0xbdaa6146,
0xbf0c46f9, 0xbe38b07d, 0xbedb1e76, 0x3ed95083,
0xbde0dce8, 0x3f0ed9c1, 0x3e532678, 0x3f2e85ee,
0xbe7dd495, 0xbea83eda, 0x3d925250, 0x3df05141,
0x3eb59957, 0x3e9c26d2, 0xbf1e8de6, 0x3e236301,
0xbd911947, 0x3f78a297, 0xbe83f92e, 0x3e6872e3,
0xbf1a3aae, 0xbe8f4f32, 0x3c8030a5, 0x3e90e465,
0xbf44c604, 0x3d54c51d, 0xbcf6cd50, 0xbead4829,
0xbedb4ce3, 0x3f062359, 0x3cb02c08, 0x3ebef08d,
0xbea942e9, 0x3e7d88f5, 0xbf5c99bb, 0x3e837727,
0x3dbfac28, 0xbf532711, 0xbe3e2f58, 0xbd265514,
0x3e75c265, 0x3f2e0e67, 0x3f3579d7, 0x3ed6e5fd,
0x3eb90609, 0x3e8fbf36, 0x3ef11bcb, 0xbe887aa6,
0xbdb136f5, 0xbf145fb5, 0xbee99f4d, 0x3ef681f0,
0xbe5503d7, 0x3e8f41a9, 0x3ed83c07, 0x3e87c6ac,
0x3f066e0b, 0x3e239449, 0xbe440d1d, 0xbce2b98e,
0xbdb28d61, 0x3d1572d1, 0xbe49aaa3, 0xbf800000,
0x3f00eee8, 0xbf2e5b84, 0x3e32d9ae, 0xbec79c35,
0x3e1a00f8, 0x3d02b5bc, 0x3e39bb97, 0x3e18705f,
0xbf74f517, 0xbd1f7657, 0xbd2a78c1, 0x3e40b93a,
0xbe61a727, 0xbe9dcec9, 0x3ecc2fb6, 0x3e40fd61,
0x3e53bc63, 0xbe8e14e6, 0x3f06f503, 0x3f11fca7,
0xbf448ee1, 0x3ea06804, 0x3f27a2d7, 0x3e9ad6ab,
0xbf0fda39, 0x3e8f581b, 0x3e47452a, 0xbd3e5a96,
0x3e291ffd, 0x3eaf9a07, 0x3e07e2e2, 0x3d8f474a,
0xbe7c6ca0, 0xbcdd5961, 0xbdce1bb4, 0xbe9b70ef,
0xbcb46650, 0xbdb97088, 0x3e9e6481, 0x3e4d9feb,
0xbf23c5cc, 0x3ea4dcad, 0xbe806f3c, 0xbdcfd2b0,
0xbe8b78d8, 0xbe841014, 0x3e12bdfe, 0xbd4ac247,
0xbf064349, 0xbe1148a3, 0x3e60cb5f, 0x3ccdad9a,
0xbf5d0a67, 0x3d1e8358, 0xbef4ba4a, 0xbebfb9a0,
0x3e72e8a4, 0xbdf8c09d, 0x3e34bef7, 0x3c8dcc54,
0x3d841048, 0x3ebbc2f3, 0xbf10016f, 0x3d553741,
0x3ee40bc8, 0x3e0307c5, 0xbe19672b, 0x3ef594d3,
0x3d4338fc, 0xbdd5104b, 0xbdda83e6, 0xbedaca7c,
0x3f07f627, 0xbea1f735, 0xbed6bf10, 0x3e853663,
0x3dfa7d8e, 0xbea6ad6c, 0x3f800000, 0x3f1726cd,
0xbe97561e, 0x3ef025c8, 0x3e45a1b2, 0x3e479dc3,
0xbe238e80, 0x3f02310c, 0x3d6da084, 0xbde38eb7,
0xbcb8169a, 0xbe0d24ea, 0xbed4e51c, 0x3f047b5a,
0xbe93dd5d, 0xbd535140, 0x3e8c81a6, 0x3e8dfd1d,
0xbe5c1831, 0x3e13b59c, 0x3f62ed36, 0xbeeef5ee,
0x3e490c92, 0xbedec01a, 0xbe561ca6, 0x3c579622,
0x3f1f4536, 0x3cfb571a, 0x3e9e466c, 0xbd6ac422,
0x3d9a7cf8, 0x3e33927f, 0x3ed43263, 0x3dde5247,
0x3e895b85, 0x3d534be7, 0xbe85bca9, 0x3e0a98fb,
0xbf14e647, 0xbeeb3e72, 0x3de97443, 0x3f00fec3,
0xbf1279b0, 0xbe7b7b44, 0xbd907f6b, 0xbf800000,
0x3ebcc52f, 0x3f043581, 0xbe90c19a, 0x3e1dd044,
0xbeb8ecde, 0xbf1e9804, 0x3e118491, 0x3d982d2b,
0xbddb503a, 0x3ee37546, 0xbb2a88ab, 0x3e2da9fc,
0xbedcff52, 0xbea73def, 0x3f0ef856, 0xbd818f86,
0xbeb73cc2, 0xbd8c70d2, 0x3e0b0eca, 0xbd4df4bd,
0x3eebc112, 0x3e148265, 0xbe6bbdff, 0xbd6c4544,
0x3e246078, 0xbd13a7a6, 0xbe16c93a, 0xbe8317d5,
0x3ea5b98e, 0x3e43c4b0, 0x3e92f4b7, 0x3cb3643d,
0x3e9392b6, 0x3f1b005b, 0x3e1696a1, 0xbbf9c324,
0x3e837d2b, 0x3ddb037d, 0xbf39b885, 0xbe6c705f,
0x3e306d0a, 0xbe9c0954, 0xbddba52d, 0xbe97bd78,
0x3d203fd3, 0xbd9091ed, 0x3e71c49d, 0xbdd7e0ef,
0x3b8c37e5, 0xbbe3bb18, 0xbf6a682a, 0x3dadd654,
0x3ea9ee3e, 0x3f33ca7f, 0x3d8b467f, 0xbd24459f,
0xbf0435fa, 0x3eceb6c6, 0xbed22ea0, 0xbf04e774,
0xbec0a001, 0x3f32a8f1, 0x3f27b7c4, 0x3ead2cf2,
0x3d05b071, 0xbed9d648, 0x3cac09a0, 0xbd0cc0a4,
0x3e45a208, 0x3ec336e1, 0x3e06473d, 0x3e50b977,
0xbd177f55, 0x3edccb41, 0x3eefacdd, 0xbe1ce17f,
0xbd4229b8, 0x3e2f67d2, 0xbf0641af, 0xbe11540b,
0xbf03577a, 0x3eb508b6, 0x3e91d69b, 0x3e9b0c17,
0x3f488b32, 0xbf2cd92e, 0x3b057da6, 0xbd1d73da,
0x3f6099b0, 0x3f1e3263, 0xbd5cdb9a, 0x3e310315,
0x3e449522, 0x3dbd7104, 0x3ea2c7fd, 0xbed7b2b4,
0x3c30e512, 0xbdfc24bc, 0x3f4b0eed, 0x3e53b3f0,
0x3b8dcb82, 0x3effd804, 0xbf800000, 0x3e11254d,
0xbef3e0ac, 0xbd84cb6b, 0x3e7fff25, 0x3ec198df,
0x3e0b5663, 0xbee4e1f2, 0x3e8e4ad8, 0xbe0fa4e1,
0xbedcac93, 0xbe8e9bb2, 0xbebcacc7, 0x3e8f9a75,
0xbeb5e618, 0xbe2def7a, 0xbf35d262, 0xbe50332d,
0x3d1941ec, 0x3f219d56, 0x3e5bf0d7, 0x3dc74983,
0x3ca1f01f, 0xbecdc74d, 0x3e2c64d6, 0xbf0aad54,
0xbd1b18aa, 0x3f035e23, 0xbd2030fc, 0xbd138736,
0x3ea544d9, 0x3f218e8a, 0x3e33e80d, 0xbece90e7,
0xbec58b69, 0xbd688be9, 0xbf2c5fca, 0xbd625f22,
0xbebe7d1d, 0x3e29347f, 0xbe73b7b6, 0x3ea2672e,
0x3e52e892, 0x3ec7738d, 0xbea06553, 0x3f038fe0,
0xbe2a3f90, 0x3de68aa0, 0xbf1a2402, 0xbdc45c50,
0xbf32f6bc, 0x3e9a5951, 0x3c8bd7da, 0xbda8bf2d,
0xbc8e6449, 0xbdf4ce2f, 0x3d283307, 0xbdee603c,
0x3dd64ade, 0x3d4d027b, 0x3e79aa68, 0x3dc54600,
0xbefe855a, 0x3f800000, 0x3e3fcaf6, 0xbddfc308,
0xbc9438cc, 0x3d8d02df, 0x3e37fa1f, 0xbebc13da,
0x3ebc60a0, 0x3e1a55c9, 0xbe912d2a, 0x3d02093d,
0x3edcf733, 0xbdb577cb, 0xbe607b8e, 0x3e708504,
0x3efb43df, 0xbe378dd3, 0x3df688ca, 0xbf3c456e,
0xbd8e875f, 0x3ae0f8ed, 0x3ed48be3, 0xbefde4e0,
0xbd2cd62f, 0xbefb7c53, 0x3f117c90, 0x3ec0e974,
0xbf69973e, 0x3d94ce3d, 0xbef4e49e, 0x3e5ca6a0,
0xbe9c0a45, 0x3f385f4d, 0x3f133f56, 0x3c350836,
0x3d616893, 0xbedec009, 0x3e61b8ca, 0xbe753923,
0xbca8cf3c, 0x3da07f7c, 0xbeb14f73, 0x3ddb6941,
0xbe0995b7, 0xbeac82ee, 0x3e581e4f, 0x3e1c94c9,
0xbef01ada, 0xbefa340c, 0x3eb29b10, 0x3df09414,
0x3eb0c697, 0x3d1757e9, 0xbefd6276, 0xbd1d3bb2,
0x3f285294, 0x3c2e79f2, 0xbc109b48, 0x3e856249,
0xbcb98b71, 0xbf4f4344, 0xbc87053c, 0x3e9babd8,
0x3e8cf9e3, 0xbdfa1a9b, 0x3cd60580, 0xbcf3eab9,
0x3f1cd2a2, 0x3d8602fd, 0xbca0ff83, 0x3dca746e,
0xbe74103b, 0xbe9343e6, 0x3ecfb610, 0x3e4ead92,
0xbe821d93, 0x3e71d6b9, 0xbf068750, 0xbedf0ff1,
0x3e8af15e, 0x3eccacae, 0xbe8bee84, 0x3e8bca8f,
0xbef4a01a, 0xbeab6dc3, 0xbed10c4d, 0xbc0fe30c,
0xbe1ad88a, 0xbecb7c13, 0xbf015d24, 0xbed8c923,
0xbc0e132b, 0xbdb9e5f6, 0xbea56300, 0x3dcc8f39,
0x3eb7f0d4, 0xbee5c6cd, 0x3e8fdff8, 0x3ddbc636,
0xbe22fbb4, 0x3f1d8e51, 0xbcf7001c, 0x3ea26e06,
0x3f1321a5, 0xbcc01a68, 0xbd8b8219, 0x3e67c96a,
0x3f07f1ec, 0x3e44fe5e, 0x3f0b4634, 0xbdc24617,
0xbeb4ffcd, 0xbf800000, 0xbdff1121, 0xbea281d0,
0xbecfea1f, 0x3e195b8d, 0xbf063280, 0x3e185510,
0x3ddd1bd8, 0xbf2f5970, 0x3da88c70, 0x3e830234,
0x3e6770ed, 0x3eeb6c3f, 0x3e964747, 0xbc6a8adc,
0x3edc95b9, 0xbf5c0e9d, 0xbe3860ca, 0x3e5e2c66,
0x3e1c746e, 0xbeb27ca0, 0x3e13bc81, 0x3f050da9,
0xbe0ce80f, 0x3ef4ec13, 0xbe68a5f3, 0xbf4299de,
0x3dcfc728, 0x3d55bcaa, 0xbf1a2dab, 0xbbf41e50,
0xbec3733b, 0x3eea6690, 0xbea55ac4, 0x3edb45e2,
0xbde1ba61, 0x3edef1b5, 0x3dff66be, 0xbdb24bf7,
0xbec4bf78, 0x3d10bec0, 0x3f58f04a, 0xbf1e0d88,
0xbdd22003, 0x3e81d11f, 0xbe38757b, 0xbe25b0b6,
0x3dea4f49, 0x3f278b3d, 0x3e88e56f, 0xbd71cffe,
0xbeb4dd3c, 0x3e80f29d, 0x3ec96896, 0xbe2a11bf,
0x3e2aebbe, 0xbf47cdad, 0xbf1a9d57, 0xbf1a3a49,
0x3e0fecc9, 0xbf24bc8b, 0x3d5aac17, 0xbe85ede4,
0x3da6fb86, 0xbf343f67, 0x3f2fc61c, 0x3e271f88,
0xbe94d8c7, 0x3dc875ad, 0x3d86e23f, 0xbde6e6a4,
0xbed512ee, 0xbe4d52af, 0x3edbec70, 0xbf1f441c,
0x3e3cd321, 0xbeb3d563, 0xbe99e71c, 0x3e188fc2,
0x3e9764fc, 0x3e856460, 0x3d9fb475, 0x3df4aabf,
0x3f064018, 0xbd23f845, 0x3e524736, 0xbef5443b,
0xbe7ef173, 0xbef391a9, 0xbe9c4db0, 0xbf11bb51,
0x3db4fc37, 0xbf186079, 0xbeb38d44, 0x3da17449,
0xbe142287, 0x3f800000, 0xbec50939, 0xbdb00dfc,
0xbc02838e, 0xbf03a369, 0xbdf77093, 0xbf4cabd3,
0x3f21b621, 0xbe85114c, 0xbd373df3, 0x3e880e92,
0x3e28d5ce, 0xbe23172f, 0xbedbbf24, 0xbcfd2c77,
0x3e64f051, 0x3f05ab0b, 0xbe00a8e8, 0x3e6d1d55,
0x3d81105c, 0x3ef490d9, 0x3ee326df, 0x3d89d749,
0x3e457285, 0x3f3a0490, 0xbc519eb6, 0xbe8e724a,
0xbddf8b78, 0x3dd0a271, 0xbf02a72b, 0x3dba05b0,
0xbe990e78, 0xbd23f944, 0xbe94cf80, 0x3e3d2d9d,
0xbe3754cf, 0xbe6d034b, 0x3e090bc4, 0xbf25366d,
0x3ed08531, 0xbe91686c, 0xbd4bd717, 0x3dcf6ed9,
0xbe94e9cf, 0xbf1e1aa2, 0xbef3f99c, 0x3d4f7796,
0x3ef6e188, 0xbd3e8636, 0x3e1671c6, 0xbe90b782,
0x3f466789, 0xbdf36074, 0xbd6202ab, 0xbec321ff,
0x3d400b28, 0x3e9978ce, 0xbe4882d7, 0x3e1bb0e9,
0xbe664070, 0x3e016312, 0xbe9146f7, 0x3f21ffa9,
0x3ec5095f, 0x3eee7527, 0x3cc7cc3c, 0x3e3d84c4,
0x3e065736, 0xbebbb9c3, 0xbef920d5, 0x3ce58cc4,
0xbea2c5f9, 0x3e85ebdf, 0x3f0a31da, 0xbf120a45,
0xbeb1f1fd, 0x3dfb8604, 0x3e72e40a, 0xbf5cef81,
0xbf141695, 0x3e8b6b1b, 0x3e69c2ca, 0xbe3365c2,
0xbf0c852d, 0x3e9225f1, 0x3e947687, 0x3e8a06e2,
0x3ddfb90d, 0xbe73e96c, 0x3d90f3ac, 0x3e205a49,
0x3e0f690d, 0xbe3745bb, 0x3f800000, 0x3dc84f2e,
0x3d67ae33, 0x3e5ece9a, 0xbcecbe18, 0xbe81f976,
0xbdb8322b, 0x3e5cb61e, 0x3e1637b4, 0x3f454049,
0x3c561fc4, 0xbe749a02, 0x3c9f61d2, 0x3d829baa,
0x3e62c254, 0xbedb21fd, 0xbc95e954, 0xbec7a559,
0x3f25bc46, 0x3dcc4c30, 0xbe947320, 0x3e6cbc35
};
static const uint32_t in_coeff_decim[564] = {
0x3e4ccccd, 0x3e088889, 0x3d888889, 0x3e888889,
0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab, 0x3e088889,
0x3dcccccd, 0x3d888889, 0x3d088889, 0x3e906907,
0x3e834835, 0x3e6c4ec5, 0x3e520d21, 0x3e37cb7d,
0x3e1d89d9, 0x3e034835, 0x3dd20d21, 0x3d9d89d9,
0x3d520d21, 0x3cd20d21, 0x3e638e39, 0x3e2aaaab,
0x3de38e39, 0x3d638e39, 0x3e8ba2e9, 0x3e783e10,
0x3e59364e, 0x3e3a2e8c, 0x3e1b26ca, 0x3df83e10,
0x3dba2e8c, 0x3d783e10, 0x3cf83e10, 0x3e924925,
0x3e861862, 0x3e73cf3d, 0x3e5b6db7, 0x3e430c31,
0x3e2aaaab, 0x3e124925, 0x3df3cf3d, 0x3dc30c31,
0x3d924925, 0x3d430c31, 0x3cc30c31, 0x3e4ccccd,
0x3e088889, 0x3d888889, 0x3e888889, 0x3e6eeeef,
0x3e4ccccd, 0x3e2aaaab, 0x3e088889, 0x3dcccccd,
0x3d888889, 0x3d088889, 0x3e906907, 0x3e834835,
0x3e6c4ec5, 0x3e520d21, 0x3e37cb7d, 0x3e1d89d9,
0x3e034835, 0x3dd20d21, 0x3d9d89d9, 0x3d520d21,
0x3cd20d21, 0x3e638e39, 0x3e2aaaab, 0x3de38e39,
0x3d638e39, 0x3e8ba2e9, 0x3e783e10, 0x3e59364e,
0x3e3a2e8c, 0x3e1b26ca, 0x3df83e10, 0x3dba2e8c,
0x3d783e10, 0x3cf83e10, 0x3e924925, 0x3e861862,
0x3e73cf3d, 0x3e5b6db7, 0x3e430c31, 0x3e2aaaab,
0x3e124925, 0x3df3cf3d, 0x3dc30c31, 0x3d924925,
0x3d430c31, 0x3cc30c31, 0x3e4ccccd, 0x3e088889,
0x3d888889, 0x3e888889, 0x3e6eeeef, 0x3e4ccccd,
0x3e2aaaab, 0x3e088889, 0x3dcccccd, 0x3d888889,
0x3d088889, 0x3e906907, 0x3e834835, 0x3e6c4ec5,
0x3e520d21, 0x3e37cb7d, 0x3e1d89d9, 0x3e034835,
0x3dd20d21, 0x3d9d89d9, 0x3d520d21, 0x3cd20d21,
0x3e638e39, 0x3e2aaaab, 0x3de38e39, 0x3d638e39,
0x3e8ba2e9, 0x3e783e10, 0x3e59364e, 0x3e3a2e8c,
0x3e1b26ca, 0x3df83e10, 0x3dba2e8c, 0x3d783e10,
0x3cf83e10, 0x3e924925, 0x3e861862, 0x3e73cf3d,
0x3e5b6db7, 0x3e430c31, 0x3e2aaaab, 0x3e124925,
0x3df3cf3d, 0x3dc30c31, 0x3d924925, 0x3d430c31,
0x3cc30c31, 0x3e4ccccd, 0x3e088889, 0x3d888889,
0x3e888889, 0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab,
0x3e088889, 0x3dcccccd, 0x3d888889, 0x3d088889,
0x3e906907, 0x3e834835, 0x3e6c4ec5, 0x3e520d21,
0x3e37cb7d, 0x3e1d89d9, 0x3e034835, 0x3dd20d21,
0x3d9d89d9, 0x3d520d21, 0x3cd20d21, 0x3e638e39,
0x3e2aaaab, 0x3de38e39, 0x3d638e39, 0x3e8ba2e9,
0x3e783e10, 0x3e59364e, 0x3e3a2e8c, 0x3e1b26ca,
0x3df83e10, 0x3dba2e8c, 0x3d783e10, 0x3cf83e10,
0x3e924925, 0x3e861862, 0x3e73cf3d, 0x3e5b6db7,
0x3e430c31, 0x3e2aaaab, 0x3e124925, 0x3df3cf3d,
0x3dc30c31, 0x3d924925, 0x3d430c31, 0x3cc30c31,
0x3e4ccccd, 0x3e088889, 0x3d888889, 0x3e888889,
0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab, 0x3e088889,
0x3dcccccd, 0x3d888889, 0x3d088889, 0x3e906907,
0x3e834835, 0x3e6c4ec5, 0x3e520d21, 0x3e37cb7d,
0x3e1d89d9, 0x3e034835, 0x3dd20d21, 0x3d9d89d9,
0x3d520d21, 0x3cd20d21, 0x3e638e39, 0x3e2aaaab,
0x3de38e39, 0x3d638e39, 0x3e8ba2e9, 0x3e783e10,
0x3e59364e, 0x3e3a2e8c, 0x3e1b26ca, 0x3df83e10,
0x3dba2e8c, 0x3d783e10, 0x3cf83e10, 0x3e924925,
0x3e861862, 0x3e73cf3d, 0x3e5b6db7, 0x3e430c31,
0x3e2aaaab, 0x3e124925, 0x3df3cf3d, 0x3dc30c31,
0x3d924925, 0x3d430c31, 0x3cc30c31, 0x3e4ccccd,
0x3e088889, 0x3d888889, 0x3e888889, 0x3e6eeeef,
0x3e4ccccd, 0x3e2aaaab, 0x3e088889, 0x3dcccccd,
0x3d888889, 0x3d088889, 0x3e906907, 0x3e834835,
0x3e6c4ec5, 0x3e520d21, 0x3e37cb7d, 0x3e1d89d9,
0x3e034835, 0x3dd20d21, 0x3d9d89d9, 0x3d520d21,
0x3cd20d21, 0x3e638e39, 0x3e2aaaab, 0x3de38e39,
0x3d638e39, 0x3e8ba2e9, 0x3e783e10, 0x3e59364e,
0x3e3a2e8c, 0x3e1b26ca, 0x3df83e10, 0x3dba2e8c,
0x3d783e10, 0x3cf83e10, 0x3e924925, 0x3e861862,
0x3e73cf3d, 0x3e5b6db7, 0x3e430c31, 0x3e2aaaab,
0x3e124925, 0x3df3cf3d, 0x3dc30c31, 0x3d924925,
0x3d430c31, 0x3cc30c31, 0x3e4ccccd, 0x3e088889,
0x3d888889, 0x3e888889, 0x3e6eeeef, 0x3e4ccccd,
0x3e2aaaab, 0x3e088889, 0x3dcccccd, 0x3d888889,
0x3d088889, 0x3e906907, 0x3e834835, 0x3e6c4ec5,
0x3e520d21, 0x3e37cb7d, 0x3e1d89d9, 0x3e034835,
0x3dd20d21, 0x3d9d89d9, 0x3d520d21, 0x3cd20d21,
0x3e638e39, 0x3e2aaaab, 0x3de38e39, 0x3d638e39,
0x3e8ba2e9, 0x3e783e10, 0x3e59364e, 0x3e3a2e8c,
0x3e1b26ca, 0x3df83e10, 0x3dba2e8c, 0x3d783e10,
0x3cf83e10, 0x3e924925, 0x3e861862, 0x3e73cf3d,
0x3e5b6db7, 0x3e430c31, 0x3e2aaaab, 0x3e124925,
0x3df3cf3d, 0x3dc30c31, 0x3d924925, 0x3d430c31,
0x3cc30c31, 0x3e4ccccd, 0x3e088889, 0x3d888889,
0x3e888889, 0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab,
0x3e088889, 0x3dcccccd, 0x3d888889, 0x3d088889,
0x3e906907, 0x3e834835, 0x3e6c4ec5, 0x3e520d21,
0x3e37cb7d, 0x3e1d89d9, 0x3e034835, 0x3dd20d21,
0x3d9d89d9, 0x3d520d21, 0x3cd20d21, 0x3e638e39,
0x3e2aaaab, 0x3de38e39, 0x3d638e39, 0x3e8ba2e9,
0x3e783e10, 0x3e59364e, 0x3e3a2e8c, 0x3e1b26ca,
0x3df83e10, 0x3dba2e8c, 0x3d783e10, 0x3cf83e10,
0x3e924925, 0x3e861862, 0x3e73cf3d, 0x3e5b6db7,
0x3e430c31, 0x3e2aaaab, 0x3e124925, 0x3df3cf3d,
0x3dc30c31, 0x3d924925, 0x3d430c31, 0x3cc30c31,
0x3e4ccccd, 0x3e088889, 0x3d888889, 0x3e888889,
0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab, 0x3e088889,
0x3dcccccd, 0x3d888889, 0x3d088889, 0x3e906907,
0x3e834835, 0x3e6c4ec5, 0x3e520d21, 0x3e37cb7d,
0x3e1d89d9, 0x3e034835, 0x3dd20d21, 0x3d9d89d9,
0x3d520d21, 0x3cd20d21, 0x3e638e39, 0x3e2aaaab,
0x3de38e39, 0x3d638e39, 0x3e8ba2e9, 0x3e783e10,
0x3e59364e, 0x3e3a2e8c, 0x3e1b26ca, 0x3df83e10,
0x3dba2e8c, 0x3d783e10, 0x3cf83e10, 0x3e924925,
0x3e861862, 0x3e73cf3d, 0x3e5b6db7, 0x3e430c31,
0x3e2aaaab, 0x3e124925, 0x3df3cf3d, 0x3dc30c31,
0x3d924925, 0x3d430c31, 0x3cc30c31, 0x3e4ccccd,
0x3e088889, 0x3d888889, 0x3e888889, 0x3e6eeeef,
0x3e4ccccd, 0x3e2aaaab, 0x3e088889, 0x3dcccccd,
0x3d888889, 0x3d088889, 0x3e906907, 0x3e834835,
0x3e6c4ec5, 0x3e520d21, 0x3e37cb7d, 0x3e1d89d9,
0x3e034835, 0x3dd20d21, 0x3d9d89d9, 0x3d520d21,
0x3cd20d21, 0x3e638e39, 0x3e2aaaab, 0x3de38e39,
0x3d638e39, 0x3e8ba2e9, 0x3e783e10, 0x3e59364e,
0x3e3a2e8c, 0x3e1b26ca, 0x3df83e10, 0x3dba2e8c,
0x3d783e10, 0x3cf83e10, 0x3e924925, 0x3e861862,
0x3e73cf3d, 0x3e5b6db7, 0x3e430c31, 0x3e2aaaab,
0x3e124925, 0x3df3cf3d, 0x3dc30c31, 0x3d924925,
0x3d430c31, 0x3cc30c31, 0x3e4ccccd, 0x3e088889,
0x3d888889, 0x3e888889, 0x3e6eeeef, 0x3e4ccccd,
0x3e2aaaab, 0x3e088889, 0x3dcccccd, 0x3d888889,
0x3d088889, 0x3e906907, 0x3e834835, 0x3e6c4ec5,
0x3e520d21, 0x3e37cb7d, 0x3e1d89d9, 0x3e034835,
0x3dd20d21, 0x3d9d89d9, 0x3d520d21, 0x3cd20d21,
0x3e638e39, 0x3e2aaaab, 0x3de38e39, 0x3d638e39,
0x3e8ba2e9, 0x3e783e10, 0x3e59364e, 0x3e3a2e8c,
0x3e1b26ca, 0x3df83e10, 0x3dba2e8c, 0x3d783e10,
0x3cf83e10, 0x3e924925, 0x3e861862, 0x3e73cf3d,
0x3e5b6db7, 0x3e430c31, 0x3e2aaaab, 0x3e124925,
0x3df3cf3d, 0x3dc30c31, 0x3d924925, 0x3d430c31,
0x3cc30c31, 0x3e4ccccd, 0x3e088889, 0x3d888889,
0x3e888889, 0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab,
0x3e088889, 0x3dcccccd, 0x3d888889, 0x3d088889,
0x3e906907, 0x3e834835, 0x3e6c4ec5, 0x3e520d21,
0x3e37cb7d, 0x3e1d89d9, 0x3e034835, 0x3dd20d21,
0x3d9d89d9, 0x3d520d21, 0x3cd20d21, 0x3e638e39,
0x3e2aaaab, 0x3de38e39, 0x3d638e39, 0x3e8ba2e9,
0x3e783e10, 0x3e59364e, 0x3e3a2e8c, 0x3e1b26ca,
0x3df83e10, 0x3dba2e8c, 0x3d783e10, 0x3cf83e10,
0x3e924925, 0x3e861862, 0x3e73cf3d, 0x3e5b6db7,
0x3e430c31, 0x3e2aaaab, 0x3e124925, 0x3df3cf3d,
0x3dc30c31, 0x3d924925, 0x3d430c31, 0x3cc30c31
};
static const uint32_t in_config_decim[288] = {
0x00000001, 0x00000003, 0x00000003, 0x00000003,
0x00000001, 0x00000008, 0x00000003, 0x00000003,
0x00000001, 0x0000000B, 0x00000003, 0x00000003,
0x00000001, 0x00000004, 0x00000003, 0x00000003,
0x00000001, 0x00000009, 0x00000003, 0x00000003,
0x00000001, 0x0000000C, 0x00000003, 0x00000003,
0x00000001, 0x00000003, 0x00000008, 0x00000008,
0x00000001, 0x00000008, 0x00000008, 0x00000008,
0x00000001, 0x0000000B, 0x00000008, 0x00000008,
0x00000001, 0x00000004, 0x00000008, 0x00000008,
0x00000001, 0x00000009, 0x00000008, 0x00000008,
0x00000001, 0x0000000C, 0x00000008, 0x00000008,
0x00000001, 0x00000003, 0x0000000B, 0x0000000B,
0x00000001, 0x00000008, 0x0000000B, 0x0000000B,
0x00000001, 0x0000000B, 0x0000000B, 0x0000000B,
0x00000001, 0x00000004, 0x0000000B, 0x0000000B,
0x00000001, 0x00000009, 0x0000000B, 0x0000000B,
0x00000001, 0x0000000C, 0x0000000B, 0x0000000B,
0x00000002, 0x00000003, 0x00000006, 0x00000003,
0x00000002, 0x00000008, 0x00000006, 0x00000003,
0x00000002, 0x0000000B, 0x00000006, 0x00000003,
0x00000002, 0x00000004, 0x00000006, 0x00000003,
0x00000002, 0x00000009, 0x00000006, 0x00000003,
0x00000002, 0x0000000C, 0x00000006, 0x00000003,
0x00000002, 0x00000003, 0x00000010, 0x00000008,
0x00000002, 0x00000008, 0x00000010, 0x00000008,
0x00000002, 0x0000000B, 0x00000010, 0x00000008,
0x00000002, 0x00000004, 0x00000010, 0x00000008,
0x00000002, 0x00000009, 0x00000010, 0x00000008,
0x00000002, 0x0000000C, 0x00000010, 0x00000008,
0x00000002, 0x00000003, 0x00000016, 0x0000000B,
0x00000002, 0x00000008, 0x00000016, 0x0000000B,
0x00000002, 0x0000000B, 0x00000016, 0x0000000B,
0x00000002, 0x00000004, 0x00000016, 0x0000000B,
0x00000002, 0x00000009, 0x00000016, 0x0000000B,
0x00000002, 0x0000000C, 0x00000016, 0x0000000B,
0x00000004, 0x00000003, 0x0000000C, 0x00000003,
0x00000004, 0x00000008, 0x0000000C, 0x00000003,
0x00000004, 0x0000000B, 0x0000000C, 0x00000003,
0x00000004, 0x00000004, 0x0000000C, 0x00000003,
0x00000004, 0x00000009, 0x0000000C, 0x00000003,
0x00000004, 0x0000000C, 0x0000000C, 0x00000003,
0x00000004, 0x00000003, 0x00000020, 0x00000008,
0x00000004, 0x00000008, 0x00000020, 0x00000008,
0x00000004, 0x0000000B, 0x00000020, 0x00000008,
0x00000004, 0x00000004, 0x00000020, 0x00000008,
0x00000004, 0x00000009, 0x00000020, 0x00000008,
0x00000004, 0x0000000C, 0x00000020, 0x00000008,
0x00000004, 0x00000003, 0x0000002C, 0x0000000B,
0x00000004, 0x00000008, 0x0000002C, 0x0000000B,
0x00000004, 0x0000000B, 0x0000002C, 0x0000000B,
0x00000004, 0x00000004, 0x0000002C, 0x0000000B,
0x00000004, 0x00000009, 0x0000002C, 0x0000000B,
0x00000004, 0x0000000C, 0x0000002C, 0x0000000B,
0x00000008, 0x00000003, 0x00000018, 0x00000003,
0x00000008, 0x00000008, 0x00000018, 0x00000003,
0x00000008, 0x0000000B, 0x00000018, 0x00000003,
0x00000008, 0x00000004, 0x00000018, 0x00000003,
0x00000008, 0x00000009, 0x00000018, 0x00000003,
0x00000008, 0x0000000C, 0x00000018, 0x00000003,
0x00000008, 0x00000003, 0x00000040, 0x00000008,
0x00000008, 0x00000008, 0x00000040, 0x00000008,
0x00000008, 0x0000000B, 0x00000040, 0x00000008,
0x00000008, 0x00000004, 0x00000040, 0x00000008,
0x00000008, 0x00000009, 0x00000040, 0x00000008,
0x00000008, 0x0000000C, 0x00000040, 0x00000008,
0x00000008, 0x00000003, 0x00000058, 0x0000000B,
0x00000008, 0x00000008, 0x00000058, 0x0000000B,
0x00000008, 0x0000000B, 0x00000058, 0x0000000B,
0x00000008, 0x00000004, 0x00000058, 0x0000000B,
0x00000008, 0x00000009, 0x00000058, 0x0000000B,
0x00000008, 0x0000000C, 0x00000058, 0x0000000B
};
static const uint32_t in_val_interp[264] = {
0x3f3394bb, 0xbf800000, 0x3f0e7ea0, 0x3ca3f4b8,
0x3f800000, 0x3eb97421, 0x3e7ca010, 0xbec29f0b,
0xbe9d549a, 0xbf444ebd, 0xbd798b2b, 0x3e82e097,
0xbf59344e, 0xbf800000, 0x3ebe5c80, 0xbe2a7142,
0xbc359fcf, 0xbf800000, 0x3e8c3bb3, 0xbeed5808,
0x3ce1b788, 0xbd5a455d, 0xbf0a2f7c, 0x3f3a15f0,
0x3f06c912, 0xbf800000, 0x3ee4fd50, 0xbecc75a4,
0xbf2ff39d, 0x3e54554b, 0x3f05da0f, 0xbf564b3a,
0x3e93ca61, 0x3e54f412, 0xbf800000, 0xbdd74be8,
0xbf081c0d, 0x3f1d3b6d, 0xbf54d3e9, 0x3e6da069,
0xbdb5f015, 0xbf18cd8b, 0xbf16e70a, 0x3f0c9dd4,
0x3e1db9f3, 0x3f16d684, 0xbf800000, 0xbf800000,
0xbe08a36b, 0xbf1d67d3, 0x3e6cb3b0, 0x3b9cee2e,
0x3e9903ad, 0xbe59e4dc, 0xbf3f0641, 0xbed73b84,
0x3f800000, 0x3e6ad633, 0x3e52634c, 0xbf38a327,
0xbf800000, 0xbe9f4b58, 0x3f2263e4, 0xbf1e8507,
0x3e93899c, 0xbf68a14d, 0xbf800000, 0xbf65d985,
0xbf44b8c6, 0xbe7efc4c, 0x3ec30ba6, 0x3ec1f8c8,
0xbdab5e89, 0x3e54d5fe, 0xbdaa32db, 0x3f024b22,
0xbedc013a, 0xbf334be7, 0x3f5ed3eb, 0x3e8b51a6,
0xbe9f6446, 0xbf4b1e71, 0x3e6c6ccc, 0x3f800000,
0xbe224ad8, 0x3ed317fc, 0x3c9b4cd0, 0xbe9f3940,
0xbebbb6f0, 0x3e83bee4, 0xbf800000, 0x3f4d6539,
0x3f267094, 0x3f800000, 0xbea936cc, 0x3ead1793,
0x3f088a4f, 0xbedb2211, 0x3f800000, 0x3cff10c1,
0x3dcf2324, 0xbe54a399, 0x3e8b57b7, 0xbf4748ca,
0xbe8860a9, 0xbf1306de, 0xbf800000, 0xbe1e689e,
0x3e363957, 0xbee0bd83, 0x3f2dec40, 0xbed73cae,
0xbf17d851, 0xbf30bf09, 0x3e881dc6, 0x3f5fbe29,
0x3d91c614, 0x3f622e8a, 0x3ec933b1, 0x3f800000,
0xbee56006, 0x3f2926e4, 0xbf800000, 0xbf286213,
0x3f1684d5, 0xbe87b1d2, 0x3e834878, 0x3eec0080,
0x3edf0f0b, 0x3f0a24d5, 0x3eadfa1c, 0x3ef86e55,
0x3e5b4b00, 0x3ece6eed, 0xbf800000, 0x3f363b47,
0xbf800000, 0x3f3e8673, 0xbeb86f35, 0xbf117e64,
0x3f2d5044, 0xbeb7fca9, 0xbf800000, 0x3ef2c6bf,
0x3f259da0, 0x3ea51a36, 0x3d6e037f, 0x3f800000,
0x3df35a60, 0x3f1d51ea, 0xbeb7a1ad, 0x3ea93620,
0xbf7ad862, 0xbea26ad7, 0xbe9b480c, 0xbe8de8e9,
0xbe3c97ad, 0xbe3455f8, 0x3da251a0, 0x3d810ba8,
0x3e718beb, 0xbeb13416, 0xbdd64f20, 0xbf800000,
0x3e91b72c, 0xbf5e43d7, 0x3f0b3bc9, 0xbf16e4c6,
0x3db57f0f, 0x3f14bc5e, 0x3f726c84, 0x3f800000,
0x3f6f5f64, 0x3dfc1f47, 0x3efe9f9d, 0xbe3ee9dc,
0x3f800000, 0x3eac88d2, 0x3f5386c3, 0xbe7758fd,
0x3f800000, 0x3da34e54, 0x3ebf7e27, 0xbe7a58bc,
0x3f094c60, 0x3d7500a6, 0x3f800000, 0xbef2b12d,
0xbf28e296, 0xbe978a2c, 0xbe019d4e, 0xbf7a8feb,
0x3e8ccbce, 0x3c653371, 0x3f2cfb71, 0x3ba52232,
0xbf29b88e, 0xbf800000, 0x3e24f9e8, 0xbd368bf0,
0x3f800000, 0x3e195c68, 0xbe8334f0, 0x3f1d13ec,
0x3dadf096, 0x3e66ab9b, 0x3f08f07b, 0x3f46bbac,
0xbf065a3f, 0xbd929abd, 0xbf7f45f0, 0xbe6a59c8,
0xbf7444fd, 0xbf72b2d1, 0x3efb3b29, 0x3db1e1ea,
0xbda18a5b, 0x3ed0a0b5, 0xbf800000, 0xbe8bdad3,
0x3ea9ff26, 0x3f800000, 0xbe89a04b, 0x3e3909b9,
0xbf800000, 0xbd75538d, 0x3e6ccdb3, 0xbf800000,
0xbe9ee089, 0xbe2a38bc, 0x3dd6d514, 0xbe25d57e,
0xbf6a10ef, 0xbf28dba7, 0xbf2926bd, 0x3e5fdfc7,
0x3eb810c9, 0x3f396f3f, 0x3ef31591, 0xbe5a3d65,
0x3e71d603, 0xbf800000, 0x3f166eb8, 0x3f800000,
0xbed54670, 0xbc6e88ca, 0xbe188f3a, 0xbe7a251f,
0x3eb20de0, 0xbf506bae, 0xbea36937, 0x3f67b208,
0xbf09c1cd, 0xbe91ef4f, 0xbe71e734, 0xbddd7d1e,
0x3cbfa90d, 0x3ee47516, 0x3df27640, 0x3dabb48d,
0x3eb52c66, 0x3e742218, 0x3f800000, 0x3e99e6e4
};
static const uint32_t in_coeff_interp[1044] = {
0x3e638e39, 0x3e2aaaab, 0x3de38e39, 0x3d638e39,
0x3e888889, 0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab,
0x3e088889, 0x3dcccccd, 0x3d888889, 0x3d088889,
0x3e638e39, 0x3e2aaaab, 0x3de38e39, 0x3d638e39,
0x3e888889, 0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab,
0x3e088889, 0x3dcccccd, 0x3d888889, 0x3d088889,
0x3e638e39, 0x3e2aaaab, 0x3de38e39, 0x3d638e39,
0x3e888889, 0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab,
0x3e088889, 0x3dcccccd, 0x3d888889, 0x3d088889,
0x3e888889, 0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab,
0x3e088889, 0x3dcccccd, 0x3d888889, 0x3d088889,
0x3e97b426, 0x3e8e38e4, 0x3e84bda1, 0x3e7684be,
0x3e638e39, 0x3e5097b4, 0x3e3da12f, 0x3e2aaaab,
0x3e17b426, 0x3e04bda1, 0x3de38e39, 0x3dbda12f,
0x3d97b426, 0x3d638e39, 0x3d17b426, 0x3c97b426,
0x3e888889, 0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab,
0x3e088889, 0x3dcccccd, 0x3d888889, 0x3d088889,
0x3e97b426, 0x3e8e38e4, 0x3e84bda1, 0x3e7684be,
0x3e638e39, 0x3e5097b4, 0x3e3da12f, 0x3e2aaaab,
0x3e17b426, 0x3e04bda1, 0x3de38e39, 0x3dbda12f,
0x3d97b426, 0x3d638e39, 0x3d17b426, 0x3c97b426,
0x3e888889, 0x3e6eeeef, 0x3e4ccccd, 0x3e2aaaab,
0x3e088889, 0x3dcccccd, 0x3d888889, 0x3d088889,
0x3e97b426, 0x3e8e38e4, 0x3e84bda1, 0x3e7684be,
0x3e638e39, 0x3e5097b4, 0x3e3da12f, 0x3e2aaaab,
0x3e17b426, 0x3e04bda1, 0x3de38e39, 0x3dbda12f,
0x3d97b426, 0x3d638e39, 0x3d17b426, 0x3c97b426,
0x3e97b426, 0x3e8e38e4, 0x3e84bda1, 0x3e7684be,
0x3e638e39, 0x3e5097b4, 0x3e3da12f, 0x3e2aaaab,
0x3e17b426, 0x3e04bda1, 0x3de38e39, 0x3dbda12f,
0x3d97b426, 0x3d638e39, 0x3d17b426, 0x3c97b426,
0x3ea0a0a1, 0x3e9b9b9c, 0x3e969697, 0x3e919192,
0x3e8c8c8d, 0x3e878788, 0x3e828283, 0x3e7afafb,
0x3e70f0f1, 0x3e66e6e7, 0x3e5cdcdd, 0x3e52d2d3,
0x3e48c8c9, 0x3e3ebebf, 0x3e34b4b5, 0x3e2aaaab,
0x3e20a0a1, 0x3e169697, 0x3e0c8c8d, 0x3e028283,
0x3df0f0f1, 0x3ddcdcdd, 0x3dc8c8c9, 0x3db4b4b5,
0x3da0a0a1, 0x3d8c8c8d, 0x3d70f0f1, 0x3d48c8c9,
0x3d20a0a1, 0x3cf0f0f1, 0x3ca0a0a1, 0x3c20a0a1,
0x3e97b426, 0x3e8e38e4, 0x3e84bda1, 0x3e7684be,
0x3e638e39, 0x3e5097b4, 0x3e3da12f, 0x3e2aaaab,
0x3e17b426, 0x3e04bda1, 0x3de38e39, 0x3dbda12f,
0x3d97b426, 0x3d638e39, 0x3d17b426, 0x3c97b426,
0x3ea0a0a1, 0x3e9b9b9c, 0x3e969697, 0x3e919192,
0x3e8c8c8d, 0x3e878788, 0x3e828283, 0x3e7afafb,
0x3e70f0f1, 0x3e66e6e7, 0x3e5cdcdd, 0x3e52d2d3,
0x3e48c8c9, 0x3e3ebebf, 0x3e34b4b5, 0x3e2aaaab,
0x3e20a0a1, 0x3e169697, 0x3e0c8c8d, 0x3e028283,
0x3df0f0f1, 0x3ddcdcdd, 0x3dc8c8c9, 0x3db4b4b5,
0x3da0a0a1, 0x3d8c8c8d, 0x3d70f0f1, 0x3d48c8c9,
0x3d20a0a1, 0x3cf0f0f1, 0x3ca0a0a1, 0x3c20a0a1,
0x3e97b426, 0x3e8e38e4, 0x3e84bda1, 0x3e7684be,
0x3e638e39, 0x3e5097b4, 0x3e3da12f, 0x3e2aaaab,
0x3e17b426, 0x3e04bda1, 0x3de38e39, 0x3dbda12f,
0x3d97b426, 0x3d638e39, 0x3d17b426, 0x3c97b426,
0x3ea0a0a1, 0x3e9b9b9c, 0x3e969697, 0x3e919192,
0x3e8c8c8d, 0x3e878788, 0x3e828283, 0x3e7afafb,
0x3e70f0f1, 0x3e66e6e7, 0x3e5cdcdd, 0x3e52d2d3,
0x3e48c8c9, 0x3e3ebebf, 0x3e34b4b5, 0x3e2aaaab,
0x3e20a0a1, 0x3e169697, 0x3e0c8c8d, 0x3e028283,
0x3df0f0f1, 0x3ddcdcdd, 0x3dc8c8c9, 0x3db4b4b5,
0x3da0a0a1, 0x3d8c8c8d, 0x3d70f0f1, 0x3d48c8c9,
0x3d20a0a1, 0x3cf0f0f1, 0x3ca0a0a1, 0x3c20a0a1,
0x3e9b26ca, 0x3e9364d9, 0x3e8ba2e9, 0x3e83e0f8,
0x3e783e10, 0x3e68ba2f, 0x3e59364e, 0x3e49b26d,
0x3e3a2e8c, 0x3e2aaaab, 0x3e1b26ca, 0x3e0ba2e9,
0x3df83e10, 0x3dd9364e, 0x3dba2e8c, 0x3d9b26ca,
0x3d783e10, 0x3d3a2e8c, 0x3cf83e10, 0x3c783e10,
0x3ea28a29, 0x3e9e79e8, 0x3e9a69a7, 0x3e965966,
0x3e924925, 0x3e8e38e4, 0x3e8a28a3, 0x3e861862,
0x3e820821, 0x3e7befbf, 0x3e73cf3d, 0x3e6baebb,
0x3e638e39, 0x3e5b6db7, 0x3e534d35, 0x3e4b2cb3,
0x3e430c31, 0x3e3aebaf, 0x3e32cb2d, 0x3e2aaaab,
0x3e228a29, 0x3e1a69a7, 0x3e124925, 0x3e0a28a3,
0x3e020821, 0x3df3cf3d, 0x3de38e39, 0x3dd34d35,
0x3dc30c31, 0x3db2cb2d, 0x3da28a29, 0x3d924925,
0x3d820821, 0x3d638e39, 0x3d430c31, 0x3d228a29,
0x3d020821, 0x3cc30c31, 0x3c820821, 0x3c020821,
0x3e9b26ca, 0x3e9364d9, 0x3e8ba2e9, 0x3e83e0f8,
0x3e783e10, 0x3e68ba2f, 0x3e59364e, 0x3e49b26d,
0x3e3a2e8c, 0x3e2aaaab, 0x3e1b26ca, 0x3e0ba2e9,
0x3df83e10, 0x3dd9364e, 0x3dba2e8c, 0x3d9b26ca,
0x3d783e10, 0x3d3a2e8c, 0x3cf83e10, 0x3c783e10,
0x3ea28a29, 0x3e9e79e8, 0x3e9a69a7, 0x3e965966,
0x3e924925, 0x3e8e38e4, 0x3e8a28a3, 0x3e861862,
0x3e820821, 0x3e7befbf, 0x3e73cf3d, 0x3e6baebb,
0x3e638e39, 0x3e5b6db7, 0x3e534d35, 0x3e4b2cb3,
0x3e430c31, 0x3e3aebaf, 0x3e32cb2d, 0x3e2aaaab,
0x3e228a29, 0x3e1a69a7, 0x3e124925, 0x3e0a28a3,
0x3e020821, 0x3df3cf3d, 0x3de38e39, 0x3dd34d35,
0x3dc30c31, 0x3db2cb2d, 0x3da28a29, 0x3d924925,
0x3d820821, 0x3d638e39, 0x3d430c31, 0x3d228a29,
0x3d020821, 0x3cc30c31, 0x3c820821, 0x3c020821,
0x3e9b26ca, 0x3e9364d9, 0x3e8ba2e9, 0x3e83e0f8,
0x3e783e10, 0x3e68ba2f, 0x3e59364e, 0x3e49b26d,
0x3e3a2e8c, 0x3e2aaaab, 0x3e1b26ca, 0x3e0ba2e9,
0x3df83e10, 0x3dd9364e, 0x3dba2e8c, 0x3d9b26ca,
0x3d783e10, 0x3d3a2e8c, 0x3cf83e10, 0x3c783e10,
0x3ea28a29, 0x3e9e79e8, 0x3e9a69a7, 0x3e965966,
0x3e924925, 0x3e8e38e4, 0x3e8a28a3, 0x3e861862,
0x3e820821, 0x3e7befbf, 0x3e73cf3d, 0x3e6baebb,
0x3e638e39, 0x3e5b6db7, 0x3e534d35, 0x3e4b2cb3,
0x3e430c31, 0x3e3aebaf, 0x3e32cb2d, 0x3e2aaaab,
0x3e228a29, 0x3e1a69a7, 0x3e124925, 0x3e0a28a3,
0x3e020821, 0x3df3cf3d, 0x3de38e39, 0x3dd34d35,
0x3dc30c31, 0x3db2cb2d, 0x3da28a29, 0x3d924925,
0x3d820821, 0x3d638e39, 0x3d430c31, 0x3d228a29,
0x3d020821, 0x3cc30c31, 0x3c820821, 0x3c020821,
0x3ea0a0a1, 0x3e9b9b9c, 0x3e969697, 0x3e919192,
0x3e8c8c8d, 0x3e878788, 0x3e828283, 0x3e7afafb,
0x3e70f0f1, 0x3e66e6e7, 0x3e5cdcdd, 0x3e52d2d3,
0x3e48c8c9, 0x3e3ebebf, 0x3e34b4b5, 0x3e2aaaab,
0x3e20a0a1, 0x3e169697, 0x3e0c8c8d, 0x3e028283,
0x3df0f0f1, 0x3ddcdcdd, 0x3dc8c8c9, 0x3db4b4b5,
0x3da0a0a1, 0x3d8c8c8d, 0x3d70f0f1, 0x3d48c8c9,
0x3d20a0a1, 0x3cf0f0f1, 0x3ca0a0a1, 0x3c20a0a1,
0x3ea57eb5, 0x3ea2e8ba, 0x3ea052bf, 0x3e9dbcc5,
0x3e9b26ca, 0x3e9890cf, 0x3e95fad4, 0x3e9364d9,
0x3e90cede, 0x3e8e38e4, 0x3e8ba2e9, 0x3e890cee,
0x3e8676f3, 0x3e83e0f8, 0x3e814afd, 0x3e7d6a05,
0x3e783e10, 0x3e73121a, 0x3e6de624, 0x3e68ba2f,
0x3e638e39, 0x3e5e6243, 0x3e59364e, 0x3e540a58,
0x3e4ede62, 0x3e49b26d, 0x3e448677, 0x3e3f5a81,
0x3e3a2e8c, 0x3e350296, 0x3e2fd6a0, 0x3e2aaaab,
0x3e257eb5, 0x3e2052bf, 0x3e1b26ca, 0x3e15fad4,
0x3e10cede, 0x3e0ba2e9, 0x3e0676f3, 0x3e014afd,
0x3df83e10, 0x3dede624, 0x3de38e39, 0x3dd9364e,
0x3dcede62, 0x3dc48677, 0x3dba2e8c, 0x3dafd6a0,
0x3da57eb5, 0x3d9b26ca, 0x3d90cede, 0x3d8676f3,
0x3d783e10, 0x3d638e39, 0x3d4ede62, 0x3d3a2e8c,
0x3d257eb5, 0x3d10cede, 0x3cf83e10, 0x3ccede62,
0x3ca57eb5, 0x3c783e10, 0x3c257eb5, 0x3ba57eb5,
0x3ea0a0a1, 0x3e9b9b9c, 0x3e969697, 0x3e919192,
0x3e8c8c8d, 0x3e878788, 0x3e828283, 0x3e7afafb,
0x3e70f0f1, 0x3e66e6e7, 0x3e5cdcdd, 0x3e52d2d3,
0x3e48c8c9, 0x3e3ebebf, 0x3e34b4b5, 0x3e2aaaab,
0x3e20a0a1, 0x3e169697, 0x3e0c8c8d, 0x3e028283,
0x3df0f0f1, 0x3ddcdcdd, 0x3dc8c8c9, 0x3db4b4b5,
0x3da0a0a1, 0x3d8c8c8d, 0x3d70f0f1, 0x3d48c8c9,
0x3d20a0a1, 0x3cf0f0f1, 0x3ca0a0a1, 0x3c20a0a1,
0x3ea57eb5, 0x3ea2e8ba, 0x3ea052bf, 0x3e9dbcc5,
0x3e9b26ca, 0x3e9890cf, 0x3e95fad4, 0x3e9364d9,
0x3e90cede, 0x3e8e38e4, 0x3e8ba2e9, 0x3e890cee,
0x3e8676f3, 0x3e83e0f8, 0x3e814afd, 0x3e7d6a05,
0x3e783e10, 0x3e73121a, 0x3e6de624, 0x3e68ba2f,
0x3e638e39, 0x3e5e6243, 0x3e59364e, 0x3e540a58,
0x3e4ede62, 0x3e49b26d, 0x3e448677, 0x3e3f5a81,
0x3e3a2e8c, 0x3e350296, 0x3e2fd6a0, 0x3e2aaaab,
0x3e257eb5, 0x3e2052bf, 0x3e1b26ca, 0x3e15fad4,
0x3e10cede, 0x3e0ba2e9, 0x3e0676f3, 0x3e014afd,
0x3df83e10, 0x3dede624, 0x3de38e39, 0x3dd9364e,
0x3dcede62, 0x3dc48677, 0x3dba2e8c, 0x3dafd6a0,
0x3da57eb5, 0x3d9b26ca, 0x3d90cede, 0x3d8676f3,
0x3d783e10, 0x3d638e39, 0x3d4ede62, 0x3d3a2e8c,
0x3d257eb5, 0x3d10cede, 0x3cf83e10, 0x3ccede62,
0x3ca57eb5, 0x3c783e10, 0x3c257eb5, 0x3ba57eb5,
0x3ea0a0a1, 0x3e9b9b9c, 0x3e969697, 0x3e919192,
0x3e8c8c8d, 0x3e878788, 0x3e828283, 0x3e7afafb,
0x3e70f0f1, 0x3e66e6e7, 0x3e5cdcdd, 0x3e52d2d3,
0x3e48c8c9, 0x3e3ebebf, 0x3e34b4b5, 0x3e2aaaab,
0x3e20a0a1, 0x3e169697, 0x3e0c8c8d, 0x3e028283,
0x3df0f0f1, 0x3ddcdcdd, 0x3dc8c8c9, 0x3db4b4b5,
0x3da0a0a1, 0x3d8c8c8d, 0x3d70f0f1, 0x3d48c8c9,
0x3d20a0a1, 0x3cf0f0f1, 0x3ca0a0a1, 0x3c20a0a1,
0x3ea57eb5, 0x3ea2e8ba, 0x3ea052bf, 0x3e9dbcc5,
0x3e9b26ca, 0x3e9890cf, 0x3e95fad4, 0x3e9364d9,
0x3e90cede, 0x3e8e38e4, 0x3e8ba2e9, 0x3e890cee,
0x3e8676f3, 0x3e83e0f8, 0x3e814afd, 0x3e7d6a05,
0x3e783e10, 0x3e73121a, 0x3e6de624, 0x3e68ba2f,
0x3e638e39, 0x3e5e6243, 0x3e59364e, 0x3e540a58,
0x3e4ede62, 0x3e49b26d, 0x3e448677, 0x3e3f5a81,
0x3e3a2e8c, 0x3e350296, 0x3e2fd6a0, 0x3e2aaaab,
0x3e257eb5, 0x3e2052bf, 0x3e1b26ca, 0x3e15fad4,
0x3e10cede, 0x3e0ba2e9, 0x3e0676f3, 0x3e014afd,
0x3df83e10, 0x3dede624, 0x3de38e39, 0x3dd9364e,
0x3dcede62, 0x3dc48677, 0x3dba2e8c, 0x3dafd6a0,
0x3da57eb5, 0x3d9b26ca, 0x3d90cede, 0x3d8676f3,
0x3d783e10, 0x3d638e39, 0x3d4ede62, 0x3d3a2e8c,
0x3d257eb5, 0x3d10cede, 0x3cf83e10, 0x3ccede62,
0x3ca57eb5, 0x3c783e10, 0x3c257eb5, 0x3ba57eb5,
0x3ea1af28, 0x3e9d3167, 0x3e98b3a6, 0x3e9435e5,
0x3e8fb824, 0x3e8b3a63, 0x3e86bca2, 0x3e823ee1,
0x3e7b823f, 0x3e7286bd, 0x3e698b3a, 0x3e608fb8,
0x3e579436, 0x3e4e98b4, 0x3e459d31, 0x3e3ca1af,
0x3e33a62d, 0x3e2aaaab, 0x3e21af28, 0x3e18b3a6,
0x3e0fb824, 0x3e06bca2, 0x3dfb823f, 0x3de98b3a,
0x3dd79436, 0x3dc59d31, 0x3db3a62d, 0x3da1af28,
0x3d8fb824, 0x3d7b823f, 0x3d579436, 0x3d33a62d,
0x3d0fb824, 0x3cd79436, 0x3c8fb824, 0x3c0fb824,
0x3ea60dd6, 0x3ea3bf6c, 0x3ea17102, 0x3e9f2298,
0x3e9cd42e, 0x3e9a85c4, 0x3e98375a, 0x3e95e8f0,
0x3e939a86, 0x3e914c1c, 0x3e8efdb2, 0x3e8caf47,
0x3e8a60dd, 0x3e881273, 0x3e85c409, 0x3e83759f,
0x3e812735, 0x3e7db196, 0x3e7914c2, 0x3e7477ee,
0x3e6fdb19, 0x3e6b3e45, 0x3e66a171, 0x3e62049d,
0x3e5d67c9, 0x3e58caf4, 0x3e542e20, 0x3e4f914c,
0x3e4af478, 0x3e4657a4, 0x3e41bad0, 0x3e3d1dfb,
0x3e388127, 0x3e33e453, 0x3e2f477f, 0x3e2aaaab,
0x3e260dd6, 0x3e217102, 0x3e1cd42e, 0x3e18375a,
0x3e139a86, 0x3e0efdb2, 0x3e0a60dd, 0x3e05c409,
0x3e012735, 0x3df914c2, 0x3defdb19, 0x3de6a171,
0x3ddd67c9, 0x3dd42e20, 0x3dcaf478, 0x3dc1bad0,
0x3db88127, 0x3daf477f, 0x3da60dd6, 0x3d9cd42e,
0x3d939a86, 0x3d8a60dd, 0x3d812735, 0x3d6fdb19,
0x3d5d67c9, 0x3d4af478, 0x3d388127, 0x3d260dd6,
0x3d139a86, 0x3d012735, 0x3cdd67c9, 0x3cb88127,
0x3c939a86, 0x3c5d67c9, 0x3c139a86, 0x3b939a86,
0x3ea1af28, 0x3e9d3167, 0x3e98b3a6, 0x3e9435e5,
0x3e8fb824, 0x3e8b3a63, 0x3e86bca2, 0x3e823ee1,
0x3e7b823f, 0x3e7286bd, 0x3e698b3a, 0x3e608fb8,
0x3e579436, 0x3e4e98b4, 0x3e459d31, 0x3e3ca1af,
0x3e33a62d, 0x3e2aaaab, 0x3e21af28, 0x3e18b3a6,
0x3e0fb824, 0x3e06bca2, 0x3dfb823f, 0x3de98b3a,
0x3dd79436, 0x3dc59d31, 0x3db3a62d, 0x3da1af28,
0x3d8fb824, 0x3d7b823f, 0x3d579436, 0x3d33a62d,
0x3d0fb824, 0x3cd79436, 0x3c8fb824, 0x3c0fb824,
0x3ea60dd6, 0x3ea3bf6c, 0x3ea17102, 0x3e9f2298,
0x3e9cd42e, 0x3e9a85c4, 0x3e98375a, 0x3e95e8f0,
0x3e939a86, 0x3e914c1c, 0x3e8efdb2, 0x3e8caf47,
0x3e8a60dd, 0x3e881273, 0x3e85c409, 0x3e83759f,
0x3e812735, 0x3e7db196, 0x3e7914c2, 0x3e7477ee,
0x3e6fdb19, 0x3e6b3e45, 0x3e66a171, 0x3e62049d,
0x3e5d67c9, 0x3e58caf4, 0x3e542e20, 0x3e4f914c,
0x3e4af478, 0x3e4657a4, 0x3e41bad0, 0x3e3d1dfb,
0x3e388127, 0x3e33e453, 0x3e2f477f, 0x3e2aaaab,
0x3e260dd6, 0x3e217102, 0x3e1cd42e, 0x3e18375a,
0x3e139a86, 0x3e0efdb2, 0x3e0a60dd, 0x3e05c409,
0x3e012735, 0x3df914c2, 0x3defdb19, 0x3de6a171,
0x3ddd67c9, 0x3dd42e20, 0x3dcaf478, 0x3dc1bad0,
0x3db88127, 0x3daf477f, 0x3da60dd6, 0x3d9cd42e,
0x3d939a86, 0x3d8a60dd, 0x3d812735, 0x3d6fdb19,
0x3d5d67c9, 0x3d4af478, 0x3d388127, 0x3d260dd6,
0x3d139a86, 0x3d012735, 0x3cdd67c9, 0x3cb88127,
0x3c939a86, 0x3c5d67c9, 0x3c139a86, 0x3b939a86,
0x3ea1af28, 0x3e9d3167, 0x3e98b3a6, 0x3e9435e5,
0x3e8fb824, 0x3e8b3a63, 0x3e86bca2, 0x3e823ee1,
0x3e7b823f, 0x3e7286bd, 0x3e698b3a, 0x3e608fb8,
0x3e579436, 0x3e4e98b4, 0x3e459d31, 0x3e3ca1af,
0x3e33a62d, 0x3e2aaaab, 0x3e21af28, 0x3e18b3a6,
0x3e0fb824, 0x3e06bca2, 0x3dfb823f, 0x3de98b3a,
0x3dd79436, 0x3dc59d31, 0x3db3a62d, 0x3da1af28,
0x3d8fb824, 0x3d7b823f, 0x3d579436, 0x3d33a62d,
0x3d0fb824, 0x3cd79436, 0x3c8fb824, 0x3c0fb824,
0x3ea60dd6, 0x3ea3bf6c, 0x3ea17102, 0x3e9f2298,
0x3e9cd42e, 0x3e9a85c4, 0x3e98375a, 0x3e95e8f0,
0x3e939a86, 0x3e914c1c, 0x3e8efdb2, 0x3e8caf47,
0x3e8a60dd, 0x3e881273, 0x3e85c409, 0x3e83759f,
0x3e812735, 0x3e7db196, 0x3e7914c2, 0x3e7477ee,
0x3e6fdb19, 0x3e6b3e45, 0x3e66a171, 0x3e62049d,
0x3e5d67c9, 0x3e58caf4, 0x3e542e20, 0x3e4f914c,
0x3e4af478, 0x3e4657a4, 0x3e41bad0, 0x3e3d1dfb,
0x3e388127, 0x3e33e453, 0x3e2f477f, 0x3e2aaaab,
0x3e260dd6, 0x3e217102, 0x3e1cd42e, 0x3e18375a,
0x3e139a86, 0x3e0efdb2, 0x3e0a60dd, 0x3e05c409,
0x3e012735, 0x3df914c2, 0x3defdb19, 0x3de6a171,
0x3ddd67c9, 0x3dd42e20, 0x3dcaf478, 0x3dc1bad0,
0x3db88127, 0x3daf477f, 0x3da60dd6, 0x3d9cd42e,
0x3d939a86, 0x3d8a60dd, 0x3d812735, 0x3d6fdb19,
0x3d5d67c9, 0x3d4af478, 0x3d388127, 0x3d260dd6,
0x3d139a86, 0x3d012735, 0x3cdd67c9, 0x3cb88127,
0x3c939a86, 0x3c5d67c9, 0x3c139a86, 0x3b939a86
};
static const uint32_t in_config_interp[144] = {
0x00000001, 0x00000004, 0x00000003, 0x00000003,
0x00000001, 0x00000008, 0x00000003, 0x00000003,
0x00000001, 0x00000004, 0x00000008, 0x00000008,
0x00000001, 0x00000008, 0x00000008, 0x00000008,
0x00000001, 0x00000004, 0x0000000B, 0x0000000B,
0x00000001, 0x00000008, 0x0000000B, 0x0000000B,
0x00000002, 0x00000008, 0x00000003, 0x00000006,
0x00000002, 0x00000010, 0x00000003, 0x00000006,
0x00000002, 0x00000008, 0x00000008, 0x00000010,
0x00000002, 0x00000010, 0x00000008, 0x00000010,
0x00000002, 0x00000008, 0x0000000B, 0x00000016,
0x00000002, 0x00000010, 0x0000000B, 0x00000016,
0x00000004, 0x00000010, 0x00000003, 0x0000000C,
0x00000004, 0x00000020, 0x00000003, 0x0000000C,
0x00000004, 0x00000010, 0x00000008, 0x00000020,
0x00000004, 0x00000020, 0x00000008, 0x00000020,
0x00000004, 0x00000010, 0x0000000B, 0x0000002C,
0x00000004, 0x00000020, 0x0000000B, 0x0000002C,
0x00000005, 0x00000014, 0x00000003, 0x0000000F,
0x00000005, 0x00000028, 0x00000003, 0x0000000F,
0x00000005, 0x00000014, 0x00000008, 0x00000028,
0x00000005, 0x00000028, 0x00000008, 0x00000028,
0x00000005, 0x00000014, 0x0000000B, 0x00000037,
0x00000005, 0x00000028, 0x0000000B, 0x00000037,
0x00000008, 0x00000020, 0x00000003, 0x00000018,
0x00000008, 0x00000040, 0x00000003, 0x00000018,
0x00000008, 0x00000020, 0x00000008, 0x00000040,
0x00000008, 0x00000040, 0x00000008, 0x00000040,
0x00000008, 0x00000020, 0x0000000B, 0x00000058,
0x00000008, 0x00000040, 0x0000000B, 0x00000058,
0x00000009, 0x00000024, 0x00000003, 0x0000001B,
0x00000009, 0x00000048, 0x00000003, 0x0000001B,
0x00000009, 0x00000024, 0x00000008, 0x00000048,
0x00000009, 0x00000048, 0x00000008, 0x00000048,
0x00000009, 0x00000024, 0x0000000B, 0x00000063,
0x00000009, 0x00000048, 0x0000000B, 0x00000063
};
static const uint32_t ref_decim[528] = {
0x3ba53eeb, 0x3d9d3066, 0x3ddcf3f0, 0x3ab3cad4,
0xbcfa97b7, 0xbd8f4818, 0xbbc47a35, 0x3c5fa00c,
0x3d3cf0c5, 0xbd638e39, 0xbd8dda12, 0xbda2faa6,
0xbcf83e10, 0xbd88f0dd, 0xbdc86fde, 0xbc9aabc9,
0xbc6496c2, 0x3c0d0730, 0x3b960b45, 0x3ccb3790,
0x3de4c39c, 0x3e419db6, 0x3e5d715b, 0xbc38e81c,
0xbd0833fa, 0x3c1ddbdf, 0x3ba02e35, 0x397b9a35,
0x3cecf3ed, 0x3d9d096c, 0x3e186fb4, 0x3e74b1db,
0x3eaab6e0, 0x3ece3b65, 0x3cbd4609, 0x3d23b226,
0x3d80ef56, 0x3d94f1be, 0x3d859be8, 0x3d358a78,
0x3c918fdc, 0x3c8a17ea, 0xbc001aab, 0xbc606a62,
0xbd09233a, 0xbd83cb45, 0xbc9e4534, 0xbb7feb54,
0x3d9d8ef2, 0x3e5a42d4, 0xbab51008, 0xbb8e4b0d,
0x3bc8a1b8, 0x3c570b61, 0x3c8a4c53, 0x3c06f366,
0xbc6eaa57, 0xbd8a9886, 0x3c8f8cf4, 0x3c55e510,
0x3c2a206f, 0x3c9bf8ad, 0x3b7ea78f, 0xbc46f942,
0xbcae41f4, 0xbd029ad5, 0xbd888889, 0xbe2218aa,
0xbe85c7f9, 0xbd7f69d4, 0x3d7d31f6, 0x3e100c95,
0x3d9f412b, 0x3d410b96, 0x3e17f237, 0x3d9709ed,
0xbcf2a777, 0xbbc63170, 0xbbf32d5b, 0xbce1a42b,
0xbd426efb, 0xbd9bb0f0, 0xbdf11a7c, 0xbe062ce3,
0xbe1fba4c, 0xbdf60a19, 0xbe3cf783, 0xbc1ad625,
0xbcd20d21, 0xbd57b828, 0xbdb27e64, 0xbdf911b9,
0xbe1e1022, 0xbe2b8f99, 0xbe43c701, 0xbe5b3c66,
0xbe6ecc2a, 0xbe7e3053, 0xbe89816b, 0xba01b17d,
0x3d4cdf6f, 0x3e1fd4f7, 0x3e818788, 0x3eb31024,
0x3e306b4d, 0xbd8acfb6, 0xbbb0eb2a, 0x3cacb749,
0x3db80a84, 0x3d80a358, 0xbcc9971f, 0xbd3e0a89,
0xbd3cd7ed, 0xbc7e1925, 0x3c830f46, 0x3d1057af,
0x3d3e0158, 0x3dacfbef, 0x3e032ffd, 0x3ed41cc4,
0x3eea74a4, 0x38e7da05, 0x3b3c64d4, 0xbbfb76a7,
0xbc92c237, 0xbd0c67da, 0xbd93c748, 0xbdf77dff,
0xbe3b6100, 0xbe7d75dc, 0xbeabf61f, 0xbedd7d2b,
0x3d50e942, 0x3d8b3b1e, 0xbddac2b1, 0xbd088889,
0xbd8286bf, 0xbdae2cfa, 0x3ba54379, 0xbcab9ec7,
0xbd40845b, 0xbcc68b74, 0xbe2329a3, 0xbe9dbe2f,
0xbbd76f44, 0xbd6b1b09, 0xbdb5273b, 0x3c660e8f,
0x3d45f52a, 0x3dfd39b1, 0xbb62397a, 0x3d87caf0,
0x3e8278d3, 0xbdec298f, 0xbd41c2ef, 0x3d968de7,
0x3d7ce4f0, 0xbc9772ae, 0xbbf3e5d9, 0xbd2e7e0a,
0xbde47c79, 0xbe5f2ee8, 0xbe9b5fc7, 0xbe8cca54,
0xbde9a78b, 0x3cf28b1f, 0xbc4cfad6, 0xbd87abb4,
0xbd8c1e09, 0xbba14e6d, 0x3d001066, 0x3dcd8f70,
0x3f19c3c3, 0x3eff3323, 0xbd0ad93a, 0xbe2a5642,
0x3ca0391b, 0x3eab66c5, 0x3c24d4f1, 0x3de2160b,
0x3da28560, 0xbe3473e8, 0xbc10f5ae, 0x3ce6e42b,
0x3cfbeaf4, 0xbc9ae55c, 0xbd5b335b, 0xbe5b9fb1,
0xbda79bce, 0x3eccd696, 0x3c2d087c, 0x3d8bcd63,
0x3dc54c09, 0x3e000188, 0x3e09679e, 0x3e030d0a,
0x3bcfff00, 0xbe74aa79, 0xbd24fb1f, 0xbe66fd81,
0xbcc28968, 0xbd7dc21f, 0x3e31a3cb, 0x3d71a29b,
0x3d0343f1, 0xbddc2526, 0xbb0a97c5, 0xbd560c34,
0xbc03d51e, 0x3bf9e469, 0x3c84ebab, 0x3d01d39b,
0x3db485b2, 0x3d805746, 0x3e26913b, 0x3cd68ec1,
0xbe7ee576, 0xbddb503a, 0x3c792ade, 0x3e95adc1,
0x3c8db514, 0x3d3d6e72, 0x3d87c601, 0x3db50555,
0x3daeb299, 0x3dba8911, 0xbe2e9d03, 0xbe23f24a,
0xbe717e16, 0xbded5b72, 0xbe0f61c3, 0xbd1759ef,
0xbe4a7a0b, 0xbe63366a, 0xbc8ee4bd, 0x3d11e653,
0x3e0d22ae, 0x3db3505a, 0x3dc60d69, 0x3e1dcee2,
0x3dc38439, 0xbdba92ba, 0xbcc9c5cc, 0xbdb0229e,
0xbe1f5cc6, 0xbe4c76fa, 0xbe73607a, 0xbdbd3869,
0xbd640b56, 0xbe828aaf, 0xbeebad05, 0xbe150ae4,
0xbe6e493f, 0xbb6e12ba, 0x3c56fc04, 0x3c864c83,
0xbbb9663e, 0xbd172983, 0xbd3fc1db, 0x3cbb31f7,
0xbe19f5d4, 0xbd94b92e, 0x3e14413d, 0x3d995b27,
0x3d1d14ba, 0xbbcd9159, 0x3dc9a51b, 0xbc6485af,
0xbe68a7a2, 0xbec37b0e, 0xbc6daa25, 0xbc05812c,
0x3d51f43a, 0x3d638e39, 0xbe51b6c7, 0x3e77f842,
0xbc5e958f, 0xbe8a6929, 0xbee813a1, 0xbc9e812e,
0xbd368b3f, 0x3e0600eb, 0xbc91b1bb, 0x3c7bdb14,
0xbc36b352, 0xbe58e754, 0xbcf18566, 0x3df26522,
0xbb01f809, 0x3dfb05a0, 0x3aa0e34e, 0xba8ee470,
0x3d0817bc, 0x3e7fd5de, 0x3eeeb1e5, 0x3e0668cc,
0x3dce60b5, 0x3d47f096, 0xbbfc19b2, 0x3d864984,
0x3e2239a4, 0x3e03a1a1, 0xbd5c22cf, 0xbe534ab2,
0xbda7a474, 0xbda714d0, 0x3c145504, 0xbd6de9fb,
0xbe0e0da6, 0xbabe96cd, 0x3d8dfbcb, 0x3da5d84f,
0xbe1d5a5b, 0x3c8004a3, 0xbb1a2bac, 0xbd58b9d5,
0xbd1ac072, 0xbdc6ab75, 0xbe9395f3, 0xbe51d70a,
0x3e9ef9ea, 0x3d997167, 0x3bb45098, 0x3d00a16f,
0x3d979c64, 0xbc85c736, 0xbe190690, 0xbe9a664c,
0xbd91f656, 0xbea8489c, 0xb90ba15f, 0xbe20de72,
0x3e1a4ca4, 0x3dd59daa, 0xbda7e2fb, 0x3e06b786,
0x3e12cac7, 0x3cb788d3, 0x3dbacf53, 0xbc407a48,
0x3d2cb6d8, 0x3ca604d4, 0x3e349b19, 0x3dd14434,
0xbe1cafe7, 0x3e0324fd, 0x3df2bcbc, 0x3de28567,
0x3e89e49c, 0x3e9b6573, 0x3e6185d5, 0x3e8a3566,
0x3c63e1dd, 0xbc846b96, 0xbda33f4b, 0xbe80d4af,
0xbe21397d, 0x3d9c7991, 0x3d12c526, 0xbde66ce7,
0xbd863466, 0xbeb41a6d, 0xbec0d28b, 0x3c49220c,
0x3ddacd8d, 0x3e9b2029, 0x3dd0e360, 0xbdc492ae,
0x3dd91781, 0x3e533e0e, 0xbd639507, 0x3bc78bfb,
0xbe2bbfe5, 0xbdc17ee6, 0xbbe5540f, 0x3d34026b,
0x3d15e80f, 0xbcde4fb8, 0x3ddf44bd, 0xbe8bc3bb,
0xbea23e2c, 0xbe1aaee7, 0xbe1460ec, 0x3d010621,
0x3e0d7688, 0x3b548e08, 0x3ae72496, 0x3b8a446d,
0xbd9cd4ab, 0xbe0f79f9, 0xbe76a6de, 0xbda4b0dd,
0x3e73968b, 0x3e401b79, 0xbd2ee2f0, 0x3e1d68fb,
0x3c0dcbc3, 0xbd604afe, 0x3cb51338, 0xbc82008d,
0xbdf34500, 0xbeb89a06, 0x3c4dbe71, 0xbe88d990,
0xbf3bc918, 0xbc412028, 0x3cf90b6c, 0xbe177484,
0x3c26f218, 0xbe0dcd5e, 0xbcf5331e, 0x3b012025,
0xbe189ab6, 0xbe989844, 0x3c2d7d71, 0xbe3364d1,
0xbc85ca75, 0x3d3fbe15, 0xbe75281e, 0xbe248bb1,
0xbd20016b, 0xbe2fa82e, 0x3bde3156, 0x3cad0555,
0x3e081727, 0xbea67435, 0x3d28210b, 0xbbe884d3,
0x3df2f9df, 0xbe366e60, 0x3b50301c, 0x3c916cda,
0xbf219b51, 0xbedc3d11, 0xbe6e51aa, 0x3e9c3247,
0x3e0ead98, 0x3d688da0, 0x3be9c96b, 0x3e191fbf,
0x3e0841e7, 0xbddb6b63, 0x3d2d43aa, 0xbdaec321,
0xbd901259, 0xbce86df5, 0xbc958e3c, 0xbea5c703,
0x3b27ac62, 0xbad1d8ee, 0x3dedb8c6, 0x3e6786bb,
0xbe7dea3e, 0xbd0d2551, 0xbc95c231, 0x3cbb6148,
0x3e4b66cc, 0xbdfb841a, 0xbe2c37f8, 0xbe83312d,
0x3dbb5c67, 0x3d2a21b2, 0xbc2e75de, 0xbd08dd7d,
0x3e0338c2, 0x3d728953, 0xbd95717b, 0xbdfba0a3,
0x3cff8178, 0x3da29d33, 0xbd30433d, 0x3da2e5b4,
0xbe285710, 0x391590f5, 0xbd8053ef, 0x3ce1a8c7,
0xbbe3f230, 0x3e049f79, 0x3e93d5ad, 0x3e70d20e,
0x3e1e3954, 0x3daba5b0, 0xbe89e908, 0x3e2b1a5b,
0xbc22167e, 0xbe83ddf6, 0x3daf33dd, 0xbea2e161,
0x3df9a8e1, 0x3d831549, 0x3ca948ba, 0xbe40c5ad,
0x3db76927, 0x3d938ea6, 0xbe35b692, 0xbaa4edba,
0x3c021982, 0x3c44af42, 0x3d40d3a3, 0xbe61591d,
0xbd4c09cb, 0x3d1c0242, 0xbe9a0341, 0xbdc7b2f4,
0xbe40f546, 0xbc2a35dd, 0xbb5ae347, 0x3d8cb0b5,
0x3d94916a, 0xbe0dd631, 0xbe275091, 0xbe11eefc,
0x3d0fa6bf, 0xbd857e18, 0xbdf89c8f, 0xbe5dc720,
0x3c3a7c0b, 0xbb2a51e2, 0xbe06db7a, 0xbe3874d9,
0xbe81eac5, 0x3d749abd, 0x3e460b58, 0x3d60ceac,
0xbdd21942, 0x3e00a51b, 0x3e33b2b1, 0x3e0e4d44
};
static const uint32_t ref_interp[1276] = {
0x3d1fa0a6, 0x3cb76626, 0x3d166ef1, 0x3a2ee2e6,
0x3d0dffa0, 0x3da55c00, 0x3c608e47, 0x3bce3c84,
0xbc95024e, 0xbdaea460, 0xbe65a7d1, 0xbe412fac,
0xbe4c13ba, 0xbdf752e5, 0x3c4b0d56, 0x3c9d99cc,
0x3cd2a600, 0xba95edd7, 0xbc9a9939, 0xbd553478,
0xbdacaca2, 0xbdf26252, 0xbcf5a9c0, 0xbca081d6,
0x3ca4446d, 0x3b87b8f7, 0x3e26ee94, 0xbcb5822f,
0xbe6bc2f4, 0xbd032353, 0xbe1ad5a6, 0xbdda4999,
0x3d666584, 0x3be3267a, 0xbc9f7dd4, 0xbd4a3d08,
0xbdc6a952, 0xbdfe466a, 0xbe375246, 0xbe679598,
0xbe8d7097, 0xbed137a2, 0xbe521f55, 0xbe5fd55f,
0x3ba83dd0, 0x3c283dd0, 0x3d0f8997, 0x3d7503b9,
0x3d51f554, 0x3d2ee6ee, 0xbc97b426, 0xbd17b426,
0xbd6dad4a, 0xbda1d337, 0xbde4218a, 0xbe1337ee,
0x3bfc7b67, 0x3c7c7b67, 0x3cbeab56, 0x3cff18f9,
0x3d489115, 0x3d88cad7, 0x3d9ec66a, 0x3db4c1fe,
0x3b9c78d2, 0xbc8bd4c0, 0xbd5eab96, 0xbdb918d5,
0xbe3b1ace, 0xbe480da3, 0xbe0bce45, 0xbe09a9cc,
0x3b79593e, 0x3bf9593e, 0xbafe8b31, 0xbc3c4f6b,
0xbd220d6f, 0xbd8a8382, 0xbdcfccfd, 0xbe0a8b3c,
0xbe212894, 0xbe37c5eb, 0xbe5a2143, 0xbe7c7c9b,
0xbe8cb089, 0xbe9b22c5, 0xbeb232af, 0xbec94299,
0xbd088889, 0xbd888889, 0xbe050bf0, 0xbe45d39b,
0xbe906b06, 0xbebdec3e, 0xbeefad66, 0xbf10b747,
0xbeb315ba, 0xbecd456e, 0xbe2e29fd, 0xbe36f568,
0x3d25d3b5, 0x3d60246a, 0x3e1a345e, 0x3e38609f,
0x3dbd5f69, 0x3dda0a00, 0x3cc2bc9e, 0x3d2c7716,
0x3d91db98, 0x3d9fc8d7, 0xbc547fe2, 0xbcd47fe2,
0xbcbab405, 0xbca0e829, 0xbc3ba965, 0xbb5609e4,
0xba5cfdc2, 0x3acf1606, 0xbc2f266b, 0xbcbc17cc,
0xbcfd95bf, 0xbd1f89d9, 0xbce8dd7f, 0xbc92a74c,
0xbc28f85f, 0xbb328898, 0x3e6e949c, 0x3e85b9bd,
0x3c80aa46, 0x3ce6759c, 0xbd5056d5, 0xbd49abab,
0xbbde7a00, 0xbc5e7a00, 0xbca6db80, 0xbcde7a00,
0xbcef0f59, 0xbcffa4b2, 0xbd081d06, 0xbd1067b2,
0xbd648c71, 0xbd9c5898, 0xbdc66af8, 0xbdf07d58,
0x3c00e024, 0x3c80e024, 0x3cc15036, 0x3d00e024,
0x3d3b33e0, 0x3d75879c, 0x3d97edac, 0x3db5178a,
0x3de6557c, 0x3e0bc9b7, 0x3e2468b0, 0x3e3d07a9,
0xbbc88ccc, 0xbc488ccc, 0xbc966999, 0xbcc88ccc,
0xbcc766a3, 0xbcc6407b, 0xbcc51a53, 0xbcc3f42b,
0xbc63c8b3, 0xbb7ea43b, 0x3bc8ed2a, 0x3c844b1c,
0x3c956d48, 0x3ca68f73, 0x3cb7b19f, 0x3cc8d3ca,
0x3e18c010, 0x3e341f40, 0x3e4f7e71, 0x3e6adda1,
0x3e19d817, 0x3e2f6542, 0x3e44f26e, 0x3e5a7f99,
0x3d8c0e74, 0x3da6c45d, 0x3dc17a45, 0x3ddc302e,
0x3e80bdfe, 0x3e89824a, 0x3e924696, 0x3e9b0ae2,
0x3b2edc82, 0x3baedc82, 0x3c032561, 0x3c2edc82,
0x3bbb1233, 0x3a435b13, 0xbb8a3b6e, 0xbc16711f,
0xbc8946c3, 0xbcc754f6, 0xbd02b194, 0xbd21b8ae,
0xbd57cfea, 0xbd86f393, 0xbda1ff31, 0xbdbd0ad0,
0xbdec2a82, 0xbe0da51a, 0xbe2534f3, 0xbe3cc4cc,
0xbe55e238, 0xbe6effa5, 0xbe840e88, 0xbe909d3f,
0xbe9c4748, 0xbea7f152, 0xbeb39b5c, 0xbebf4566,
0xbecd237d, 0xbedb0195, 0xbee8dfac, 0xbef6bdc4,
0x3c4e217c, 0x3cce217c, 0x3d1a991d, 0x3d4e217c,
0x3d61c6ca, 0x3d756c19, 0x3d8488b4, 0x3d8e5b5b,
0x3d81af26, 0x3d6a05e1, 0x3d50ad76, 0x3d37550c,
0x3cd33c34, 0x3bdf3941, 0xbc473f27, 0xbcff0d78,
0xbe84a435, 0xbe9246d4, 0xbe9fe973, 0xbead8c13,
0xbe5e458b, 0xbe60ff32, 0xbe63b8d9, 0xbe667280,
0xbd227128, 0xbcf5e7c9, 0xbca6ed41, 0xbc2fe571,
0x3e6e33cd, 0x3e8af5ea, 0x3e9ed1ed, 0x3eb2adf0,
0x3e9f69d5, 0x3eb47a66, 0x3ec98af7, 0x3ede9b88,
0x3e608eaa, 0x3e8689bf, 0x3e9ccc28, 0x3eb30e92,
0x3eb99881, 0x3ecaeebd, 0x3edc44fa, 0x3eed9b36,
0x3bd444e2, 0x3c5444e2, 0x3c9f33aa, 0x3cd444e2,
0x3cb905cb, 0x3c9dc6b3, 0x3c82879b, 0x3c4e9107,
0x3b39af94, 0xbbe3727a, 0xbc88ef30, 0xbcd901c1,
0xbcf9db96, 0xbd0d5ab6, 0xbd1dc7a1, 0xbd2e348c,
0xbd494600, 0xbd645774, 0xbd7f68e7, 0xbd8d3d2e,
0xbd959fed, 0xbd9e02ac, 0xbda6656b, 0xbdaec82b,
0xbdade9a4, 0xbdad0b1d, 0xbdac2c96, 0xbdab4e0f,
0xbda1b032, 0xbd981255, 0xbd8e7478, 0xbd84d69c,
0xbe898c47, 0xbe87c076, 0xbe85f4a4, 0xbe8428d3,
0x3d93f527, 0x3db60b17, 0x3dd82108, 0x3dfa36f9,
0x3eb676e8, 0x3ec4b91f, 0x3ed2fb56, 0x3ee13d8d,
0x3b54a5d1, 0x3bd4a5d1, 0x3c1f7c5d, 0x3c54a5d1,
0x3c84e7a3, 0x3cd187bd, 0x3d0f13ec, 0x3d3563f9,
0x3d5bb406, 0x3d81020a, 0x3d6a449d, 0x3d528526,
0x3d3ac5af, 0x3d230639, 0x3d0b46c2, 0x3bb91fc6,
0x3c391fc6, 0x3c8ad7d5, 0x3cb91fc6, 0x3ce767b8,
0x3cd4ab99, 0x3cc1ef7a, 0x3caf335c, 0x3c9c773d,
0x3c89bb1e, 0x3ca76229, 0x3cc50934, 0x3ce2b03e,
0x3d002ba5, 0x3d0eff2a, 0xbbb2d871, 0xbc32d871,
0xbc862255, 0xbcb2d871, 0xbcdf8e8d, 0xbd2967c2,
0xbd63083e, 0xbd8e545d, 0xbdab249b, 0xbdc7f4d9,
0xbdcfc31e, 0xbdd79163, 0xbddf5fa8, 0xbde72dee,
0xbdeefc33, 0xbe00f887, 0xbe0a72f4, 0xbe13ed62,
0xbe1d67cf, 0xbe26e23d, 0xbd950502, 0xbdbbd418,
0xbde2a32e, 0xbe04b922, 0xbe1820ad, 0x3ca7fd18,
0x3c8e2675, 0x3c689fa3, 0x3c34f25d, 0x3c014516,
0xbe4db1a9, 0xbe5163ec, 0xbe551630, 0xbe58c873,
0xbe5c7ab6, 0xbdcc2e11, 0xbdbe6a6b, 0xbdb0a6c4,
0xbda2e31e, 0xbd951f78, 0x39f1caaa, 0x3a71caaa,
0x3ab557ff, 0x3af1caaa, 0x3b171eaa, 0x3c2f5e20,
0x3c9c7a4b, 0x3ce14586, 0x3d130860, 0x3d356dfe,
0x3d5bb078, 0x3d80f979, 0x3d941ab7, 0x3da73bf4,
0x3dba5d31, 0x3dd77b81, 0x3df499d1, 0x3e08dc11,
0x3e176b39, 0x3e25fa61, 0x3e319f59, 0x3e3d4452,
0x3e48e94b, 0x3e548e43, 0x3e60333c, 0x3e6e87cb,
0x3e7cdc5b, 0x3e859875, 0x3e8cc2bd, 0x3e93ed05,
0x3e971bfd, 0x3e9a4af6, 0x3e9d79ef, 0x3ea0a8e8,
0x3ea3d7e1, 0x3ea5bcdd, 0x3ea7a1d8, 0x3ea986d3,
0x3eab6bcf, 0x3ead50ca, 0xbb969370, 0xbc169370,
0xbc61dd29, 0xbc969370, 0xbcbc384d, 0xbd022215,
0xbd262805, 0xbd4a2df4, 0xbd6e33e3, 0xbd891ce9,
0xbda0d6e6, 0xbdb890e3, 0xbdd04ae0, 0xbde804dc,
0xbdffbed9, 0xbe0e77e7, 0xbe1d1061, 0xbe2ba8dc,
0xbe3a4156, 0xbe48d9d1, 0xbde6cd79, 0xbdf81f9d,
0xbe04b8e1, 0xbe0d61f3, 0xbe160b05, 0xbd86d6d7,
0xbd8d9ab1, 0xbd945e8a, 0xbd9b2263, 0xbda1e63c,
0xbca5535c, 0xbc8c3f68, 0xbc6656ea, 0xbc342f04,
0xbc02071e, 0x3d3c1235, 0x3d3e0f72, 0x3d400cae,
0x3d4209ea, 0x3d440726, 0x3cb0754d, 0x3c9d9c55,
0x3c8ac35d, 0x3c6fd4ca, 0x3c4a22da, 0xbcce23f4,
0xbd32770e, 0xbd7ddc23, 0xbda4a09c, 0xbdca5326,
0xbe407382, 0xbe528b4a, 0xbe64a311, 0xbe76bad8,
0xbe846950, 0xbbe1cb03, 0xbc61cb03, 0xbca95842,
0xbce1cb03, 0xbd0d1ee2, 0xbd17aa10, 0xbd22353f,
0xbd2cc06d, 0xbd374b9c, 0xbd41d6ca, 0xbd5f8b36,
0xbd7d3fa2, 0xbd8d7a07, 0xbd9c543d, 0xbdab2e73,
0xbdb897e8, 0xbdc6015d, 0xbdd36ad2, 0xbde0d447,
0xbdee3dbc, 0xbdf235a5, 0xbdf62d8e, 0xbdfa2577,
0xbdfe1d60, 0xbe010aa4, 0xbdf6a8d8, 0xbdeb3c67,
0xbddfcff6, 0xbdd46385, 0xbdc8f715, 0xbdad49a0,
0xbd919c2b, 0xbd6bdd6c, 0xbd348283, 0xbcfa4f32,
0xbc1d9cb3, 0x3c3964fe, 0x3d0419ac, 0x3d59da18,
0x3d97cd42, 0x3ec1d17c, 0x3ed090c5, 0x3edf500f,
0x3eee0f58, 0x3efccea2, 0x3eb2f680, 0x3ec18557,
0x3ed0142f, 0x3edea307, 0x3eed31df, 0x3f2e9911,
0x3f36b218, 0x3f3ecb1e, 0x3f46e425, 0x3f4efd2c,
0x3c20a0a1, 0x3ca0a0a1, 0x3cf0f0f1, 0x3d20a0a1,
0x3d48c8c9, 0x3d70f0f1, 0x3d8c8c8d, 0x3da0a0a1,
0x3dbb78d1, 0x3dd65101, 0x3df12932, 0x3e0600b1,
0x3e136cc9, 0x3e20d8e1, 0x3e2e44fa, 0x3e3bb112,
0x3e5168b9, 0x3e672061, 0x3e7cd808, 0x3e8947d8,
0x3e9423ab, 0x3e9eff7f, 0x3ea9db53, 0x3eb4b726,
0xba9fe6c8, 0xbb1fe6c8, 0xbb6fda2c, 0xbb9fe6c8,
0xbbc7e07a, 0xbbefda2c, 0xbc0be9ef, 0xbc1fe6c8,
0xbbc2488c, 0xbb098712, 0x3ae305e8, 0x3bb6467d,
0x3c19e5c0, 0x3c58a842, 0x3c8bb562, 0x3cab16a2,
0x3ccdc476, 0x3cf07249, 0x3d09900e, 0x3d1ae6f8,
0x3d2c3de1, 0x3d3d94cb, 0x3d4eebb5, 0x3d60429e,
0x3b704dff, 0x3bf04dff, 0x3c343a7f, 0x3c704dff,
0x3c9630bf, 0x3cb43a7f, 0x3cd2443f, 0x3cf04dff,
0x3cfab52e, 0x3d028e2e, 0x3d07c1c5, 0x3d0cf55d,
0x3d1228f4, 0x3d175c8b, 0x3d1c9023, 0x3d21c3ba,
0x3d3c80ca, 0x3d573dda, 0x3d71faea, 0x3d865bfd,
0x3d93ba85, 0x3da1190d, 0x3dae7794, 0x3dbbd61c,
0x3dca6819, 0x3dd8fa15, 0x3de78c11, 0x3df61e0d,
0x3e025805, 0x3e09a103, 0x3e10ea01, 0x3e1832ff,
0x3d36773e, 0x3d6cbe7f, 0x3d9182e0, 0x3daca680,
0x3dc7ca20, 0x3de2edc0, 0x3dfe1161, 0x3e0c9a81,
0x3e6668b0, 0x3e71ac9a, 0x3e7cf084, 0x3e841a37,
0x3e89bc2c, 0x3e8f5e21, 0x3e950016, 0x3e9aa20c,
0x3e083a66, 0x3e077c78, 0x3e06be8b, 0x3e06009e,
0x3e0542b1, 0x3e0484c3, 0x3e03c6d6, 0x3e0308e9,
0x3dd702a3, 0x3dce61fd, 0x3dc5c157, 0x3dbd20b1,
0x3db4800c, 0x3dabdf66, 0x3da33ec0, 0x3d9a9e1a,
0xba279515, 0xbaa79515, 0xbafb5f9f, 0xbb279515,
0xbb517a5a, 0xbb7b5f9f, 0xbb92a272, 0xbba79515,
0xbc2f413f, 0xbc855bfa, 0xbcb31754, 0xbce0d2ae,
0xbd074704, 0xbd1e24b1, 0xbd35025f, 0xbd4be00c,
0xbd5d0d68, 0xbd6e3ac5, 0xbd7f6821, 0xbd884abf,
0xbd90e16d, 0xbd99781b, 0xbda20ec9, 0xbdaaa577,
0xbdb3171b, 0xbdbb88be, 0xbdc3fa61, 0xbdcc6c05,
0xbdd4dda8, 0xbddd4f4b, 0xbde5c0ef, 0xbdee3292,
0xbdefa6fa, 0xbdf11b63, 0xbdf28fcb, 0xbdf40434,
0xbdf5789c, 0xbdf6ed04, 0xbdf8616d, 0xbdf9d5d5,
0xbdfb3ce6, 0xbdfca3f6, 0xbdfe0b06, 0xbdff7217,
0xbe006c93, 0xbe01201c, 0xbe01d3a4, 0xbe02872c,
0xbe06a874, 0xbe0ac9bc, 0xbe0eeb03, 0xbe130c4b,
0xbe172d93, 0xbe1b4edb, 0xbe1f7023, 0xbe23916a,
0xbe2cdea8, 0xbe362be5, 0xbe3f7923, 0xbe48c660,
0xbe52139e, 0xbe5b60db, 0xbe64ae19, 0xbe6dfb56,
0x3acf0769, 0x3b4f0769, 0x3b9b458f, 0x3bcf0769,
0x3c0164a2, 0x3c1b458f, 0x3c35267c, 0x3c4f0769,
0x3c61bfb7, 0x3c747804, 0x3c839828, 0x3c8cf44f,
0x3c965076, 0x3c9fac9c, 0x3ca908c3, 0x3cb264e9,
0x3d0608b0, 0x3d32deec, 0x3d5fb527, 0x3d8645b1,
0x3d9cb0cf, 0x3db31bed, 0x3dc9870a, 0x3ddff228,
0x3df95f16, 0x3e096602, 0x3e161c78, 0x3e22d2ef,
0x3e2f8966, 0x3e3c3fdd, 0x3e48f654, 0x3e55acca,
0x3e2a70bd, 0x3e32f689, 0x3e3b7c56, 0x3e440223,
0x3e4c87ef, 0x3e550dbc, 0x3e5d9389, 0x3e661955,
0x3e81c5ee, 0x3e895692, 0x3e90e735, 0x3e9877d8,
0x3ea0087c, 0x3ea7991f, 0x3eaf29c3, 0x3eb6ba66,
0x3d48943a, 0x3d605a49, 0x3d782058, 0x3d87f334,
0x3d93d63b, 0x3d9fb943, 0x3dab9c4a, 0x3db77f52,
0x3d4958dd, 0x3d64270c, 0x3d7ef53c, 0x3d8ce1b5,
0x3d9a48cd, 0x3da7afe5, 0x3db516fc, 0x3dc27e14,
0x3e42375e, 0x3e50dc49, 0x3e5f8133, 0x3e6e261e,
0x3e7ccb09, 0x3e85b7fa, 0x3e8d0a6f, 0x3e945ce4,
0x3de7c5bc, 0x3e0429f9, 0x3e147113, 0x3e24b82d,
0x3e34ff48, 0x3e454662, 0x3e558d7c, 0x3e65d497,
0x3e54b3be, 0x3e5edbc7, 0x3e6903cf, 0x3e732bd7,
0x3e7d53df, 0x3e83bdf3, 0x3e88d1f7, 0x3e8de5fc,
0xb9bd8c97, 0xba3d8c97, 0xba8e2971, 0xbabd8c97,
0xbaecefbd, 0xbb0e2971, 0xbb25db04, 0xbb3d8c97,
0xbc07d2c1, 0xbc60425c, 0xbc9c58fb, 0xbcc890c9,
0xbcf4c897, 0xbd108032, 0xbd269c19, 0xbd3cb800,
0xbd578fe5, 0xbd7267cb, 0xbd869fd8, 0xbd940bcb,
0xbda177be, 0xbdaee3b1, 0xbdbc4fa4, 0xbdc9bb96,
0xbde1061f, 0xbdf850a8, 0xbe07cd98, 0xbe1372dd,
0xbe1f1821, 0xbe2abd65, 0xbe3662aa, 0xbe4207ee,
0xbe52945d, 0xbe6320cd, 0xbe73ad3c, 0xbe821cd6,
0xbe8a630d, 0xbe92a945, 0xbe9aef7d, 0xbea335b4,
0xbeaa3719, 0xbeb1387e, 0xbeb839e3, 0xbebf3b47,
0xbec63cac, 0xbecd3e11, 0xbed43f75, 0xbedb40da,
0xbee208bf, 0xbee8d0a5, 0xbeef988a, 0xbef66070,
0xbefd2855, 0xbf01f81d, 0xbf055c10, 0xbf08c003,
0xbf0c3e11, 0xbf0fbc1f, 0xbf133a2d, 0xbf16b83c,
0xbf1a364a, 0xbf1db458, 0xbf213266, 0xbf24b074,
0xbf21a38e, 0xbf24830b, 0xbf276289, 0xbf2a4207,
0xbf2d2185, 0xbf300103, 0xbf32e080, 0xbf35bffe,
0xbecc3a6d, 0xbed1fb49, 0xbed7bc26, 0xbedd7d03,
0xbee33de0, 0xbee8febc, 0xbeeebf99, 0xbef48076,
0xbed47eae, 0xbeda5cde, 0xbee03b0d, 0xbee6193c,
0xbeebf76c, 0xbef1d59b, 0xbef7b3cb, 0xbefd91fa,
0x3b3edf9b, 0x3bbedf9b, 0x3c0f27b5, 0x3c3edf9b,
0x3c6e9782, 0x3c8f27b5, 0x3ca703a8, 0x3cbedf9b,
0x3cd6bb8f, 0x3d1b39ca, 0x3d4b15cd, 0x3d7af1d0,
0x3d9566e9, 0x3dad54ea, 0x3dc542ec, 0x3ddd30ed,
0x3df51eef, 0x3e068678, 0x3e10135c, 0x3e19a041,
0x3e232d25, 0x3e2cba0a, 0x3e3646ee, 0x3e3fd3d2,
0x3e4960b7, 0x3e52ed9b, 0x3e5c7a80, 0x3a55608c,
0x3ad5608c, 0x3b200869, 0x3b55608c, 0x3b855c57,
0x3ba00869, 0x3bbab47a, 0x3bd5608c, 0x3bf00c9d,
0x3b6e3c52, 0xb868259c, 0xbb757d7f, 0xbbf3ad34,
0xbc364dd4, 0xbc72c50e, 0xbc979e24, 0xbcb5d9c1,
0xbcd4155e, 0xbcf486c8, 0xbd0a7c18, 0xbd1ab4cd,
0xbd2aed82, 0xbd3b2636, 0xbd4b5eeb, 0xbd5b97a0,
0xbd6bd054, 0xbd7c0909, 0x3b04f13c, 0x3b84f13c,
0x3bc769da, 0x3c04f13c, 0x3c262d8b, 0x3c4769da,
0x3c68a629, 0x3c84f13c, 0x3c958f63, 0x3c3ca2f2,
0x3b9c4e39, 0xbb0152e1, 0xbc0ed08d, 0xbc7d4c62,
0xbcb5e41c, 0xbced2206, 0xbd122ff8, 0xbd2dceee,
0xbd549419, 0xbd7b5945, 0xbd910f38, 0xbda471ce,
0xbdb7d464, 0xbdcb36fa, 0xbdde9990, 0xbdf1fc26,
0xbe02af5e, 0xbe0ddee9, 0xbe190e75, 0xbe243e00,
0xbe2f6d8c, 0xbe3a9d17, 0xbe45cca3, 0xbe50fc2e,
0xbe5c2bba, 0xbe675b45, 0xbe9f3a88, 0xbea56395,
0xbeab8ca1, 0xbeb1b5ae, 0xbeb7debb, 0xbebe07c7,
0xbec430d4, 0xbeca59e1, 0xbed082ed, 0xbdc4e50e,
0xbdce7b08, 0xbdd81103, 0xbde1a6fd, 0xbdeb3cf7,
0xbdf4d2f2, 0xbdfe68ec, 0xbe03ff73, 0xbe08ca71,
0xbd3aa9ca, 0xbd63897d, 0xbd863498, 0xbd9aa471,
0xbdaf144b, 0xbdc38424, 0xbdd7f3fe, 0xbdec63d7,
0xbe0069d8, 0xbdb29e68, 0xbdcfeb45, 0xbded3823,
0xbe054280, 0xbe13e8ef, 0xbe228f5d, 0xbe3135cc,
0xbe3fdc3b, 0xbe4e82a9, 0xbb430eb0, 0xbbc30eb0,
0xbc124b04, 0xbc430eb0, 0xbc73d25c, 0xbc924b04,
0xbcaaacda, 0xbcc30eb0, 0xbcdb7086, 0xbcebc112,
0xbcfc119e, 0xbd063115, 0xbd0e595b, 0xbd1681a1,
0xbd1ea9e7, 0xbd26d22d, 0xbd2efa73, 0xbd3722b9,
0xbd38a8f3, 0xbd3a2f2d, 0xbd3bb567, 0xbd3d3ba1,
0xbd3ec1db, 0xbd404815, 0xbd41ce4f, 0xbd435489,
0xbd44dac4, 0xbd3903a4, 0xbd2d2c84, 0xbd215564,
0xbd157e44, 0xbd09a725, 0xbcfba00a, 0xbce3f1ca,
0xbccc438a, 0xbcb4954b, 0xbc8b6208, 0xbc445d89,
0xbbe3ee06, 0xbafc83e7, 0x3b4b5825, 0x3c053c8f,
0x3c57a316, 0x3c9504ce, 0x3cbe3811, 0x3cdf8e04,
0x3d0071fc, 0x3d111cf6, 0x3d21c7ef, 0x3d3272e9,
0x3d431de3, 0x3d53c8dc, 0x3d6473d6, 0x3d751ed0,
0x3d8512a4, 0x3d8f95e0, 0x3d9a191d, 0x3da49c59,
0x3daf1f95, 0x3db9a2d1, 0x3dc4260e, 0x3dcea94a,
0x3dd92c86, 0x3dda761a, 0x3ddbbfae, 0x3ddd0942,
0x3dde52d6, 0x3ddf9c6a, 0x3de0e5fe, 0x3de22f92,
0x3de37926, 0x3de4c2ba, 0x3ba8e81b, 0x3c28e81b,
0x3c7d5c28, 0x3ca8e81b, 0x3cd32222, 0x3cfd5c28,
0x3d13cb18, 0x3d28e81b, 0x3d3e051e, 0x3d77102b,
0x3d980d9b, 0x3db49322, 0x3dd118a8, 0x3ded9e2e,
0x3e0511da, 0x3e13549d, 0x3e219760, 0x3e2fda23,
0x3e3a5f08, 0x3e44e3ed, 0x3e4f68d2, 0x3e59edb8,
0x3e64729d, 0x3e6ef782, 0x3e797c67, 0x3e8200a6,
0x3e874318, 0x3e8c74ce, 0x3e91a683, 0x3e96d838,
0x3e9c09ed, 0x3ea13ba3, 0x3ea66d58, 0x3eab9f0d,
0x3eb0d0c3, 0x3eb60278, 0x3e31c564, 0x3e358af7,
0x3e39508a, 0x3e3d161c, 0x3e40dbaf, 0x3e44a142,
0x3e4866d5, 0x3e4c2c67, 0x3e4ff1fa, 0xbdf5a802,
0xbe023bab, 0xbe09a355, 0xbe110aff, 0xbe1872aa,
0xbe1fda54, 0xbe2741fe, 0xbe2ea9a8, 0xbe361152,
0xbd3fa0d9, 0xbd41c94f, 0xbd43f1c5, 0xbd461a3c,
0xbd4842b2, 0xbd4a6b28, 0xbd4c939e, 0xbd4ebc14,
0xbd50e48a, 0xbd5cf2b3, 0xbd7bd5c3, 0xbd8d5c6a,
0xbd9ccdf2, 0xbdac3f7a, 0xbdbbb102, 0xbdcb228a,
0xbdda9413, 0xbdea059b, 0xbd9c2b54, 0xbdaeab84,
0xbdc12bb3, 0xbdd3abe2, 0xbde62c11, 0xbdf8ac41,
0xbe059638, 0xbe0ed650, 0xbe181667, 0xbd900aa5,
0xbd8de4fc, 0xbd8bbf52, 0xbd8999a9, 0xbd877400,
0xbd854e56, 0xbd8328ad, 0xbd810303, 0xbd7dbab3,
0xbe36c57a, 0xbe3da7b9, 0xbe4489f8, 0xbe4b6c38,
0xbe524e77, 0xbe5930b6, 0xbe6012f6, 0xbe66f535,
0xbe6dd775, 0xbaa84902, 0xbb284902, 0xbb7c6d82,
0xbba84902, 0xbbd25b42, 0xbbfc6d82, 0xbc133fe1,
0xbc284902, 0xbc3d5222, 0xbc63ca7b, 0xbc85216a,
0xbc985d96, 0xbcab99c3, 0xbcbed5ef, 0xbcd2121c,
0xbce54e48, 0xbcf88a75, 0xbd05e351, 0xbd118039,
0xbd1d1d21, 0xbd28ba0a, 0xbd3456f2, 0xbd3ff3db,
0xbd4b90c3, 0xbd572dab, 0xbd62ca94, 0xbd6e677c,
0xbd7995e3, 0xbd826225, 0xbd87f958, 0xbd8d908b,
0xbd9327bf, 0xbd98bef2, 0xbd9e5625, 0xbda3ed59,
0xbda9848c, 0xbdaafdf6, 0xbdac7761, 0xbdadf0cb,
0xbdaf6a35, 0xbdb0e39f, 0xbdb25d0a, 0xbdb3d674,
0xbdb54fde, 0xbdb6c948, 0xbdb72b1a, 0xbdb78cec,
0xbdb7eebe, 0xbdb85090, 0xbdb8b261, 0xbdb91433,
0xbdb97605, 0xbdb9d7d7, 0xbdba39a8, 0xbdb9d57a,
0xbdb9714b, 0xbdb90d1c, 0xbdb8a8ed, 0xbdb844be,
0xbdb7e08f, 0xbdb77c60, 0xbdb71832, 0xbdb6b403,
0xbdb30c25, 0xbdaf6447, 0xbdabbc6a, 0xbda8148c,
0xbda46cae, 0xbda0c4d1, 0xbd9d1cf3, 0xbd997515,
0xbd95cd38, 0x3cc003de, 0x3ce1f414, 0x3d01f225,
0x3d12ea40, 0x3d23e25b, 0x3d34da76, 0x3d45d290,
0x3d56caab, 0x3d67c2c6, 0x3e125700, 0x3e1c48ce,
0x3e263a9c, 0x3e302c6b, 0x3e3a1e39, 0x3e441008,
0x3e4e01d6, 0x3e57f3a5, 0x3e61e573, 0x3e88d257,
0x3e8ebc92, 0x3e94a6cc, 0x3e9a9107, 0x3ea07b41,
0x3ea6657c, 0x3eac4fb6, 0x3eb239f0, 0x3eb8242b
};
| Max | 2 | psychogenic/zephyr | tests/lib/cmsis_dsp/filtering/src/decim_f32.pat | [
"Apache-2.0"
] |
<p class="for-paddle-users">is your card about to expire, or got a new paypal account? you can update your payment method here.</p>
<p class="for-stripe-users">is your card about to expire, or got a new bank account? you can update your payment method here.</p>
<p> </p>
<button id="update-payment-method-button" class="bold" onclick="updatePaymentMethod();">update payment method</button> | Kit | 2 | pws1453/web-client | source/imports/app/account-tab-plan-payments-payment-method.kit | [
"MIT"
] |
# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_generate_changelog.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_GENERATE_CHANGELOG()
#
# DESCRIPTION
#
# Builds a rule for generating a ChangeLog file from version control
# system commit messages. Currently, the only supported VCS is git, but
# support for others could be added in future.
#
# Defines GENERATE_CHANGELOG_RULES which should be substituted in your
# Makefile.
#
# Usage example:
#
# configure.ac:
#
# AX_GENERATE_CHANGELOG
#
# Makefile.am:
#
# @GENERATE_CHANGELOG_RULES@
# CHANGELOG_START = 0.2.3^
# dist-hook: dist-ChangeLog
#
# ChangeLog (stub committed to VCS):
#
# The ChangeLog is auto-generated when releasing.
# If you are seeing this, use 'git log' for a detailed list of changes.
#
# This results in a "dist-ChangeLog" rule being added to the Makefile.
# When run, "dist-ChangeLog" will generate a ChangeLog in the
# $(top_distdir), using $(CHANGELOG_GIT_FLAGS) to format the output from
# "git log" being run in $(CHANGELOG_GIT_DIR).
#
# Unless Automake is initialised with the 'foreign' option, a dummy
# ChangeLog file must be committed to VCS in $(top_srcdir), containing the
# text above (for example). It will be substituted by the automatically
# generated ChangeLog during "make dist".
#
# LICENSE
#
# Copyright (c) 2015 David King <amigadave@amigadave.com>
# Copyright (c) 2015 Philip Withnall <philip.withnall@collabora.co.uk>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice
# and this notice are preserved. This file is offered as-is, without any
# warranty.
#serial 1
AC_DEFUN([AX_GENERATE_CHANGELOG],[
# Find git, defaulting to the 'missing' script so the user gets a nice
# message if git is missing, rather than a plain 'command not found'.
AC_PATH_PROG([GIT],[git],[${am_missing_run}git])
AC_SUBST([GIT])
# Build the ChangeLog rules.
m4_pattern_allow([AM_V_GEN])
GENERATE_CHANGELOG_RULES='
# Generate ChangeLog
#
# Optional:
# - CHANGELOG_START: git commit ID or tag name to output changelogs from
# (exclusive). (Default: include all commits)
# - CHANGELOG_GIT_FLAGS: General flags to pass to git-log when generating the
# ChangeLog. (Default: various)
# - CHANGELOG_GIT_DIR: .git directory to use. (Default: $(top_srcdir)/.git)
# git-specific
CHANGELOG_GIT_FLAGS ?= --stat -M -C --name-status --no-color
CHANGELOG_GIT_DIR ?= $(top_srcdir)/.git
ifeq ($(CHANGELOG_START),)
CHANGELOG_GIT_RANGE =
else
CHANGELOG_GIT_RANGE = $(CHANGELOG_START)..
endif
# Generate a ChangeLog in $(top_distdir)
dist-ChangeLog:
$(AM_V_GEN)if $(GIT) \
--git-dir=$(CHANGELOG_GIT_DIR) --work-tree=$(top_srcdir) log \
$(CHANGELOG_GIT_FLAGS) $(CHANGELOG_GIT_RANGE) \
| fmt --split-only >.ChangeLog.tmp; \
then mv -f .ChangeLog.tmp "$(top_distdir)/ChangeLog"; \
else rm -f .ChangeLog.tmp; exit 1; fi
.PHONY: dist-ChangeLog
'
AC_SUBST([GENERATE_CHANGELOG_RULES])
m4_ifdef([_AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE([GENERATE_CHANGELOG_RULES])])
])
| M4 | 4 | cssl-unist/tweezer | Docker/gperftools/m4/ax_generate_changelog.m4 | [
"MIT"
] |
%require "3.5"
%{
#define YYDEBUG 1
%}
%code requires {
#include "parser-util.h"
#include "debug/pront.h"
#include <malloc.h>
#include <string.h>
extern int yylex (parser_ctx_t *ctx);
extern void yyerror(parser_ctx_t *ctx, char *msg);
}
%param { parser_ctx_t *ctx };
%union {
pos_t pos;
ival_t ival;
strval_t strval;
ident_t ident;
idents_t idents;
funcdef_t func;
expr_t expr;
exprs_t exprs;
stmt_t stmt;
stmts_t stmts;
strval_t garbage;
}
%token <pos> TKN_AUTO "auto" TKN_FUNC "func"
%token <pos> TKN_IF "if" TKN_ELSE "else" TKN_WHILE "while" TKN_RETURN "return" TKN_ASM "asm"
%token TKN_THEN "then"
%token <pos> TKN_LPAR "(" TKN_RPAR ")" TKN_LBRAC "{" TKN_RBRAC "}" TKN_LSBRAC "[" TKN_RSBRAC "]"
%token <pos> TKN_SEMI ";" TKN_COLON ":" TKN_COMMA ","
%token <ival> TKN_IVAL
%token <strval> TKN_STRVAL
%token <ident> TKN_IDENT
%token <garbage> TKN_GARBAGE
%token <pos> TKN_ADD "+" TKN_SUB "-" TKN_ASSIGN "=" TKN_AMP "&"
%token <pos> TKN_MUL "*" TKN_DIV "/" TKN_REM "%"
%token <pos> TKN_NOT "!" TKN_INV "~" TKN_XOR "^" TKN_OR "|"
%token <pos> TKN_SHL "<<" TKN_SHR ">>"
%token <pos> TKN_LT "<" TKN_LE "<=" TKN_GT ">" TKN_GE ">=" TKN_EQ "==" TKN_NE "!="
%type <idents> opt_idents
%type <idents> idents
%type <func> funcdef
%type <expr> expr
%type <exprs> opt_exprs
%type <exprs> exprs
%type <stmts> stmts
%type <stmt> stmt
%type <stmt> inline_asm
%type <idents> vardecls
// Precedence: lowest.
%right "="
%left "||"
%left "&&"
%left "|"
%left "^"
//%left "&"
%left "==" "!="
%left "<" ">" "<=" ">="
%left "<<" ">>"
%left "+" //"-"
%left "%" "/" //"*"
%right "!" "~" "*" "&" "-"
%precedence "(" "["
%precedence "then"
%precedence "else"
// Precedence: highest.
%%
library: global library
| %empty;
global: funcdef {function_added(ctx, &$1);}
| vardecls;
funcdef: "func" TKN_IDENT "(" opt_idents ")"
"{" stmts "}" {$$=funcdef_decl(&$2, &$4, &$7);};
vardecls: "auto" idents ";" {$$=$2;};
opt_idents: idents {$$=$1;}
| %empty {$$=idents_empty();};
idents: idents "," TKN_IDENT {$$=idents_cat (&$1, &$3);}
| TKN_IDENT {$$=idents_one (&$1);};
stmts: stmts stmt {$$=stmts_cat (&$1, &$2);}
| %empty {$$=stmts_empty ();};
stmt: "{" stmts "}" {$$=stmt_multi (&$2);}
| "if" "(" expr ")" stmt %prec "then" {$$=stmt_if (&$3, &$5, NULL);}
| "if" "(" expr ")" stmt
"else" stmt {$$=stmt_if (&$3, &$5, &$7);}
| "while" "(" expr ")" stmt {$$=stmt_while (&$3, &$5);}
| "return" ";" {$$=stmt_ret (NULL);}
| "return" expr ";" {$$=stmt_ret (&$2);}
| vardecls {$$=stmt_var (&$1);}
| expr ";" {$$=stmt_expr (&$1);}
| inline_asm ";" {$$=$1;};
opt_exprs: exprs
| %empty;
exprs: expr "," exprs
| expr;
expr: TKN_IVAL {$$=expr_icnst(&$1);}
| TKN_STRVAL {$$=expr_scnst(&$1);}
| TKN_IDENT {$$=expr_ident(&$1);}
| expr "(" opt_exprs ")" {$$=expr_call (&$1, &$3);}
| expr "[" expr "]" {$$=expr_math2(OP_INDEX, &$1, &$3);}
| "(" expr ")" {$$=$2;}
| "-" expr {$$=expr_math1(OP_0_MINUS, &$2);}
| "!" expr {$$=expr_math1(OP_LOGIC_NOT, &$2);}
| "~" expr {$$=expr_math1(OP_BIT_NOT, &$2);}
| "&" expr {$$=expr_math1(OP_ADROF, &$2);}
| "*" expr {$$=expr_math1(OP_DEREF, &$2);}
| expr "*" expr {$$=expr_math2(OP_MUL, &$1, &$3);}
| expr "/" expr %prec "*" {$$=expr_math2(OP_DIV, &$1, &$3);}
| expr "%" expr %prec "*" {$$=expr_math2(OP_MOD, &$1, &$3);}
| expr "+" expr {$$=expr_math2(OP_ADD, &$1, &$3);}
| expr "-" expr %prec "+" {$$=expr_math2(OP_SUB, &$1, &$3);}
| expr "<" expr {$$=expr_math2(OP_LT, &$1, &$3);}
| expr "<=" expr %prec "<" {$$=expr_math2(OP_LE, &$1, &$3);}
| expr ">" expr %prec "<" {$$=expr_math2(OP_GT, &$1, &$3);}
| expr ">=" expr %prec "<" {$$=expr_math2(OP_GE, &$1, &$3);}
| expr "==" expr {$$=expr_math2(OP_NE, &$1, &$3);}
| expr "!=" expr %prec "==" {$$=expr_math2(OP_EQ, &$1, &$3);}
| expr "&" expr {$$=expr_math2(OP_BIT_AND, &$1, &$3);}
| expr "^" expr {$$=expr_math2(OP_BIT_XOR, &$1, &$3);}
| expr "|" expr {$$=expr_math2(OP_BIT_OR, &$1, &$3);}
| expr "<<" expr {$$=expr_math2(OP_SHIFT_L, &$1, &$3);}
| expr ">>" expr %prec "<<" {$$=expr_math2(OP_SHIFT_R, &$1, &$3);}
| expr "&&" expr {$$=expr_math2(OP_LOGIC_AND, &$1, &$3);}
| expr "||" expr {$$=expr_math2(OP_LOGIC_OR, &$1, &$3);}
| expr "=" expr {$$=expr_math2(OP_ASSIGN, &$1, &$3);};
inline_asm: "asm" "(" TKN_STRVAL
":" opt_asm_regs
":" opt_asm_regs
":" opt_asm_strs ")"
| "asm" "(" TKN_STRVAL
":" opt_asm_regs
":" opt_asm_regs ")"
| "asm" "(" TKN_STRVAL
":" opt_asm_regs ")"
| "asm" "(" TKN_STRVAL ")" {$$=stmt_iasm(&$3, NULL, NULL, NULL);};
opt_asm_strs: asm_strs
| %empty;
asm_strs: TKN_STRVAL "," asm_strs
| TKN_STRVAL;
opt_asm_regs: asm_regs
| %empty;
asm_regs: TKN_STRVAL "(" expr ")" "," asm_regs
| TKN_STRVAL "(" expr ")";
%%
void *make_copy(void *mem, size_t size) {
if (!mem) return NULL;
void *copy = malloc(size);
memcpy(copy, mem, size);
return copy;
}
| Bison | 5 | robotman2412/lilly-c | src/parser.bison | [
"MIT"
] |
(test (= (try _ 42) 42))
(test (= (try ((foo(x) (+ x 35)))
(call (restart 'foo) 7))
42))
(test (= (try ((foo(x) (+ x 35)))
(try _
(call (restart 'foo) 7)))
42))
(test (= (try ((foo() 'bar))
(try ((foo() 'baz))
(call (restart 'foo))))
'baz))
(test (= (catch ((_ (restart 'done 21)))
(try ((done(n) (* 2 n)))
(throw 'foo)))
42))
(test (= (catch (((Int e) (restart 'done e)))
(try ((done(n) (* 2 n)))
(throw 21)))
42))
(test (= (catch (((EUnknown _)
(restart 'use-val 42)))
(try _ not-found))
42)) | Grammatical Framework | 3 | daota2/fffff | v1/test/restart.gf | [
"MIT"
] |
#![crate_type = "dylib"]
extern crate m1;
pub fn m2() { m1::m1() }
| Rust | 2 | Eric-Arellano/rust | src/test/run-make-fulldeps/dylib-chain/m2.rs | [
"ECL-2.0",
"Apache-2.0",
"MIT-0",
"MIT"
] |
new function pairwiseSort(array, f, l, g = 1) {
if f == l - g {
return;
}
for b = f + g; b < l; b += 2 * g {
compSwap(array, b - g, b);
}
if ((l - f) // g) % 2 == 0 {
pairwiseSort(array, f, l, g * 2);
pairwiseSort(array, f + g, l + g, g * 2);
} else {
pairwiseSort(array, f, l + g, g * 2);
pairwiseSort(array, f + g, l, g * 2);
}
for a = 1; a < (l - f) // g; a = (a * 2) + 1 {}
for b = f + g; b + g < l; b += 2 * g {
new int c = a;
while c > 1 {
c //= 2;
if b + (c * g) < l {
compSwap(array, b, b + (c * g));
}
}
}
}
@Sort(
"Concurrent Sorts",
"Pairwise Sorting Network",
"Pairwise"
);
new function pairwiseSortRun(array) {
pairwiseSort(array, 0, len(array));
} | Opal | 3 | thatsOven/sorting-visualizer | sorts/PairwiseSortingNetwork.opal | [
"MIT"
] |
"* The Computer Language Benchmarks Game
http://benchmarksgame.alioth.debian.org/
contributed by Andres Valloud *"!
!SequenceableCollection methodsFor: 'computer language shootout'!
substringFrequencies5: aLength using: aDictionary
| buffer |
buffer := String new: aLength.
1 to: self size - aLength + 1 do:
[:i |
| answer |
buffer replaceFrom: 1 to: aLength with: self startingAt: i.
answer := aDictionary
at: buffer
putValueOf: [:sum | sum + 1]
ifAbsentPutValueOf: 1.
answer = 1 ifTrue: [buffer := String new: aLength].
].
^aDictionary! !
!Dictionary methodsFor: 'computer language shootout'!
at: key putValueOf: putBlock ifAbsentPutValueOf: absentBlock
"* Set the value at key to be the value of evaluating putBlock
with the existing value. If key is not found, create a new
entry for key and set is value to the evaluation of
absentBlock. Answer the result of evaluating either block. *"
| index element anObject |
key == nil ifTrue:
[^self
subscriptBoundsErrorFor: #at:putValueOf:ifAbsentPutValueOf:
index: key
value: absentBlock value].
index := self findKeyOrNil: key.
element := self basicAt: index.
element == nil
ifTrue: [self atNewIndex: index put:
(self createKey: key value: (anObject := absentBlock value))]
ifFalse: [element value: (anObject := putBlock value: element value)].
^anObject ! !
!Tests class methodsFor: 'benchmarking'!
readFasta: sequenceName from: input
| prefix newline buffer description line char |
prefix := '>',sequenceName.
newline := Character lf.
"* find start of particular fasta sequence *"
[(input atEnd) or: [
(input peek = $>)
ifTrue: [((line := input upTo: newline)
indexOfSubCollection: prefix startingAt: 1) = 1]
ifFalse: [input skipThrough: newline. false]]
] whileFalse.
"* line-by-line read - it would be a lot faster to block read *"
description := line.
buffer := ReadWriteStream on: (String new: 1028).
[(input atEnd) or: [(char := input peek) = $>]] whileFalse: [
(char = $;)
ifTrue: [input upTo: newline]
ifFalse: [buffer nextPutAll: (input upTo: newline)]
].
^Association key: description value: buffer contents ! !
!Tests class methodsFor: 'benchmarking'!
knucleotide5From: input to: output
"Same as av3, but create less strings while updating the frequencies"
| sequence writeFrequencies writeCount |
sequence := (self readFasta: 'THREE' from: input) value asUppercase.
writeFrequencies :=
[:k | | frequencies count |
frequencies := SortedCollection sortBlock: [:a :b|
(a value = b value) ifTrue: [b key < a key] ifFalse: [b value < a value]].
count := 0.0.
(sequence substringFrequencies5: k using: (Dictionary new: 1024))
associationsDo: [:each|
frequencies add: each. count := count + each value].
frequencies do: [:each | | percentage |
percentage := (each value / count) * 100.0.
output
nextPutAll: each key; space;
print: percentage digits: 3; nl]].
writeCount := [:nucleotideFragment | | frequencies count |
frequencies := sequence substringFrequencies5: nucleotideFragment size
using: (Dictionary new: 1024).
count := frequencies at: nucleotideFragment ifAbsent: [0].
output print: count; tab; nextPutAll: nucleotideFragment; nl].
writeFrequencies value: 1. output nl.
writeFrequencies value: 2. output nl.
writeCount value: 'GGT'.
writeCount value: 'GGTA'.
writeCount value: 'GGTATT'.
writeCount value: 'GGTATTTTAATT'.
writeCount value: 'GGTATTTTAATTTATAGT'.! !
!Tests class methodsFor: 'benchmark scripts'!
knucleotide5
self knucleotide5From: self stdinSpecial to: self stdout.
^''! ! | Gosu | 4 | danglotb/Energy-Languages | Smalltalk/k-nucleotide/knucleotide5.gst | [
"MIT"
] |
\section{IDS types}
\begin{code}
{-# LANGUAGE MagicHash #-}
module Types where
import GHC.Exts
data F a = FN | F1 a | F2 a a | F3 a a a
| F4 a a a a
| F5 a a a a a (F a)
data FI = FIN | FI1 Int# | FI2 Int# Int# | FI3 Int# Int# Int#
| FI4 Int# Int# Int# Int#
| FI5 Int# Int# Int# Int# Int# FI
data FC = FCN | FC1 Char# | FC2 Char# Char#
| FC3 Char# Char# Char#
| FC4 Char# Char# Char# Char#
| FC5 Char# Char# Char# Char# Char# FC
\end{code}
\begin{code}
data F2 a b = F2N | F21 a b | F22 a b a b | F23 a b a b a b
| F24 a b a b a b a b
| F25 a b a b a b a b a b (F2 a b)
data F3 a b c = F3N | F31 a b c | F32 a b c a b c
| F33 a b c a b c a b c
| F34 a b c a b c a b c a b c
| F35 a b c a b c a b c a b c a b c (F3 a b c)
data F3I = F3IN
| F3I1 Int# Int# Int#
| F3I2 Int# Int# Int# Int# Int# Int#
| F3I3 Int# Int# Int# Int# Int# Int# Int# Int# Int#
| F3I4 Int# Int# Int# Int# Int# Int# Int# Int# Int#
Int# Int# Int#
| F3I5 Int# Int# Int# Int# Int# Int# Int# Int# Int#
Int# Int# Int# Int# Int# Int# F3I
\end{code}
\begin{code}
data S a = SN | S1 a (S a) | S2 a a (S a) | S3 a a a (S a)
| S4 a a a a (S a)
| S5 a a a a a (S a)
data SI = SIN | SI1 Int# SI | SI2 Int# Int# SI
| SI3 Int# Int# Int# SI
| SI4 Int# Int# Int# Int# SI
| SI5 Int# Int# Int# Int# Int# SI
data SC = SCN | SC1 Char# SC | SC2 Char# Char# SC
| SC3 Char# Char# Char# SC
| SC4 Char# Char# Char# Char# SC
| SC5 Char# Char# Char# Char# Char# SC
\end{code}
| Literate Haskell | 3 | ocharles/ghc | testsuite/tests/programs/cvh_unboxing/Types.lhs | [
"BSD-3-Clause"
] |
package com.serverless;
import com.amazonaws.services.lambda.runtime.Context;
import com.amazonaws.services.lambda.runtime.RequestHandler;
import com.amazonaws.services.lambda.runtime.events.S3Event;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
public class RequestHandlerS3Event implements RequestHandler<S3Event, Object> {
static S3Event input;
@Override
public Object handleRequest(S3Event event, Context context) {
input = event;
ObjectMapper objectMapper = new ObjectMapper().findAndRegisterModules();
try {
System.out.println("Input received:" + objectMapper.writeValueAsString(input));
} catch (JsonProcessingException e) {
System.out.println("Input received:" + input.toString());
throw new RuntimeException("Failed to convert to JSON.", e);
}
return "RequestHandlerS3Event invoke Complete.";
}
}
| Java | 3 | Arun-kc/serverless | lib/plugins/aws/invokeLocal/runtimeWrappers/java/src/test/java/com/serverless/RequestHandlerS3Event.java | [
"MIT"
] |
#![feature(associated_type_defaults)]
#![feature(generic_associated_types)]
trait Trait1 {
fn foo();
}
trait Trait2 {
type Associated: Trait1 = Self;
//~^ ERROR: the trait bound `Self: Trait1` is not satisfied
//~| the size for values of type `Self` cannot be known
}
impl Trait2 for () {}
fn call_foo<T: Trait2>() {
T::Associated::foo()
}
fn main() {
call_foo::<()>()
}
| Rust | 4 | mbc-git/rust | src/test/ui/generic-associated-types/issue-74816.rs | [
"ECL-2.0",
"Apache-2.0",
"MIT-0",
"MIT"
] |
@prefix ia: <http://lv2plug.in/ns/ext/instance-access#> .
@prefix lv2: <http://lv2plug.in/ns/lv2core#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
<http://lv2plug.in/ns/ext/instance-access>
a lv2:Feature ;
rdfs:seeAlso <instance-access.h> ,
<lv2-instance-access.doap.ttl> ;
lv2:documentation """
<p>This extension defines a feature which allows plugin UIs to get a direct
handle to an LV2 plugin instance (LV2_Handle), if possible.</p>
<p>Note that the use of this extension by UIs violates the important principle
of UI/plugin separation, and is potentially a source of many problems.
Accordingly, <strong>use of this extension is highly discouraged</strong>, and
plugins should not expect hosts to support it, since it is often impossible to
do so.</p>
<p>To support this feature the host must pass an LV2_Feature struct to the UI
instantiate method with URI LV2_INSTANCE_ACCESS_URI and data pointed directly
to the LV2_Handle of the plugin instance.</p>
""" .
| Turtle | 4 | joshrose/audacity | lib-src/lv2/lv2/lv2/instance-access/instance-access.ttl | [
"CC-BY-3.0"
] |
class_name Pawn
extends Node2D
enum CellType { ACTOR, OBSTACLE, OBJECT }
#warning-ignore:unused_class_variable
export(CellType) var type = CellType.ACTOR
var active = true setget set_active
func set_active(value):
active = value
set_process(value)
set_process_input(value)
| GDScript | 4 | jonbonazza/godot-demo-projects | 2d/role_playing_game/grid_movement/pawns/Pawn.gd | [
"MIT"
] |
FIVE
;List and count the months between 1/1900 and 12/2100 that have 5 full weekends
;Extra credit - list and count years with no months with five full weekends
;Using the test that the 31st of a month is on a Sunday
;Uses the VA's public domain routine %DTC (Part of the Kernel) named here DIDTC
NEW YEAR,MONTH,X,Y,CNTMON,NOT,NOTLIST
; YEAR is the year we're testing
; MONTH is the month we're testing
; X is the date in "internal" format, as an input to DOW^DIDTC
; Y is the day of the week (0=Sunday, 1=Monday...) output from DOW^DIDTC
; CNTMON is a count of the months that have 5 full weekends
; NOT is a flag if there were no months with 5 full weekends yet that year
; NOTLIST is a list of years that do not have any months with 5 full weekends
SET CNTMON=0,NOTLIST=""
WRITE !!,"The following months have five full weekends:"
FOR YEAR=200:1:400 DO ;years since 12/31/1700 epoch
. SET NOT=0
. FOR MONTH="01","03","05","07","08","10","12" DO
. . SET X=YEAR_MONTH_"31"
. . DO DOW^DIDTC
. . IF (Y=0) DO
. . . SET NOT=NOT+1,CNTMON=CNTMON+1
. . . WRITE !,MONTH_"-"_(YEAR+1700)
. SET:(NOT=0) NOTLIST=NOTLIST_$SELECT($LENGTH(NOTLIST)>1:",",1:"")_(YEAR+1700)
WRITE !,"For a total of "_CNTMON_" months."
WRITE !!,"There are "_$LENGTH(NOTLIST,",")_" years with no five full weekends in any month."
WRITE !,"They are: "_NOTLIST
KILL YEAR,MONTH,X,Y,CNTMON,NOT,NOTLIST
QUIT
F ;Same logic as the main entry point, shortened format
N R,M,X,Y,C,N,L S C=0,L=""
W !!,"The following months have five full weekends:"
F R=200:1:400 D
. S N=0 F M="01","03","05","07","08","10","12" S X=R_M_"31" D DOW^DIDTC I 'Y S N=N+1,C=C+1 W !,M_"-"_(R+1700)
. S:'N L=L_$S($L(L):",",1:"")_(R+1700)
W !,"For a total of "_C_" months.",!!,"There are "_$L(L,",")_" years with no five full weekends in any month.",!,"They are: "_L
Q
| M | 4 | LaudateCorpus1/RosettaCodeData | Task/Five-weekends/MUMPS/five-weekends.mumps | [
"Info-ZIP"
] |
#/** @file
# This is a very simple shell script to test how the interpreter parses the parameters.
#
# Copyright (c) 2015, Intel Corporation. All rights reserved.<BR>
# This program and the accompanying materials
# are licensed and made available under the terms and conditions of the BSD License
# which accompanies this distribution. The full text of the license may be found at
# http://opensource.org/licenses/bsd-license.php
#
# THE PROGRAM IS DISTRIBUTED UNDER THE BSD LICENSE ON AN "AS IS" BASIS,
# WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
#
#**/
echo -on
set Var_EFCF356F_228C_47C2_AD0C_3B5DAC9A8CFA ValueOfGuid
set Sharp_E8528E46_A008_4221_8DE0_D5AB42A9C580 ^#
set Quote_E95DEE8B_E3AA_4155_9ED5_6916394104FC ^"
set Var_ShellCTestApp_EE6E8BC6_71A6_44A5_BED3_D8F901105CDE ShellCTestApp_EE6E8BC6_71A6_44A5_BED3_D8F901105CDE
alias ShellCTestApp_EE6E8BC6_71A6_44A5_BED3_D8F901105CDE ShellCTestApp
#
# '^' should escape all special characters (including space)
# but has no impact to non-special characters
#
ShellCTestApp ^^
ShellCTestApp ^#
ShellCTestApp ^%Var_EFCF356F_228C_47C2_AD0C_3B5DAC9A8CFA%
ShellCTestApp ^"
ShellCTestApp ^ 1
ShellCTestApp ^
ShellCTestApp ^1
ShellCTestApp ^^^"
ShellCTestApp ^^^
#
# '#' should be processed before %% replacement, and inside '"'
#
ShellCTestApp #%Var_EFCF356F_228C_47C2_AD0C_3B5DAC9A8CFA%
#ShellCTestApp "#"
ShellCTestApp %Sharp_E8528E46_A008_4221_8DE0_D5AB42A9C580%
#
# '%' should be processed before grouping parameters
#
ShellCTestApp "%Var_EFCF356F_228C_47C2_AD0C_3B5DAC9A8CFA% 2%Quote_E95DEE8B_E3AA_4155_9ED5_6916394104FC%
#
# alias should be processed after %% replacement
#
%Var_ShellCTestApp_EE6E8BC6_71A6_44A5_BED3_D8F901105CDE%
#
# '"' should be stripped, space inside '"' should be kept,
#
ShellCTestApp "p 1"
ShellCTestApp "p"1
ShellCTestApp "p 1"e"x"""
set -d Var_EFCF356F_228C_47C2_AD0C_3B5DAC9A8CFA
set -d Sharp_E8528E46_A008_4221_8DE0_D5AB42A9C580
set -d Quote_E95DEE8B_E3AA_4155_9ED5_6916394104FC
set -d Var_ShellCTestApp_EE6E8BC6_71A6_44A5_BED3_D8F901105CDE
alias -d ShellCTestApp_EE6E8BC6_71A6_44A5_BED3_D8F901105CDE
echo -off | NSIS | 4 | CEOALT1/RefindPlusUDK | ShellPkg/Application/ShellCTestApp/TestArgv.nsh | [
"BSD-2-Clause"
] |
#%RAML 0.8
title: Kafka Web Console API
version: 1.0
baseUri: http://{hostname}:{port}
mediaType: application/json
/zookeepers.json/{group}:
get:
/zookeepers.json:
put:
body:
schema: !include zookeeper.json
/zookeepers.json/{name}:
delete:
/topics.json:
get:
/topics.json/{topic}/{zookeeper}:
get:
/brokers.json:
get:
/consumergroups.json/{consumerGroup}/{topic}/{zookeeper}:
get:
/offsethistory.json/{consumerGroup}/{topic}/{zookeeper}:
get:
/settings.json:
get:
post:
body:
schema: !include settings.json | RAML | 3 | cfchou/try-kafka-web-console | public/api-console/kafka-web-console.raml | [
"Apache-2.0"
] |
/* Copyright 2015 The TensorFlow Authors. All Rights Reserved.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
==============================================================================*/
#include <condition_variable>
#include "tensorflow/core/platform/cpu_info.h"
#include "tensorflow/core/platform/env_time.h"
#include "tensorflow/core/platform/mem.h"
#include "tensorflow/core/platform/mutex.h"
#include "tensorflow/core/platform/test.h"
#include "tensorflow/core/platform/threadpool.h"
namespace tensorflow {
namespace port {
TEST(Port, AlignedMalloc) {
for (size_t alignment = 1; alignment <= 1 << 20; alignment <<= 1) {
void* p = AlignedMalloc(1, alignment);
ASSERT_TRUE(p != nullptr) << "AlignedMalloc(1, " << alignment << ")";
uintptr_t pval = reinterpret_cast<uintptr_t>(p);
EXPECT_EQ(pval % alignment, 0);
AlignedFree(p);
}
}
TEST(Port, GetCurrentCPU) {
const int cpu = GetCurrentCPU();
#if !defined(__APPLE__)
// GetCurrentCPU does not currently work on MacOS.
EXPECT_GE(cpu, 0);
EXPECT_LT(cpu, NumTotalCPUs());
#endif
}
TEST(ConditionVariable, WaitForMilliseconds_Timeout) {
mutex m;
mutex_lock l(m);
condition_variable cv;
ConditionResult result = kCond_MaybeNotified;
time_t start = time(nullptr);
// Condition variables are subject to spurious wakeups on some platforms,
// so need to check for a timeout within a loop.
while (result == kCond_MaybeNotified) {
result = WaitForMilliseconds(&l, &cv, 3000);
}
EXPECT_EQ(result, kCond_Timeout);
time_t finish = time(nullptr);
EXPECT_GE(finish - start, 3);
}
TEST(ConditionVariable, WaitForMilliseconds_Signalled) {
thread::ThreadPool pool(Env::Default(), "test", 1);
mutex m;
mutex_lock l(m);
condition_variable cv;
time_t start = time(nullptr);
// Sleep for just 1 second then notify. We have a timeout of 3 secs,
// so the condition variable will notice the cv signal before the timeout.
pool.Schedule([&m, &cv]() {
Env::Default()->SleepForMicroseconds(1 * 1000 * 1000);
mutex_lock l(m);
cv.notify_all();
});
EXPECT_EQ(WaitForMilliseconds(&l, &cv, 3000), kCond_MaybeNotified);
time_t finish = time(nullptr);
EXPECT_LT(finish - start, 3);
}
TEST(ConditionalCriticalSections, AwaitWithDeadline_Timeout) {
bool always_false = false;
mutex m;
m.lock();
time_t start = time(nullptr);
bool result =
m.AwaitWithDeadline(Condition(&always_false),
EnvTime::NowNanos() + 3 * EnvTime::kSecondsToNanos);
time_t finish = time(nullptr);
m.unlock();
EXPECT_EQ(result, false);
EXPECT_GE(finish - start, 3);
}
TEST(ConditionalCriticalSections, AwaitWithDeadline_Woken) {
thread::ThreadPool pool(Env::Default(), "test", 1);
bool woken = false;
mutex m;
m.lock();
time_t start = time(nullptr);
// Sleep for just 1 second then set the boolean. We have a timeout of 3
// secs, so the mutex implementation will notice the boolean state change
// before the timeout.
pool.Schedule([&m, &woken]() {
Env::Default()->SleepForMicroseconds(1 * 1000 * 1000);
m.lock();
woken = true;
m.unlock();
});
bool result = m.AwaitWithDeadline(
Condition(&woken), EnvTime::NowNanos() + 3 * EnvTime::kSecondsToNanos);
time_t finish = time(nullptr);
m.unlock();
EXPECT_EQ(result, true);
EXPECT_LT(finish - start, 3);
}
// Return the negation of *b. Used as an Await() predicate.
static bool Invert(bool* b) { return !*b; }
// The Value() method inverts the value of the boolean specified in
// the constructor.
class InvertClass {
public:
explicit InvertClass(bool* value) : value_(value) {}
bool Value() { return !*this->value_; }
private:
InvertClass();
bool* value_;
};
TEST(ConditionalCriticalSections, Await_PingPong) {
thread::ThreadPool pool(Env::Default(), "test", 1);
bool ping_pong = false;
bool done = false;
mutex m;
pool.Schedule([&m, &ping_pong, &done]() {
m.lock();
for (int i = 0; i != 1000; i++) {
m.Await(Condition(&ping_pong));
ping_pong = false;
}
done = true;
m.unlock();
});
m.lock();
InvertClass invert(&ping_pong);
for (int i = 0; i != 1000; i++) {
m.Await(Condition(&Invert, &ping_pong));
ping_pong = true;
}
m.Await(Condition(&done));
m.unlock();
}
TEST(ConditionalCriticalSections, Await_PingPongMethod) {
thread::ThreadPool pool(Env::Default(), "test", 1);
bool ping_pong = false;
bool done = false;
mutex m;
pool.Schedule([&m, &ping_pong, &done]() {
m.lock();
for (int i = 0; i != 1000; i++) {
m.Await(Condition(&ping_pong));
ping_pong = false;
}
done = true;
m.unlock();
});
m.lock();
InvertClass invert(&ping_pong);
for (int i = 0; i != 1000; i++) {
m.Await(Condition(&invert, &InvertClass::Value));
ping_pong = true;
}
m.Await(Condition(&done));
m.unlock();
}
TEST(TestCPUFeature, TestFeature) {
// We don't know what the result should be on this platform, so just make
// sure it's callable.
const bool has_avx = TestCPUFeature(CPUFeature::AVX);
LOG(INFO) << "has_avx = " << has_avx;
const bool has_avx2 = TestCPUFeature(CPUFeature::AVX2);
LOG(INFO) << "has_avx2 = " << has_avx2;
}
} // namespace port
} // namespace tensorflow
| C++ | 4 | yage99/tensorflow | tensorflow/core/platform/port_test.cc | [
"Apache-2.0"
] |
package com.alibaba.json.bvt.issue_1200;
import com.alibaba.fastjson.JSON;
import com.alibaba.fastjson.annotation.JSONField;
import junit.framework.TestCase;
import java.io.Serializable;
import java.util.List;
/**
* Created by wenshao on 01/07/2017.
*/
public class Issue1299 extends TestCase {
public void test_for_issue() throws Exception {
String jsonStr = "{\"code\":201,\"data\":{\"materials\":[{\"material\":\"locale\",\"success\":true,"
+ "\"material_id\":356,\"id\":\"5099\"}],\"unitInfo\":{\"languages\":[\"'en_US'\",\"ru_RU\"],"
+ "\"unitName\":\"PC_ROCKBROS\",\"sceneKey\":\"shop_activity_page\",\"domain\":\"shopcdp.aliexpress"
+ ".com\",\"format\":\"HTML\",\"unitId\":\"1625\",\"id\":1761,\"rootPath\":\"shopcdp\","
+ "\"userId\":\"jianqing.zengjq\",\"platforms\":[\"pc\",\"mobile\"],\"status\":2}},\"success\":true}";
UnitsSaveResponse response = JSON.parseObject(jsonStr, UnitsSaveResponse.class);
Class<?> dataClass = response.getData().getClass();
System.out.println(dataClass);
}
public static class ServiceResult<T> extends BaseResultDo implements Serializable {
@JSONField(
name = "data"
)
private T data;
public ServiceResult() {
}
public T getData() {
return this.data;
}
public void setData(T data) {
this.data = data;
}
}
public static class UnitsSaveResponse extends ServiceResult<UnitSave> {
}
public static class UnitSave implements Serializable {
private SaveUnitInfo unitInfo;
private List materials;
public SaveUnitInfo getUnitInfo() {
return unitInfo;
}
public void setUnitInfo(SaveUnitInfo unitInfo) {
this.unitInfo = unitInfo;
}
public List getMaterials() {
return materials;
}
public void setMaterials(List materials) {
this.materials = materials;
}
}
public static class SaveUnitInfo {
}
public static class BaseResultDo{
}
}
| Java | 3 | Czarek93/fastjson | src/test/java/com/alibaba/json/bvt/issue_1200/Issue1299.java | [
"Apache-2.0"
] |
t ia2 -3a 1 1 0 1
t ia2 -ca enable
t ia2 -adj ae
t ia2 -ae on
| AGS Script | 0 | waltersgrey/autoexechack | CA/1/autoexec.ash | [
"MIT"
] |
<%
from rllab.misc.mako_utils import compute_rect_vertices
link_len = opts['link_len']
link_width = 0.1
%>
<box2d>
<world timestep="0.01" velitr="20" positr="20">
<body name="link1" type="dynamic" position="0,0">
<fixture
density="5.0"
group="-1"
shape="polygon"
vertices="${compute_rect_vertices([0,0], [0, -link_len], link_width/2)}"
/>
</body>
<body name="link2" type="dynamic" position="0,${-link_len}">
<fixture
density="5.0"
group="-1"
shape="polygon"
vertices="${compute_rect_vertices([0,0], [0,-link_len], link_width/2)}"
/>
</body>
<body name="track" type="static" position="0,-0.1">
<fixture group="-1" shape="polygon" box="100,0.1"/>
</body>
<joint type="revolute" name="link_joint_1" bodyA="track" bodyB="link1" anchor="0,0"/>
<joint type="revolute" name="link_joint_2" bodyA="link1" bodyB="link2" anchor="0,${-link_len}"/>
<!-- <control type="torque" joint="link_joint_1" ctrllimit="-3,3"/> -->
<control type="torque" joint="link_joint_2" ctrllimit="-50,50" />
<state type="apos" body="link1" transform="sin"/>
<state type="apos" body="link1" transform="cos"/>
<state type="avel" body="link1"/>
<state type="apos" body="link2" transform="sin"/>
<state type="apos" body="link2" transform="cos"/>
<state type="avel" body="link2"/>
</world>
</box2d>
| Mako | 3 | RussellM2020/maml_gps | rllab/envs/box2d/models/double_pendulum.xml.mako | [
"MIT"
] |
import ../Coro
version(windows) {
include windows
CoroWin32: class extends Coro {
fiber: Pointer
parent: Pointer
init: func
initializeMainCoro: func {
isMain = true
if(GetCurrentFiber() == 0x1e00 as Pointer) {
ConvertThreadToFiber(this)
}
fiber = GetCurrentFiber()
}
startCoro: func(other: Coro, callback: Func) {
other setup(this, ||
callback()
other switchTo(this)
)
switchTo(other)
}
switchTo: func(next: Coro) {
SwitchToFiber(next as This fiber)
}
yield: func {
if(isMain) {
raise("Scheduler error: yielded from main coro")
}
SwitchToFiber(parent)
}
setup: func(coro: Coro, callback: Func) {
if(fiber != null && !isMain) {
DeleteFiber(fiber)
}
fiber = CreateFiber(DEFAULT_STACK_SIZE, callback as Closure thunk, callback as Closure context)
if(!fiber) {
raise("Could not create fiber")
}
parent = coro as This fiber
}
// Freeing a main fiber results in exiting the thread it was executed in
free: func {
if(fiber) {
DeleteFiber(fiber)
}
}
}
DeleteFiber: extern func(Pointer)
SwitchToFiber: extern func(Pointer)
CreateFiber: extern func(Int, Pointer, Pointer) -> Pointer
GetCurrentFiber: extern func -> Pointer
ConvertThreadToFiber: extern func(Pointer)
}
| ooc | 4 | fredrikbryntesson/launchtest | sdk/os/native/CoroWin32.ooc | [
"MIT"
] |
package opal: import *;
package random: import randint, uniform;
new <Vector> RESOLUTION = Vector(1280, 720);
new int FIREWORK_SIZE = 4,
PARTICLE_SIZE = 2,
MIN_PARTICLE_QTY = 80,
MAX_PARTICLE_QTY = 120,
LIFESPAN_DECREASE = 3,
ALPHA_CHANGE = 25,
ROCKET_FREQ_PERC = 10;
new float PARTICLE_VELOCITY_MULTIPLIER = 0.98,
PARTICLE_MAX_INIT_VELOCITY = 5,
ROCKET_MAX_INIT_VELOCITY = 17,
ROCKET_MIN_INIT_VELOCITY = 8;
new bool RAINBOW_EXPLOSION = False;
new <Vector> GRAVITY = Vector(0, 0.2);
new <Graphics> graphics = Graphics(RESOLUTION, caption = "Fireworks");
new class Particle {
new method __init__(pos, color = (255, 255, 255), exploder = False) {
this.pos = pos;
this.acceleration = Vector();
if exploder {
this.velocity = Vector(uniform(-1, 1), uniform(-1, 1));
this.velocity *= uniform(1, PARTICLE_MAX_INIT_VELOCITY);
} else {
this.velocity = Vector(0, uniform(-ROCKET_MAX_INIT_VELOCITY, -ROCKET_MIN_INIT_VELOCITY));
}
this.color = color;
this.lifeSpan = 255;
this.alive = True;
this.exploder = exploder;
}
new method applyForce(f) {
this.acceleration += f;
}
new method update() {
if this.exploder {
this.velocity *= PARTICLE_VELOCITY_MULTIPLIER;
this.lifeSpan -= LIFESPAN_DECREASE;
}
this.velocity += this.acceleration;
this.pos += this.velocity;
this.acceleration *= 0;
if this.pos.y >= RESOLUTION.y or this.pos.x < 0 or this.pos.x >= RESOLUTION.x {
this.alive = False;
}
}
new method isAlive() {
return this.lifeSpan >= 0 and this.alive;
}
new method show() {
if this.exploder {
graphics.circle(this.pos, PARTICLE_SIZE, this.color, this.lifeSpan);
} else {
graphics.fastCircle(this.pos, FIREWORK_SIZE, this.color);
}
}
}
new class Explosion {
new method __init__(pos, color = None) {
this.pos = pos;
if color is None {
this.color = (randint(0, 255), randint(0, 255), randint(0, 255));
} else {
this.color = color;
}
this.particles = [];
}
new method explode(pos = None) {
if pos is not None {
this.pos = pos;
}
if RAINBOW_EXPLOSION {
repeat randint(MIN_PARTICLE_QTY, MAX_PARTICLE_QTY) {
this.particles.append(Particle(this.pos, (randint(0, 255), randint(0, 255), randint(0, 255)), True));
}
} else {
repeat randint(MIN_PARTICLE_QTY, MAX_PARTICLE_QTY) {
this.particles.append(Particle(this.pos, this.color, True));
}
}
}
new method update() {
for particle in this.particles {
particle.applyForce(GRAVITY);
particle.update();
}
this.particles = [particle for particle in this.particles if particle.isAlive()];
}
new method isAlive() {
return len(this.particles) > 0;
}
new method show() {
for particle in this.particles {
particle.show();
}
}
}
new class Firework {
new method __init__(pos = None) {
this.color = (randint(0, 255), randint(0, 255), randint(0, 255));
if pos is None {
this.rocket = Particle(Vector(randint(0, RESOLUTION.x), RESOLUTION.y), this.color);
} else {
this.rocket = Particle(pos, this.color);
}
this.explosion = Explosion(this.rocket.pos, this.color);
this.exploded = False;
}
new method update() {
if not this.exploded {
this.rocket.applyForce(GRAVITY);
this.rocket.update();
if this.rocket.velocity.y >= 0 {
this.exploded = True;
this.explosion.explode(this.rocket.pos);
}
}
if this.exploded {
this.explosion.update();
}
}
new method isAlive() {
return this.explosion.isAlive() or not this.exploded;
}
new method show() {
if not this.exploded {
this.rocket.show();
} else {
this.explosion.show();
}
}
}
new list fireworks = [],
explosions = [];
@graphics.event(MOUSEBUTTONDOWN);
new function click(event) {
global fireworks, explosions;
match event.button {
case 1 {
fireworks.append(Firework(graphics.getMousePos()));
}
case 3 {
explosions.append(Explosion(graphics.getMousePos()));
explosions[-1].explode();
}
}
}
@graphics.update;
new function draw() {
global fireworks, explosions;
if randint(0, 100) < ROCKET_FREQ_PERC {
fireworks.append(Firework());
}
graphics.fillAlpha((0, 0, 0), ALPHA_CHANGE);
for firework in fireworks {
firework.update();
firework.show();
}
for explosion in explosions {
explosion.update();
explosion.show();
}
fireworks = [ firework for firework in fireworks if firework.isAlive()];
explosions = [explosion for explosion in explosions if explosion.isAlive()];
}
main {
graphics.run(drawBackground = False);
}
| Opal | 5 | thatsOven/opal-lang | examples/fireworks.opal | [
"MIT"
] |
Hi! I'm Jennifer Dewalt and I taught myself to code by making 180 websites in 180 days.
You can check out the project at https://jenniferdewalt.com.
| RDoc | 1 | nadiaschutz/jennifer_dewalt | README.rdoc | [
"MIT"
] |
package com.baeldung.di.aspectj;
import org.springframework.stereotype.Service;
@Service
public class IdService {
private static int count;
int generateId() {
return ++count;
}
}
| Java | 3 | DBatOWL/tutorials | spring-di-2/src/main/java/com/baeldung/di/aspectj/IdService.java | [
"MIT"
] |
// Whitney music box in one line - by Nathaniel Virgo
play{mean({|i|99**(-1-LFSaw.kr(i+1/180,1))*SinOsc.ar(i+1*55)}!48)!2}
// Explanations by Jim B:
// {|i| i.postln; }!10; // basic iterator
// Envelope generation:
// {LFSaw.kr(2,1)}.plot(1); // produces ascending ramp from -1 to 1
// {-1 - LFSaw.kr(2,1)}.plot(1); // produces descending ramp from 0 - -2
// {99**(-1-LFSaw.kr(2,1))}.plot(1); // Produces a nice envelope from 1 to 0 at the desired rate
// 99 ** 0 is 1 99 ** -2 is a small value
// mean() is used to mix all the signals so we don't have to explicitly sent amplitude to 1/n
// !2 is for the stereo channels | SuperCollider | 4 | Haroenv/Whitney-Music-Box-Examples | supercollider/whitney_oneliner.scd | [
"AAL"
] |
server {
server_name homestead.app;
root /var/www/default;
index index.php;
client_max_body_size 100M;
fastcgi_read_timeout 1800;
location / {
try_files $uri $uri/ /index.php;
}
location ~* \.(js|css|png|jpg|jpeg|gif|ico)$ {
expires max;
log_not_found off;
access_log off;
}
sendfile off;
location ~ \.php$ {
try_files $uri =404;
include fastcgi_params;
fastcgi_index index.php;
fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
#fastcgi_pass unix:/var/run/php5-fpm.sock; #UNCOMMENT TO USING PHP-FPM
fastcgi_pass unix:/var/run/hhvm/hhvm.sock; #UNCOMMENT TO USING HHVM
fastcgi_intercept_errors off;
fastcgi_buffer_size 16k;
fastcgi_buffers 4 16k;
fastcgi_connect_timeout 300;
fastcgi_send_timeout 300;
fastcgi_read_timeout 300;
}
}
| ApacheConf | 4 | tanlinhnd/docker-fullstack-php | sites/homestead.app.vhost | [
"MIT"
] |
def each_line1(file)
File.read_lines(file).each_with_index do |line, index0|
yield line, index0 + 1
end
end
repo_base_dir = "#{__DIR__}/../../"
tmp_build_dir = File.join(repo_base_dir, ".build")
Dir.mkdir_p(tmp_build_dir)
input = ARGV[0]
bin = File.join(tmp_build_dir, "debug_test_case")
debugger_script = File.join(tmp_build_dir, "./debugger.script")
Process.run(ENV["CRYSTAL_SPEC_COMPILER_BIN"]? || "#{repo_base_dir}/bin/crystal", ["build", "--debug", input, "-o", bin])
File.open(debugger_script, "w") do |script|
lldb_crystal_formatters = File.expand_path(File.join(repo_base_dir, "etc", "lldb", "crystal_formatters.py"))
script.puts "version"
script.puts "command script import #{lldb_crystal_formatters}"
each_line1(input) do |line, line_number|
if line.match(/# break\b/)
script.puts "breakpoint set --file #{input} --line #{line_number}"
end
end
script.puts "run"
each_line1(input) do |line|
if md = line.match(/# lldb-command: (.*)/)
script.puts md[1]
end
end
end
session_output_dir = File.join(repo_base_dir, "tmp", "debug")
Dir.mkdir_p(session_output_dir)
session_log = File.join(session_output_dir, File.basename(input, File.extname(input)) + ".lldb-session")
session_assert = File.join(session_output_dir, File.basename(input, File.extname(input)) + ".lldb-assert")
File.open(session_assert, "w") do |assert|
each_line1(input) do |line|
if md = line.match(/# lldb-command: (.*)/)
assert.puts "CHECK: (lldb) #{md[1]}"
elsif md = line.match(/# lldb-check: (.*)/)
assert.puts "CHECK-NEXT: #{md[1]}"
end
end
end
`/usr/bin/lldb -b --source #{debugger_script} #{bin} > #{session_log}`
`FileCheck #{session_assert} < #{session_log}`
exit $?.exit_code
| Crystal | 3 | jessedoyle/crystal | spec/debug/driver.cr | [
"Apache-2.0"
] |
<%= "evaluated string" %> | Gosu | 0 | tcmoore32/sheer-madness | gosu-test/src/test/gosu/gw/internal/gosu/template/NoArgEval.gst | [
"Apache-2.0"
] |
Button {
background-color: transparent;
border-color: transparent;
border-width: 1;
text-transform: capitalize;
android-elevation: 0;
android-dynamic-elevation-offset: 0;
padding: 0;
margin: 0;
}
.component-label{
margin-left: 12;
min-width: 100;
}
.component-select-fix{
padding-top: 6;
text-align: right;
vertical-align: middle;
padding-right: 8;
}
.header{
font-size: 20px;
font-weight: bold;
}
.code-text-view-fix{
font-size: 15px;
}
.go-back{
font-family: "ns-playground-font";
font-size: 30;
color: #3350ff;
}
.header-label{
padding-top: 8%;
padding-left: 40%;
font-size: 20px;
color: black;
}
.components-header-label{
padding-top: 8%;
text-align: center;
font-size: 20px;
color: black;
}
.components-link{
color: #3350ff;
font-size: 20px;
padding-top: 8%;
margin-left: -25px;
}
.navigation-bar{
background-color: #f4f4f5;
height: 5%;
max-height: 3;
}
.navigation-bar-components{
background-color: #f4f4f5;
height: 8%;
}
.segmented-bar{
background-color: #f4f4f5;
padding-bottom: 10%
}
.custom-segmented-bar-root-fix{
padding-top: 15%;
}
.custom-segmented-bar-border-fix{
border-radius: 15px;
border-width: 5px;
}
.selected-segment{
color: #f4f4f5;
padding-top: 5%;
background-color: #3350ff;
text-align: center;
}
.unselected-segment{
color: #3350ff;
padding-top: 5%;
background-color: #f4f4f5;
text-align: center;
}
.action-item-details{
color: #007aff;
font-size: 20px;
padding-right: 15;
}
.listview-separator{
margin-left: 66;
background-color: #949494;
height: 1px;
}
.icon-around{
background-color: #3350ff;
height: 42;
width: 42;
border-radius: 3;
vertical-align: middle;
text-align: center;
}
.list-view-row{
padding: 6 0 6 12;
}
.list-group{
background-color: white;
padding-top: 6;
}
| CSS | 3 | tralves/NativeScript | apps/toolbox/src/app-platform.android.css | [
"Apache-2.0"
] |
.non-selectable
user-select: none !important
.scroll
overflow: auto
.scroll, .scroll-x, .scroll-y
-webkit-overflow-scrolling: touch
will-change: scroll-position
.scroll-x
overflow-x: auto
.scroll-y
overflow-y: auto
.no-scroll
overflow: hidden !important
.no-pointer-events,
.no-pointer-events--children,
.no-pointer-events--children *
pointer-events: none !important
.all-pointer-events
pointer-events: all !important
.cursor
&-pointer
cursor: pointer !important
&-not-allowed
cursor: not-allowed !important
&-inherit
cursor: inherit !important
&-none
cursor: none !important
[aria-busy='true']
cursor: progress
[aria-controls]
cursor: pointer
[aria-disabled]
cursor: default
| Sass | 3 | ygyg70/quasar | ui/src/css/core/mouse.sass | [
"MIT"
] |
<cfcomponent>
<cffunction name="myFunction" hint="My function">
<cftry>
<!--- do something --->
<cfcatch type="any">
<cfreturn "Error: #CFCATCH.Message#">
</cfcatch>
</cftry>
<cfreturn "Success">
</cffunction>
<cfcomponent> | ColdFusion CFC | 4 | tonym128/CFLint | src/test/resources/com/cflint/tests/GlobalVarChecker/cfcatch_tag.cfc | [
"BSD-3-Clause"
] |
# This is a decimal.
<s> <p> -123.0 .
| Turtle | 0 | joshrose/audacity | lib-src/lv2/serd/tests/TurtleTests/turtle-syntax-number-06.ttl | [
"CC-BY-3.0"
] |
i 00001 00 010 2000 00 011 0000
i 00002 00 27 00013 00 010 2000
i 00003 00 011 2000 00 012 2000
i 00004 00 27 00013 00 010 2001
i 00005 00 011 2001 00 012 2001
i 00006 00 27 00013 00 010 2001
i 00007 00 011 2002 00 27 00013
i 00010 00 010 2001 00 015 2002
i 00011 00 012 2000 00 27 00013
i 00012 06 33 12345 00 22 00000
i 00013 02 33 76543 00 22 00000
d 02000 7777 7777 7777 7777
d 02001 5252 5252 5252 5252
d 02002 2525 2525 2525 2525
| Octave | 1 | besm6/mesm6 | test/aax_aox_aex/aax_aox_aex.oct | [
"MIT"
] |
diff --git a/include/git2/cert.h b/include/git2/cert.h
index e8cd2d180..54293cd31 100644
--- a/include/git2/cert.h
+++ b/include/git2/cert.h
@@ -111,6 +111,14 @@ typedef struct {
* have the SHA-256 hash of the hostkey.
*/
unsigned char hash_sha256[32];
+
+ /**
+ * Hostkey itself.
+ */
+ int hostkey_type;
+ size_t hostkey_len;
+ unsigned char hostkey[1024];
+
} git_cert_hostkey;
/**
diff --git a/src/transports/ssh.c b/src/transports/ssh.c
index f4ed05bb1..ec6366a5f 100644
--- a/src/transports/ssh.c
+++ b/src/transports/ssh.c
@@ -523,6 +523,7 @@ static int _git_ssh_setup_conn(
git_credential *cred = NULL;
LIBSSH2_SESSION* session=NULL;
LIBSSH2_CHANNEL* channel=NULL;
+ char *host_and_port;
t->current_stream = NULL;
@@ -566,6 +567,12 @@ post_extract:
cert.parent.cert_type = GIT_CERT_HOSTKEY_LIBSSH2;
+ key = libssh2_session_hostkey(session, &cert.hostkey_len, &cert.hostkey_type);
+ bzero(&cert.hostkey, sizeof(cert.hostkey));
+ if (cert.hostkey_len > sizeof(cert.hostkey))
+ cert.hostkey_len = sizeof(cert.hostkey);
+ memcpy(&cert.hostkey, key, cert.hostkey_len);
+
#ifdef LIBSSH2_HOSTKEY_HASH_SHA256
key = libssh2_hostkey_hash(session, LIBSSH2_HOSTKEY_HASH_SHA256);
if (key != NULL) {
@@ -597,7 +604,15 @@ post_extract:
cert_ptr = &cert;
- error = t->owner->certificate_check_cb((git_cert *) cert_ptr, 0, urldata.host, t->owner->message_cb_payload);
+ if (atoi(urldata.port) == SSH_DEFAULT_PORT) {
+ host_and_port = urldata.host;
+ } else {
+ size_t n = strlen(urldata.host) + strlen(urldata.port) + 2;
+ host_and_port = alloca(n);
+ sprintf(host_and_port, "%s:%s", urldata.host, urldata.port);
+ }
+
+ error = t->owner->certificate_check_cb((git_cert *) cert_ptr, 0, host_and_port, t->owner->message_cb_payload);
if (error < 0 && error != GIT_PASSTHROUGH) {
if (!git_error_last())
| Diff | 3 | jonas-schulze/julia | deps/patches/libgit2-hostkey.patch | [
"MIT"
] |
#[warn(clippy::double_neg)]
#[allow(clippy::no_effect)]
fn main() {
let x = 1;
-x;
-(-x);
--x;
}
| Rust | 1 | ohno418/rust | src/tools/clippy/tests/ui/double_neg.rs | [
"ECL-2.0",
"Apache-2.0",
"MIT-0",
"MIT"
] |
tell application "Finder"
if not (exists window 1) then
make new Finder window
set target of front window to path to home folder as string
end if
activate
end tell
| AppleScript | 3 | FedorZaytsev/MTMR | MTMR/AppleScripts/Finder.scpt | [
"MIT"
] |
#world {
line-width: 2;
line-color: #024;
}
| CartoCSS | 0 | nimix/carto | test/rendering/issue_394.mss | [
"Apache-2.0"
] |
<GameProjectFile>
<PropertyGroup Type="Node" Name="BagItem" ID="fcd1fab6-83ff-4cfc-84f4-2d8df7a5f1ce" Version="2.0.0.0" />
<Content ctype="GameProjectContent">
<Content>
<Animation Duration="0" Speed="1" />
<ObjectData Name="Node" CanEdit="False" ctype="SingleNodeObjectData">
<Position X="0" Y="0" />
<Scale ScaleX="1" ScaleY="1" />
<AnchorPoint />
<CColor A="255" R="255" G="255" B="255" />
<Size X="0" Y="0" />
<PrePosition X="0" Y="0" />
<PreSize X="0" Y="0" />
<Children>
<NodeObjectData Name="Sprite_1" ActionTag="1045408199" Tag="61" ObjectIndex="1" ctype="SpriteObjectData">
<Position X="0" Y="0" />
<Scale ScaleX="1" ScaleY="1" />
<AnchorPoint />
<CColor A="255" R="255" G="255" B="255" />
<Size X="105" Y="131" />
<PrePosition X="0" Y="0" />
<PreSize X="0" Y="0" />
<FileData Type="Normal" Path="Inventory/rolebg.png" />
</NodeObjectData>
<NodeObjectData Name="Sprite_2" ActionTag="1045408200" Tag="62" ObjectIndex="2" ctype="SpriteObjectData">
<Position X="57.35335" Y="62.94159" />
<Scale ScaleX="1" ScaleY="1" />
<AnchorPoint ScaleX="0.5" ScaleY="0.5" />
<CColor A="255" R="255" G="255" B="255" />
<Size X="112" Y="72" />
<PrePosition X="0" Y="0" />
<PreSize X="0" Y="0" />
<FileData Type="Normal" Path="Inventory/ic_egyviper_blue.png" />
</NodeObjectData>
<NodeObjectData Name="Sprite_3" ActionTag="1045408201" Tag="63" ObjectIndex="3" ctype="SpriteObjectData">
<Position X="45.5882" Y="24.70599" />
<Scale ScaleX="1" ScaleY="1" />
<AnchorPoint ScaleX="0.5" ScaleY="0.5" />
<CColor A="255" R="255" G="255" B="255" />
<Size X="23" Y="25" />
<PrePosition X="0" Y="0" />
<PreSize X="0" Y="0" />
<FileData Type="PlistSubImage" Path="fx_starshining_cell-xingxing.png" Plist="MissionSelect/fx_starshining.plist" />
</NodeObjectData>
<NodeObjectData Name="Sprite_3_Copy" ActionTag="1045408202" Tag="64" ObjectIndex="4" ctype="SpriteObjectData">
<Position X="56.56863" Y="24.70599" />
<Scale ScaleX="1" ScaleY="1" />
<AnchorPoint ScaleX="0.5" ScaleY="0.5" />
<CColor A="255" R="255" G="255" B="255" />
<Size X="23" Y="25" />
<PrePosition X="0" Y="0" />
<PreSize X="0" Y="0" />
<FileData Type="PlistSubImage" Path="fx_starshining_cell-xingxing.png" Plist="MissionSelect/fx_starshining.plist" />
</NodeObjectData>
<NodeObjectData Name="Sprite_3_Copy_Copy" ActionTag="1045408203" Tag="65" ObjectIndex="5" ctype="SpriteObjectData">
<Position X="67.54906" Y="24.70599" />
<Scale ScaleX="1" ScaleY="1" />
<AnchorPoint ScaleX="0.5" ScaleY="0.5" />
<CColor A="255" R="255" G="255" B="255" />
<Size X="23" Y="25" />
<PrePosition X="0" Y="0" />
<PreSize X="0" Y="0" />
<FileData Type="PlistSubImage" Path="fx_starshining_cell-xingxing.png" Plist="MissionSelect/fx_starshining.plist" />
</NodeObjectData>
<NodeObjectData Name="Sprite_3_Copy_Copy_0" ActionTag="1045408204" Tag="66" ObjectIndex="6" ctype="SpriteObjectData">
<Position X="78.5295" Y="24.70599" />
<Scale ScaleX="1" ScaleY="1" />
<AnchorPoint ScaleX="0.5" ScaleY="0.5" />
<CColor A="255" R="255" G="255" B="255" />
<Size X="23" Y="25" />
<PrePosition X="0" Y="0" />
<PreSize X="0" Y="0" />
<FileData Type="PlistSubImage" Path="fx_starshining_cell-xingxing.png" Plist="MissionSelect/fx_starshining.plist" />
</NodeObjectData>
</Children>
</ObjectData>
</Content>
</Content>
</GameProjectFile> | Csound | 3 | chukong/CocosStudioSamples | DemoMicroCardGame/CocosStudioResources/cocosstudio/InventoryItem.csd | [
"MIT"
] |
// run-pass
#![feature(generic_const_exprs)]
#![allow(incomplete_features)]
struct Foo<const B: bool>;
fn test<const N: usize>() -> Foo<{ !(N > 10) }> where Foo<{ !(N > 10) }>: Sized {
Foo
}
fn main() {
let _: Foo<false> = test::<12>();
let _: Foo<true> = test::<9>();
}
| Rust | 3 | mbc-git/rust | src/test/ui/const-generics/generic_const_exprs/unop.rs | [
"ECL-2.0",
"Apache-2.0",
"MIT-0",
"MIT"
] |
-module(bif1).
%% Other set of warnings due to removed of functions from
%% erl_bif_types.
-export([ets_rename/0, string_chars/0]).
ets_rename() ->
A = ets:new(fipp, []),
true = not is_atom(A),
ets:rename(A, fopp). % No warning
string_chars() ->
L2 = bif1_adt:opaque_string(),
S = $A,
string:chars(S, 10, L2). % Warning
| Erlang | 3 | jjhoo/otp | lib/dialyzer/test/small_SUITE_data/src/bif1/bif1.erl | [
"Apache-2.0"
] |
- dashboard: error_overivew
title: Error Overivew
layout: newspaper
elements:
- name: Top Assumed User Types
title: Top Assumed User Types
model: aws_athena_cloudtrail
explore: cloudtrail_logs
type: looker_column
fields:
- cloudtrail_logs.total_errors
- cloudtrail_logs.assumed_user_name
filters:
sorts:
- cloudtrail_logs.total_errors desc
limit: 10
column_limit: 50
stacking: ''
show_value_labels: false
label_density: 25
legend_position: center
x_axis_gridlines: false
y_axis_gridlines: true
show_view_names: false
limit_displayed_rows: false
y_axis_combined: true
show_y_axis_labels: true
show_y_axis_ticks: true
y_axis_tick_density: default
y_axis_tick_density_custom: 5
show_x_axis_label: true
show_x_axis_ticks: true
x_axis_scale: auto
y_axis_scale_mode: linear
ordering: none
show_null_labels: false
show_totals_labels: false
show_silhouette: false
totals_color: "#808080"
series_colors:
cloudtrail_logs.total_errors: "#1f3e5a"
x_axis_label_rotation: -30
colors:
- 'palette: Looker Classic'
series_types:
errors_as_a_percent_of_events: line
hidden_series: []
y_axes:
- label: ''
maxValue:
minValue:
orientation: left
showLabels: true
showValues: true
tickDensity: default
tickDensityCustom: 5
type: linear
unpinAxis: false
valueFormat:
series:
- id: errors_as_a_percent_of_events
name: Errors as a Percent of Events
__FILE: aws_athena_cloudtrail/error_overview.dashboard.lookml
__LINE_NUM: 180
__FILE: aws_athena_cloudtrail/error_overview.dashboard.lookml
__LINE_NUM: 168
- label:
maxValue:
minValue:
orientation: right
showLabels: true
showValues: true
tickDensity: default
tickDensityCustom: 5
type: linear
unpinAxis: false
valueFormat:
series:
- id: total_errors
name: Total Errors
__FILE: aws_athena_cloudtrail/error_overview.dashboard.lookml
__LINE_NUM: 194
__FILE: aws_athena_cloudtrail/error_overview.dashboard.lookml
__LINE_NUM: 182
listen:
Date: cloudtrail_logs.event_time_date
row: 8
col: 15
width: 9
height: 7
- name: Errors by User Type
title: Errors by User Type
model: aws_athena_cloudtrail
explore: cloudtrail_logs
type: looker_pie
fields:
- cloudtrail_logs.total_errors
- cloudtrail_logs.user_type
filters:
sorts:
- cloudtrail_logs.total_errors desc
limit: 10
column_limit: 50
value_labels: legend
label_type: labPer
stacking: ''
show_value_labels: false
label_density: 25
legend_position: center
x_axis_gridlines: false
y_axis_gridlines: true
show_view_names: true
limit_displayed_rows: false
y_axis_combined: true
show_y_axis_labels: true
show_y_axis_ticks: true
y_axis_tick_density: default
y_axis_tick_density_custom: 5
show_x_axis_label: true
show_x_axis_ticks: true
x_axis_scale: auto
y_axis_scale_mode: linear
ordering: none
show_null_labels: false
show_totals_labels: false
show_silhouette: false
totals_color: "#808080"
show_row_numbers: true
truncate_column_names: false
hide_totals: false
hide_row_totals: false
table_theme: gray
enable_conditional_formatting: false
conditional_formatting_ignored_fields: []
conditional_formatting_include_totals: false
conditional_formatting_include_nulls: false
series_types: {}
series_colors:
cloudtrail_logs.total_errors: "#1f3e5a"
AssumedRole: "#1f3e5a"
x_axis_label_rotation: -30
inner_radius: 45
listen:
Date: cloudtrail_logs.event_time_date
row: 8
col: 0
width: 9
height: 7
- name: Errors by Source
title: Errors by Source
model: aws_athena_cloudtrail
explore: cloudtrail_logs
type: table
fields:
- cloudtrail_logs.total_errors
- cloudtrail_logs.event_source
filters:
cloudtrail_logs.total_errors: ">0"
sorts:
- cloudtrail_logs.total_errors desc
limit: 500
column_limit: 50
show_view_names: true
show_row_numbers: true
truncate_column_names: false
hide_totals: false
hide_row_totals: false
table_theme: gray
limit_displayed_rows: false
enable_conditional_formatting: false
conditional_formatting_ignored_fields: []
conditional_formatting_include_totals: false
conditional_formatting_include_nulls: false
stacking: ''
show_value_labels: false
label_density: 25
legend_position: center
x_axis_gridlines: false
y_axis_gridlines: true
y_axis_combined: true
show_y_axis_labels: true
show_y_axis_ticks: true
y_axis_tick_density: default
y_axis_tick_density_custom: 5
show_x_axis_label: true
show_x_axis_ticks: true
x_axis_scale: auto
y_axis_scale_mode: linear
ordering: none
show_null_labels: false
show_totals_labels: false
show_silhouette: false
totals_color: "#808080"
series_types: {}
listen:
Date: cloudtrail_logs.event_time_date
row: 8
col: 9
width: 6
height: 7
- name: Errors and Events Over Time
title: Errors and Events Over Time
model: aws_athena_cloudtrail
explore: cloudtrail_logs
type: looker_column
fields:
- cloudtrail_logs.errors_percent_events
- cloudtrail_logs.total_errors
- cloudtrail_logs.count
- cloudtrail_logs.event_time_minute30
fill_fields:
- cloudtrail_logs.event_time_minute30
sorts:
- cloudtrail_logs.event_time_minute30
limit: 500
column_limit: 50
query_timezone: America/Los_Angeles
stacking: ''
show_value_labels: false
label_density: 25
legend_position: center
x_axis_gridlines: false
y_axis_gridlines: true
show_view_names: false
limit_displayed_rows: false
y_axis_combined: true
show_y_axis_labels: true
show_y_axis_ticks: true
y_axis_tick_density: default
y_axis_tick_density_custom: 5
show_x_axis_label: true
show_x_axis_ticks: true
x_axis_scale: auto
y_axis_scale_mode: linear
ordering: none
show_null_labels: false
show_totals_labels: false
show_silhouette: false
totals_color: "#808080"
show_row_numbers: true
truncate_column_names: false
hide_totals: false
hide_row_totals: false
table_theme: editable
enable_conditional_formatting: false
conditional_formatting_ignored_fields: []
conditional_formatting_include_totals: false
conditional_formatting_include_nulls: false
show_null_points: true
point_style: none
interpolation: linear
series_types:
errors_as_a_percent_of_events: line
cloudtrail_logs.errors_percent_events: line
series_colors:
errors_as_a_percent_of_events: "#a9c574"
total_errors: "#1f3e5a"
cloudtrail_logs.total_errors: "#1f3e5a"
cloudtrail_logs.errors_percent_events: "#a9c574"
cloudtrail_logs.count: "#1f3e5a"
hidden_fields:
- cloudtrail_logs.total_errors
y_axes:
- label:
maxValue:
minValue:
orientation: left
showLabels: true
showValues: true
tickDensity: default
tickDensityCustom:
type: linear
unpinAxis: false
valueFormat:
series:
- id: cloudtrail_logs.errors_percent_events
name: Errors As A Percent Of Events
__FILE: aws_athena_cloudtrail/error_overview.dashboard.lookml
__LINE_NUM: 280
__FILE: aws_athena_cloudtrail/error_overview.dashboard.lookml
__LINE_NUM: 268
- label:
maxValue:
minValue:
orientation: right
showLabels: true
showValues: true
tickDensity: default
tickDensityCustom:
type: linear
unpinAxis: false
valueFormat:
series:
- id: cloudtrail_logs.count
name: Total Events
__FILE: aws_athena_cloudtrail/error_overview.dashboard.lookml
__LINE_NUM: 294
__FILE: aws_athena_cloudtrail/error_overview.dashboard.lookml
__LINE_NUM: 282
hidden_series: []
colors:
- 'palette: Looker Classic'
listen:
Date: cloudtrail_logs.event_time_date
row: 0
col: 0
width: 24
height: 8
- name: Top Events with Errors
title: Top Events with Errors
model: aws_athena_cloudtrail
explore: cloudtrail_logs
type: looker_bar
fields:
- cloudtrail_logs.count
- cloudtrail_logs.event_name
filters:
cloudtrail_logs.errorcode: "-NULL"
cloudtrail_logs.errormessage: "-NULL"
sorts:
- cloudtrail_logs.count desc
limit: 10
column_limit: 50
stacking: ''
show_value_labels: false
label_density: 25
legend_position: center
x_axis_gridlines: false
y_axis_gridlines: true
show_view_names: false
limit_displayed_rows: false
y_axis_combined: true
show_y_axis_labels: true
show_y_axis_ticks: true
y_axis_tick_density: default
y_axis_tick_density_custom: 5
show_x_axis_label: true
show_x_axis_ticks: true
x_axis_scale: auto
y_axis_scale_mode: linear
ordering: none
show_null_labels: false
show_totals_labels: false
show_silhouette: false
totals_color: "#808080"
label: Top AWS Event Errors
show_row_numbers: true
truncate_column_names: false
hide_totals: false
hide_row_totals: false
table_theme: gray
enable_conditional_formatting: false
conditional_formatting_ignored_fields: []
conditional_formatting_include_totals: false
conditional_formatting_include_nulls: false
series_types: {}
series_colors:
cloudtrail_logs.count: "#1f3e5a"
x_axis_label_rotation: -45
listen:
Date: cloudtrail_logs.event_time_date
row: 15
col: 0
width: 12
height: 10
- name: Top Error Codes
title: Top Error Codes
model: aws_athena_cloudtrail
explore: cloudtrail_logs
type: looker_bar
fields:
- cloudtrail_logs.count
- cloudtrail_logs.errorcode
filters:
cloudtrail_logs.errorcode: "-NULL"
cloudtrail_logs.errormessage: "-NULL"
sorts:
- cloudtrail_logs.count desc
limit: 10
column_limit: 50
stacking: ''
show_value_labels: false
label_density: 25
legend_position: center
x_axis_gridlines: false
y_axis_gridlines: true
show_view_names: false
limit_displayed_rows: false
y_axis_combined: true
show_y_axis_labels: true
show_y_axis_ticks: true
y_axis_tick_density: default
y_axis_tick_density_custom: 5
show_x_axis_label: true
show_x_axis_ticks: true
x_axis_scale: auto
y_axis_scale_mode: linear
ordering: none
show_null_labels: false
show_totals_labels: false
show_silhouette: false
totals_color: "#808080"
label: Top AWS Event Errors
show_row_numbers: true
truncate_column_names: false
hide_totals: false
hide_row_totals: false
table_theme: gray
enable_conditional_formatting: false
conditional_formatting_ignored_fields: []
conditional_formatting_include_totals: false
conditional_formatting_include_nulls: false
series_types: {}
series_colors:
cloudtrail_logs.count: "#1f3e5a"
x_axis_label_rotation: -45
listen:
Date: cloudtrail_logs.event_time_date
row: 15
col: 12
width: 12
height: 10
- name: Assumed IAM User Errors (Full Detail)
title: Assumed IAM User Errors (Full Detail)
model: aws_athena_cloudtrail
explore: cloudtrail_logs
type: table
fields:
- cloudtrail_logs.assumed_user_name
- cloudtrail_logs.event_name
- cloudtrail_logs.errorcode
- cloudtrail_logs.errormessage
- cloudtrail_logs.count
- cloudtrail_logs.event_source
filters:
cloudtrail_logs.errorcode: "-NULL"
cloudtrail_logs.count: ">1"
sorts:
- cloudtrail_logs.count desc
limit: 500
column_limit: 50
label: Top AWS Event Errors
show_view_names: false
show_row_numbers: true
truncate_column_names: false
hide_totals: false
hide_row_totals: false
table_theme: gray
limit_displayed_rows: false
enable_conditional_formatting: false
conditional_formatting_ignored_fields: []
conditional_formatting_include_totals: false
conditional_formatting_include_nulls: false
listen:
Date: cloudtrail_logs.event_time_date
row: 25
col: 0
width: 24
height: 8
filters:
- name: Date
title: Date
type: date_filter
default_value: 48 hours
model:
explore:
field:
listens_to_filters: []
allow_multiple_values: true
| LookML | 4 | voltagebots/aws_cloudtrail_block | error_overview.dashboard.lookml | [
"MIT"
] |
<%= render(SharedView, "_drift_js.html") %>
<article class="sponsor_story">
<div class="sponsor_story-content richtext">
<h1>Podcast sponsorship styles</h1>
<h3>Endorsement</h3>
<p>This is our most popular ad style and is read by a member of our ad team. We will take care of all the creative writing based on the goals and strategy we set with you. We can focus on different aspects of the service, a big promotion, an upcoming event you're hosting — or work together to come up with ideas on how to direct people to your current marketing goals and funnels. We like to get creative!</p>
<h3>Insider Story</h3>
<p>Talking to someone inside your company really helps to humanize who you are and allows you tell the developer world who you are in your own words. This prodution is created by having our ad team speak with someone inside your company — an engineer, developer, support, design — really anyone who can speak to the product or service, the work they do, and how that might help the listener to learn more and why they should give it a try. The call to record the initial conversation is around 20-40 minutes.</p>
<h3>Customer Story / Endorsement</h3>
<p>Customer stories are powerful and we are experts at getting your customers talking and sharing details that get the listeners attention. This is a chance to have a future customer hear from one of their peers on why they choose your product or service and why it works for them. This is also a great example of social proof.</p>
<p>This prodution is created by having our ad team speak with one of your customers or users. The person we speak with should be well spoken and can be anyone that is in charge of decisions or someone who's directly impacted by the product or service. The call to record the initial conversation is around 20-40 minutes.</p>
<h3>Team Culture / Hiring</h3>
<p>We're helping engineering teams to tell their story and attract the best talent. We'll work closely with you to determine what the developer community needs to know about your teams and point them in the right direction to learn more and take the first step.</p>
<hr>
</div>
<div class="sponsor_story-examples">
<h3>Sponsorship Examples</h3>
<div class="grid_table">
<div class="grid_table-header">
<div class="grid_table-header-column"><p>Campaign type</p></div>
<div class="grid_table-header-column"><p>Campaign name</p></div>
<div class="grid_table-header-column"><p>Campaign production</p></div>
</div>
<%= for example <- Changelog.SponsorStyle.all() do %>
<div class="grid_table-row">
<div class="grid_table-row-column"><p><%= example.type %></p></div>
<div class="grid_table-row-column"><p><%= example.name %></p></div>
<div class="grid_table-row-column">
<%= render(SharedView, "_mini_player.html", title: example.name, audio: example.audio, duration: example.duration) %>
</div>
</div>
<% end %>
</div>
</div>
</article> | HTML+EEX | 3 | PsOverflow/changelog.com | lib/changelog_web/templates/page/sponsor_styles.html.eex | [
"MIT"
] |
const std = @import("std");
pub fn main() anyerror!void {
std.log.info("All your codebase are belong to us.", .{});
}
test "basic test" {
try std.testing.expectEqual(10, 3 + 7);
}
| Zig | 3 | lukekras/zig | lib/std/special/init-exe/src/main.zig | [
"MIT"
] |
require "spec"
describe "GC" do
it "compiles GC.stats" do
typeof(GC.stats).should eq(GC::Stats)
end
it "raises if calling enable when not disabled" do
expect_raises(Exception, "GC is not disabled") do
GC.enable
end
end
end
| Crystal | 3 | n00p3/crystal | spec/std/gc_spec.cr | [
"Apache-2.0"
] |
module.exports (terms) =
moduleTerm = terms.term {
constructor (statements, global: false, returnLastStatement: false, bodyStatements: nil) =
self.statements = statements
self.isModule = true
self.global = global
self.bodyStatements = (bodyStatements || statements)
generateModule () =
scope = new (terms.SymbolScope (nil))
self.code (
self.statements.generateStatements (scope, global: self.global, inClosure: true)
)
}
module (statements, inScope: true, global: false, returnLastStatement: false, bodyStatements: bodyStatements) =
if (returnLastStatement)
statements.rewriteLastStatementToReturn (async: false)
if (inScope)
scope = terms.closure ([], statements, returnLastStatement: returnLastStatement, redefinesSelf: true, definesModuleConstants: true)
args = [terms.variable (['this'])]
methodCall = terms.methodCall (terms.subExpression (scope), ['call'], args)
call = if (statements.isAsync)
methodCall
else
methodCall
moduleTerm (terms.statements [call], bodyStatements: statements, global: global)
else
moduleTerm (statements, global: global, returnLastStatement: returnLastStatement, bodyStatements: bodyStatements)
| PogoScript | 4 | Sotrek/Alexa | Alexa_Cookbook/Workshop/StatePop/4_IOT/tests/node_modules/aws-sdk/node_modules/cucumber/node_modules/pogo/lib/terms/module.pogo | [
"MIT"
] |
DROP TABLE IF EXISTS `t_user`;
CREATE TABLE `t_user` (
`id` int(11) NOT NULL AUTO_INCREMENT COMMENT '主键',
`username` varchar(32) NOT NULL COMMENT '用户名',
`password` varchar(32) NOT NULL COMMENT '加密后的密码',
`salt` varchar(32) NOT NULL COMMENT '加密使用的盐',
`email` varchar(32) NOT NULL COMMENT '邮箱',
`phone_number` varchar(15) NOT NULL COMMENT '手机号码',
`status` int(2) NOT NULL DEFAULT '1' COMMENT '状态，-1：逻辑删除，0：禁用，1：启用',
`create_time` datetime NOT NULL DEFAULT CURRENT_TIMESTAMP COMMENT '创建时间',
`last_login_time` datetime DEFAULT NULL COMMENT '上次登录时间',
`last_update_time` datetime NOT NULL DEFAULT CURRENT_TIMESTAMP COMMENT '上次更新时间',
PRIMARY KEY (`id`),
UNIQUE KEY `username` (`username`),
UNIQUE KEY `email` (`email`),
UNIQUE KEY `phone_number` (`phone_number`)
) ENGINE=InnoDB AUTO_INCREMENT=3 DEFAULT CHARSET=utf8 COMMENT='1.0-用户表';
| SQL | 4 | zcy2095/spring-boot-demo | demo-flyway/src/main/resources/db/migration/V1_0__INIT.sql | [
"MIT"
] |
(*
Count Messages in All Mailboxes
Copyright 2002-2012 Apple Inc. All rights reserved.
You may incorporate this Apple sample code into your program(s) without
restriction. This Apple sample code has been provided "AS IS" and the
responsibility for its operation is yours. You are not permitted to
redistribute this Apple sample code as "Apple sample code" after having
made changes. If you're going to redistribute the code, we require
that you make it clear that the code was descended from Apple sample
code, but that you've made changes.
*)
(*
This script goes through each mailbox, gets the total message count and
the unread count, then displays the final output in a new email message.
*)
tell application "Mail"
set localMailboxes to every mailbox
if (count of localMailboxes) is greater than 0 then
set messageCountDisplay to "Local mailboxes (On My Mac)" & return & my getMessageCountsForMailboxes(localMailboxes)
else
set messageCountDisplay to ""
end if
set everyAccount to every account
repeat with eachAccount in everyAccount
set accountMailboxes to every mailbox of eachAccount
if (count of accountMailboxes) is greater than 0 then
set messageCountDisplay to messageCountDisplay & return & "Mailboxes for Account: " & name of eachAccount & return & my getMessageCountsForMailboxes(accountMailboxes)
end if
end repeat
set outputMessage to make new outgoing message with properties {content:messageCountDisplay, subject:"Message counts for all my mailboxes", visible:true}
tell outputMessage
set font to "Courier"
set size to 12
end tell
end tell
on getMessageCountsForMailboxes(theMailboxes)
-- (list of mailboxes)
-- returns string
set displayString to ""
tell application "Mail"
repeat with eachMailbox in theMailboxes
set mailboxName to name of eachMailbox
set messageCount to (count of (messages of eachMailbox)) as string
set unreadCount to unread count of eachMailbox as string
set displayString to displayString & " " & my padString(mailboxName, 40) & " " & messageCount & " (" & unreadCount & " unread)" & return
end repeat
end tell
return displayString
end getMessageCountsForMailboxes
on padString(theString, fieldLength)
-- (string, integer)
-- returns string
set stringLength to length of theString
if stringLength is greater than fieldLength then
set paddedString to (text from character 1 to character (fieldLength - 3) of theString) & "..."
else -- stringLength is less than or equal to fieldLength
set paddedString to theString
set paddingLength to fieldLength - stringLength
repeat paddingLength times
set paddedString to paddedString & space
end repeat
end if
return paddedString
end padString | AppleScript | 5 | JavascriptID/sourcerer-app | src/test/resources/samples/langs/AppleScript/Count Messages in All Mailboxes.applescript | [
"MIT"
] |
package com.baeldung.propertyeditor;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
@SpringBootApplication
public class PropertyEditorApplication {
public static void main(String[] args) {
SpringApplication.run(PropertyEditorApplication.class, args);
}
}
| Java | 3 | zeesh49/tutorials | spring-rest/src/main/java/com/baeldung/propertyeditor/PropertyEditorApplication.java | [
"MIT"
] |
/* The characters 'ı' and 'ſ' have lengths 2 */;
/* but their upper case 'I' and 'S" have length 1 */;
/* Code that relies on indices extracted from ToUpper will fail on this table*/;
CREATE TABLE `ı` (
`ſ` varchar(5) NOT NULL
) ENGINE=InnoDB;
| SQL | 3 | imtbkcat/tidb-lightning | lightning/mydump/examples/mocker_test.i-schema.sql | [
"Apache-2.0"
] |
fs=${1%.fs}
# let's *not* delete this directory; it's okay if previously-downloaded
# excess packages hang around in case we need them later.
#rm -rf "$fs"
mkdir -p "$fs"
redo-ifchange debootstrap.options
debootstrap \
--download-only \
--keep-debootstrap-dir \
$(cat debootstrap.options) \
"$fs" >&2
redo-ifchange "$fs/debootstrap/debootstrap.log"
| Stata | 4 | BlameJohnny/redo | docs/cookbook/container/debdownload.fs.do | [
"Apache-2.0"
] |
/*M///////////////////////////////////////////////////////////////////////////////////////
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
// By downloading, copying, installing or using the software you agree to this license.
// If you do not agree to this license, do not download, install,
// copy or use the software.
//
//
// License Agreement
// For Open Source Computer Vision Library
//
// Copyright (C) 2018 Ya-Chiu Wu, all rights reserved.
// Third party copyrights are property of their respective owners.
//
// @Authors
// Ya-Chiu Wu, yacwu@cs.nctu.edu.tw
//
// Redistribution and use in source and binary forms, with or without modification,
// are permitted provided that the following conditions are met:
//
// * Redistribution's of source code must retain the above copyright notice,
// this list of conditions and the following disclaimer.
//
// * Redistribution's in binary form must reproduce the above copyright notice,
// this list of conditions and the following disclaimer in the documentation
// and/or other materials provided with the distribution.
//
// * The name of the copyright holders may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// This software is provided by the copyright holders and contributors "as is" and
// any express or implied warranties, including, but not limited to, the implied
// warranties of merchantability and fitness for a particular purpose are disclaimed.
// In no event shall the Intel Corporation or contributors be liable for any direct,
// indirect, incidental, special, exemplary, or consequential damages
// (including, but not limited to, procurement of substitute goods or services;
// loss of use, data, or profits; or business interruption) however caused
// and on any theory of liability, whether in contract, strict liability,
// or tort (including negligence or otherwise) arising in any way out of
// the use of this software, even if advised of the possibility of such damage.
//
//M*/
#if CN==1
#define T_MEAN float
#define F_ZERO (0.0f)
#define frameToMean(a, b) (b) = *(a);
#define meanToFrame(a, b) *b = convert_uchar_sat(a);
#else
#define T_MEAN float4
#define F_ZERO (0.0f, 0.0f, 0.0f, 0.0f)
#define meanToFrame(a, b)\
b[0] = convert_uchar_sat(a.x); \
b[1] = convert_uchar_sat(a.y); \
b[2] = convert_uchar_sat(a.z);
#define frameToMean(a, b)\
b.x = a[0]; \
b.y = a[1]; \
b.z = a[2]; \
b.w = 0.0f;
#endif
__kernel void knn_kernel(__global const uchar* frame, int frame_step, int frame_offset, int frame_row, int frame_col,
__global const uchar* nNextLongUpdate,
__global const uchar* nNextMidUpdate,
__global const uchar* nNextShortUpdate,
__global uchar* aModelIndexLong,
__global uchar* aModelIndexMid,
__global uchar* aModelIndexShort,
__global uchar* flag,
__global uchar* sample,
__global uchar* fgmask, int fgmask_step, int fgmask_offset,
int nLongCounter, int nMidCounter, int nShortCounter,
float c_Tb, int c_nkNN, float c_tau
#ifdef SHADOW_DETECT
, uchar c_shadowVal
#endif
)
{
int x = get_global_id(0);
int y = get_global_id(1);
if( x < frame_col && y < frame_row)
{
__global const uchar* _frame = (frame + mad24(y, frame_step, mad24(x, CN, frame_offset)));
T_MEAN pix;
frameToMean(_frame, pix);
uchar foreground = 255; // 0 - the pixel classified as background
int Pbf = 0;
int Pb = 0;
uchar include = 0;
int pt_idx = mad24(y, frame_col, x);
int idx_step = frame_row * frame_col;
__global T_MEAN* _sample = (__global T_MEAN*)(sample);
for (uchar n = 0; n < (NSAMPLES) * 3 ; ++n)
{
int n_idx = mad24(n, idx_step, pt_idx);
T_MEAN c_mean = _sample[n_idx];
uchar c_flag = flag[n_idx];
T_MEAN diff = c_mean - pix;
float dist2 = dot(diff, diff);
if (dist2 < c_Tb)
{
Pbf++;
if (c_flag)
{
Pb++;
if (Pb >= c_nkNN)
{
include = 1;
foreground = 0;
break;
}
}
}
}
if (Pbf >= c_nkNN)
{
include = 1;
}
#ifdef SHADOW_DETECT
if (foreground)
{
int Ps = 0;
for (uchar n = 0; n < (NSAMPLES) * 3 ; ++n)
{
int n_idx = mad24(n, idx_step, pt_idx);
uchar c_flag = flag[n_idx];
if (c_flag)
{
T_MEAN c_mean = _sample[n_idx];
float numerator = dot(pix, c_mean);
float denominator = dot(c_mean, c_mean);
if (denominator == 0)
break;
if (numerator <= denominator && numerator >= c_tau * denominator)
{
float a = numerator / denominator;
T_MEAN dD = mad(a, c_mean, -pix);
if (dot(dD, dD) < c_Tb * a * a)
{
Ps++;
if (Ps >= c_nkNN)
{
foreground = c_shadowVal;
break;
}
}
}
}
}
}
#endif
__global uchar* _fgmask = fgmask + mad24(y, fgmask_step, x + fgmask_offset);
*_fgmask = (uchar)foreground;
__global const uchar* _nNextLongUpdate = nNextLongUpdate + pt_idx;
__global const uchar* _nNextMidUpdate = nNextMidUpdate + pt_idx;
__global const uchar* _nNextShortUpdate = nNextShortUpdate + pt_idx;
__global uchar* _aModelIndexLong = aModelIndexLong + pt_idx;
__global uchar* _aModelIndexMid = aModelIndexMid + pt_idx;
__global uchar* _aModelIndexShort = aModelIndexShort + pt_idx;
uchar nextLongUpdate = _nNextLongUpdate[0];
uchar nextMidUpdate = _nNextMidUpdate[0];
uchar nextShortUpdate = _nNextShortUpdate[0];
uchar modelIndexLong = _aModelIndexLong[0];
uchar modelIndexMid = _aModelIndexMid[0];
uchar modelIndexShort = _aModelIndexShort[0];
int offsetLong = mad24(mad24(2, (NSAMPLES), modelIndexLong), idx_step, pt_idx);
int offsetMid = mad24((NSAMPLES)+modelIndexMid, idx_step, pt_idx);
int offsetShort = mad24(modelIndexShort, idx_step, pt_idx);
if (nextLongUpdate == nLongCounter)
{
_sample[offsetLong] = _sample[offsetMid];
flag[offsetLong] = flag[offsetMid];
_aModelIndexLong[0] = (modelIndexLong >= ((NSAMPLES)-1)) ? 0 : (modelIndexLong + 1);
}
if (nextMidUpdate == nMidCounter)
{
_sample[offsetMid] = _sample[offsetShort];
flag[offsetMid] = flag[offsetShort];
_aModelIndexMid[0] = (modelIndexMid >= ((NSAMPLES)-1)) ? 0 : (modelIndexMid + 1);
}
if (nextShortUpdate == nShortCounter)
{
_sample[offsetShort] = pix;
flag[offsetShort] = include;
_aModelIndexShort[0] = (modelIndexShort >= ((NSAMPLES)-1)) ? 0 : (modelIndexShort + 1);
}
}
}
__kernel void getBackgroundImage2_kernel(__global const uchar* flag,
__global const uchar* sample,
__global uchar* dst, int dst_step, int dst_offset, int dst_row, int dst_col)
{
int x = get_global_id(0);
int y = get_global_id(1);
if(x < dst_col && y < dst_row)
{
int pt_idx = mad24(y, dst_col, x);
T_MEAN meanVal = (T_MEAN)F_ZERO;
__global T_MEAN* _sample = (__global T_MEAN*)(sample);
int idx_step = dst_row * dst_col;
for (uchar n = 0; n < (NSAMPLES) * 3 ; ++n)
{
int n_idx = mad24(n, idx_step, pt_idx);
uchar c_flag = flag[n_idx];
if(c_flag)
{
meanVal = _sample[n_idx];
break;
}
}
__global uchar* _dst = dst + mad24(y, dst_step, mad24(x, CN, dst_offset));
meanToFrame(meanVal, _dst);
}
}
| OpenCL | 4 | thisisgopalmandal/opencv | modules/video/src/opencl/bgfg_knn.cl | [
"BSD-3-Clause"
] |
D:/gitee/open/tinyriscv/tests/riscv-compliance/build_generated/rv32i/I-ECALL-01.elf: file format elf32-littleriscv
Disassembly of section .text.init:
00000000 <_start>:
0: 04c0006f j 4c <reset_vector>
00000004 <trap_vector>:
4: 34202f73 csrr t5,mcause
8: 00800f93 li t6,8
c: 03ff0a63 beq t5,t6,40 <write_tohost>
10: 00900f93 li t6,9
14: 03ff0663 beq t5,t6,40 <write_tohost>
18: 00b00f93 li t6,11
1c: 03ff0263 beq t5,t6,40 <write_tohost>
20: 00000f17 auipc t5,0x0
24: fe0f0f13 addi t5,t5,-32 # 0 <_start>
28: 000f0463 beqz t5,30 <trap_vector+0x2c>
2c: 000f0067 jr t5
30: 34202f73 csrr t5,mcause
34: 000f5463 bgez t5,3c <handle_exception>
38: 0040006f j 3c <handle_exception>
0000003c <handle_exception>:
3c: 5391e193 ori gp,gp,1337
00000040 <write_tohost>:
40: 00001f17 auipc t5,0x1
44: fc3f2023 sw gp,-64(t5) # 1000 <tohost>
48: ff9ff06f j 40 <write_tohost>
0000004c <reset_vector>:
4c: 00000193 li gp,0
50: 00000297 auipc t0,0x0
54: fb428293 addi t0,t0,-76 # 4 <trap_vector>
58: 30529073 csrw mtvec,t0
5c: 30005073 csrwi mstatus,0
60: 00000297 auipc t0,0x0
64: 02028293 addi t0,t0,32 # 80 <begin_testcode>
68: 34129073 csrw mepc,t0
6c: 00000293 li t0,0
70: 10000337 lui t1,0x10000
74: 01030313 addi t1,t1,16 # 10000010 <_end+0xfffde0c>
78: 00532023 sw t0,0(t1)
7c: 30200073 mret
00000080 <begin_testcode>:
80: 00000097 auipc ra,0x0
84: 02c08093 addi ra,ra,44 # ac <_trap_handler>
88: 30509ff3 csrrw t6,mtvec,ra
8c: 00002097 auipc ra,0x2
90: f7408093 addi ra,ra,-140 # 2000 <begin_signature>
94: 11111137 lui sp,0x11111
98: 11110113 addi sp,sp,273 # 11111111 <_end+0x1110ef0d>
9c: 00000073 ecall
a0: 0000a023 sw zero,0(ra)
a4: 305f9073 csrw mtvec,t6
a8: 0280006f j d0 <test_end>
000000ac <_trap_handler>:
ac: 34102f73 csrr t5,mepc
b0: 004f0f13 addi t5,t5,4
b4: 341f1073 csrw mepc,t5
b8: 34202f73 csrr t5,mcause
bc: 01e0a023 sw t5,0(ra)
c0: 0020a223 sw sp,4(ra)
c4: 0000a423 sw zero,8(ra)
c8: 00c08093 addi ra,ra,12
cc: 30200073 mret
000000d0 <test_end>:
d0: 00002297 auipc t0,0x2
d4: f3028293 addi t0,t0,-208 # 2000 <begin_signature>
d8: 10000337 lui t1,0x10000
dc: 00830313 addi t1,t1,8 # 10000008 <_end+0xfffde04>
e0: 00532023 sw t0,0(t1)
e4: 00002297 auipc t0,0x2
e8: f2c28293 addi t0,t0,-212 # 2010 <end_signature>
ec: 10000337 lui t1,0x10000
f0: 00c30313 addi t1,t1,12 # 1000000c <_end+0xfffde08>
f4: 00532023 sw t0,0(t1)
f8: 00100293 li t0,1
fc: 10000337 lui t1,0x10000
100: 01030313 addi t1,t1,16 # 10000010 <_end+0xfffde0c>
104: 00532023 sw t0,0(t1)
108: 00000013 nop
10c: 00100193 li gp,1
110: 00000073 ecall
00000114 <end_testcode>:
114: c0001073 unimp
...
Disassembly of section .tohost:
00001000 <tohost>:
...
00001100 <fromhost>:
...
Disassembly of section .data:
00002000 <begin_signature>:
2000: ffff 0xffff
2002: ffff 0xffff
2004: ffff 0xffff
2006: ffff 0xffff
2008: ffff 0xffff
200a: ffff 0xffff
200c: ffff 0xffff
200e: ffff 0xffff
00002010 <end_signature>:
...
00002100 <begin_regstate>:
2100: 0080 addi s0,sp,64
...
00002200 <end_regstate>:
2200: 0004 0x4
...
| ObjDump | 3 | DuBirdFly/TinyRISCV_Learn | tests/riscv-compliance/build_generated/rv32i/I-ECALL-01.elf.objdump | [
"Apache-2.0"
] |
a:after { content: '\invalid' } | CSS | 0 | vjpr/swc | css/parser/tests/fixture/esbuild/misc/Q_wA-fPw3o2m3R7gyWNxbQ/input.css | [
"Apache-2.0",
"MIT"
] |
POST /upload HTTP/1.1
Host: localhost:8080
Content-Type: multipart/form-data; boundary=----TLV0SrKD4z1TRxRhAPUvZ
Content-Length: 31
------TLV0SrKD4z1TRxRhAPUvZ--
| HTTP | 2 | xifeiwu/node-formidable | test/fixture/http/misc/empty-multipart2.http | [
"MIT"
] |
# Package 'sri24-atlas' is not installed, so not removed
# Package 'libatlas-cpp-0.6-0-dev' is not installed, so not removed
# Package 'libatlas.so.3gf' is not installed, so not removed
# Package 'matlab-dev' is not installed, so not removed
# Package 'matlab-spm8' is not installed, so not removed
# Package 'fsl-atlases' is not installed, so not removed
# Package 'libatlas3gf-sse' is not installed, so not removed
# Package 'libatlas3gf-sse2' is not installed, so not removed
# Package 'libatlas3gf-3dnow' is not installed, so not removed
# Package 'libatlas-sse-dev' is not installed, so not removed
# Package 'libatlas-sse2-dev' is not installed, so not removed
# Package 'libatlas-3dnow-dev' is not installed, so not removed
# Package 'matlab' is not installed, so not removed
# Package 'gtkatlantic' is not installed, so not removed
# Package 'libatlas-cpp-0.6-1' is not installed, so not removed
# Package 'libatlas-cpp-0.6-1-dbg' is not installed, so not removed
# Package 'libatlas-cpp-0.6-dev'
#
#
# This file provides configuration information about non-Python dependencies for
# numpy.distutils-using packages. Create a file like this called "site.cfg" next
# to your package's setup.py file and fill in the appropriate sections. Not all
# packages will use all sections so you should leave out sections that your
# package does not use.
# To assist automatic installation like easy_install, the user's home directory
# will also be checked for the file ~/.numpy-site.cfg .
# The format of the file is that of the standard library's ConfigParser module.
#
# http://www.python.org/doc/current/lib/module-ConfigParser.html
#
# Each section defines settings that apply to one particular dependency. Some of
# the settings are general and apply to nearly any section and are defined here.
# Settings specific to a particular section will be defined near their section.
#
# libraries
# Comma-separated list of library names to add to compile the extension
# with. Note that these should be just the names, not the filenames. For
# example, the file "libfoo.so" would become simply "foo".
# libraries = lapack,f77blas,cblas,atlas
#
# library_dirs
# List of directories to add to the library search path when compiling
# extensions with this dependency. Use the character given by os.pathsep
# to separate the items in the list. Note that this character is known to
# vary on some unix-like systems; if a colon does not work, try a comma.
# This also applies to include_dirs and src_dirs (see below).
# On UN*X-type systems (OS X, most BSD and Linux systems):
# library_dirs = /usr/lib:/usr/local/lib
# On Windows:
# library_dirs = c:\mingw\lib,c:\atlas\lib
# On some BSD and Linux systems:
# library_dirs = /usr/lib,/usr/local/lib
#
# include_dirs
# List of directories to add to the header file earch path.
# include_dirs = /usr/include:/usr/local/include
#
# src_dirs
# List of directories that contain extracted source code for the
# dependency. For some dependenciPackage 'sri24-atlas' is not installed, so not removed
Package 'libatlas-cpp-0.6-0-dev' is not installed, so not removed
Package 'libatlas.so.3gf' is not installed, so not removed
Package 'matlab-dev' is not installed, so not removed
Package 'matlab-spm8' is not installed, so not removed
Package 'fsl-atlases' is not installed, so not removed
Package 'libatlas3gf-sse' is not installed, so not removed
Package 'libatlas3gf-sse2' is not installed, so not removed
Package 'libatlas3gf-3dnow' is not installed, so not removed
Package 'libatlas-sse-dev' is not installed, so not removed
Package 'libatlas-sse2-dev' is not installed, so not removed
Package 'libatlas-3dnow-dev' is not installed, so not removed
Package 'matlab' is not installed, so not removed
Package 'gtkatlantic' is not installed, so not removed
Package 'libatlas-cpp-0.6-1' is not installed, so not removed
Package 'libatlas-cpp-0.6-1-dbg' is not installed, so not removed
Package 'libatlas-cpp-0.6-dev' es, numpy.distutils will be able to build
# them from source if binaries cannot be found. The FORTRAN BLAS and
# LAPACK libraries are one example. However, most dependencies are more
# complicated and require actual installation that you need to do
# yourself.
# src_dirs = /home/rkern/src/BLAS_SRC:/home/rkern/src/LAPACK_SRC
#
# search_static_first
# Boolean (one of (0, false, no, off) for False or (1, true, yes, on) for
# True) to tell numpy.distutils to prefer static libraries (.a) over
# shared libraries (.so). It is turned off by default.
# search_static_first = false
# Defaults
# ========
# The settings given here will apply to all other sections if not overridden.
# This is a good place to add general library and include directories like
# /usr/local/{lib,include}
#
[DEFAULT]
library_dirs = /usr/local/atlas/lib
include_dirs = /usr/local/atlas/include
[atlas]
search_static_first = true
libraries = lapack,ptf77blas,ptcblas,atlas,satlas,tatlas,atlas,cblas,f77blas,lapack,ptf77blas,ptcblas
library_dirs = /usr/local/atlas/lib
include_dirs = /usr/local/atlas/include
# OpenBLAS
# --------
# OpenBLAS is another open source optimized implementation of BLAS and Lapack
# and can be seen as an alternative to Atlas. To build numpy against OpenBLAS
# instead of Atlas, use this section instead of the above, adjusting as needed
# for your configuration (in the following example we installed OpenBLAS with
# ``make install PREFIX=/opt/OpenBLAS``.
#
# **Warning**: OpenBLAS, by default, is built in multithreaded mode. Due to the
# way Python's multiprocessing is implemented, a multithreaded OpenBLAS can
# cause programs using both to hang as soon as a worker process is forked on
# POSIX systems (Linux, Mac).
# This is fixed in Openblas 0.2.9 for the pthread build, the OpenMP build using
# GNU openmp is as of gcc-4.9 not fixed yet.
# Python 3.4 will introduce a new feature in multiprocessing, called the
# "forkserver", which solves this problem. For older versions, make sure
# OpenBLAS is built using pthreads or use Python threads instead of
# multiprocessing.
# (This problem does not exist with multithreaded ATLAS.)
#
# http://docs.python.org/3.4/library/multiprocessing.html#contexts-and-start-methods
# https://github.com/xianyi/OpenBLAS/issues/294
#
#[openblas]
#search_static_first = false
#libraries = openblas
#library_dirs = /opt/openblas/lib
#include_dirs = /opt/openblas/include
#
# MKL
#----
# MKL is Intel's very optimized yet proprietary implementation of BLAS and
# Lapack.
# For recent (9.0.21, for example) mkl, you need to change the names of the
# lapack library. Assuming you installed the mkl in /opt, for a 32 bits cpu:
# [mkl]
# library_dirs = /opt/intel/mkl/9.1.023/lib/32/
# lapack_libs = mkl_lapack
#
# For 10.*, on 32 bits machines:
#[mkl]
#library_dirs = /opt/intel/mkl/lib/intel64
#include_dirs = /opt/intel/mkl/include
#lapack_libs = mkl_lapack
#blas_libs = mkl_blas95, mkl_blas
#mkl_libs = mkl
# UMFPACK
# -------
# The UMFPACK library is used in scikits.umfpack to factor large sparse matrices.
# It, in turn, depends on the AMD library for reordering the matrices for
# better performance. Note that the AMD library has nothing to do with AMD
# (Advanced Micro Devices), the CPU company.
#
# UMFPACK is not used by numpy.
#
# http://www.cise.ufl.edu/research/sparse/umfpack/
# http://www.cise.ufl.edu/research/sparse/amd/
# http://scikits.appspot.com/umfpack
#
#[amd]
#amd_libs = amd
#
#[umfpack]
#umfpack_libs = umfpack
# FFT libraries
# -------------
# There are two FFT libraries that we can configure here: FFTW (2 and 3) and djbfft.
# Note that these libraries are not used by for numpy or scipy.
#
# http://fftw.org/
# http://cr.yp.to/djbfft.html
#
# Given only this section, numpy.distutils will try to figure out which version
# of FFTW you are using.
#[fftw]
#libraries = fftw3
#
# For djbfft, numpy.distutils will look for either djbfft.a or libdjbfft.a .
#[djbfft]
#include_dirs = /usr/local/djbfft/include
#library_dirs = /usr/local/djbfft/lib
| NumPy | 4 | JoeSuber/OpenCV-Max-Build-Package- | vital.config/site.cfg.numpy | [
"Intel"
] |
Complete the :pep:`654` implementation: add ``except*``. | reStructuredText | 5 | lostbeta/cpython | Misc/NEWS.d/next/Core and Builtins/2021-11-22-13-05-32.bpo-45292.pfEouJ.rst | [
"0BSD"
] |
---
title: "rgdal - vector tutorial"
author: "Paulo Arevalo"
date: "January 25, 2016"
output: html_document
---
##Objectives
The objective of this tutorial is to show some basic functionality of the rgdal package to deal with vector data in R. This tutorial assumes that GDAL is properly installed in the system. For options depending on which OS you are using, you can check [here](https://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries)
##Installing and loading the library
The package can be installled and loaded using the following commands. Note that the CRAN mirror is used as an example, but you might want to change it depending on your location.
```{r, message=FALSE}
#install.packages("rgdal", repos='http://cran.us.r-project.org')
library(rgdal)
```
##Loading an example dataset and obtaining information
This layer contains polygons with multiple land cover classes. They could be used as training data for land cover classification. We can use the following commands to download the file from Github:
```{r}
if (file.exists('training_data.shp') == F) {
download.file(url = 'https://raw.githubusercontent.com/parevalo/EF_Activities/master/rgdal-vector_tutorial_shp.zip',
destfile = 'rgdal-vector_tutorial_shp.zip', method = 'auto')
unzip('rgdal-vector_tutorial_shp.zip')
}
```
In order to read the dataset, we use the `readOGR` function.
```{r}
training <- readOGR('training_data.shp', layer='training_data')
```
The function `summary` shows detailed information about the object we just read into R:
```{r}
summary(training)
```
The file has three fields, corresponding to "id" (sequential number), "class" (which is numerical, for now) and "Comment", which is a string field. You can also see the extent coordinates and the spatial projection. If we only want to see information contained in the attribute table we could use:
```{r}
head(training@data)
```
We can also see the overall structure of the file, if we need to use other information from it:
```{r}
str(training, max.level = 2)
```
##Modifying data
We can alter the attribute table almost the same way we would with a regular dataframe:
```{r}
lut <- data.frame(classes=c(1,2,3,4,5,6), labels=c("Forest", "Grasslands", "Shrublands", "Croplands", "Secondary", "Water"))
training@data$label <- lut$labels[match(training@data$Class,lut$classes)]
head(training@data)
```
In this case we created a new column, and assign it the string values using a lookup table.
## Reprojection
We can use the function `spTransform` in order to reproject our shapefile to a different coordinate system. In our case, we can reproject from a plane cordinate system to a geographic (lat-long) coordinate system
```{r}
training@proj4string # We check the proj. system
training_wgs84 <- spTransform(training, CRS("+proj=longlat +datum=WGS84")) # Reprojection
training_wgs84@proj4string # We check the proj. system again
```
## Plotting
Plotting is very simple, we can use the `plot` command, and color the polygons according to the class they belong to:
```{r}
plot(training, col=unique(training@data$Class))
```
We could manually modify the fill color and other graphic properties using additional options in the plot function. We can also plot the file along with other datasets, such as a raster stack. In order to do that, we will download an example raster and then we will do the plotting on top of it. These two files are in the same projection, but reprojection would be needed otherwise.
```{r}
library(raster)
if (file.exists('LE70070592003004_clip.tif') == F) {
download.file(url='https://www.dropbox.com/s/odoeqge9277io6i/LE70070592003004_clip.tif?dl=1',
destfile='LE70070592003004_clip.tif', method='auto', mode='wb')
}
example_raster <- brick('LE70070592003004_clip.tif')
plotRGB(example_raster, stretch="lin")
plot(training, col=unique(training@data$Class), add=T)
```
## Conversion between formats
Conversion to another file format (e.g. KML) is done using the function `writeOGR`:
```{r}
writeOGR(training_wgs84, dsn = "training_wgs84.kml", layer = "training_wgs84", driver = "KML")
``` | RMarkdown | 5 | klreinl/EF_Course | tutorials/rgdal-vector_tutorial.rmd | [
"MIT"
] |
⍝ Standard way to calculate the Euclidean distance
⍝ (As the sqrt of the sum of the square difference)
euclidean_distance ← {
(+/(⍺ - ⍵) * 2) * ÷ 2
}
⍝ Using the Euclidean Norm to calculate the distance.
⍝ Since the distance between 2 Points is only the length of the difference.
euclidean_distance_via_norm ← {
euclidean_norm ⍺ - ⍵
}
⍝ This function is only used in one calculation of the euclidean distance
⍝ You can find it here: https://github.com/kennyledet/Algorithm-Implementations/blob/master/Euclidean_Norm/APL/jcla1/euclidean_norm.apl
euclidean_norm ← {
(+/⍵ × ⍵) * ÷ 2
} | APL | 4 | Mynogs/Algorithm-Implementations | Euclidean_distance/APL/jcla1/euclidean_distance.apl | [
"MIT"
] |
size: 2048px 1024px;
dpi: 240;
limit-x: 1404278100 1404299700;
axes {
label-format-left: scientific();
title-left: "Value";
title-font-size-left: 14pt;
label-format-right: scientific();
title-right: "Value";
title-rotate-right: 90;
title-font-size-right: 14pt;
label-format-top: datetime("%H:%M");
title-top: "Time";
title-font-size-top: 14pt;
label-format-bottom: datetime("%H:%M");
title-bottom: "Time";
title-font-size-bottom: 14pt;
}
lines {
data-x: csv("test/testdata/measurement.csv" time);
data-y: csv("test/testdata/measurement.csv" value1);
}
| CLIPS | 3 | asmuth-archive/travistest | test/examples/charts_custom_axis_titles.clp | [
"Apache-2.0"
] |
/*---------------------------------------------------------------------------------------------
* Copyright (c) Microsoft Corporation. All rights reserved.
* Licensed under the MIT License. See License.txt in the project root for license information.
*--------------------------------------------------------------------------------------------*/
declare module 'vscode' {
// https://github.com/microsoft/vscode/issues/145307
export interface Extension<T> {
/**
* `true` when the extension is associated to another extension host.
*
* *Note* that an extension from another extension host cannot export
* API, e.g {@link Extension.exports its exports} are always `undefined`.
*/
readonly isFromDifferentExtensionHost: boolean;
}
export namespace extensions {
/**
* Get an extension by its full identifier in the form of: `publisher.name`.
*
* @param extensionId An extension identifier.
* @param includeDifferentExtensionHosts Include extensions from different extension host
* @return An extension or `undefined`.
*/
export function getExtension<T = any>(extensionId: string, includeDifferentExtensionHosts: boolean): Extension<T> | undefined;
/**
* All extensions across all extension hosts.
*
* @see {@link Extension.isFromDifferentExtensionHost}
*/
export const allAcrossExtensionHosts: readonly Extension<void>[];
}
}
| TypeScript | 4 | w0lramD/vscode | src/vscode-dts/vscode.proposed.extensionsAny.d.ts | [
"MIT"
] |
<div class="capability-element">
<h4 class="capability-title">{{ c-title }}</h4>
<div class="capability-copy">{{ c-copy }}</div>
</div> | Liquid | 1 | noahcb/lit | website/src/_includes/partials/capability-element.liquid | [
"Apache-2.0"
] |
package {
import GZ.Gfx.Shape;
import GZ.Gfx.Object;
import GZ.File.RcImg;
public class GpuObject {
public function GpuObject( ):Void;
public function fIniRender():Void;
public function fFinishRender():Void;
public function fDraw( _oSource : Object, _nX_Start : Int, _nX_End : Int, _nY_Start : Int, _nY_End : Int):Void;
static public function fLoadImg(_aImg : CArray<Int, 1>, _nWidth : Int, _nHeight : Int):UInt32;
}
} | Redcode | 4 | VLiance/GZE | src/SubLib_System/Lib_GzWeb_Emsc/WebGL/Sys/GpuObj/GpuObject.cw | [
"Apache-2.0"
] |
import "m2" as x;
def f: 42 | x::g;
| JSONiq | 1 | Abhibob/gojq | cli/testdata/m1/m1.jq | [
"MIT"
] |
module openconfig-sampling-sflow {
yang-version "1";
// namespace
namespace "http://openconfig.net/yang/sampling/sflow";
prefix "oc-sflow";
// import some basic types
import openconfig-extensions { prefix oc-ext; }
import openconfig-inet-types { prefix oc-inet; }
import openconfig-interfaces { prefix oc-if; }
import openconfig-yang-types { prefix oc-yang; }
import openconfig-network-instance { prefix oc-netinst; }
// meta
organization "OpenConfig working group";
contact
"OpenConfig working group
www.openconfig.net";
description
"This module defines configuration and operational state data
related to data plane traffic sampling based on sFlow.
RFC 3176 - InMon Corporation's sFlow: A Method for
Monitoring Traffic in Switched and Routed Networks";
oc-ext:openconfig-version "0.1.0";
revision "2020-06-26" {
description
"Initial revision";
reference "0.1.0";
}
grouping sflow-interfaces-config {
description
"Configuration data for sFlow data on interfaces.";
leaf name {
type oc-if:base-interface-ref;
description
"Reference to the interface for sFlow configuration and
state.";
}
leaf enabled {
type boolean;
description
"Enables or disables sFlow on the interface. If sFlow is
globally disabled, this leaf is ignored. If sFlow
is globally enabled, this leaf may be used to disable it
for a specific interface.";
}
leaf sampling-rate {
type uint32;
description
"If sFlow is enabled on the interface, this leaf may be
used to override the global sampling rate for a specific
interface. The sampling rate semantics are the same as the
system-wide leaf.";
}
}
grouping sflow-interfaces-state {
description
"Operational state data for sFlow data on interfaces";
leaf packets-sampled {
type oc-yang:counter64;
description
"Total number of packets sampled from the interface.";
}
}
grouping sflow-interfaces-top {
description
"Top-level grouping for sFlow data on an interface.";
container interfaces {
description
"Enclosing container for list of sFlow interfaces.";
list interface {
key "name";
description
"List of interfaces with sFlow data.";
leaf name {
type leafref {
path "../config/name";
}
description
"Reference to list key.";
}
container config {
description
"Configuration data for sFlow data on interfaces.";
uses sflow-interfaces-config;
}
container state {
config false;
description
"Operational state data for sFlow data on interfaces.";
uses sflow-interfaces-config;
uses sflow-interfaces-state;
}
}
}
}
grouping sflow-collectors-config {
description
"Configuration data for sFlow collectors.";
leaf address {
type oc-inet:ip-address;
description
"IP address of the sFlow collector.";
}
leaf port {
type oc-inet:port-number;
default 6343;
description
"UDP port number for the sFlow collector.";
}
leaf network-instance {
type oc-netinst:network-instance-ref;
description
"Reference to the network instance used to reach the
sFlow collector. If uspecified, the collector destination
is reachable in the default network instance.";
}
}
grouping sflow-collectors-state {
description
"Operational state data for sFlow collectors.";
leaf packets-sent {
type oc-yang:counter64;
description
"The total number of packets sampled and sent to the
collector.";
}
}
grouping sflow-collectors-top {
description
"Top-level grouping for data related to sFlow collectors.";
container collectors {
description
"Enclosing container for list of sFlow collectors.";
list collector {
key "address port";
description
"List of sFlow collectors to send sampling data. Packet
samples are sent to all collectors specified.";
leaf address {
type leafref {
path "../config/address";
}
description
"Reference to address list key.";
}
leaf port {
type leafref {
path "../config/port";
}
description
"Reference to port list key.";
}
container config {
description
"Configuration data for sFlow collectors.";
uses sflow-collectors-config;
}
container state {
config false;
description
"Operational state data for sFlow collectors.";
uses sflow-collectors-config;
uses sflow-collectors-state;
}
}
}
}
grouping sflow-global-config {
description
"Configuration data for global sflow";
leaf enabled {
type boolean;
default false;
description
"Enables or disables sFlow sampling for the device.";
}
leaf source-address {
type oc-inet:ip-address;
description
"Sets the source IP address for sFlow datagrams sent to
sFlow collectors.";
}
leaf sampling-rate {
type uint32;
description
"Sets the global packet sampling rate. The rate is
is expressed as an integer N, where the intended sampling
rate is 1/N packets. An implementation may implement the
sampling rate as a statistical average, rather than a strict
periodic sampling.
The allowable sampling rate range is generally a
property of the system, e.g., determined by the
capability of the hardware.";
}
leaf sample-size {
type uint16;
units bytes;
default 128;
description
"Sets the maximum number of bytes to be copied from a
sampled packet.";
reference
"RFC 3176 - InMon Corporation's sFlow: A Method for
Monitoring Traffic in Switched and Routed Networks";
}
}
grouping sflow-global-state {
description
"Operational state data for global sFlow.";
}
grouping sflow-global-top {
description
"Top-level grouping for global sFlow";
container sflow {
description
"Top-level container for sFlow data.";
container config {
description
"Configuration data for global sFlow.";
uses sflow-global-config;
}
container state {
config false;
description
"Operational state data for global sFlow.";
uses sflow-global-config;
uses sflow-global-state;
}
uses sflow-collectors-top;
uses sflow-interfaces-top;
}
}
grouping sampling-top {
description
"Top-level grouping for traffic sampling data.";
container sampling {
description
"Top-level container for data related to traffic sampling
protocols.";
uses sflow-global-top;
}
}
// data definition statements
uses sampling-top;
}
| YANG | 5 | wenovus/public | release/models/sampling/openconfig-sampling-sflow.yang | [
"Apache-2.0"
] |
Add Trove classifier and create binary wheels for 3.10. -- :user:`hugovk`.
| Cucumber | 1 | loven-doo/aiohttp | CHANGES/6079.feature | [
"Apache-2.0"
] |
pub trait Array {
type Element;
}
pub trait Visit {
fn visit() {}
}
impl Array for () {
type Element = ();
}
impl<'a> Visit for () where
(): Array<Element=&'a ()>,
{}
fn main() {
<() as Visit>::visit(); //~ ERROR: type mismatch resolving
}
| Rust | 4 | Eric-Arellano/rust | src/test/ui/associated-types/issue-44153.rs | [
"ECL-2.0",
"Apache-2.0",
"MIT-0",
"MIT"
] |
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