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testbed/biopragmatics__bioregistry/.github/workflows/docker.yml

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+name: Build and Push to Dockerhub
+
+on:
+  workflow_dispatch:
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          # See: https://github.com/docker/build-push-action/blob/master/docs/advanced/multi-platform.md
+          platforms: linux/amd64,linux/arm64
+          tags: biopragmatics/bioregistry:latest
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

testbed/biopragmatics__bioregistry/.readthedocs.yml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  apt_packages:
+    - graphviz
+  tools:
+    python: "3.12"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - gha
+        - align
+        - export
+        - charts
+        - web

testbed/biopragmatics__bioregistry/CITATION.cff

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+cff-version: 1.2.0
+message: Please cite the Bioregistry manuscript when using this software.
+type: article
+authors:
+- family-names: "Hoyt"
+  given-names: "Charles Tapley"
+  orcid: "https://orcid.org/0000-0003-4423-4370"
+- family-names: "Balk"
+  given-names: "Meghan"
+  orcid: "https://orcid.org/0000-0003-2699-3066"
+- family-names: "Callahan"
+  given-names: "Tiffany J."
+  orcid: "https://orcid.org/0000-0002-8169-9049"
+- family-names: "Domingo-Fernandez"
+  given-names: "Daniel"
+  orcid: "https://orcid.org/0000-0002-2046-6145"
+- family-names: "Haendel"
+  given-names: "Melissa A."
+  orcid: "https://orcid.org/0000-0001-9114-8737"
+- family-names: "Hegde"
+  given-names: "Harshad B."
+  orcid: "https://orcid.org/0000-0002-2411-565X"
+- family-names: "Himmelstein"
+  given-names: "Daniel S."
+  orcid: "https://orcid.org/0000-0002-3012-7446"
+- family-names: "Karis"
+  given-names: "Klas"
+  orcid: "https://orcid.org/0000-0003-1699-7776"
+- family-names: "Kunze"
+  given-names: "John"
+  orcid: "https://orcid.org/0000-0001-7604-8041"
+- family-names: "Lubiana"
+  given-names: "Tiago"
+  orcid: "https://orcid.org/0000-0003-2473-2313"
+- family-names: "Matentzoglu"
+  given-names: "Nicolas"
+  orcid: "https://orcid.org/0000-0002-7356-1779"
+- family-names: "McMurry"
+  given-names: "Julie"
+  orcid: "https://orcid.org/0000-0002-9353-5498"
+- family-names: "Moxon"
+  given-names: "Sierra"
+  orcid: "https://orcid.org/0000-0002-8719-7760"
+- family-names: "Mungall"
+  given-names: "Christopher J."
+  orcid: "https://orcid.org/0000-0002-6601-2165"
+- family-names: "Rutz"
+  given-names: "Adriano"
+  orcid: "https://orcid.org/0000-0003-0443-9902"
+- family-names: "Unni"
+  given-names: "Deepak R."
+  orcid: "https://orcid.org/0000-0002-8424-0604"
+- family-names: "Willighagen"
+  given-names: "Egon"
+  orcid: "https://orcid.org/0000-0001-7542-0286"
+- family-names: "Winston"
+  given-names: "Donald"
+  orcid: "https://orcid.org/0000-0002-8424-0604"
+- family-names: "Gyori"
+  given-names: "Benjamin M."
+  orcid: "https://orcid.org/0000-0001-9439-5346"
+doi: 10.1038/s41597-022-01807-3
+identifiers:
+  - type: doi
+    value: 10.1038/s41597-022-01807-3
+keywords:
+  - The Bioregistry
+  - biocuration
+  - biosemantics
+  - bioinformatics
+  - clinical informatics
+  - systems biology
+  - semantics
+  - semantic web
+  - CURIE
+  - URI
+  - identifiers
+  - chemistry
+  - cheminformatics
+  - agriculture
+  - molecular biology
+title: >-
+  Unifying the Identification of Biomedical Entities with the Bioregistry

testbed/biopragmatics__bioregistry/Dockerfile

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+# Local building/testing instructions:
+# 1. docker build --tag bioregistry:dev .
+# 2. docker run -p 8766:8766 bioregistry:dev
+# 3. Navgiate in the web browser to http://localhost:8766
+
+FROM python:3.11-alpine
+
+RUN python -m pip install --upgrade pip
+RUN python -m pip install --upgrade wheel
+RUN python -m pip install bioregistry[web]
+ENTRYPOINT python -m bioregistry web --port 8766 --host "0.0.0.0"

testbed/biopragmatics__bioregistry/LICENSE

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+MIT License
+
+Copyright (c) 2020-2024 Charles Tapley Hoyt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

testbed/biopragmatics__bioregistry/README.md

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+<p align="center">
+  <img src="https://github.com/biopragmatics/bioregistry/raw/main/docs/source/logo.png" height="150">
+</p>
+
+<h1 align="center">
+    Bioregistry
+</h1>
+
+<p align="center">
+    <a href="https://github.com/biopragmatics/bioregistry/actions?query=workflow%3ATests">
+        <img alt="Tests" src="https://github.com/biopragmatics/bioregistry/workflows/Tests/badge.svg" />
+    </a>
+    <a href="https://pypi.org/project/bioregistry">
+        <img alt="PyPI" src="https://img.shields.io/pypi/v/bioregistry" />
+    </a>
+    <a href="https://pypi.org/project/bioregistry">
+        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/bioregistry" />
+    </a>
+    <a href="https://github.com/biopragmatics/bioregistry/blob/main/LICENSE">
+        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/bioregistry" />
+    </a>
+    <a href='https://bioregistry.readthedocs.io/en/latest/?badge=latest'>
+        <img src='https://readthedocs.org/projects/bioregistry/badge/?version=latest' alt='Documentation Status' />
+    </a>
+    <a href="https://zenodo.org/badge/latestdoi/319481281">
+        <img src="https://zenodo.org/badge/319481281.svg" alt="DOI">
+    </a>
+    <a href="https://github.com/psf/black">
+        <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code style: black">
+    </a>
+    <a href="https://github.com/biopragmatics/bioregistry/blob/main/.github/CODE_OF_CONDUCT.md">
+        <img alt="Contributor Covenant" src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" />
+    </a>
+</p>
+
+<p align="center">
+   A community-driven integrative meta-registry of life science databases, ontologies, and other resources.
+   <br />More information <a href="https://bioregistry.io/summary">here</a>.
+</p>
+
+The Bioregistry can be accessed, searched, and queried through its associated website at
+https://bioregistry.io.
+
+### 📥 Download
+
+The underlying data of the Bioregistry can be downloaded (or edited) directly
+from [here](https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/data/).
+Several exports to YAML, TSV, and RDF, including consensus views over the
+registry, are built on a weekly basis and can be downloaded via the
+[`exports/`](https://github.com/biopragmatics/bioregistry/tree/main/exports) directory.
+
+The manually curated portions of these data are available under the
+[CC0 1.0 Universal License](https://creativecommons.org/publicdomain/zero/1.0/).
+Aggregated data are redistributed under their original licenses.
+
+## 🙏 Contributing
+
+Contributions are both welcomed and encouraged. Contribution guidelines for new
+prefix requests, record edits, record removals, and code updates are available
+in [CONTRIBUTING.md](docs/CONTRIBUTING.md).
+
+The most simple contribution is to submit an issue:
+
+- Submit a new prefix using the [issue template](https://github.com/biopragmatics/bioregistry/issues/new?assignees=cthoyt&labels=New%2CPrefix&template=new-prefix.yml&title=Add+prefix+%5BX%5D). A new pull request will be generated automatically for you.
+- Update an existing record using one of the [existing issue templates](https://github.com/biopragmatics/bioregistry/issues/new/choose) (e.g., for updating a record's regular expression, merging two prefixes).
+- For any updates that don't have a corresponding template, feel free to start with a [blank issue](https://github.com/biopragmatics/bioregistry/issues/new).
+
+If you want to make a direct contribution, feel free to make edits directly to
+the [bioregistry.json](https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/data/bioregistry.json)
+file either through the GitHub interface or locally by [forking the repository](https://github.com/biopragmatics/bioregistry/blob/main/docs/CONTRIBUTING.md#code-contribution).
+
+If you want to make a contribution but don't know where to start, you can check
+[this list](https://biopragmatics.github.io/bioregistry/curation/) of curation
+To-Do's that's automatically generated weekly, including more detailed
+information on how to contribute.
+
+## ⚖️ Governance
+
+The Bioregistry is maintained by a Review Team and Core Development team
+whose memberships and duties are described in the
+[Project Governance](docs/GOVERNANCE.md).
+
+## 🧹 Maintenance
+
+### 🫀 Health Report
+
+The Bioregistry runs some automated tests weekly to check that various metadata haven't gone stale. For example,
+it checks that the homepages are still available and that each provider URL is still able to resolve.
+
+It has a dedicated [dashboard](https://biopragmatics.github.io/bioregistry/health) that is not part of the main
+Bioregistry site.
+
+### ♻️ Update
+
+The database is automatically updated daily thanks to scheduled workflows in GitHub Actions. The workflow's
+configuration can be found [here](https://github.com/biopragmatics/bioregistry/blob/main/.github/workflows/update.yml)
+and the last run can be seen [here](https://github.com/biopragmatics/bioregistry/actions?query=workflow%3A%22Update+Data%22).
+Further, a [changelog](https://github.com/biopragmatics/bioregistry/commits?author=actions-user) can be recapitulated from the
+commits of the GitHub Actions bot.
+
+If you want to manually update the database, run the following:
+
+```shell
+$ tox -e update
+```
+
+Make sure that you have valid environment variables or `pystow` configurations
+for `BIOPORTAL_API_KEY`, `ECOPORTAL_API_KEY`, `AGROPORTAL_API_KEY`,
+`FAIRSHARING_LOGIN`, and `FAIRSHARING_PASSWORD`.
+
+## 🚀 Installation
+
+The Bioregistry can be installed from [PyPI](https://pypi.org/project/bioregistry/) with:
+
+```shell
+$ pip install bioregistry
+```
+
+It can be installed in development mode for local curation with:
+
+```shell
+$ git clone https://github.com/biopragmatics/bioregistry.git
+$ cd bioregistry
+$ pip install --editable .
+```
+
+Build the docs locally with `tox -e docs` then view by opening
+`docs/build/html/index.html`.
+
+## 💪 Usage
+
+### Normalizing Prefixes
+
+The Bioregistry can be used to normalize prefixes across MIRIAM and all the (very plentiful) variants that pop up in
+ontologies in OBO Foundry and the OLS with the `normalize_prefix()` function.
+
+```python
+from bioregistry import normalize_prefix
+
+# Doesn't affect canonical prefixes
+assert 'ncbitaxon' == normalize_prefix('ncbitaxon')
+
+# This works for uppercased prefixes, like:
+assert 'chebi' == normalize_prefix("CHEBI")
+
+# This works for mixed case prefixes like
+assert 'fbbt' == normalize_prefix("FBbt")
+
+# This works for synonym prefixes, like:
+assert 'ncbitaxon' == normalize_prefix('taxonomy')
+
+# This works for common mistaken prefixes, like:
+assert 'pubchem.compound' == normalize_prefix('pubchem')
+
+# This works for prefixes that are often written many ways, like:
+assert 'eccode' == normalize_prefix('ec-code')
+assert 'eccode' == normalize_prefix('EC_CODE')
+
+# If a prefix is not registered, it gives back `None`
+assert normalize_prefix('not a real key') is None
+```
+
+### Parsing CURIEs
+
+The Bioregistry supports parsing a CURIE into a pair of normalized prefix
+and identifier using the `parse_curie()` function:
+
+```python
+from bioregistry import parse_curie
+
+# Obvious for canonical CURIEs
+assert ('chebi', '1234') == parse_curie('chebi:1234')
+
+# Normalize mixed case prefixes
+assert ('fbbt', '00007294') == parse_curie('FBbt:00007294')
+
+# Normalize common mistaken prefixes
+assert ('pubchem.compound', '1234') == parse_curie('pubchem:1234')
+
+# Remove the redundant prefix and normalize
+assert ('go', '1234') == parse_curie('GO:GO:1234')
+```
+
+This will also apply the same normalization rules for prefixes from the previous
+section on normalizing prefixes for the remaining examples.
+
+### Normalizing CURIEs
+
+The Bioregistry supports converting a CURIE to a canonical CURIE by normalizing
+the prefix and removing redundant namespaces embedded in LUIs with the
+`normalize_curie()` function.
+
+```python
+from bioregistry import normalize_curie
+
+# Idempotent to canonical CURIEs
+assert 'chebi:1234' == normalize_curie('chebi:1234')
+
+# Normalize common mistaken prefixes
+assert 'pubchem.compound:1234' == normalize_curie('pubchem:1234')
+
+# Normalize mixed case prefixes
+assert 'fbbt:1234' == normalize_curie('FBbt:1234')
+
+# Remove the redundant prefix and normalize
+assert 'go:1234' == normalize_curie('GO:GO:1234')
+```
+
+### Parsing IRIs
+
+The Bioregistry can be used to parse CURIEs from IRIs due to its vast registry of provider URL
+strings and additional programmatic logic implemented with Python. It can parse OBO Library PURLs,
+IRIs from the OLS and identifiers.org, IRIs from the Bioregistry website, and any other IRIs
+from well-formed providers registered in the Bioregistry. The `parse_iri()` function
+gets a pre-parsed CURIE, while the `curie_from_iri()` function makes a canonical CURIE
+from the pre-parsed CURIE.
+
+```python
+from bioregistry import curie_from_iri, parse_iri
+
+# First-party IRI
+assert ('chebi', '24867') == parse_iri('https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24867')
+assert 'chebi:24867' == curie_from_iri('https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24867')
+
+# OBO Library PURL
+assert ('chebi', '24867') == parse_iri('http://purl.obolibrary.org/obo/CHEBI_24867')
+assert 'chebi:24867' == curie_from_iri('http://purl.obolibrary.org/obo/CHEBI_24867')
+
+# OLS IRI
+assert ('chebi', '24867') == parse_iri('https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http://purl.obolibrary.org/obo/CHEBI_24867')
+assert 'chebi:24867' == curie_from_iri('https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http://purl.obolibrary.org/obo/CHEBI_24867')
+
+# Identifiers.org IRIs (with varying usage of HTTP(s) and colon/slash separator
+assert ('chebi', '24867') == parse_iri('https://identifiers.org/CHEBI:24867')
+assert ('chebi', '24867') == parse_iri('http://identifiers.org/CHEBI:24867')
+assert ('chebi', '24867') == parse_iri('https://identifiers.org/CHEBI/24867')
+assert ('chebi', '24867') == parse_iri('http://identifiers.org/CHEBI/24867')
+
+# Bioregistry IRI
+assert ('chebi', '24867') == parse_iri('https://bioregistry.io/chebi:24867')
+```
+
+In general, the Bioregistry knows how to parse both the http and https variants
+of any given URI:
+
+```python
+from bioregistry import parse_iri
+
+assert ('neuronames', '268') == parse_iri("http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=268")
+assert ('neuronames', '268') == parse_iri("https://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=268")
+```
+
+### Generating IRIs
+
+You can generate an IRI from either a CURIE or a pre-parsed CURIE
+(i.e., a 2-tuple of a prefix and identifier) with the `get_iri()` function.
+By default, it uses the following priorities:
+
+1. Custom prefix map (`custom`)
+2. First-party IRI (`default`)
+3. Identifiers.org / MIRIAM (`miriam`)
+4. Ontology Lookup Service (`ols`)
+5. OBO PURL (`obofoundry`)
+6. Name-to-Thing (`n2t`)
+7. BioPortal (`bioportal`)
+
+```python
+from bioregistry import get_iri
+
+assert get_iri("chebi", "24867") == 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24867'
+assert get_iri("chebi:24867") == 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24867'
+```
+
+It's possible to change the default priority list by passing an alternate
+sequence of metaprefixes to the `priority` keyword (see above). For example, if
+you're working with OBO ontologies, you might want to make OBO PURLs the highest
+priority and when OBO PURLs can't be generated, default to something else:
+
+```python
+from bioregistry import get_iri
+
+priority = ["obofoundry", "default", "miriam", "ols", "n2t", "bioportal"]
+assert get_iri("chebi:24867", priority=priority) == 'http://purl.obolibrary.org/obo/CHEBI_24867'
+assert get_iri("hgnc:1234", priority=priority) == 'https://bioregistry.io/hgnc:1234' 
+```
+
+Even deeper, you can add (or override) any of the Bioregistry's default prefix
+map with the `prefix_map` keyword:
+
+```python
+from bioregistry import get_iri
+
+prefix_map = {
+   "myprefix": "https://example.org/myprefix/",
+   "chebi": "https://example.org/chebi/",
+}
+assert get_iri("chebi:24867", prefix_map=prefix_map) == 'https://example.org/chebi/24867'
+assert get_iri("myprefix:1234", prefix_map=prefix_map) == 'https://example.org/myprefix/1234'
+```
+
+A custom prefix map can be supplied in combination with a priority list, using
+the `"custom"` key for changing the priority of the custom prefix map.
+
+```python
+from bioregistry import get_iri
+
+prefix_map = {"lipidmaps": "https://example.org/lipidmaps/"}
+priority = ["obofoundry", "custom", "default", "bioregistry"]
+assert get_iri("chebi:24867", prefix_map=prefix_map, priority=priority) == \
+    'http://purl.obolibrary.org/obo/CHEBI_24867'
+assert get_iri("lipidmaps:1234", prefix_map=prefix_map, priority=priority) == \
+    'https://example.org/lipidmaps/1234'
+```
+
+Alternatively, there are direct functions for generating IRIs for different
+registries:
+
+```python
+import bioregistry as br
+
+# Bioregistry IRI
+assert br.get_bioregistry_iri('chebi', '24867') == 'https://bioregistry.io/chebi:24867'
+
+# Default Provider
+assert br.get_default_iri('chebi', '24867') == 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24867'
+
+# OBO Library
+assert br.get_obofoundry_iri('chebi', '24867') == 'http://purl.obolibrary.org/obo/CHEBI_24867'
+
+# OLS IRI
+assert br.get_ols_iri('chebi', '24867') ==
+       'https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http://purl.obolibrary.org/obo/CHEBI_24867'
+
+# Bioportal IRI
+assert br.get_bioportal_iri('chebi', '24867') == \
+    'https://bioportal.bioontology.org/ontologies/CHEBI/?p=classes&conceptid=http://purl.obolibrary.org/obo/CHEBI_24867'
+
+# Identifiers.org IRI
+assert br.get_identifiers_org_iri('chebi', '24867') == 'https://identifiers.org/CHEBI:24867'
+
+# Name-to-Thing IRI
+assert br.get_n2t_iri('chebi', '24867') == 'https://n2t.net/chebi:24867'
+```
+
+Each of these functions could also return `None` if there isn't a provider available or if the prefix
+can't be mapped to the various resources.
+
+### Prefix Map
+
+The Bioregistry can be used to generate prefix maps with various flavors
+depending on your context. Prioritization works the same way as when generating
+IRIs.
+
+```python
+from bioregistry import get_prefix_map
+
+# Standard
+prefix_map = get_prefix_map()
+
+# Prioritize OBO prefixes over bioregistry
+priority = ["obofoundry", "default", "miriam", "ols", "n2t", "bioportal"]
+prefix_map = get_prefix_map(uri_prefix_priority=priority)
+
+# Provide custom remapping that doesn't have prioritization logic
+remapping = {"chebi": "CHEBI"}
+prefix_map = get_prefix_map(remapping=remapping)
+```
+
+### Getting Metadata
+
+The pattern for an entry in the Bioregistry can be looked up quickly with `get_pattern()` if
+it exists. It prefers the custom curated, then MIRIAM, then Wikidata pattern.
+
+```python
+import bioregistry
+
+assert '^GO:\\d{7}$' == bioregistry.get_pattern('go')
+```
+
+Entries in the Bioregistry can be checked for deprecation with the `is_deprecated()` function. MIRIAM and OBO Foundry
+don't often agree - OBO Foundry takes precedence since it seems to be updated more often.
+
+```python
+import bioregistry
+
+assert bioregistry.is_deprecated('nmr')
+assert not bioregistry.is_deprecated('efo')
+```
+
+Entries in the Bioregistry can be looked up with the `get_resource()` function.
+
+```python
+import bioregistry
+
+entry = bioregistry.get_resource('taxonomy')
+# there are lots of mysteries to discover in this dictionary!
+```
+
+The full Bioregistry can be read in a Python project using:
+
+```python
+import bioregistry
+
+registry = bioregistry.read_registry()
+```
+
+### 🕸️ Resolver App
+
+After installation with the `[web]` extras, the Bioregistry web application
+can be run with the following code:
+
+```shell
+$ python -m pip install bioregistry[web]
+$ bioregistry web
+```
+
+to run a web app that functions like Identifiers.org, but backed by the Bioregistry.
+A public instance of this app is hosted by the [Gyori Lab for Computational Biomedicine](https://gyorilab.github.io) at
+https://bioregistry.io.
+
+## 👋 Attribution
+
+### ⚖️ License
+
+The code in this repository is licensed under the
+[MIT License](https://github.com/biopragmatics/bioregistry/blob/main/LICENSE).
+
+### 📛 Badge
+
+If you use the Bioregistry in your code, support us by including our
+badge in your project's README.md:
+
+```markdown
+[![Powered by the Bioregistry](https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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)](https://github.com/biopragmatics/bioregistry)
+```
+
+If your README uses reStructuredText (.rst), use this instead:
+
+```
+.. image:: https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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
+    :target: https://github.com/biopragmatics/bioregistry
+    :alt: Powered by the Bioregistry
+```
+
+It looks like this: [![Powered by the Bioregistry](https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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)](https://github.com/biopragmatics/bioregistry)
+
+### 📖 Citation
+
+> [Unifying the identification of biomedical entities with the Bioregistry](https://bioregistry.io/doi:10.1038/s41597-022-01807-3)
+> <br />Hoyt, C. T., Balk, M., Callahan, T. J., Domingo-Fernandez, D., Haendel, M. A., Hegde, H. B., Himmelstein, D. S., Karis, K., Kunze, J., Lubiana, T., Matentzoglu, N., McMurry, J., Moxon, S., Mungall, C. J., Rutz, A., Unni, D. R., Willighagen, E., Winston, D., and Gyori, B. M. (2022)
+> <br />*Nature Scientific Data*, s41597-022-01807-3
+
+```bibtex
+@article{Hoyt2022Bioregistry,
+    author = {Hoyt, Charles Tapley and Balk, Meghan and Callahan, Tiffany J and Domingo-Fern{\'{a}}ndez, Daniel and Haendel, Melissa A and Hegde, Harshad B and Himmelstein, Daniel S and Karis, Klas and Kunze, John and Lubiana, Tiago and Matentzoglu, Nicolas and McMurry, Julie and Moxon, Sierra and Mungall, Christopher J and Rutz, Adriano and Unni, Deepak R and Willighagen, Egon and Winston, Donald and Gyori, Benjamin M},
+    doi = {10.1038/s41597-022-01807-3},
+    issn = {2052-4463},
+    journal = {Sci. Data},
+    number = {1},
+    pages = {714},
+    title = {{Unifying the identification of biomedical entities with the Bioregistry}},
+    url = {https://doi.org/10.1038/s41597-022-01807-3},
+    volume = {9},
+    year = {2022}
+}
+```
+
+Talks on the Bioregistry:
+
+- [Future Curation in the Bioregistry](https://bit.ly/wpci2022-bioregistry-maintenance) (WPCI, December 2022)
+- [The Bioregistry - Governance and Review Team](https://bit.ly/wpci2022-bioregistry-governance) (WPCI, December 2022)
+- [Development, Maintenance, and Expansion of the Bioregistry](https://bit.ly/sorger-lab-bioregistry-2022)
+  (Sorger Lab Meeting, October 2022)
+- [The Bioregistry, CURIEs, and OBO Community Health](https://bit.ly/icbo2022-cth) (ICBO 2022 (September))
+- [Introduction to the Bioregistry](https://bit.ly/bioregistry-short-talk) (Sorger Lab Meeting, July 2021)
+
+### 🎁 Support
+
+The Bioregistry was primarily developed by the [Gyori Lab for Computational Biomedicine](https://gyorilab.github.io)
+at Northeastern University, which was previously a part of the
+[Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/)
+in the [Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu)
+at [Harvard Medical School](https://hms.harvard.edu/).
+
+### 💰 Funding
+
+1. Chan Zuckerberg Initiative (CZI) 2023-329850
+2. DARPA Automating Scientific Knowledge Extraction and Modeling (ASKEM) HR00112220036
+3. DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).

testbed/biopragmatics__bioregistry/docs/CODE_OF_CONDUCT.md

@@ -0,0 +1,138 @@
+---
+layout: page
+title: Code of Conduct
+permalink: /conduct/
+---
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission. As a slight departure from the
+  verbatim text from the Contributor Covenant, we relax this restriction when
+  related to the publicly available contact information for individuals related
+  to the data in the Bioregistry (i.e., contributors, reviewers, contact people).
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+{{ site.email }}.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available
+at [https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

testbed/biopragmatics__bioregistry/docs/CONTRIBUTING.md

@@ -0,0 +1,418 @@
+---
+layout: page
+title: Contributing
+permalink: /contributing/
+---
+
+Contributions to the Bioregistry are welcomed and encouraged. Thanks for
+considering to participate.
+
+All contributors, maintainers, and participants of the Bioregistry project
+are expected to follow our [Code of Conduct](CODE_OF_CONDUCT.md).
+This document is organized as follows:
+
+1. [Content Contribution](#content-contribution)
+    1. [Submitting New Prefixes](#submitting-new-prefixes)
+    2. [Editing Records](#editing-records)
+    3. [Removing Records](#removing-records)
+2. [Code Contribution](#code-contribution)
+
+## Content Contribution
+
+There are several ways to request a new prefix in the Bioregistry:
+
+1. Fill out the [new prefix request form](https://github.com/biopragmatics/bioregistry/issues/new?assignees=cthoyt&labels=New%2CPrefix&template=new-prefix.yml&title=%5BResource%5D%3A%20xxxxx)
+   on our GitHub issue tracker with as much information about the resource as
+   possible (e.g., name, homepage, format URL pattern, example identifier,
+   pattern). Don't worry if you don't understand everything, our Review Team
+   will guide you through the process.
+2. ~Add an entry yourself
+   by [editing the Bioregistry](https://github.com/biopragmatics/bioregistry/edit/main/src/bioregistry/data/bioregistry.json)
+   in GitHub through the web browser.~ As the Bioregistry has surpassed the size limit of in-browser editing on GitHub,
+   this is no longer possible.
+3. Make a pull request directly to the upstream repository
+   [biopragmatics/bioregistry](https://github.com/biopragmatics/bioregistry). Make sure that you
+   run `tox -e bioregistry-lint` from the shell after editing the source JSON files in order to canonically order the
+   data.
+
+### Submitting New Prefixes
+
+#### Who Can Request a New Prefix
+
+A prefix can be requested by anyone, even if it is for a resource they do not
+themselves maintain. A main goal of the Bioregistry is to be a detailed,
+descriptive resource - expertise is welcome from anywhere. Ideally, the
+requester should provide contact information for the main responsible person for
+the resource or include them in discussion on GitHub directly. In many cases,
+it's much easier for the resource responsible person to provide certain metadata
+that's required to go with a given prefix.
+
+#### Minimum New Prefix Requirements
+
+1. New prefixes are allowed to contain letters [a-z], numbers [0-9], and a
+   single dot `.` if a subspace is requested. More discussion on subspacing
+   policy can be found https://github.com/biopragmatics/bioregistry/issues/133
+   and https://github.com/biopragmatics/bioregistry/issues/65.
+2. New prefixes must start with a letter.
+3. New prefixes must be at least two characters. Ideally, prefixes should be
+   three or more characters for legibility.
+4. Subspaces must start with a letter.
+5. Subspaces must be at least two characters. Ideally, subspaces should be three
+   or more characters for legibility.
+6. New prefixes must be lowercase. However, lexical variants can be stored as
+   synonyms for reference (e.g., FBbt).
+7. New prefixes must validate against the following regular expression:
+   `^[a-z][a-z0-9]+(\.[a-z][a-z0-9]+?)$`
+8. New prefixes must pass all metadata checks, which are canonically defined by
+   the quality assurance workflow.
+
+Unfortunately, these requirements can not be applied retroactively and can not
+be trivially applied to automatically imported prefixes. In some cases,
+historical prefixes can be modified to follow these requirements. For example,
+Identifiers.org's `ec-code` was renamed to `eccode` while maintaining `ec-code`
+as a synonym.
+
+Original discussion about minimum prefix requirements can be found at
+https://github.com/biopragmatics/bioregistry/issues/158.
+
+#### Miscellaneous Requirements
+
+- Do not include titles (e.g., Dr.) in contact information for the requester, reviewer, nor contact for a resource.
+
+#### Choosing a Good Prefix
+
+1. Prefixes should be chosen in a way to minimize confusion (e.g., prefixes
+   should correspond to the name of the resource they are minted for. Most
+   commonly, people use acronyms.)
+2. Multiple prefixes will not be issued for multiple versions of a resource (
+   e.g., the fact that there is a `mesh.2012` and `mesh.2013` prefix registered in
+   Identifiers.org was a huge mistake and causes massive confusion)
+3. Prefixes must not be too generic or common entity types like gene or
+   chemical. Reviewers will use their best judgment since it's hard to list all
+   possible generic entity types. For example, gene would be bad while `hgnc.gene`
+   would be better.
+4. Subspacing should not be used unnecessarily, i.e., when a nomenclature only
+   has one entity type. For example, `chebi.chemical` would be bad while `chebi`
+   would be better.
+5. Prefixes should not end in "O" for "Ontology", "T" for "Terminology" or any
+   letters denoting related words about vocabularies
+6. New prefixes should not end with "ID" as a way to signify that the prefix is used for
+   identifiers, like in `doid` for the Disease Ontology or `caid` for ClinGen Canonical Allele identifier.
+
+These policies were developed in parallel with the OBO Foundry policy on
+choosing a prefix (i.e., IDSPACE) at http://obofoundry.org/id-policy.html.
+
+#### Handling Collisions
+
+While they have proven to be rather infrequent between high quality resources,
+collisions do happen. The Bioregistry has the following policy for handling
+collisions:
+
+- New prefixes must not collide with any canonical prefixes, preferred prefixes,
+  synonyms, or normalized variants thereof.
+  See https://github.com/biopragmatics/bioregistry/issues/359 for an example of
+  a prefix request that duplicated the synonyms of an existing prefix and how it
+  was able to be resolved.
+- New prefixes should not collide with any prefixes in external registries, even
+  if they are not explicitly imported in the Bioregistry. In these cases, a
+  thoughtful discussion should take place explaining why the prefix is being
+  reused (e.g., it has been parked by an inactive or low-quality resource in
+  Bioportal).
+- If a new contributor wants to register a prefix that is already present in the
+  Bioregistry, then precedence will be given to the already existing prefix and
+  the contributor will be asked to choose a different prefix.
+
+It has not happened often that prefixes have even collided. One example is two
+maintained resources, Gene Expression Omnibus vs. Geographical Entity Ontology,
+collided on using `geo` when Geographical Entity Ontology was added to the OBO
+Foundry. This was resolved
+in https://github.com/biopragmatics/bioregistry/issues/67 after deciding to
+change the prefix used in Geographical Entity Ontology due to the fact that the
+Gene Expression Omnibus was both much older and more well-known. This particular
+case motivated the OBO Foundry to update its ontology registration guidelines to
+require conflicts with existing Bioregistry records
+in https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1519. Another
+example is the disease class annotation (legacy classification from the hard
+fork of the Disease Ontology that later became MONDO) and Dublin Core, where one
+is subjectively more important than the other.
+
+#### Bulk Contribution
+
+If you would like to submit more than 5 prefixes at once, you can fill out the
+[bulk prefix request template](bulk_prefix_request_template.tsv)
+spreadsheet and submit it in
+an [issue](https://github.com/biopragmatics/bioregistry/issues/new). The
+template contains several examples - please review them then delete them before
+submission. Please number all of the rows in sequential order the first
+column (`request_id`). The first columns of the template are all required, even
+if some of the examples don't have an entry there for historic reasons. All
+optional fields are marked as such.
+
+Anyone is welcome to submit a bulk prefix request, but ideally submitters have a
+large working knowledge of the Bioregistry, its requirements, etc. as reviewing
+issues in a bulk request is much less ergonomic and more time-consuming than in
+individual prefix requests, which each get their own discussion thread, pull
+request, and CI/CD runs. Submitters of bulk prefix requests that contain many
+issues may be asked to re-submit as individual prefix requests.
+
+#### Prefix Parking
+
+A prefix and its corresponding semantic space are **substantiated** when it's
+provable that a semantic space exists by one or more of the following:
+
+1. There's a public place where you can get the entire list of terms.
+   Ontologies (e.g., [Gene Ontology](https://bioregistry.io/go)) and databases
+   (e.g., [HGNC](https://bioregistry.io/hgnc)) usually make this pretty
+   straightforwards by offering download links for the ontology or full
+   database.
+2. There's a working, public URI format string that either lets you get HTML,
+   JSON, RDF, or some other kind of information artifact for a given local
+   unique identifier. For example, [OMIM.PS](https://bioregistry.io/omim.ps)
+   doesn't have a way to get a full list of terms but if you have a given local
+   unique identifier, you can use it with the URI format string to retrieve some
+   information about the entity corresponding to that LUI.
+
+A potential less strict third criteria for substantiation could be when
+references to entities in a semantic space (i.e., in the form of CURIEs) can be
+found in public resources or ontologies that are external to the resource in
+which the prefix/semantic space are defined. This is more common for historical
+prefixes (e.g., OpenCyc references appear quite frequently, but this resource
+was taken down more than a decade ago) and is less applicable to new prefix
+requests. Therefore, this relaxed criteria will not be considered as sufficient
+for substantiation.
+
+We define **prefix parking** as a special case of a prefix request in which the
+corresponding resource/semantic space for the prefix does not yet exist or is
+currently under development (and by definition, is not yet substantiated). The
+Bioregistry does not explicitly discourage prefix parking, but new prefix
+requests qualifying as prefix parking require additional guidelines, partially
+motivated by the difficulty of the discussion on
+https://github.com/biopragmatics/bioregistry/issues/359.
+
+1. While it's not typically under the purview of the Bioregistry Review Team to
+   judge the utility of a prefix nor comment on its corresponding design
+   decisions (e.g., choice of local unique identifier scheme, regular expression
+   pattern, URI format string), submitters seeking to park a prefix must both
+   actively publicly seek out and seriously consider suggestions and advice from
+   the Bioregistry Review Team with regards to these matters (e.g., in the issue
+   corresponding to a new prefix request). Submissions unable/unwilling to
+   follow these guidelines may be dismissed and asked to re-submit after their
+   prefix has been substantiated.
+2. Submissions to park a prefix must include a primary contact person for the
+   resource that is available for public discussion on GitHub. Even though this
+   is likely the same as the submitter, it is important that this person can be
+   contacted. If they are unresponsive within two weeks of contact regarding the
+   parked prefix, then the parked prefix is subject to removal.
+3. Parked prefixes that are not substantiated within three months are subject to
+   removal. In the case that someone else wants to use that prefix, the fact
+   that the parked prefix has not been substantiated will, by definition, result
+   in no impact or confusion that would normally result from the removal of a
+   prefix. It is the responsibility of the submitter/primary contact person for
+   the prefix to inform the Bioregistry Review Team of the updates and/or to
+   submit the updates to their prefix record themselves that demonstrates it has
+   been substantiated.
+4. It's not the job of the Bioregistry to support parking prefixes for semantic
+   spaces that will not be public or that won't be used in other public
+   resources - these can be rejected without further discussion.
+
+Original discussion about prefix parking can be found at
+https://github.com/biopragmatics/bioregistry/issues/365.
+
+#### Review of New Prefix Requests
+
+Review of new prefix requests is handled by the Bioregistry Review Team, whose
+membership and conduct is described in the Bioregistry's
+[Project Governance](GOVERNANCE.md).
+
+### Editing Records
+
+There are several ways to update a prefix's record in the Bioregistry:
+
+1. Fill out one of the issue templates on our GitHub issue tracker with the
+   requested information. If no template exists for your update, feel free to
+   fill out a blank issue. We will help make the update and attribute you
+   properly.
+2. ~Edit an entry yourself by [editing the Bioregistry](https://github.com/biopragmatics/bioregistry/edit/main/src/bioregistry/data/bioregistry.json)
+   in GitHub through the web browser.~ As the Bioregistry has surpassed the size limit of in-browser editing on GitHub,
+   this is no longer possible.
+3. Make a pull request directly to the upstream repository
+   [biopragmatics/bioregistry](https://github.com/biopragmatics/bioregistry). Make sure that you
+   run `tox -e bioregistry-lint` from the shell after editing the source JSON files in order to
+   canonically order the data.
+
+#### Who can edit an existing prefix's record
+
+A prefix's record can be edited by anyone, even if it is for a resource they do
+not themselves maintain. A main goal of the Bioregistry is to be a detailed,
+descriptive resource - expertise is welcome from anywhere. In many cases,
+editing an existing prefix's record is useful to override incorrect information
+from integrated repositories, such as Identifiers.org.
+
+#### Change of Prefix
+
+Typically, prefixes should not be changed since the Bioregistry acts as an
+archive of all usages, even deprecated ones. As an alternative, someone wishing
+to change a prefix can do the following:
+
+1. Mark the old prefix as deprecated
+2. Include in the `comment` field information about when and why the prefix was
+   deprecated
+3. Add a `has_canonical` relationship from the old prefix's record to the new
+   prefix
+
+Like with all edits, these are subject to review by the Bioregistry Review team.
+Extra care should be given with this kind of edit.
+
+#### Review of Edits
+
+Review of edits to existing records is handled by the Bioregistry Review Team,
+whose membership and conduct is described in the Bioregistry's
+[Project Governance](GOVERNANCE.md).
+
+### Removing Records
+
+Typically, prefixes should not be removed from the Bioregistry, even if they
+correspond to subsumed, abandoned, or dead resources, because it is also a
+historical archive and reference for anyone who might run into legacy prefixes
+in legacy resources.
+
+#### Review of Removals
+
+Review of removals of existing records is handled by the Bioregistry Review
+Team, whose membership and conduct is described in the Bioregistry's
+[Project Governance](GOVERNANCE.md).
+
+## Adding a new Registry
+
+New registries can be added by anyone, similarly to prefixes, but there is a lot more required curation.
+See the source [metaregistry.json](https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/data/metaregistry.json)
+file for inspiration. Entries in this file should follow the schema defined by the 
+[`Registry` pydantic model class](https://bioregistry.readthedocs.io/en/latest/api/bioregistry.Registry.html#bioregistry.Registry).
+See also the corresponding entry in the Bioregistry's [JSON schema](https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/schema/schema.json)
+
+While not strictly required, it's also useful for each registry to add a corresponding getter script and aligner
+class in `bioregistry.external`. See examples there, or get in touch on the
+issue tracker for help.
+
+## Code Contribution
+
+This project uses the [GitHub Flow](https://guides.github.com/introduction/flow)
+model for code contributions. Follow these steps:
+
+1. [Create a fork](https://help.github.com/articles/fork-a-repo) of the upstream
+   repository
+   at [`biopragmatics/bioregistry`](https://github.com/biopragmatics/bioregistry)
+   on your GitHub account (or in one of your organizations)
+2. [Clone your fork](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
+   with `git clone https://github.com/<your namespace here>/bioregistry.git`
+3. Make changes to the code
+4. Test that your code passes quality assurance by running `tox`
+5. Commit changes to your fork with `git commit`
+6. Push changes to your fork with `git push`
+7. Repeat steps 3-6 as needed
+8. Submit a pull request back to the upstream repository
+
+### Merge Model
+
+The Bioregistry
+uses [squash merges](https://docs.github.com/en/github/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-pull-request-commits)
+to group all related commits in a given pull request into a single commit upon
+acceptance and merge into the main branch. This has several benefits:
+
+1. Keeps the commit history on the main branch focused on high-level narrative
+2. Enables people to make lots of small commits without worrying about muddying
+   up the commit history
+3. Commits correspond 1-to-1 with pull requests
+
+### Code Style
+
+This project encourages the use of optional static typing. It
+uses [`mypy`](http://mypy-lang.org/) as a type checker
+and [`sphinx_autodoc_typehints`](https://github.com/agronholm/sphinx-autodoc-typehints)
+to automatically generate documentation based on type hints. You can check if
+your code passes `mypy` with `tox -e mypy`.
+
+This project uses [`black`](https://github.com/psf/black) to automatically
+enforce a consistent code style. You can apply `black` and other pre-configured
+linters with `tox -e lint`.
+
+This project uses [`flake8`](https://flake8.pycqa.org) and several plugins for
+additional checks of documentation style, security issues, good variable
+nomenclature, and more (
+see [`tox.ini`](tox.ini) for a list of flake8 plugins). You can check if your
+code passes `flake8` with `tox -e flake8`.
+
+Each of these checks are run on each commit using GitHub Actions as a continuous
+integration service. Passing all of them is required for accepting a
+contribution. If you're unsure how to address the feedback from one of these
+tools, please say so either in the description of your pull request or in a
+comment, and we will help you.
+
+### Logging
+
+Python's builtin `print()` should not be used (except when writing to files),
+it's checked by the
+[`flake8-print`](https://github.com/jbkahn/flake8-print) plugin to `flake8`. If
+you're in a command line setting or `main()` function for a module, you can use
+`click.echo()`. Otherwise, you can use the builtin `logging` module by adding
+`logger = logging.getLogger(__name__)` below the imports at the top of your
+file.
+
+### Documentation
+
+All public functions (i.e., not starting with an underscore `_`) must be
+documented using
+the [sphinx documentation format](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html#the-sphinx-docstring-format).
+The [`darglint`](https://github.com/terrencepreilly/darglint) plugin to `flake8`
+reports on functions that are not fully documented.
+
+This project uses [`sphinx`](https://www.sphinx-doc.org) to automatically build
+documentation into a narrative structure. You can check that the documentation
+properly builds with `tox -e docs-test`.
+
+### Testing
+
+Functions in this repository should be unit tested. These can either be written
+using the `unittest` framework in the `tests/` directory or as embedded
+doctests. You can check that the unit tests pass with `tox -e py` and that the
+doctests pass with `tox -e doctests`. These tests are required to pass for
+accepting a contribution.
+
+### Syncing your fork
+
+If other code is updated before your contribution gets merged, you might need to
+resolve conflicts against the main branch. After cloning, you should add the
+upstream repository with
+
+```shell
+$ git remote add biopragmatics https://github.com/biopragmatics/bioregistry.git
+```
+
+Then, you can merge upstream code into your branch. You can also use the GitHub
+UI to do this by following [this tutorial](https://docs.github.com/en/github/collaborating-with-pull-requests/working-with-forks/syncing-a-fork).
+
+### Python Version Compatibility
+
+This project aims to support all versions of Python that have not passed their
+end-of-life dates. After end-of-life, the version will be removed from the Trove
+qualifiers in the [`setup.cfg`](https://github.com/biopragmatics/bioregistry/blob/main/setup.cfg)
+and from the GitHub Actions testing configuration.
+
+See https://endoflife.date/python for a timeline of Python release and
+end-of-life dates.
+
+#### Review of Pull Requests
+
+Review of edits to existing records is handled by the Bioregistry Core
+Development Team, whose membership and conduct is described in the Bioregistry's
+[Project Governance](GOVERNANCE.md).
+
+## Meta-contributions
+
+### Retroactive Application of Curation Guidelines
+
+As the Bioregistry matures, new fields may be added and more strict curation
+guidelines may be imposed (both from a philosophical and technical perspective).
+When imposing new rules, reasonable efforts should be made to backfill existing
+records. Alternatively, existing prefixes can be "grandfathered" in to less
+strict requirements.

testbed/biopragmatics__bioregistry/docs/GOVERNANCE.md

@@ -0,0 +1,171 @@
+---
+layout: page
+title: Project Governance
+permalink: /governance/
+---
+# Governance
+
+The goal of the Bioregistry is to enable community-driven curation and
+maintenance of a registry of prefixes and their associated metadata. This is a
+first suggestion for some minimal governance (heavily inspired
+by https://github.com/mapping-commons/SSSOM/issues/82, since that is a similar
+community-driven effort). Discussion for this governance is taking place
+on https://github.com/biopragmatics/bioregistry/issues/156.
+
+## Manually Updating the Bioregistry
+
+- Manual updates to the contents of the Bioregistry (e.g., adding a new prefix,
+  merging prefixes, splitting prefixes, or updating a prefix's associated
+  metadata) must be done either in the form of an issue or a pull request.
+- The only updates that aren't considered manual are the ones done by the CI
+  system on a chronological basis.
+- Manual updates can be accepted if all continuous integration tests pass and a
+  member of the Bioregistry Review Team approves. It's best practice that a
+  member of the Review Team does not approve their own updates.
+- New prefixes must conform to
+  https://github.com/biopragmatics/bioregistry/issues/158 and
+  https://github.com/biopragmatics/bioregistry/issues/133 and the
+  [contribution guidelines](CONTRIBUTING.md).
+- Attribution information for the requester and reviewer of manual updates
+  must be collected in the form of an [ORCiD identifier](https://orcid.org).
+
+## Review Team
+
+The _Bioregistry Review Team_ is responsible for reviewing requests for new
+prefixes, merging prefixes, splitting prefixes, and updating metadata associated
+with prefixes. It is implemented as a GitHub team that has "triage"
+permissions (e.g., able to maintain issues and pull requests).
+
+Until all of the potential update interactions have been codified with GitHub
+actions workflows, the review team is also responsible for either helping the
+requester create an appropriate pull request or creating an appropriate pull
+request directly if none has been given by the requester.
+
+### Membership
+
+- Membership to the Bioregistry Review Team is requested on the issue tracker
+- Membership to the Bioregistry Review Team is granted at the discretion of the
+  existing Bioregistry Review Team
+  using [Disapproval Voting](https://en.wikipedia.org/wiki/Disapproval_voting)
+- Members must join and participate the OBO Foundry Slack, the #prefixes
+  channel, and the Review Team private chat.
+- Members must be listed alphabetically by family name [below](#members)
+
+#### Member Onboarding
+
+- Add to private channel on OBO Foundry Slack
+- Add to the GitHub [review team](https://github.com/orgs/biopragmatics/teams/bioregistry-reviewers)
+  (note that GitHub hasn't yet enabled teams to be publicly viewed, and this
+  link currently results in a 404 error)
+- Add to membership list below in alphabetical order by last name in along with
+  their GitHub handle, ORCID identifier, and date of joining.
+
+#### Removing Members
+
+- Members who unresponsive for 3 or more months can be removed by another member
+  of the Bioregistry Review Team
+- Members who do not conduct themselves according to
+  the Bioregistry [Code of Conduct](CODE_OF_CONDUCT.md) can be suggested to be
+  removed by a member of the Bioregistry Review Team.
+
+#### Member Offboarding
+
+- Remove from the private channel on OBO Foundry Slack
+- Remove from the the
+  GitHub [review team](https://github.com/orgs/biopragmatics/teams/bioregistry-reviewers)
+  (note that GitHub hasn't yet enabled teams to be publicly viewed, and this 
+  link currently results in a 404 error)
+- Add the date of exit and move their name and information ot the previous
+  members list.
+
+#### Members
+
+- Meghan Balk (@megbalk; https://orcid.org/0000-0003-2699-3066; joined 2022-01)
+- Tiffany Callahan (@callahantiff; https://orcid.org/0000-0002-8169-9049; joined
+  2022-01)
+- Benjamin M. Gyori (@bgyori; https://orcid.org/0000-0001-9439-5346)
+- Charles Tapley Hoyt (@cthoyt; https://orcid.org/0000-0003-4423-4370)
+- Tiago Lubiana (@lubianat; https://orcid.org/0000-0003-2473-2313; joined
+  2022-01)
+
+#### Previous Members
+
+We're a new team and don't have any yet!
+
+## Core Development Team
+
+The _Core Development Team_ is responsible for maintaining the codebase
+associated with the Bioregistry, which includes the Python package, the
+Bioregistry web application, docker configurations/artifacts, and related GitHub
+repositories. It is implemented as a GitHub team that has "maintain"
+permissions (e.g., able to write to the repo as well as maintain issues and pull
+requests).
+
+Contributions to the Bioregistry code must be submitted as pull requests
+to https://github.com/biopragmatics/bioregistry. They must conform to
+the [contribution guidelines](CONTRIBUTING.md). Code contributions must be
+approved by a member of the Core Development Team as well as pass continuous
+integration tests before merging.
+
+### Membership
+
+- Membership to the Bioregistry Core Development Team is requested on the issue
+  tracker
+- It is required that a potential member of the Bioregistry Core Development
+  Team has previously made a contribution as an external contributor (to which
+  there are no requirements)
+- Membership to the Bioregistry Core Development Team is granted at the
+  discretion of the existing Bioregistry Core Development Team
+  using [Disapproval Voting](https://en.wikipedia.org/wiki/Disapproval_voting)
+- Members must be listed alphabetically by family name [below](#members-1)
+
+#### Members
+
+- Benjamin M. Gyori (@bgyori; https://orcid.org/0000-0001-9439-5346)
+- Charles Tapley Hoyt (@cthoyt; https://orcid.org/0000-0003-4423-4370)
+
+## Publications / Attribution
+
+All members of the core development and review teams are automatically authors
+on Bioregistry papers and can propose other co-authors.
+
+All contributors to the data underlying the Bioregistry, regardless of curation
+size, should be considered for authorship on Bioregistry papers. These
+contributions are automatically summarized at
+https://bioregistry.io/contributors.
+
+Larger external institutional contributors should be acknowledged in the 
+following places, where appropriate:
+
+- On the [support](https://github.com/biopragmatics/bioregistry#-support) and 
+  [funding](https://github.com/biopragmatics/bioregistry#-funding) sections
+  of the repository's main README.md
+- On the [acknowledgements](https://bioregistry.io/acknowledgments) page of
+  https://bioregistry.io
+
+## Bootstrapping governance
+
+This document's governance will go into effect after additional rounds of
+editing and community discussion. The Bioregistry Review Team will announce when
+it is officially in effect.
+
+## Updating governance
+
+This governance must updated through the following steps:
+
+1. Create an issue on the
+   Bioregistry's [issue tracker](https://github.com/biopragmatics/bioregistry/issues)
+   describing the desired change and reasoning.
+2. Engage potential stakeholders in discussion.
+3. Solicit the Bioregistry Review Team for a review.
+4. The Bioregistry Review Team will accept changes at their discretion.
+
+This procedure doesn't apply to cosmetic or ergonomics changes, which are
+allowed to be done in a more *ad-hoc* manner. The Bioregistry Review Team may
+later make explicit criteria for accepting changes to this governance.
+
+## Partners
+
+Please see https://github.com/biopragmatics/bioregistry/issues/755
+for discussions about a governance model for partnerships between
+the Bioregistry and identifier space owners.

testbed/biopragmatics__bioregistry/docs/README.md

@@ -0,0 +1,20 @@
+# Bioregistry Documentation
+
+This folder contains two parts:
+
+1. [`source/`](source/) which contains the Sphinx configuration and RST files to
+   create the documentation that gets deployed to ReadTheDocs
+   at https://bioregistry.readthedocs.io.
+2. Other documentation, which gets deployed as a static site using Jekyll and
+   GitHub Pages to https://biopragmatics.github.io/bioregistry
+
+## Build locally
+
+The site can be deployed locally for development using Docker with the following
+commands in the terminal:
+
+```shell
+git clone https://github.com/biopragmatics/bioregistry
+cd bioregistry/docs
+docker run --rm --volume="$PWD:/srv/jekyll" -p 4000:4000 -it jekyll/jekyll:latest jekyll serve
+```

testbed/biopragmatics__bioregistry/docs/_config.yml

@@ -0,0 +1,13 @@
+title: Bioregistry
+author: Charles Tapley Hoyt
+email: cthoyt@gmail.com
+description: >
+  An integrative meta-registry of biological databases, ontologies, and nomenclatures.
+
+github_username:  bioregistry
+
+theme: minima
+plugins:
+  - jekyll-feed
+  - jekyll-sitemap
+  - jekyll-paginate

testbed/biopragmatics__bioregistry/docs/_data/warnings.yml

@@ -0,0 +1,539 @@
+embedding_rewrites: []
+license_conflict: []
+prefix_rewrites: []
+wrong_patterns:
+- correct: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
+  homepage: https://arks.org
+  miriam: ^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
+  name: Archival Resource Key
+  prefix: ark
+- correct: ^([a-zA-Z]+-)?\d+(\.\d)?$
+  homepage: https://www.lgcstandards-atcc.org
+  miriam: ^\d+$
+  name: American Type Culture Collection
+  prefix: atcc
+- correct: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
+  homepage: https://biofactoid.org/
+  miriam: ^[0-9a-f]{8}-[0-9a-f]{4}-[1-5][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}$
+  name: Biofactoid
+  prefix: biofactoid
+- correct: ^\d+$
+  homepage: https://github.com/SED-ML/KiSAO
+  miriam: ^KISAO_\d+$
+  name: Kinetic Simulation Algorithm Ontology
+  prefix: biomodels.kisao
+- correct: ^\d+$
+  homepage: http://teddyontology.sourceforge.net/
+  miriam: ^TEDDY_\d{7}$
+  name: Terminology for Description of Dynamics
+  prefix: biomodels.teddy
+- correct: ^(\d+)|(\w+)$
+  homepage: http://bioportal.bioontology.org/
+  miriam: ^\d+$
+  name: BioPortal
+  prefix: bioportal
+- correct: ^\d{7}$
+  homepage: http://www.brenda-enzymes.org
+  miriam: ^BTO:\d{7}$
+  name: BRENDA Tissue Ontology
+  prefix: bto
+- correct: ^\w+$
+  homepage: http://www.semantic-systems-biology.org/apo
+  miriam: ^CCO:\w+$
+  name: Cell Cycle Ontology
+  prefix: cco
+- correct: ^[A-Z0-9]{4}$
+  homepage: https://cellosaurus.org
+  miriam: ^CVCL_[A-Z0-9]{4}(\.txt)?$
+  name: Cellosaurus
+  prefix: cellosaurus
+- correct: ^\d+$
+  homepage: http://www.ebi.ac.uk/chebi
+  miriam: ^CHEBI:\d+$
+  name: Chemical Entities of Biological Interest
+  prefix: chebi
+- correct: ^\d{6}$
+  homepage: https://github.com/semanticchemistry/semanticchemistry
+  miriam: ^CHEMINF:\d+$
+  name: Chemical Information Ontology
+  prefix: cheminf
+- correct: ^\d{7}$
+  homepage: https://obophenotype.github.io/cell-ontology/
+  miriam: ^CL:\d{7}$
+  name: Cell Ontology
+  prefix: cl
+- correct: ^\d{7}$
+  homepage: http://classyfire.wishartlab.com/
+  miriam: ^C[0-9]{7}$
+  name: ClassyFire
+  prefix: classyfire
+- correct: ^COG\d+$
+  homepage: https://www.ncbi.nlm.nih.gov/research/cog/
+  miriam: ^COG[0-9]+$
+  name: Cluster of orthologous genes
+  prefix: cog
+- correct: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$
+  homepage: https://w3c-ccg.github.io/did-spec/
+  miriam: ^did:[a-z0-9]+:[A-Za-z0-9.\-:]+$
+  name: Decentralized Identifier
+  prefix: did
+- correct: ^10.\d{2,9}/.*$
+  homepage: https://www.doi.org/
+  miriam: ^(doi\:)?10\.\d+/.*$
+  name: Digital Object Identifier
+  prefix: doi
+- correct: ^\d+$
+  homepage: http://www.disease-ontology.org
+  miriam: ^DOID:\d+$
+  name: Human Disease Ontology
+  prefix: doid
+- correct: ^\d+$
+  homepage: http://drugcentral.org
+  miriam: ^[0-9]+$
+  name: Drug Central
+  prefix: drugcentral
+- correct: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$
+  homepage: https://www.enzyme-database.org/
+  miriam: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$
+  name: Enzyme Commission Code
+  prefix: eccode
+- correct: ^\d{7}$
+  homepage: https://www.evidenceontology.org
+  miriam: ECO:\d{7}$
+  name: Evidence and Conclusion Ontology
+  prefix: eco
+- correct: ^\d+$
+  homepage: https://www.ebi.ac.uk/pdbe/emdb
+  miriam: EMPIAR-\d{5,}
+  name: Electron Microscopy Public Image Archive
+  prefix: empiar
+- correct: ^\d{7,8}$
+  homepage: http://environmentontology.org/
+  miriam: ^ENVO:\d{7,8}$
+  name: Environment Ontology
+  prefix: envo
+- correct: ^\d{7}$
+  homepage: http://planteome.org/
+  miriam: ^(P)?EO\:\d{7}$
+  name: Plant Environment Ontology
+  prefix: eo
+- correct: ^(bsg-[dscp]?\d{6})|(FAIRsharing\.\w+)$
+  homepage: https://fairsharing.org/
+  miriam: ^bsg-[dscp]?\d{6}$
+  name: FAIRsharing
+  prefix: fairsharing
+- correct: ^\d+$
+  homepage: http://si.washington.edu/projects/fma
+  miriam: ^FMA:\d+$
+  name: Foundational Model of Anatomy
+  prefix: fma
+- correct: ^[0-9]{8}$
+  homepage: https://foodon.org/
+  miriam: ^FOODON:[0-9]{8}$
+  name: The Food Ontology
+  prefix: foodon
+- correct: ^\d{9}$
+  homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki
+  miriam: ^GEO_[0-9]{9}$
+  name: Geographical Entity Ontology
+  prefix: geogeo
+- correct: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$
+  homepage: https://github.com/
+  miriam: ^[a-zA-Z0-9-_]+/[a-zA-Z0-9-_]+$
+  name: GitHub username
+  prefix: github
+- correct: ^.*/.*$
+  homepage: https://gitlab.com/
+  miriam: ^[0-9A-Za-z_][0-9A-Za-z-_()\. ]*/[0-9A-Za-z_][0-9A-Za-z-_\. ]*$
+  name: GitLab
+  prefix: gitlab
+- correct: ^GN_[A-Za-z0-9_:]+$
+  homepage: https://www.noguchi.or.jp/
+  miriam: ^GN_[A-Za-z]*[_]*[A-Za-z0-9-:_]+$
+  name: GlycoNAVI
+  prefix: glyconavi
+- correct: ^\d{7}$
+  homepage: http://geneontology.org/
+  miriam: ^GO:\d{7}$
+  name: Gene Ontology
+  prefix: go
+- correct: ^\d{7}$
+  homepage: http://www.geneontology.org/cgi-bin/references.cgi
+  miriam: ^GO_REF:\d{7}$
+  name: Gene Ontology Database references
+  prefix: go.ref
+- correct: ^[A-Z]{2,4}\d+([A-Z])?([0-9])?$
+  homepage: https://www.google.com/patents/
+  miriam: ^[A-Z]{2}\d+([A-Z])?$
+  name: Google Patents
+  prefix: google.patent
+- correct: ^\d{7}$
+  homepage: http://www.gramene.org/plant_ontology/
+  miriam: ^GRO:\d+$
+  name: Gramene Growth Stage Ontology
+  prefix: gramene.growthstage
+- correct: ^\d+$
+  homepage: http://www.gramene.org/
+  miriam: ^GR\_tax\:\d+$
+  name: Gramene Taxonomy
+  prefix: gramene.taxonomy
+- correct: ^\d{6}$
+  homepage: https://gsso.research.cchmc.org/
+  miriam: ^GSSO:\d{6}$
+  name: Gender, Sex, and Sexual Orientation Ontology
+  prefix: gsso
+- correct: ^\d{1,5}$
+  homepage: http://www.genenames.org
+  miriam: ^((HGNC|hgnc):)?\d{1,5}$
+  name: HUGO Gene Nomenclature Committee
+  prefix: hgnc
+- correct: ^\d{7}$
+  homepage: http://www.human-phenotype-ontology.org/
+  miriam: ^HP:\d{7}$
+  name: Human Phenotype Ontology
+  prefix: hp
+- correct: ^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\.[0-9]))?))$
+  homepage: https://icd.who.int/browse10
+  miriam: ^[A-Z]\d+(\.[-\d+])?$
+  name: International Classification of Diseases, 10th Revision
+  prefix: icd10
+- correct: ^\d{7}$
+  homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology
+  miriam: ^[0-9]+$
+  name: Infectious Disease Ontology
+  prefix: ido
+- correct: ^\d+(-\d+)?$
+  homepage: https://www.imexconsortium.org/
+  miriam: ^IM-\d+(-?)(\d+?)$
+  name: International Molecular Exchange
+  prefix: imex
+- correct: ^\d+$
+  homepage: https://openbiolink.github.io/ITOExplorer/
+  miriam: ^.+$
+  name: Intelligence Task Ontology
+  prefix: ito
+- correct: ^(LCL|LDC|ES|LSC|LPC)-\d+$
+  homepage: http://lincsportal.ccs.miami.edu/cells/
+  miriam: (^LCL-\d+$)|(^LDC-\d+$)|(^ES-\d+$)|(^LSC-\d+$)|(^LPC-\d+$)
+  name: LINCS Cell
+  prefix: lincs.cell
+- correct: ^\d+$
+  homepage: http://www.lrg-sequence.org/
+  miriam: ^LRG_\d+$
+  name: Locus Reference Genomic
+  prefix: lrg
+- correct: ^\d+$
+  homepage: https://github.com/obophenotype/mouse-anatomy-ontology
+  miriam: ^MA:\d+$
+  name: Mouse adult gross anatomy
+  prefix: ma
+- correct: ^\d{7}$
+  homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/
+  miriam: ^MAMO_\d{7}$
+  name: Mathematical modeling ontology
+  prefix: mamo
+- correct: ^\d{7}$
+  homepage: https://github.com/monarch-initiative/MAxO
+  miriam: \d{7}
+  name: Medical Action Ontology
+  prefix: maxo
+- correct: ^\d{7}$
+  homepage: https://github.com/UTHealth-Ontology/MCRO
+  miriam: ^MCRO:\d+$
+  name: Model Card Report Ontology
+  prefix: mcro
+- correct: ^\d+\w?$
+  homepage: https://mediadive.dsmz.de/media
+  miriam: ^[A-Z]?[0-9]{1,5}[a-z]?$
+  name: MediaDive Medium
+  prefix: mediadive.medium
+- correct: ^[SCTAGMNUI]\d{2}\.([AB]\d{2}|\d{3})$
+  homepage: http://merops.sanger.ac.uk/index.htm
+  miriam: ^I\d{2}\.\d{3}$
+  name: MEROPS Entry
+  prefix: merops.entry
+- correct: ^(MAM\d{5}\w)|(MAR\d{5})$
+  homepage: https://metabolicatlas.org
+  miriam: ^MA[MR]\d{5}[a-z]?$
+  name: Metabolic Atlas
+  prefix: metatlas
+- correct: ^\d+$
+  homepage: http://aclame.ulb.ac.be/
+  miriam: ^mge:\d+$
+  name: Aclame
+  prefix: mge
+- correct: ^\d+$
+  homepage: http://www.informatics.jax.org/
+  miriam: ^MGI:\d+$
+  name: Mouse Genome Informatics
+  prefix: mgi
+- correct: ^\d{4}$
+  homepage: https://github.com/HUPO-PSI/psi-mi-CV
+  miriam: ^MI:\d{4}$
+  name: Molecular Interactions Controlled Vocabulary
+  prefix: mi
+- correct: ^\d{1,7}$
+  homepage: https://mint.bio.uniroma2.it
+  miriam: ^MINT\-\d{1,7}$
+  name: Molecular Interaction Database
+  prefix: mint
+- correct: ^\d{8}$
+  homepage: https://registry.identifiers.org/registry
+  miriam: ^MIR:\d{8}$
+  name: Identifiers.org Registry
+  prefix: mir
+- correct: ^[0-9a-z_:\.-]+$
+  homepage: https://www.ebi.ac.uk
+  miriam: ^[a-z_\.]+$
+  name: Identifiers.org namespace
+  prefix: miriam
+- correct: ^000\d{5}$
+  homepage: https://www.ebi.ac.uk/miriam/
+  miriam: ^MIR:000\d{5}$
+  name: MIRIAM Registry collection
+  prefix: miriam.collection
+- correct: ^001\d{5}$
+  homepage: https://www.ebi.ac.uk/miriam/
+  miriam: ^MIR:001\d{5}$
+  name: MIRIAM Legacy Registry Identifier
+  prefix: miriam.resource
+- correct: ^\d{5}$
+  homepage: http://www.psidev.info/MOD
+  miriam: ^MOD:\d{5}
+  name: Protein modification
+  prefix: mod
+- correct: ^\d{7}$
+  homepage: https://www.informatics.jax.org/vocab/mp_ontology/
+  miriam: ^MP:\d{7}$
+  name: Mammalian Phenotype Ontology
+  prefix: mp
+- correct: ^\d{7}$
+  homepage: http://www.psidev.info/groups/controlled-vocabularies
+  miriam: ^MS:\d{7}$
+  name: Mass spectrometry ontology
+  prefix: ms
+- correct: ^.+$
+  homepage: http://www.psidev.info/usi
+  miriam: ^mzspec:(PDX|USI|PXD)[0-9]{6}:[^:]+:(scan|index|nativeId):[0-9]+(:.*)?$
+  name: Universal Spectrum Identifier
+  prefix: mzspec
+- correct: ^\d+$
+  homepage: https://nanbyodata.jp/
+  miriam: ^NANDO:[0-9]+$
+  name: Nanbyo Disease Ontology
+  prefix: nando
+- correct: ^\d+$
+  homepage: https://github.com/SciCrunch/NIF-Ontology
+  miriam: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$
+  name: 'NIF Standard Ontology: Neurolex'
+  prefix: neurolex
+- correct: ^.{2,}$
+  homepage: https://microbiomedata.org/
+  miriam: ^[A-Za-z0-9._~\-\:]+$
+  name: National Microbiome Data Collaborative
+  prefix: nmdc
+- correct: ^\d+$
+  homepage: http://msi-ontology.sourceforge.net/
+  miriam: ^NMR:\d+$
+  name: NMR-instrument specific component of metabolomics investigations
+  prefix: nmr
+- correct: ^\d{7}$
+  homepage: https://github.com/obcs/obcs
+  miriam: ^OBCS:\d+$
+  name: Ontology of Biological and Clinical Statistics
+  prefix: obcs
+- correct: ^\d{7}$
+  homepage: http://obi-ontology.org
+  miriam: (^OBI:\d{7}$)|(^OBI_\d{7}$)
+  name: Ontology for Biomedical Investigations
+  prefix: obi
+- correct: ^[0-9]{12}$
+  homepage: https://ontochem.com/
+  miriam: ocid:[0-9]{12}
+  name: Ontology Concept Identifiers
+  prefix: ocid
+- correct: ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$
+  homepage: https://omabrowser.org
+  miriam: ^HOG:[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$
+  name: OMA HOGs
+  prefix: oma.hog
+- correct: ^\d{6}(-\d+)?$
+  homepage: https://omia.org
+  miriam: ^\d+$
+  name: Online Mendelian Inheritance in Animals
+  prefix: omia
+- correct: ^\d+$
+  homepage: https://omim.org/
+  miriam: ^[*#+%^]?\d{6}$
+  name: Online Mendelian Inheritance in Man
+  prefix: omim
+- correct: ^\d+$
+  homepage: http://bioportal.bioontology.org/ontologies/OPB
+  miriam: ^OPB_\d+$
+  name: Ontology of Physics for Biology
+  prefix: opb
+- correct: ^\d{7}$
+  homepage: https://github.com/OPL-ontology/OPL
+  miriam: ^OPL:\d+$
+  name: Ontology for Parasite LifeCycle
+  prefix: opl
+- correct: ^C?\d+$
+  homepage: https://www.ebi.ac.uk/ols4/ontologies/ordo
+  miriam: ^Orphanet(_|:)C?\d+$
+  name: Orphanet Rare Disease Ontology
+  prefix: orphanet.ordo
+- correct: ^(G|P|U|C|S)\d{5}$
+  homepage: http://www.pantherdb.org/
+  miriam: ^[GPUCS]\d{5}$
+  name: PANTHER Pathway Component
+  prefix: panther.pthcmp
+- correct: ^\d{7}$
+  homepage: https://github.com/pato-ontology/pato/
+  miriam: ^PATO:\d{7}$
+  name: Phenotype And Trait Ontology
+  prefix: pato
+- correct: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$
+  homepage: http://pid.nci.nih.gov/
+  miriam: ^\w+$
+  name: 'NCI Pathway Interaction Database: Pathway'
+  prefix: pid.pathway
+- correct: ^PMC\d+(\.\d+)?$
+  homepage: http://europepmc.org/
+  miriam: PMC\d+
+  name: PubMed Central
+  prefix: pmc
+- correct: ^\d+$
+  homepage: http://browser.planteome.org/amigo
+  miriam: ^PO:\d+$
+  name: Plant Ontology
+  prefix: po
+- correct: ^(?:\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\d+)?)$
+  homepage: http://proconsortium.org
+  miriam: ^PR:P?\d+$
+  name: Protein Ontology
+  prefix: pr
+- correct: ^\d{7}$
+  homepage: https://github.com/PRIDE-Utilities/pride-ontology
+  miriam: ^\d+$
+  name: PRIDE Controlled Vocabulary
+  prefix: pride
+- correct: ^(c|k)\d{7}$
+  homepage: http://probonto.org
+  miriam: ^PROB_c\d+$
+  name: Probability Distribution Ontology
+  prefix: probonto
+- correct: ^\d+$
+  homepage: https://www.psidev.info/psi-par
+  miriam: ^PAR:\d+$
+  name: Protein Affinity Reagents
+  prefix: psipar
+- correct: ^\d{7}$
+  homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
+  miriam: ^PW:\d{7}$
+  name: Pathway ontology
+  prefix: pw
+- correct: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$
+  homepage: https://www.reactome.org/
+  miriam: (^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$)
+  name: Reactome
+  prefix: reactome
+- correct: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\d+)|(NZ_[A-Z]{2,4}\d+))(\.\d+)?$
+  homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/
+  miriam: ^(((WP|AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+)|(NZ\_[A-Z]{2,4}\d+))(\.\d+)?$
+  name: Reference Sequence Collection
+  prefix: refseq
+- correct: ^(HOM)?\d{7}$
+  homepage: https://oborel.github.io/
+  miriam: ^RO_\d{7}$
+  name: Relation Ontology
+  prefix: ro
+- correct: ^[a-zA-Z]+.+$
+  homepage: https://rrid.site
+  miriam: ^RRID:[a-zA-Z]+.+$
+  name: Research Resource Identification
+  prefix: rrid
+- correct: ^\d{7}$
+  homepage: http://www.ebi.ac.uk/sbo/
+  miriam: ^SBO:\d{7}$
+  name: Systems Biology Ontology
+  prefix: sbo
+- correct: ^\d{6}$
+  homepage: https://github.com/micheldumontier/semanticscience
+  miriam: ^SIO_\d{6,6}$
+  name: Semanticscience Integrated Ontology
+  prefix: sio
+- correct: ^\d+$
+  homepage: http://www.swisslipids.org/#/
+  miriam: ^SLM:\d+$
+  name: SwissLipid
+  prefix: slm
+- correct: ^\d{7}$
+  homepage: http://www.sequenceontology.org/
+  miriam: ^SO:\d{7}$
+  name: Sequence types and features ontology
+  prefix: so
+- correct: ^\d{7}$
+  homepage: http://stato-ontology.org/
+  miriam: ^STATO:\d+$
+  name: The Statistical Methods Ontology
+  prefix: stato
+- correct: ^(STUDY|FILE|DATASET)\d+$
+  homepage: https://www.storedb.org/
+  miriam: ^STOREDB:(STUDY|FILE|DATASET)\d+$
+  name: Store DB
+  prefix: storedb
+- correct: ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$
+  homepage: https://archive.softwareheritage.org
+  miriam: ^swh:[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$
+  name: Software Heritage
+  prefix: swh
+- correct: ^\d{7}$
+  homepage: http://arabidopsis.org/index.jsp
+  miriam: ^Gene:\d{7}$
+  name: TAIR Gene
+  prefix: tair.gene
+- correct: ^\d+$
+  homepage: http://arabidopsis.org/index.jsp
+  miriam: ^\d{7}$
+  name: The Arabidopsis Information Resource
+  prefix: tair.locus
+- correct: ^\d{10}$
+  homepage: http://arabidopsis.org/index.jsp
+  miriam: ^AASequence:\d{10}$
+  name: TAIR Protein
+  prefix: tair.protein
+- correct: ^\d+$
+  homepage: http://uberon.org
+  miriam: ^UBERON:\d+$
+  name: Uber Anatomy Ontology
+  prefix: uberon
+- correct: ^\d{7}$
+  homepage: https://github.com/bio-ontology-research-group/unit-ontology
+  miriam: ^UO:\d{7}?
+  name: Units of measurement ontology
+  prefix: uo
+- correct: ^(\d{1,2},?\d{3},?\d{3}|(PP|RE|AI|RX)\d{2},?\d{3}|(D|T|H|X)\d{3},?\d{3})$
+  homepage: http://patft.uspto.gov/netahtml/PTO/index.html
+  miriam: ^(D|PP|R|T|H|X|AI)?\d+$
+  name: United States Patent and Trademark Office
+  prefix: uspto
+- correct: ^\d+$
+  homepage: http://variationontology.org
+  miriam: ^VariO:\d+$
+  name: Variation Ontology
+  prefix: vario
+- correct: ^\d{1,9}$
+  homepage: https://vertebrate.genenames.org
+  miriam: ^((VGNC|vgnc):)?\d{1,9}$
+  name: Vertebrate Gene Nomenclature Committee
+  prefix: vgnc
+- correct: ^\S+$
+  homepage: http://en.wikipedia.org/wiki/Main_Page
+  miriam: ^[A-Za-z-0-9_]+$
+  name: Wikipedia
+  prefix: wikipedia.en
+- correct: ^(CE[0-9]{5}|WB[A-Z][a-z]+\d+)$
+  homepage: https://www.wormbase.org/
+  miriam: ^WB[A-Z][a-z]+\d+$
+  name: WormBase
+  prefix: wormbase

testbed/biopragmatics__bioregistry/docs/bulk_prefix_request_template.tsv

@@ -0,0 +1,10 @@
+request_id	prefix	name	description	pattern	uri_format	homepage	example	contributor_name	contributor_github	contributor_orcid	contributor_email	repository (optional)	license (optional)	version (optional)	part_of (optional)	provides (optional)	download_owl (optional)	download_obo (optional)	download_json (optional)	banana (optional)	deprecated (optional)	synonyms (optional)	references (optional)	appears_in (optional)	depends_on (optional)	namespace_in_lui (optional)	no_own_terms (optional)	comment (optional)	proprietary (optional)	has_canonical (optional)	preferred_prefix (optional)	twitter (optional)	contact_name (optional)	contact_github (optional)	contact_orcid (optional)	contact_email (optional)
+example_1 (delete this row)	chebi	Chemical Entities of Biological Interest	Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.	^\d+$	https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1	http://www.ebi.ac.uk/chebi	24867					https://github.com/ebi-chebi/ChEBI	CC BY 4.0	210			http://purl.obolibrary.org/obo/chebi.owl	http://purl.obolibrary.org/obo/chebi.obo		CHEBI		CHEBI|CHEBIID|ChEBI				True					CHEBI	chebit	Adnan Malik	amalik01	0000-0001-8123-5351	amalik@ebi.ac.uk
+example_2 (delete this row)	tkg	Tohoku University cell line catalog	Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells.	^\d+$	http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html	http://www2.idac.tohoku.ac.jp/dep/ccr/	0221	Charles Tapley Hoyt	cthoyt	0000-0003-4423-4370	cthoyt@gmail.com																									
+example_3 (delete this row)	mondo	Monarch Disease Ontology	A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.	^\d{7}$	http://purl.obolibrary.org/obo/MONDO_$1	https://monarch-initiative.github.io/mondo	0000001					https://github.com/monarch-initiative/mondo	CC BY 4.0	2022-05-02			http://purl.obolibrary.org/obo/mondo.owl	http://purl.obolibrary.org/obo/mondo.obo		MONDO											MONDO	MonarchInit	Nicole Vasilevsky	nicolevasilevsky	0000-0001-5208-3432	nicole@tislab.org
+example_4 (delete this row)	nmdc	National Microbiome Data Collaborative	An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.	^[\w\-.]{3,}$	https://drs.microbiomedata.org/objects/$1	https://microbiomedata.org/	y3ax-8bq3-60	Donny Winston	dwinston	0000-0002-8424-0604	donny@polyneme.xyz																						Donny Winston	dwinston	0000-0002-8424-0604	donny@polyneme.xyz
+1																																				
+2																																				
+3																																				
+4																																				
+5																																				

testbed/biopragmatics__bioregistry/docs/curation-blacklisting-external.md

@@ -0,0 +1,32 @@
+---
+layout: page
+title: Blacklist External Prefixes
+permalink: /curation/blacklist-external
+---
+When curating unaligned external prefixes, many are either out of scope or
+not possible to find minimum metadata and therefore should be explicitly
+excluded from the Bioregistry.
+
+> **Warning **
+> This is a first draft of a tutorial on explicitly curating non-alignments.
+> It's subject to change and additional polishing.
+
+1. Identify a prefix of interest from BioPortal (or another) curation
+   sheet (e.g., [here](https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/data/external/bioportal/curation.tsv))
+2. Decide if it's out of scope:
+    - Not enough information inside external registry's record to follow-up on
+      what it is (i.e., `000467` in CHEMINF)
+    - Is there evidence of this resource being used somewhere? Don't add
+      resources that are one-off (e.g., many ontologies in BioPortal) as this
+      pollutes the prefix pool and makes the burden of finding things harder
+    - Double mapping to a Bioregistry prefix (there isn't currently a way to
+      curate these)
+    - Not about biomedical, chemical, clinical, or life sciences or
+      meta-sciences
+3. If out of scope, add to the SKIP list, either in the corresponding alignment
+   python module or associated processing configuration (TODO this needs to be
+   better standardized)
+
+The PR [#41](https://github.com/semanticchemistry/semanticchemistry/issues/41)
+demonstrates curating CHEMINF mappings including adding three explicit
+blacklists.

testbed/biopragmatics__bioregistry/docs/curation-import-external.md

@@ -0,0 +1,47 @@
+---
+layout: page
+title: Importing External Prefixes
+permalink: /curation/import-external
+---
+While the Bioregistry automatically imports all prefixes from external
+registries with similar scope and sufficient minimum metadata and quality
+standards (e.g., Identifiers.org), it only partially aligns most external
+registries (e.g., BioPortal). This is a tutorial on how to import a prefix from
+one of the partially aligned registries on an *as-needed* basis. More
+specifically, it describes importing the _Food
+classification_ ([`FOODEX2`](http://agroportal.lirmm.fr/ontologies/FOODEX2))
+ontology from AgroPortal. Pull
+request [#573](https://github.com/biopragmatics/bioregistry/pull/573) contains
+the relevant diff for the changes described in this tutorial.
+
+1. Identify a prefix of interest from AgroPortal (or another) curation
+   sheet (e.g., [here](https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/data/external/agroportal/curation.tsv))
+2. Pick a prefix for the Bioregistry. This doesn't have to be the same as the
+   external one, but usually it is. If the external prefix is too short or too
+   vague, it might be a good chance to improve on this. Further, keep in mind
+   that Bioregistry requires lowercase, so the best choice here is `foodex2`
+3. Go into the `bioregistry.json` file and use the prefix as a key for a new
+   dictionary object.
+4. The only thing you need inside the object is `"mappings"` which itself is a
+   dictionary object where the key is the metaprefix for the external registry
+   (in this case `agroportal`) and the value is the external registry's prefix
+   (in this case `FOODEX2`).
+
+    ```json
+    "foodex2": {
+        "mappings": {
+            "agroportal": "FOODEX2"
+        }
+    }
+    ```
+5. Make sure the Bioregistry is installed in editable mode
+6. Run the alignment script for the registry. In this case,
+   it's `python -m bioregistry.align.bioportal`
+7. Run unit tests with `tox -e py`. This reveals that the alignment doesn't pull
+   in enough metadata to meet the minimum requirements. In this case, OntoPortal
+   instances (e.g., AgroPortal, BioPortal, etc.) don't provide a well-defined
+   example local unique identifier (though note they provide an
+   unstandardized `example_iri` field that might be helpful)
+8. Curate an example identifier. In this case, the AgroPortal's `example_iri`
+   gives enough information to pull out an example identifier.
+9. Add any additional curations

testbed/biopragmatics__bioregistry/docs/curation.md

@@ -0,0 +1,247 @@
+---
+layout: page
+title: Help Wanted
+permalink: /curation/
+---
+Welcome to the _Help Wanted_ section of the Bioregistry 👋, a place where both
+first-time contributors or veteran Bioregistras can find small, meaningful
+ways to contribute novel curations.
+
+It's one of the core values of the Bioregistry project to provide attribution
+and appreciation to curation contributors, here's how that works:
+
+1. We associate your ORCID identifier with records that you submitted or helped
+   improve. These are displayed proudly on our
+   site's [contributions page](https://bioregistry.io/contributors/).
+2. We associate your GitHub handle with the commits to the repository (even if
+   one of the Bioregistry team members or an automated workflow on GitHub makes
+   it on your behalf) to get GitHub cred.
+3. We will consider _all_ curation contributors as co-authors on Bioregistry
+   papers.
+
+**Table of Contents**:
+
+Each of the following sections has its own instructions on how to get started
+making your own curations. If there's something unclear, please let us know
+via the [GitHub issue tracker](https://github.com/biopragmatics/bioregistry/issues/new),
+and we can improve this page.
+
+1. [Improving the Metaregistry](#improving-the-metaregistry)
+2. [Aligning Wikidata database records](#wikidata)
+3. [Curating regular expression patterns](#pattern)
+4. [Curating URI format strings](#formatter)
+5. [Curating example local unique identifiers](#example)
+
+## Improving the Metaregistry
+
+The Bioregistry processes and semi-automatically aligns metadata
+from external registries such as Identifiers.org, the OBO Foundry,
+FAIRsharing, and others. These alignments constitute the Bioregistry's
+_metaregistry_. Some resources (e.g., Identifiers.org)
+have similar scope, minimum metadata standards, and curation standards
+to the Bioregistry and are imported in full. Others are aligned only when
+prefixes can be matched based on an algorithm.
+
+This means that there are potentially many records in external registries
+that are relevant for the Bioregistry, but either were not able to be mapped
+to an existing prefix, or do not have a mapping but would be valuable to import.
+
+The following table links to curation sheets for each external registry
+that show relevant metadata to help curate each record as one of the following:
+
+1. Record corresponds to a prefix in the Bioregistry. Tutorial TBD.
+2. Record is relevant but does not have a corresponding prefix in the
+   Bioregistry. See the tutorial
+   on [importing external prefixes](import-external).
+3. Record is irrelevant for the bioregistry. See the tutorial
+   on [curating explicit prefix blacklists](blacklist-external).
+
+<table>
+<thead>
+   <tr>
+      <th>Prefix</th>
+      <th>Name</th>
+   </tr>
+</thead>
+<tbody>
+{% for entry in site.data.curation["prefix_xrefs"] %}
+   <tr>
+      <td>{{ entry.metaprefix }}</td>
+      <td><a href="https://github.com/biopragmatics/bioregistry/blob/main/exports/alignment{{ entry.metaprefix }}.tsv">{{ entry.name }}</a></td>
+   </tr>
+{% endfor %}
+</tbody>
+</table>
+
+<a id="wikidata"></a>
+## Aligning Wikidata Database Records
+
+The following entries in the Bioregistry have not been annotated with
+the `["wikidata"]["database"]` entry because it either exists in Wikidata and it
+needs to be annotated, or it does not exist in Wikidata and needs to be created,
+then annotated.
+
+### Creating a Wikidata item
+
+1. Make sure an item doesn't exist already by doing a cursory search of
+   Wikidata.
+2. Create a [new item](https://www.wikidata.org/wiki/Special:NewItem).
+3. Create the first relationship `instance of` ([P31](https://www.wikidata.org/wiki/Property:P31))
+   and target `biological database` ([Q4117139](https://www.wikidata.org/wiki/Q4117139)).
+4. Add second relationship `official website` ([P856](https://www.wikidata.org/wiki/Property:P856))
+5. Fill in any other information you want! `country`, `main subject`,
+   `maintained by`, etc.
+
+### Editing the Bioregistry
+
+1. Fork the repository, clone it, create a new branch, and edit the [src/bioregistry/data/bioregistry.json](https://github.com/bioregistry/bioregistry/edit/main/src/bioregistry/data/bioregistry.json) file locally. Check the [contribution guidelines](https://github.com/biopragmatics/bioregistry/blob/main/docs/CONTRIBUTING.md) for help on working with Git and GitHub
+2. Here's an example of `3dmet`, which has the Wikidata database annotated
+   properly.
+
+   ```json
+   {
+      "3dmet": {
+         "miriam": {
+            "deprecated": false,
+            "description": "3DMET is a database collecting three-dimensional structures of natural metabolites.",
+            "id": "00000066",
+            "name": "3DMET",
+            "namespaceEmbeddedInLui": false,
+            "pattern": "^B\\d{5}$",
+            "prefix": "3dmet"
+         },
+         "n2t": {
+            "prefix": "3dmet"
+         },
+         "wikidata": {
+            "database": "Q23948774",  // <-- this is it!!
+            "property": "P2796"
+         }
+      },
+      ...
+   }
+   ```
+
+<details>
+   <summary>Entries ({{ site.data.curation["wikidata"] | size }})</summary>
+   <table>
+   <thead>
+      <tr>
+         <th>Prefix</th>
+         <th>Name</th>
+      </tr>
+   </thead>
+   <tbody>
+   {% for entry in site.data.curation["wikidata"] %}
+      <tr>
+         <td>{{ entry.prefix }}</td>
+         <td><a href="{{ entry.homepage }}">{{ entry.name }}</a></td>
+      </tr>
+   {% endfor %}
+   </tbody>
+   </table>
+</details>
+
+<a id="pattern"></a>
+## Adding a Regular Expression Pattern for Each Resource's Local Unique Identifiers
+
+Same drill for patterns - these entries need a `["pattern"]` entry that includes
+a regular expression describing the local unique identifiers for this namespace.
+
+<details>
+   <summary>Entries ({{ site.data.curation["pattern"] | size }})</summary>
+   <table>
+   <thead>
+      <tr>
+         <th>Prefix</th>
+         <th>Name</th>
+      </tr>
+   </thead>
+   <tbody>
+   {% for entry in site.data.curation["pattern"] %}
+      <tr>
+         <td>{{ entry.prefix }}</td>
+         <td><a href="{{ entry.homepage }}">{{ entry.name }}</a></td>
+      </tr>
+   {% endfor %}
+   </tbody>
+   </table>
+</details>
+
+<a id="formatter"></a>
+## Curating URI Format Strings
+
+Same drill for URL Formatters - these entries need a `["uri_format"]` entry.
+This is a URL with a `$1` character where the local unique identifier gets put.
+
+```json
+{
+  ...
+  "jax": {
+    "example": "004435",
+    "name": "Jackson Laboratories Strain",
+    "uri_format": "https://www.jax.org/strain/$1"
+    // <-- this one here
+  },
+  ...
+}
+```
+
+<details>
+   <summary>Entries ({{ site.data.curation["formatter"] | size }})</summary>
+   <table>
+   <thead>
+      <tr>
+         <th>Prefix</th>
+         <th>Name</th>
+      </tr>
+   </thead>
+   <tbody>
+   {% for entry in site.data.curation["formatter"] %}
+      <tr>
+         <td>{{ entry.prefix }}</td>
+         <td><a href="{{ entry.homepage }}">{{ entry.name }}</a></td>
+      </tr>
+   {% endfor %}
+   </tbody>
+   </table>
+</details>
+
+<a id="example"></a>
+## Example Local Unique Identifier
+
+As a courtesy to newcomers, it's nice to show an example local unique
+identifier. These entries need a `["example"]` entry.
+
+```json
+{
+  ...
+  "jax": {
+    "example": "004435",
+    // <-- this one here
+    "name": "Jackson Laboratories Strain",
+    "url": "https://www.jax.org/strain/$1"
+  },
+  ...
+}
+```
+
+<details>
+   <summary>Entries ({{ site.data.curation["example"] | size }})</summary>
+   <table>
+   <thead>
+      <tr>
+         <th>Prefix</th>
+         <th>Name</th>
+      </tr>
+   </thead>
+   <tbody>
+   {% for entry in site.data.curation["example"] %}
+      <tr>
+         <td>{{ entry.prefix }}</td>
+         <td><a href="{{ entry.homepage }}">{{ entry.name }}</a></td>
+      </tr>
+   {% endfor %}
+   </tbody>
+   </table>
+</details>

testbed/biopragmatics__bioregistry/docs/datamodel.md

@@ -0,0 +1,244 @@
+---
+layout: page
+title: Data Model
+permalink: /datamodel/
+---
+The following section describes the contents of entries in the Bioregistry. The
+associated schema is encoded in Python classes using the [Pydantic
+package](https://github.com/samuelcolvin/pydantic) which also generates a
+generally reusable JSON schema. Each element of the schema has associated unit
+tests that are run on any change to the Bioregistry to ensure that not only the
+schema is conformant, but also enables higher-level tests for style and content
+to be implemented.
+
+<details>
+   <summary>Expand for a UML diagram of the datamodel</summary>
+   <img src="https://raw.githubusercontent.com/biopragmatics/bioregistry/main/docs/img/datamodel_umls.svg" alt="Bioregistry data model in a UML diagram"/>
+</details>
+
+## Metadata and Properties
+
+### Prefixes
+
+Each entry in the Bioregistry is annotated with a required canonical prefix
+(i.e., lower case, containing no strange punctuation or characters), an optional
+preferred prefix (i.e., containing stylization), and an optional list of
+alternate prefixes (i.e., synonyms).
+
+### Status
+
+Each includes flags if the resource for the prefix is deprecated (e.g. AERO),
+proprietary (e.g., NameRXN), or doesn't contain any terms (e.g., ChIRO). These
+flags are helpful in subjectively deciding which resources could be considered
+as reliable.
+
+### Name, Description, and Homepage
+
+All entries in the Bioregistry must have a name and description. This is
+important not only for active resources, but also for deprecated resources so
+the integrative registry can be used as a research tool and reference such as
+when encountering the variety of historically obscured cross references in OBO
+Foundry ontologies. All active resources must additionally have a homepage,
+while inactive resources may not have a homepage due to their respective sites
+being taken down. Entries are highly encouraged to include reference URLs and
+contributor free text comments, especially for deprecated resources to give
+context to readers.
+
+### License
+
+License information is only readily available via the OBO Foundry and Ontology
+Lookup Service. Most use permissive licenses from the Creative Commons (either
+CC-BY or CC-0). Some licenses include license versions and some do not. There
+are several instances of conflict, often due to specification of the version of
+the Creative Commons license. Licenses only appearing a small number of times,
+such as CC-BY-SA, CC-BY-NC, and CC-BY-NC-SA were collapsed into "Other".
+Licenses that were not appropriate for data (e.g., variants of the Apache
+License, GNU GPL) and custom licenses (e.g., in the case of the Human Phenotype
+Ontology) were also collapsed into "Other".
+
+### Version
+
+The OLS is the only registry that consumes the data it references and provides
+detailed accessible artifacts, and is therefore the only registry that reports
+version information. Other lookup services like AberOWL and OntoBee consume
+ontologies but do not generate metadata reports. The OBO Foundry also references
+versioned data, but does not consume it and therefore can not report version
+information. Wikidata also contains version information for some databases, but
+is not currently viable for generally tracking version information. The other
+registries (e.g., MIRIAM, N2T) do not report version information as their
+resolution services are independent of the data versions. Alternatively, the
+Bioversions project sets out to be a registry-independent solution for
+identifying current versions of different databases, ontologies, and resources.
+
+### Local Unique Identifiers
+
+All non-deprecated entries in the Bioregistry must include one or more example
+local unique identifiers. While each optionally (highly recommended) includes a
+regular expression pattern describing local unique identifiers, there are cases
+when they are difficult to generate due to the high complexity and heterogeneity
+of identifiers (e.g., Ensembl identifiers are highly complex), the lack of
+enough examples as is often the case with deprecated identifiers, or the
+triviality of assigning a wildcard pattern to a small enumerated namespace like
+FOAF, RDF, or RDFS.
+
+While the Bioregistry imports identifier regular expression patterns from
+several registries (i.e., MIRIAM/Identifiers.org, N2T, Prefix Commons, GO, and
+Wikidata), there exist many philosophical and practical discrepancies. A major
+one arises in the definition and management of redundant prefixes embedded in
+identifiers that is common to ontologies. For example, the colloquial local
+unique identifier for apoptosis in the Gene Ontology is GO:0006915, so the
+corresponding prefixed CURIE for this entity is GO:GO:0006915. Each registry
+handles cases like this slightly differently, whether it is to include the
+redundant prefix capitalized in the pattern, to include an extra flag in the
+metadata associated with the prefix, or whether to completely handle this
+programmatically.
+
+In order to promote backwards compatibility with some MIRIAM prefixes, entries
+can contain an annotation "namespace embedded in LUI" to allow for overriding of
+MIRIAM metadata as well as the "banana" which explicitly states how the
+namespace embedded in LUI appears, for situations where it is not the same as
+the prefix itself (e.g., HOG).
+
+Because there is such low consistency, the Bioregistry introduces a new field
+called the "banana" where the potentially redundant prefix can be explicitly
+enumerated, which allows for a general solution that can apply to FBbt, VariO,
+and other mixed-case embedded prefixes. The Bioregistry Python package includes
+functions for reformatting CURIEs based on the desired context (e.g., for
+general use, for compatibility with Identifiers.org). Further discussion on this
+topic can be found at https://github.com/biopragmatics/bioregistry/issues/191.
+
+### URI Format String
+
+Each entry optionally (highly recommended) includes one or more URI format
+strings that can be used to generate URIs for a local unique identifier.
+
+All active entries should have a provider, if possible. Deprecated resources
+likely do not have providers. Two persisting issues are due to providers being
+decommissioned but not removed from registries and the propagation of resolver
+services as providers which exacerbates the first. For example, because many
+ontologies use OBO-like PURLs, they are often annotated in registries as
+providers even though they do not resolve to anything. It is a future goal to
+provide more "health" checks over each registry and the Bioregistry as a whole.
+
+### Availability
+
+Each entry includes three optional fields for when the resource is available as
+an ontology in the OWL (https://www.w3.org/TR/owl2-syntax),
+OBO (https://owlcollab.github.io/oboformat/doc/obo-syntax.html), or OBO Graph
+JSON (https://github.com/geneontology/obographs) formats. These entries are
+typically imported from the OBO Foundry and OLS and are manually annotated to
+support large-scale ontology acquisition and processing such as with ROBOT,
+Pronto, or PyOBO.
+
+### Attribution
+
+Each includes two required attribution fields for the contributor and reviewer
+that each require a minimum of an ORCiD identifier and name with optional email
+address and GitHub handle. Each also includes an optional attribution field for
+an external contact person for the resource that could have either the ORCiD
+identifier, email, GitHub handle.
+
+## Ontological Relationships Between Prefixes
+
+In addition to metadata and properties, the Bioregistry includes rich
+ontological relationships between prefixes in the Bioregistry as well as
+external prefixes.
+
+### Exact Matches
+
+The most novel aspect of the Bioregistry is its ability to store equivalence
+mappings (e.g., skos:exactMatch) between Bioregistry records and external
+records (external records' semantics are mediated by the metaregistry). Each
+entry in the Bioregistry can contain several mappings to different databases.
+Typically, each prefix can only have one exact match in each database.
+Exceptions have arisen due to duplicate records, in which case the mapping is
+curated to the canonical external record. These records support interoperability
+by enabling conversion between the standard flavor of a prefix defined by the
+Bioregistry and context-specific variants.
+
+### Depends On
+
+Each entry contains a list of external entries that its associated resource
+depends on. This is particularly useful in ontologies, since they may either
+import terms from an external ontology or use external prefixes in their xrefs,
+provenance, or relationships. These are mostly imported from the OBO Foundry but
+also have an aspect of novel manual curation. While not explicitly stored in the
+source data, the Bioregistry python package infers the inverse relationship (
+i.e. appears in) for easy access given a prefix.
+
+### Provides
+
+While prefixes in the Bioregistry are supposed to correspond to nomenclature
+authorities, this is not always true because it imports from external sources
+that don't enforce this constraint. For example, the Comparative Toxicogenomics
+Database uses NCBI Gene for naming genes and MeSH for naming diseases and
+chemicals. Identifiers.org has minted 3 prefixes (ctd.gene, ctd.disease, and
+ctd.chemical) that mostly reflect the entries of the authorities for which they
+are providers. Another example is ValidatorDB, which provides information based
+on Protein Databank records. An even more exotic example are the Gene Ontology
+Annotations provided by the EBI because it provides for several types of
+identifiers including those from UniProt, RNA Central, and the ComplexPortal.
+
+Therefore, prefixes in the Bioregistry can be annotated with the prefix for
+which they provide (e.g., ctd.gene provides mesh). Along with the part of and
+has canonical relationships (described below), this relationship can promote
+better standardization and help deconvolute multiple prefixes that use the same
+URI format string, which is problematic when generating high quality prefix maps
+for use in CURIE-IRI interconversion.
+
+### Has Canonical
+
+While there should not be redundancies in the Bioregistry, there are several
+scenarios in which two or more prefixes equally correspond to the same
+nomenclature authority. Because these can not be merged without making the data
+model for the Bioregistry much more complicated and inaccessible, the has
+canonical annotation allows for the subjective choice of which is considered
+highest priority. A few scenarios in which this annotation is used are:
+
+1. A prefix has been replaced by another one (e.g., hgnc.genefamily was replaced
+   by hgnc.genegroup)
+2. A prefix is redundant of another (e.g., glycomedb is redundant of glytoucan,
+   pdb-ccd is redundant of pdb.ligand)
+3. Multiple prefixes are used by different groups for the same shared semantic
+   space, but none of them own it (e.g., insdc.run, ena.embl)
+
+Records in the has canonical relationship do not necessarily have the same URI
+format string, but if they do, this relationship further promotes choosing a
+deterministic prefix when parsing an IRI in combination with the provides and
+part of relationships.
+
+### Part Of
+
+There are several flavors of hierarchical relationships between prefixes in the
+Bioregistry annotated with the part of relationship. For example,
+chembl.compound and chembl.target are each a part of chembl and kegg.pathway and
+kegg.ligand are each a part of kegg. Connecting these prefixes provides
+significantly more context to readers of the Bioregistry. Other scenarios
+include:
+
+1. no shared prefix, has parent prefix (e.g., fbbt, fbcv, fbrf, ... and flybase)
+2. has shared prefix, has dot delimiter, has a parent prefix (e.g., kegg with
+   kegg.pathway, kegg.ligand),
+3. has shared prefix, has dot delimiter, no parent prefix (e.g.,
+   insdc.cds/insdc.gca/insdc.sra),
+4. has shared prefix, no dot delimiter, has a parent prefix (N/A)
+5. has shared prefix, no dot delimiter, no parent prefix (e.g., dlxb/dlxb,
+   NCBIGene/NCBIProtein/NCBITaxon)
+6. prefix matching resource name and extra prefixes (e.g., biogrid and
+   biogrid.interaction)
+
+In several cases such as KEGG and ChEMBL, the parent prefix and child prefixes
+share a URI format string. Practically, the parent prefix would be sufficient,
+but it is often pertinent to use a subspace to denote entity types within the
+nomenclature. In the case of KEGG, each different entity type has a different
+identifier pattern. In the case of ChEMBL, all different entity types have the
+same identifier pattern. Ultimately, the part of relationship is the last part
+combined with the provides and has canonical relationships along with a small
+amount of additional logic to construct a high-quality prefix map.
+
+The Rat Genome Database (RGD) constitutes an edge case with its three prefixes:
+rgd, rgd.qtl, and rgd.strain. The rgd prefix is more of a bucket than a parent -
+it includes all of the entity types (e.g., genes, articles) in the RGD that are
+neither quantitative trait loci (QTLs) nor strains. Because of cases like this,
+we have begun discussions on imposing a prefix subspacing policy
+at https://github.com/biopragmatics/bioregistry/issues/133.

testbed/biopragmatics__bioregistry/docs/glossary.md

@@ -0,0 +1,135 @@
+---
+layout: page
+title: Glossary
+permalink: /glossary/
+---
+This section introduces several terms and their technical definitions when used
+throughout this manuscript.
+
+## Resource
+
+A resource assigns unique identifiers to a collection of entities. This
+definition is effectively interchangeable with *namespace* and *semantic space*
+in the context of the Bioregistry and other registries.
+
+There are many types of resources such as ontologies (e.g., [Gene Ontology (GO)](https://bioregistry.io/go)
+, [Chemical Entities of Biological Interest (ChEBI)](https://bioregistry.io/chebi)
+, [Experimental Factor Ontology (EFO)](https://bioregistry.io/efo)), controlled
+vocabularies (e.g., [Entrez Gene](https://bioregistry.io/ncbigene)
+, [InterPro](https://bioregistry.io/interpro)
+, [FamPlex](https://bioregistry.io/famplex)
+, [HUGO Genome Nomenclature Consortium (HGNC)](https://bioregistry.io/hgnc), and
+databases (e.g., [Protein Data Bank (PDB)](https://bioregistry.io/pdb)
+, [Gene Expression Omnibus (GEO)](https://bioregistry.io/geo)).
+
+Some resources only cover single entity types (e.g., HGNC), some cover a small
+number (e.g., Gene Ontology), and some are expansive (e.g., [MeSH](https://bioregistry.io/mesh),
+[UMLS](https://bioregistry.io/umls), [NCI Thesaurus (NCIT)](https://bioregistry.io/efo)).
+
+Some resources are complete by definition (e.g., [Enzyme Classification](https://bioregistry.io/eccode)), 
+some resources are complete but subject to change (e.g., HGNC), and some are
+always incomplete (e.g., PDB).
+
+Resources do not always correspond one-to-one with projects, such as how the
+ChEMBL database contains both
+the [ChEMBL Compound](https://bioregistry.io/chembl.compound)
+and [ChEMBL Target](https://bioregistry.io/chembl.target)
+resources or how the Uber Anatomy Ontology (UBERON) contains
+both [UBERON](https://bioregistry.io/uberon)) and UBPROP resources for terms and
+properties, respectively.
+
+There are a variety of patterns used for identifiers, including
+integers (`^\d+$`; e.g., PubMed), zero padded integers (`^\d{7}$`; e.g., GO,
+ChEBI, other OBO Ontologies), universally unique identifiers (UUIDs; e.g., NCI
+Pathway Interaction Database, NDEx), and many other variations.
+
+## Record
+
+A record is an entry in the Bioregistry or other external registry that has
+information about a resource, such as its prefix, title, homepage, description,
+etc.
+
+## Provider
+
+A provider returns information about entities from a given resource. A provider
+is characterized by a URI format string into which an identifier from its
+resource can be substituted for a special token (e.g., `$1`). For example, the
+following formatter can be used to get a web page about a given HGNC entity
+based on its identifier by replacing the `$1` with a given HGNC gene identifier
+like `5173` for
+HRAS: `http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$1`.
+
+Well-behaved URI format strings only have one instance of the special token that
+occurs at the end. Poorly-behaved URI format strings may have additional
+characters following the special token as
+in `http://rebase.neb.com/rebase/enz/$1.html`
+for [REBASE](https://bioregistry.io/rebase) or as
+in http://eawag-bbd.ethz.ch/$1/$1_map.html for
+the [UM-BBD Pathway database](https://bioregistry.io/umbbd.pathway). Providers
+can return information HTML as in the previous example, images (e.g., https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&chebiId=132964
+for the ChEBI entry on fluazifop-P-butyl), XML (e.g., https://www.uniprot.org/uniprot/P10636.xml
+for UniProt entry on human
+Microtubule-associated protein tau), or any other information that can be
+transferred via HTTP, FTP, or related data transfer protocols. Alternatively,
+content negotiation could be used to return multiple kinds of data from the same
+provider URL. Most resources have an associated first-party provider that
+returns information via a web page. Some resources, like ChEBI, have several
+first-party providers for different content types (e.g., HTML, image). Some
+resources, like Entrez Gene, have additional external providers, including
+databases that use its identifiers like the Comparative Toxicogenomics
+Database (CTD). Some resources, such as many OBO ontologies, do not have an
+associated first party provider and rely solely on third party browsers like
+AberOWL, OntoBee, and the Ontology Lookup Service.
+
+## Registry
+
+A registry is a special kind of resource that assigns unique identifiers to a
+collection of resources. For historical reasons, these identifiers are
+colloquially called prefixes. A registry collects additional metadata about each
+resource, though there is a wide variety of metadata standards across existing
+registries (see https://bioregistry.io/related). These metadata may include the
+name, homepage, a regular expression pattern for validating identifiers, one or
+more example identifiers, a default provider, and potentially additional
+providers. Like with resources, a high-quality registry should have an
+associated first-party provider that comprises a web site for exploring its
+entries and their associated metadata. Some registries are directly imported and
+reused in other places (e.g., GO Registry reused in
+psi-mi-CV [https://github.com/HUPO-PSI/psi-ms-CV/blob/master/db-xrefs.yaml],
+NCBI GenBank Registry reused in https://www.ddbj.nig.ac.jp/ddbj/db_xref-e.html).
+
+## Metaregistry
+
+A metaregistry is a special kind of registry that assigns unique identifiers to
+a collection of registries; it could even contain an entry about itself. It
+collects additional metadata about each registry, such as a description of its
+metadata standards and capabilities (see https://bioregistry.io/related). Most
+importantly, a metaregistry contains mappings between equivalent entries in its
+constituent registries. Before the publication of this article, to the best of
+our knowledge, there were no dedicated metaregistries. Some registries such as
+FAIRSharing and the MIRIAM/Identifiers.org registry contain limited numbers of
+entries referring to other registries (e.g., BioPortal), but they neither
+delineate these records as representing registries, provide additional metadata,
+nor provide mappings.
+
+## Resolver
+
+A resolver uses a registry to generate a URL for a given prefix/identifier pair
+based on the registry's default provider for the resource with the given prefix,
+then redirects the requester to the constructed URL. Resolvers are different
+from providers in that they are general for many resources and do not host
+content themselves. Four well-known resolvers are purl.org, the OBO PURL
+service, and Identifiers.org. Name-To-Thing also includes other resolvers and is
+therefore sometimes called a meta-resolver.
+
+## Lookup Service
+
+A lookup service is like a provider but generalized to provide for many
+resources. They typically have a URL format string into which a compact
+identifier can be placed like OntoBee, but many require more complicated
+programmatic logic to construct. Some well-known lookup services are the OLS,
+AberOWL, OntoBee, and BioPortal.
+
+## Bioregistra
+
+Noun: a developer, contributor, user, or supporter of the Bioregistry who loves cute
+names for things. Plural: _Bioregistras_

testbed/biopragmatics__bioregistry/docs/guides/README.md

@@ -0,0 +1,33 @@
+# Curation Guides
+
+This folder contains various task-specific curation guides.
+
+- [Curating new providers](curation/providers)
+- [Curating new publications and references](curation/publications)
+
+## How to add new guides
+
+1. Create a new markdown file in this directory (`bioregistry/docs/guides/`)
+2. Use appropriate front-matter so that Jekyll can give it a permalink
+   (see
+   [here](https://github.com/biopragmatics/bioregistry/blob/fe2a685503ae2c9ff863908bf885c71fd240c21d/docs/guides/providers.md?plain=1#L1-L5)
+   for an example)
+3. Add it to the list above. Don't include a forward slash `/` in the beginning of the link!
+
+## What makes a good guide
+
+A good guide is able to educate and guide a curator through a new scenario.
+
+As a guide writer, you should assume a small amount of background knowledge on the Bioregistry
+and using GitHub, but effectively none about the internal structure of the Bioregistry repository
+nor its data schema.
+
+Your guide should do the following:
+
+1. Give some high-level motivation on what curation from your guide accomplishes
+2. Explain in what files curation should be done. Give links to that file on the GitHub main branch for the
+   repository, so they can navigate in the web browser and see it. 
+3. Explain how to do the curation 
+   - Give a step-by-step guide
+   - Illustrate your guide with screenshots, code blocks (with highlighting), 
+     permalinks to files or sections of files in the Bioregistry GitHub repository

testbed/biopragmatics__bioregistry/docs/guides/publications.md

@@ -0,0 +1,76 @@
+---
+layout: page
+title: Curating Publications and References
+permalink: /curation/publications
+---
+
+The example below shows a subset of the record for
+[3D Metabolites (3dmet)](https://bioregistry.io/3dmet) that highlights the `publications` list.
+Note that each entry is a dictionary with several parts:
+
+1. `title` (required) - the title of the paper
+2. `year` (highly recommended) - the year of publication of the paper
+3. `pubmed`, `doi`, and `pmc` (one or more required) - identifiers for the paper
+
+```json
+"3dmet": {
+    "name": "3D Metabolites",
+    "publications": [
+      {
+        "doi": "10.2142/biophysico.15.0_87",
+        "pmc": "PMC5992871",
+        "pubmed": "29892514",
+        "title": "Chemical curation to improve data accuracy: recent development of the 3DMET database",
+        "year": 2018
+      },
+      {
+        "doi": "10.1021/ci300309k",
+        "pubmed": "23293959",
+        "title": "Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures",
+        "year": 2013
+      }
+    ]
+  },
+```
+
+Similarly, there are URL references that are not _publications_ that are worth curating. These can be
+stored in the `references` list. For example, the 
+[Registry of Toxic Effects of Chemical Substances (rtecs)](https://bioregistry.io/rtecs) entry appears in the
+Bioregistry because of its usage, but it is hard to find information on the internet about it. Therefore, the
+references list is perfect for storing references to PDFs and webpages that describe the resource.
+
+```json
+"rtecs": {
+   "name": "Registry of Toxic Effects of Chemical Substances",
+   "publications": [
+   {
+      "doi": "10.1016/s1074-9098%2899%2900058-1",
+      "title": "An overview of the Registry of Toxic Effects of Chemical Substances (RTECS): Critical information on chemical hazards",
+      "year": 1999
+   }
+   ],
+   "references": [
+      "https://www.cdc.gov/niosh/docs/97-119/pdfs/97-119.pdf",
+      "https://www.cdc.gov/niosh/npg/npgdrtec.html"
+   ]
+}
+```
+
+What else is good to keep track of in the references list:
+
+1. Bioregistry issue or pull requests about the resource
+2. Links to webpages describing the identifier resource
+3. Links to discussions on Slack or other platforms (keeping in mind links might not last forever)
+4. Any other context that's useful for a Bioregistry reader
+
+## Why Should I Curate Publications and References?
+
+1. They give additional context for Bioregistry readers who want to know more about the paper
+2. They make it easier to attribute usage of identifiers from a given resource to its authors
+3. They enable global landscape analysis of when and where identifier resources are being made. The following image is
+   automatically regenerated with each Bioregistry update:
+
+   ![](https://raw.githubusercontent.com/biopragmatics/bioregistry/refs/heads/main/docs/img/bibliography_years.svg)
+4. They support the training of a machine learning for semi-automated curation of additional literature. See
+   this [talk](https://docs.google.com/presentation/d/1h2IajyGkUxUPHubEi8_WE6xW6TOuOihn5zsmi4kYrrc/edit?usp=sharing)
+   from the 2022 Workshop on Prefixes, CURIEs, and IRIs.

testbed/biopragmatics__bioregistry/docs/health.md

@@ -0,0 +1,137 @@
+---
+layout: page
+title: Health Report
+permalink: /health/
+---
+
+{% assign run = site.data.health.runs[0] %}
+
+Of the {{ run.summary.total_measured }} prefixes in the Bioregistry that have
+both an example local unique identifiers and at least one URI format string,
+{{ run.summary.total_success }} ({{ run.summary.success_percent }}%)
+were able to resolve (with a HTTP 200 status code) and {{ run.summary.total_failed }}
+({{ run.summary.failure_percent }}%) were not.
+
+This comes with a few caveats:
+
+1. Some websites do not send appropriate HTTP statuses, and may return HTTP 200
+   even when redirecting to a default "Page Not Found" page. This means that this
+   number might be artificially high.
+2. There are several reasons why resolution might fail, some of which are false
+   positives (see below).
+
+## Background
+
+### Why Does Resolution Fail?
+
+1. Often, the website suffered from a temporary issue and failed to resolve during
+   check, but still works. Because this is possible, it's better to compare the
+   last few checks for any newly failing prefixes.
+2. **gone** - The website has been fully taken down. This often happens to academic websites
+3. **hijacked** - The website has been replaced with another unrelated website, and the URI
+   format does not correspond to an existing endpoint anymore (e.g., the old
+   site for `atfdb.family` has been replaced by something unrelated).
+4. **moved** - The website has been updated, and the URI format does not correspond to an
+   existing endpoint anymore (solvable with additional curation).
+5. **degraded** - The website has been modified, and it's no longer possible to link directly to a page for an entity
+   (e.g., the site switched to using form data or has a single page application)
+6. **uri-only** - The website never existed in the first place. Some URI format strings are
+   generated as artifacts of ontology curation,
+   e.g., with [Protégé](https://protege.stanford.edu), and were not meant to
+   resolve. Ontologies typically use IRIs (a superset of URIs), which do not
+   necessarily imply that their content are resolvable as a URL.
+7. **misconfigured** - The URI corresponds to a redirect that is misconfigured in the redirection
+   service (e.g., this happened for several CropOCT ontologies
+   (ref: [#527](https://github.com/biopragmatics/bioregistry/issues/527)) and
+   sporadically for the OBO PURL service).
+8. **curation-error** - The URI format string was curated incorrectly.
+
+### Why Store URI Formats for Dead Resources?
+
+It's still valuable to store URI format strings, even if the websites don't work
+anymore (or never did in the first place), because URIs based on these URI
+format strings may appear in biomedical resources like ontologies or databases.
+This makes the Bioregistry a more valuable tool for parsing these URIs and
+ultimately for standardizing data.
+
+{% if run.delta %}
+## Changes
+
+There are {{ run.delta.alive }} prefixes that remain passing and
+{{ run.delta.dead }} that remained failing.
+
+{% if run.delta.new.size > 0 or run.delta.fallen.size > 0 %}
+### New failures
+
+The following resources were passing in the previous check but not in the current check:
+
+<ul>
+{% for prefix in run.delta.new %}
+<li><a href="https://bioregistry.io/{{ prefix }}">{{ prefix }}</a> (first check)</li>
+{% endfor %}
+{% for prefix in run.delta.fallen %}
+<li><a href="https://bioregistry.io/{{ prefix }}">{{ prefix }}</a></li>
+{% endfor %}
+</ul>
+{% endif %}
+
+{% if run.delta.revived and run.delta.revived.size > 0 %}
+### Revived
+
+The following resources failed in the previous check but passed in the current check:
+
+<ul>
+{% for prefix in run.delta.revived %}
+<li><a href="https://bioregistry.io/{{ prefix }}">{{ prefix }}</a></li>
+{% endfor %}
+</ul>
+{% endif %}
+
+{% if run.delta.forgotten and run.delta.forgotten.size > 0 %}
+### Forgotten
+
+The following resources tested in the previous check but not this check:
+
+<ul>
+{% for prefix in run.delta.forgotten %}
+<li><a href="https://bioregistry.io/{{ prefix }}">{{ prefix }}</a></li>
+{% endfor %}
+</ul>
+{% endif %}
+{% endif %}
+
+## Results
+
+These results were run on {{ run.date }}.
+
+<table>
+   <thead>
+      <tr>
+         <th>Prefix</th>
+         <th>Example LUID</th>
+         <th>Status</th>
+      </tr>
+   </thead>
+   <tbody>
+   {% for record in run.results %}
+      {% if record.exception %}
+         {% assign color = "#FFDDDB" %}
+      {% elsif record.status_code == 200 %}
+         {% assign color = "#B0EEB0" %}
+      {% else %}
+         {% assign color = "#FFFFE0" %}
+      {% endif %}
+      <tr style="background-color: {{ color }}">
+         <td><a href="https://bioregistry.io/{{ record.prefix }}">{{ record.prefix }}</a></td>
+         <td><a href="{{ record.url | uri_escape }}">{{ record.example | truncate: 30 }}</a></td>
+         <td>
+            {% if record.exception %}
+                {{ record.exception }}
+            {% else %}
+                HTTP {{ record.status_code }}
+            {% endif %}
+        </td>
+      </tr>
+   {% endfor %}
+   </tbody>
+</table>

testbed/biopragmatics__bioregistry/docs/index.md

@@ -0,0 +1,11 @@
+---
+layout: home
+---
+<p align="center">
+  <img src="https://raw.githubusercontent.com/bioregistry/bioregistry/main/docs/source/logo.png" height="150">
+</p>
+
+An integrative meta-registry of biological databases, ontologies, and nomenclatures. See the full listing
+at [https://bioregistry.io/registry](https://bioregistry.io/registry/). This site hosts the curation and warning
+summary pages, automatically generated and served with GitHub Pages.
+

testbed/biopragmatics__bioregistry/docs/source/alignment.rst

@@ -0,0 +1,3 @@
+Alignment
+=========
+.. automodapi:: bioregistry.external

testbed/biopragmatics__bioregistry/docs/source/cli.rst

@@ -0,0 +1,8 @@
+Command Line Interface
+======================
+bioregistry automatically installs the command :code:`bioregistry`. See
+:code:`bioregistry --help` for usage details.
+
+.. click:: bioregistry.cli:main
+   :prog: bioregistry
+   :show-nested:

testbed/biopragmatics__bioregistry/docs/source/conf.py

@@ -0,0 +1,256 @@
+"""
+Configuration file for the Sphinx documentation builder.
+
+This file does only contain a selection of the most common options. For a
+full list see the documentation:
+http://www.sphinx-doc.org/en/master/config
+
+-- Path setup --------------------------------------------------------------
+
+If extensions (or modules to document with autodoc) are in another directory,
+add these directories to ``sys.path`` here. If the directory is relative to the
+documentation root, use ``os.path.abspath`` to make it absolute, like shown here.
+"""
+
+import os
+import re
+import sys
+from datetime import date
+
+sys.path.insert(0, os.path.abspath("../../src"))
+
+# -- Project information -----------------------------------------------------
+
+project = "bioregistry"
+copyright = f"{date.today().year}, Charles Tapley Hoyt"
+author = "Charles Tapley Hoyt"
+
+# The full version, including alpha/beta/rc tags.
+release = "0.11.19-dev"
+
+# The short X.Y version.
+parsed_version = re.match(
+    r"(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?",
+    release,
+)
+version = parsed_version.expand(r"\g<major>.\g<minor>.\g<patch>")
+
+if parsed_version.group("release"):
+    tags.add("prerelease")  # noqa: F821
+
+
+# See https://about.readthedocs.com/blog/2024/07/addons-by-default/
+# Define the canonical URL if you are using a custom domain on Read the Docs
+html_baseurl = os.environ.get("READTHEDOCS_CANONICAL_URL", "")
+
+# See https://about.readthedocs.com/blog/2024/07/addons-by-default/
+# Tell Jinja2 templates the build is running on Read the Docs
+if os.environ.get("READTHEDOCS", "") == "True":
+    if "html_context" not in globals():
+        html_context = {}
+    html_context["READTHEDOCS"] = True  # noqa: F821
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+add_module_names = False
+
+# A list of prefixes that are ignored when creating the module index. (new in Sphinx 0.6)
+modindex_common_prefix = ["bioregistry."]
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    # 'sphinx.ext.mathjax',
+    "sphinx.ext.viewcode",
+    "sphinx_click.ext",
+    "sphinx_automodapi.automodapi",
+    "sphinx_automodapi.smart_resolver",
+    "sphinxcontrib.autodoc_pydantic",
+    # 'texext',
+]
+
+# generate autosummary pages
+autosummary_generate = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = {
+    ".rst": "restructuredtext",
+}
+
+# The master toctree document.
+master_doc = "index"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#
+if os.path.exists("logo.png"):
+    html_logo = "logo.png"
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "bioregistry_doc"
+
+# -- Options for LaTeX output ------------------------------------------------
+
+# latex_elements = {
+#     The paper size ('letterpaper' or 'a4paper').
+#
+#     'papersize': 'letterpaper',
+#
+#     The font size ('10pt', '11pt' or '12pt').
+#
+#     'pointsize': '10pt',
+#
+#     Additional stuff for the LaTeX preamble.
+#
+#     'preamble': '',
+#
+#     Latex figure (float) alignment
+#
+#     'figure_align': 'htbp',
+# }
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+# latex_documents = [
+#     (
+#         master_doc,
+#         'bioregistry.tex',
+#         'Bioregistry Documentation',
+#         author,
+#         'manual',
+#     ),
+# ]
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (
+        master_doc,
+        "bioregistry",
+        "Bioregistry Documentation",
+        [author],
+        1,
+    ),
+]
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "bioregistry",
+        "Bioregistry Documentation",
+        author,
+        "Charles Tapley Hoyt",
+        "An integrative registry of biological databases, ontologies, and nomenclatures.",
+        "Miscellaneous",
+    ),
+]
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+# epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+# epub_exclude_files = ['search.html']
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+# Note: don't add trailing slashes, since sphinx adds "/objects.inv" to the end
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "rdflib": ("https://rdflib.readthedocs.io/en/stable/", None),
+    "pandas": ("https://pandas.pydata.org/docs", None),
+}
+
+autoclass_content = "both"
+
+# Don't sort alphabetically, explained at:
+# https://stackoverflow.com/questions/37209921/python-how-not-to-sort-sphinx-output-in-alphabetical-order
+autodoc_member_order = "bysource"
+
+todo_include_todos = True
+todo_emit_warnings = True

testbed/biopragmatics__bioregistry/docs/source/curation.rst

@@ -0,0 +1,7 @@
+Curation
+========
+There are several curation workflows implemented in :mod:`bioregistry.curation`.
+
+Bulk Import
+-----------
+.. automodapi:: bioregistry.curation.bulk_import

testbed/biopragmatics__bioregistry/docs/source/deployment.rst

@@ -0,0 +1,198 @@
+Deploying the Bioregistry
+=========================
+The Bioregistry web application is a part of the ``bioregistry`` Python package which is updated,
+packaged, and pushed weekly to the `Python Package Index (PyPI) <https://pypi.org/project/bioregistry/>`_.
+A new deploy can also be triggered by admins using the
+`update workflow <https://github.com/biopragmatics/bioregistry/actions/workflows/update.yml>`_ on GitHub.
+It can be installed and run interactively in the command line with the following commands:
+
+.. code-block:: shell
+
+    python -m pip install --upgrade gunicorn bioregistry[web]
+    python -m bioregistry web \
+        --with-gunicorn --workers 4 \
+        --port 8766 \
+        --host "0.0.0.0" \
+        --base-url https://example.com
+
+.. note::
+
+    The Bioregistry uses port 8766 by default. Using ``0.0.0.0`` makes sure that this
+    works on a variety of systems, including docker, Mac, and Linux. The ``--base-url``
+    should correspond to the location through which the service is accessed. In this
+    example, https://example.com is used as the base.
+
+The Bioregistry is also containerized and pushed during the weekly build to
+`Docker Hub <https://hub.docker.com/r/biopragmatics/bioregistry>`_.
+You can pull then run the latest in the command line with the following commands:
+
+.. code-block:: shell
+
+    docker pull biopragmatics/bioregistry:latest
+    docker run --detach -i --name bioregistry -p 8766:8766 biopragmatics/bioregistry:latest
+
+Note that ``-p`` says what ports to remap. Note that the base Bioregistry image uses ``8766``
+as its port, so this is simply exposed via the same port.
+
+The following shell script can be used to automatically update the containerized deployment:
+
+.. code-block:: shell
+
+    # restart.sh
+    #!/bin/bash
+
+    # Store the container's hash
+    BIOREGISTRY_CONTAINER_ID=$(docker ps --filter "name=bioregistry" -aq)
+
+    # Stop and remove the old container, taking advantage of the fact that it's named specifically
+    if [ -n "BIOREGISTRY_CONTAINER_ID" ]; then
+      docker stop $BIOREGISTRY_CONTAINER_ID
+      docker rm $BIOREGISTRY_CONTAINER_ID
+    fi
+
+    # Pull the latest
+    docker pull biopragmatics/bioregistry:latest
+
+    # Run the start script
+    docker run --detach -i --name bioregistry -p 8766:8766 biopragmatics/bioregistry:latest
+
+Deploying a custom Bioregistry
+==============================
+This is a tutorial on how to run a custom instance of the Bioregistry that contains custom content.
+If you don't need custom content, see the instructions above for deploying a vanilla copy of the Bioregistry.
+
+Creating custom content
+-----------------------
+In the following example, a slimmed down registry is generated from the base
+Bioregistry. It's also possible to add additional :class:`bioregistry.Resource`
+instances from arbitrary sources.
+
+.. code-block:: python
+
+    import bioregistry
+    from pathlib import Path
+
+    slim_prefixes = {"chebi", "go", "ncbitaxonomy"}
+    slim_registry: dict[str, bioregistry.Resource] = {
+        resource.prefix: resource
+        for resource in bioregistry.resources()
+        if resource.prefix in slim_prefixes
+    }
+    bioregistry.write_registry(
+        slim_registry,
+        path=Path.home().joinpath("Desktop", "registry.json"),
+    )
+
+This script creates a new file that will be used when running the Bioregistry
+with the ``--registry`` flag from the command line.
+
+.. note:: The same is possible for collections, contexts, and even the metaregistry.
+
+Custom configuration and branding
+---------------------------------
+The Bioregistry can be configured in several ways, including replacing various text in
+the case of custom deployments. Please use good judgement with the following features to
+best represent the Bioregistry project. The following table includes the keys that you
+can put in a configuration JSON file, an explanation of the keys, and suggestions on
+how to replace them.
+
++--------------------------------------+----------------------------------------------------------+
+| Key                                  | Description                                              |
++======================================+==========================================================+
+| ``METAREGISTRY_TITLE``               | The title on the home page, defaults to "Bioregistry".   |
++--------------------------------------+----------------------------------------------------------+
+| ``METAREGISTRY_HEADER``              | The header text on the home page. Can include arbitrary  |
+|                                      | HTML. Suggestions: use a ``<p class="lead">``.           |
++--------------------------------------+----------------------------------------------------------+
+| ``METAREGISTRY_FOOTER``              | The footer text that appears on all pages. Can include   |
+|                                      | arbitrary HTML.                                          |
++--------------------------------------+----------------------------------------------------------+
+| ``METAREGISTRY_RESOURCES_SUBHEADER`` | The second paragraph on https://bioregistry.io/registry. |
++--------------------------------------+----------------------------------------------------------+
+| ``METAREGISTRY_VERSION``             | The version to display in the top-right of each page.    |
+|                                      | Can be set to an empty string if no meaningful version   |
+|                                      | information exists.                                      |
++--------------------------------------+----------------------------------------------------------+
+| ``METAREGISTRY_EXAMPLE_PREFIX``      | An example prefix. Defaults to ``chebi``.                |
++--------------------------------------+----------------------------------------------------------+
+| ``METAREGISTRY_EXAMPLE_IDENTIFIER``  | An example local unique identifier to go with the        |
+|                                      | example prefix                                           |
++--------------------------------------+----------------------------------------------------------+
+
+Finally, after filling up a configuration JSON file and naming it something like ``config.json``,
+you can use the ``--config config.json`` flag in the Python commands to run the web service below.
+
+Running in the command line with Python
+---------------------------------------
+The Bioregistry can be run from the Python shell directly following installation
+from the Python Package Index. This example assumes ``registry.json``
+is in the same directory, but any valid paths can be given.
+
+.. code-block:: shell
+
+    python -m pip install gunicorn bioregistry[web]
+    python -m bioregistry web \
+        --with-gunicorn --workers 4 \
+        --port 8766 \
+        --host "0.0.0.0" \
+        --base-url https://example.com \
+        --registry registry.json
+
+.. note:: This is the same as deploying the vanilla Bioregistry except the usage of ``--registry registry.json``
+
+Running with Docker
+-------------------
+Create the following ``Dockerfile`` in the same directory as your ``registry.json``, ``config.json``,
+and any other custom files.
+
+.. code-block:: docker
+
+    # Dockerfile
+    FROM python:3.11-alpine
+
+    COPY registry.json
+    COPY config.json
+
+    RUN python -m pip install gunicorn bioregistry[web]
+    ENTRYPOINT python -m bioregistry web \
+        ---with-gunicorn --workers 4 \
+        --port 8766 \
+        --host "0.0.0.0" \
+        --base-url https://example.com \
+        --registry registry.json \
+        --config config.json
+
+There are two options for running the ``Dockerfile``. The first option
+is by running the following two commands in the command line:
+
+.. code-block:: shell
+
+    # Build the docker image from the same directory as the Dockerfile
+    docker build --tag bioregistry_custom:latest .
+
+    # Run the docker image, -d means "detach"
+    docker run -d -p 8766:8766 bioregistry_custom:latest
+
+The second option is to use an additional `Docker compose <https://docs.docker.com/compose/>`_
+file to orchestrate building, tagging, and running. It works by creating (yet another)
+configuration file ``docker-compose.yml`` in the same directory as ``Dockerfile`` with
+the following:
+
+.. code-block:: yaml
+
+    # docker-compose.yml
+    version: '3'
+    services:
+      app:
+        build: .
+        restart: always
+        ports:
+          - "8766:8766"
+
+.. note:: This is a relatively simple configuration, Docker Compose is capable of much more than this in general
+
+The following command can be used to bring up the docker-compose configuration:
+
+.. code-block:: shell
+
+    docker-compose up

testbed/biopragmatics__bioregistry/docs/source/index.rst

@@ -0,0 +1,66 @@
+Bioregistry |release| Documentation
+===================================
+The Bioregistry is an integrative, open, community-driven meta-registry
+of databases, ontologies, and other nomenclature resources in the life sciences.
+It relies on an open code, open data, and open infrastructure paradigm to support
+its longevity along with a sustainable governance model that enables community
+curation and discussion.
+
+This documentation is specifically for the Python package that can
+access the Bioregistry and use it for common tasks like metadata lookup,
+CURIE expansion, URI contraction, and more.
+
+.. seealso::
+
+    - `About this project <https://bioregistry.io/summary>`_
+    - `Bioregistry Website <https://bioregistry.io>`_
+    - `A list of all prefixes <https://bioregistry.io/registry/>`_
+    - `Source Code on GitHub <https://github.com/biopragmatics/bioregistry>`_
+    - `Data Downloads <https://github.com/biopragmatics/bioregistry/tree/main/exports>`_
+    - `Project Governance <https://github.com/biopragmatics/bioregistry/blob/main/docs/GOVERNANCE.md>`_
+    - `Contribution Guidelines <https://github.com/biopragmatics/bioregistry/blob/main/docs/CONTRIBUTING.md>`_
+    - `Programming language-agnostic API <https://bioregistry.io/apidocs>`_
+    - `Python Package on PyPI <https://pypi.org/project/bioregistry>`_
+    - `Docker container on DockerHub <https://hub.docker.com/r/biopragmatics/bioregistry>`_
+
+Installation
+------------
+The most recent release of the Bioregistry Python package can be installed from
+`PyPI <https://pypi.org/project/bioregistry>`_ with:
+
+.. code-block:: shell
+
+    $ pip install bioregistry
+
+The most recent code and data can be installed directly from GitHub with:
+
+.. code-block:: shell
+
+    $ pip install git+https://github.com/biopragmatics/bioregistry.git
+
+To install in development mode, use the following:
+
+.. code-block:: shell
+
+    $ git clone git+https://github.com/biopragmatics/bioregistry.git
+    $ cd bioregistry
+    $ pip install -e .
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Getting Started
+   :name: start
+
+   reference
+   alignment
+   cli
+   pandas
+   deployment
+   curation
+
+Indices and Tables
+------------------
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

testbed/biopragmatics__bioregistry/docs/source/pandas.rst

@@ -0,0 +1,4 @@
+Tabular Data Processing
+=======================
+.. automodule:: bioregistry.pandas
+    :members:

testbed/biopragmatics__bioregistry/docs/source/reference.rst

@@ -0,0 +1,9 @@
+Reference
+=========
+This page includes the reference documentation for all
+user-facing code from the Bioregistry Python package.
+
+.. automodapi:: bioregistry
+    :no-heading:
+    :no-main-docstr:
+    :no-inheritance-diagram:

testbed/biopragmatics__bioregistry/docs/users.md

@@ -0,0 +1,64 @@
+---
+layout: page
+title: Who's Using the Bioregistry?
+permalink: /usages/
+---
+
+Are you using the Bioregistry and want your project/organization on this list?
+Please let us know on the [issue tracker](https://github.com/biopragmatics/bioregistry/issues/new).
+
+To find new users, start with
+this [GitHub search for the Bioregistry](https://github.com/search?q=%22import+bioregistry%22+OR+%22from+bioregistry+import%22+-user%3Acthoyt+-user%3Asorgerlab+-user%3Abiopragmatics+-is%3Afork+-user%3Apyobo+-user%3Apybel+-user%3Agyorilab&type=code).
+Similarly, downstream users of the Bioregistry often use the [`curies`](https://github.com/cthoyt/curies) package.
+See its usages
+with [this search](https://github.com/search?q=%22import+curies%22+OR+%22from+curies+import%22+-user%3Acthoyt+-user%3Asorgerlab+-user%3Abiopragmatics+-is%3Afork+-user%3Apyobo+-user%3Apybel+-user%3Agyorilab+-repo%3ANCATS-Gamma%2Frobokop+-repo%3Anutanix%2Fcurie+language%3APython&type=code&p=4&l=Python).
+
+{% for entry in site.data.usages %}
+
+### {{ entry.name }}{% if entry.logo %}<img src="{{ entry.logo }}" style="margin-left: 5px; max-height: 35px;" />{% endif %}
+
+<table class="table">
+{% if entry.description %}
+<tr>
+<td><strong>Description</strong></td>
+<td>{{ entry.description }}</td>
+</tr>
+{% endif %}
+<tr>
+<td><strong>Type</strong></td>
+<td>{{ entry.type | capitalize }}</td>
+</tr>
+<tr>
+<td><strong>Homepage</strong></td>
+<td><a href="{{ entry.homepage }}">{{ entry.homepage }}</a></td>
+</tr>
+{% if entry.repository and entry.repository != entry.homepage %}
+<tr>
+<td><strong>Repository</strong></td>
+<td><a href="{{ entry.repository }}">{{ entry.repository }}</a></td>
+</tr>
+{% endif %}
+{% if entry.wikidata %}
+<tr>
+<td><strong>Wikidata</strong></td>
+<td><a href="https://scholia.toolforge.org/{{ entry.wikidata }}">{{ entry.wikidata }}</a></td>
+</tr>
+{% endif %}
+<tr>
+<td><strong>Usages</strong></td>
+<td>
+<ul>
+{% for usage in entry['uses'] %}
+<li>
+{{ usage['description'] }}
+{% for link in usage['links'] %}
+ <a href="{{ link }}">(ref)</a>
+{% endfor %}
+</li>
+{% endfor %}
+</ul>
+</td>
+</tr>
+</table>
+
+{% endfor %}

testbed/biopragmatics__bioregistry/docs/warnings.md

@@ -0,0 +1,115 @@
+---
+layout: page
+title: Warnings
+permalink: /warnings/
+---
+This lists any sorts of things that should be fixed upstream, but are instead
+manually curated in the Bioregistry.
+
+## License Conflicts
+
+The following chart shows which manual annotations in the OBO Foundry are
+inconsistent with those extracted by the OLS.
+
+<table>
+   <thead>
+      <tr>
+         <th>Prefix</th>
+         <th>OBO License</th>
+         <th>OLS License</th>
+      </tr>
+   </thead>
+   <tbody>
+   {% for entry in site.data.warnings["license_conflict"] %}
+      <tr>
+         <td><a href="https://bioregistry.io/{{ entry.prefix }}"><code>{{ entry.prefix }}</code></a></td>
+         <td><code>{{ entry.obo }}</code></td>
+         <td><code>{{ entry.ols }}</code></td>
+      </tr>
+   {% endfor %}
+   </tbody>
+</table>
+
+## MIRIAM
+
+The following issues are with the integrity of the data in the MIRIAM registry (
+identifiers.org).
+
+### Incorrect Pattern
+
+The following entries have an incorrect value in the `pattern` field.
+
+<table>
+   <thead>
+      <tr>
+         <th>Prefix</th>
+         <th>Name</th>
+         <th>MIRIAM</th>
+         <th>Correct</th>
+      </tr>
+   </thead>
+   <tbody>
+   {% for entry in site.data.warnings["wrong_patterns"] %}
+      <tr>
+         <td><code>{{ entry.prefix }}</code></td>
+         <td><a href="{{ entry.homepage }}">{{ entry.name }}</a></td>
+         <td><code>{{ entry.miriam }}</code></td>
+         <td><code>{{ entry.correct }}</code></td>
+      </tr>
+   {% endfor %}
+   </tbody>
+</table>
+
+### Embedding of Namespace in LUI
+
+The following entries have an incorrect value in the `namespaceEmbeddedInLui`
+field.
+
+<table>
+   <thead>
+      <tr>
+         <th>Prefix</th>
+         <th>Name</th>
+         <th>Pattern</th>
+         <th>MIRIAM</th>
+         <th>Correct</th>
+      </tr>
+   </thead>
+   <tbody>
+   {% for entry in site.data.warnings["embedding_rewrites"] %}
+      <tr>
+         <td><code>{{ entry.prefix }}</code></td>
+         <td><a href="{{ entry.homepage }}">{{ entry.name }}</a></td>
+         <td>{{ entry.pattern }}</td>
+         <td>{{ entry.miriam }}</td>
+         <td>{{ entry.correct }}</td>
+      </tr>
+   {% endfor %}
+   </tbody>
+</table>
+
+### Prefix Mismatch when Namespace Embedded in LUI
+
+When the namespace is embedded in the LUI, it's expected that the prefix should
+be uppercased. This is often not the case.
+
+<table>
+   <thead>
+      <tr>
+         <th>Prefix</th>
+         <th>Name</th>
+         <th>Pattern</th>
+         <th>Correct Prefix</th>
+      </tr>
+   </thead>
+   <tbody>
+   {% for entry in site.data.warnings["prefix_rewrites"] %}
+      <tr>
+         <td><code>{{ entry.prefix }}</code></td>
+         <td><a href="{{ entry.homepage }}">{{ entry.name }}</a></td>
+         <td><code>{{ entry.pattern }}</code></td>
+         <td><code>{{ entry.correct }}</code></td>
+      </tr>
+   {% endfor %}
+   </tbody>
+</table>

testbed/biopragmatics__bioregistry/exports/alignment/agroportal.tsv

@@ -0,0 +1,108 @@
+prefix	name	homepage	description
+AEO	Agricultural Experiments Ontology	http://lovinra.inra.fr/	AEO is an ontology aimed to represent objects related to agricultural practices.
+AFEO	Agri-Food Experiment Ontology	http://opensilex.org/vocabulary/2016/v1/afeo.owl	The Agri-Food Experiment Ontology (AFEO), a new ontology network was developed based on two existing ontology resources, i.e., OAE (Ontology for Agriculture Experiment) and OFPE (Ontology for Food Processing Experiment).
+AFO	Agriculture and Forestry Ontology		The Agriculture and Forestry Ontology (AFO) is based on the Agriforest thesaurus maintained by the Viikki Campus Library, University of Helsinki. The combination of AFO and the Finnish General Upper Ontology YSO has been created in the FinnONTO project by the Viikki Science Library in cooperation with the Semantic Computing Research Group. The ontology was created by aligning the Agriculture and Forestry Ontology with the Finnish General Upper Ontology (YSO) using the top ontology and other modelling principles of YSO. This way the equivalent and differing concepts and their links to more general concepts could be explicitly described. This combination of ontologies can be used for describing resources especially in domain of agriculture, forestry, veterinary medicine, food science, environmental science and biology.
+AGFOOD	Agri-food vocabulary	http://www.inist.fr	"This bilingual vocabulary contains 3117 concepts covering the domains of agri-food science and technology, ranging ""from farm to table"", as well as nutritional and environmental aspects, taking into account the ongoing agricultural and food transition. The terminology is enriched with a large number of alternative entries (3230 in English or French) and hidden terms for easy searching., Ce vocabulaire bilingue comprend 3117 concepts des domaines de la science et de la technologie agroalimentaire, allant « de la ferme à la table », ainsi que des aspects nutritionnels et environnementaux, tenant compte de la transition agricole et alimentaire en cours. La terminologie est enrichie d’un grand nombre d’accès synonymes (3230 en français ou en anglais) et de formes cachées facilitant la recherche. Il est aligné avec l’ontologie FoodOn., taking into account the ongoing agricultural and food transition. The terminology is enriched with a large number of alternative entries (3230 in English or French) and hidden terms for easy searching. It has been aligned with the FoodOn ontology., Este vocabulario bilingüe (francés e inglés) contiene 3117 conceptos que abarcan los ámbitos de la ciencia y la tecnología agroalimentarias, que van ""de la granja a la mesa"", así como aspectos nutricionales y medioambientales, teniendo en cuenta la transición agrícola y alimentaria en curso. La terminología se enriquece con un gran número de entradas alternativas (3230 en francés o inglés) y términos ocultos para facilitar la búsqueda. Se ha alineado con la ontología FoodOn."
+AGRONTOLOGY	AgrOntology	https://www.fao.org/agrovoc/agrontology	Agrontology is the Web Ontology Language (OWL) vocabulary providing a set of domain properties to the AGROVOC thesaurus.
+AGRORDF	AGRORDF	http://www.openagramap.org	agroXML is an XML dialect for representing and describing farm work. It provides elements and XML data types for representing data on work processes on the farm including accompanying operating supplies like fertilizers, pesticides, crops and the like. It can be used within farm management information systems as a file format for documentation purposes but also within web services and interfaces between the farm and external stakeholders as a means to exchange data in a structured, standardized and easy to use way. It covers topics relevant to on farm activity including “crop”, “cropSpecies”, “chemical substance”, “harvestDate”, “enginePower”. There exists an XML version and an RDF version.
+AHOL	Animal Health Ontology for Livestock	http://www.atol-ontology.com/	AHOL définit et organise les caractères phénotypiques des animaux d’élevage, en prenant en compte les préoccupations sociétales et les grands types de production (lait, œuf, viande, fertilité, alimentation)., AHOL (Animal Health Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). AHOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the AHOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production
+ANAEETHES	AnaEE Thesaurus	https://www.anaee-france.fr	The AnaEE thesaurus aims to provide a controlled vocabulary for the semantic description of the study of continental ecosystems and their biodiversity. It has been developed within the framework of the AnaEE-France infrastructure through an iterative process combining both top down and bottom up approaches: import of concepts from other thesauri and collection of concepts used in the AnaEE data bases and/or modeling platforms.
+ANDO	Animal Disease Ontology		L'ontologie des maladies animales est un référentiel de maladies touchant des animaux de rente et d'agents pathogènes ainsi que des relations qu'ils entretiennent. Ce référentiel est en français avec des équivalents anglais. Il contient plus de 500 couples maladie-hôtes et plus de 500 agents pathogènes associés. Il a été constitué au fil des ans par un travail de veille réglementaire à l'INRA., The Animal Diseases Ontology includes information on diseases of production animals and their related pathogenic agents in French and English. This version contains more than 500 pairs of host-disease and their more than 500 associated pathogens.
+ANT	Agricultural and Nutrition Technology Ontology		Agricultural ontology for CRP mapping.
+AQFO	Aquatic Food Ontology		The Aquatic Food Ontology (AQFO) is currently being developed to enable easy aggregation and analysis of data generated by the CGIAR Initiative on Aquatic Foods. The ontology covers two domains - aquaculture and small scale fisheries. The development of AQFO is currently led by WorldFish and supported by the Alliance of Bioversity and CIAT.
+ASCOPAIN-T	Terminology of French bread descriptors		The AsCoPain-T terminology lists and defines the main quality assessment descriptors used by bread-making professionals and those used in scientific studies. It aims at linking professional and scientific terminologies, as language can vary greatly to denote similar processing operations and observations that are made on the dough and bread. The AsCoPain-T terminology is the result of successive efforts: expert knowledge collected by the INRA AsCoPain project first resulted in the definition of the relations between bread-making control variables and the different states of the dough and bread. These relations were implemented into the expert system used to predict the state of the dough throughout the kneading process. The terminology collected during this work was then published in the form of a glossary in a document referenced by the FAO (see http://prodinra.inra.fr/record/48319). The recent adaptation of its content to the semantic web standards now allows unforeseen uses, in particular by applications. The terminology is available in French. Its translation in English will soon be under way. , La terminologie AsCoPain-T définit les descripteurs qualité utilisés usuellement par les professionnels de la panification et ceux issus des travaux scientifiques. Son objectif est d’établir un lien entre terminologies professionnelles et scientifiques ; le langage employé pour caractériser les mêmes opérations de la transformation et les nécessaires observations de la pâte étant très varié. La terminologie AsCoPain-T est issue d’un travail préalable de recueil de connaissances dans le cadre du projet INRA AsCoPain qui a permis d’intégrer les relations entre des variables de contrôle du procédé de panification et des états de la pâte et du pain dans un système expert de prédiction de l’état de la pâte tout au long de l’opération de pétrissage. Ce travail a aussi produit un glossaire terminologique publié dans un document référencé par la FAO (voir http://prodinra.inra.fr/record/48319). L’adaptation de son contenu aux standards du web sémantique permet d’envisager de nouveaux usages de la terminologie, notamment son utilisation par des programmes informatiques. La terminologie est disponible en français et une version en anglais est en projet.
+ASFA	ASFA Thesaurus	https://www.fao.org/asfa/en	The ASFA Thesaurus contains over 5000 terms related to aquatic sciences, fisheries and aquaculture. The thesaurus covers all topics within ASFA’s subject scope: science, technology, management, and conservation of marine, brackish water, and freshwater resources and environments, including their socio-economic and legal aspects. Maintained by ASFA partners and available in 40 languages, the ASFA thesaurus is an AGROVOC’s sub-scheme.
+ATC	AgronomicTaxon	http://ontology.irstea.fr/pmwiki.php/Site/AgronomicTaxon	This ontology is a module that is based on skos vocabulary, linnean taxonomy ODP and classification ODP. The module was enriched by specialising taxonomic relationship based on the AOS ontology. Taxon ranks are linked to their agrovoc concepts. Some disjoint axioms between ranks were added.
+AWS	Ontology for Meteorological Sensors		This ontology is part of the Agriculture Meteorology example showcasing the ontology developed by the W3C Semantic Sensor Networks incubator group (SSN-XG). It is published here in order to generalize the potential usage and the alignment with other standardization efforts of the SSN ontology.
+BAGO	BioAGgressor Ontology		This ontology and related knowledge graph was build during the D2KAB project. The goal is to model all the living organisms involved in cultivated plant disease appearance. The ontology and its documentation represent the point of view of some french researchers from differents intstitutions., This ontology and related knowledge graph was build during the D2KAB project. The goal is to model all the living organisms involved in cultivated plant disease appearance. The ontology and its documentation represent the point of view of some french researchers from differents institutions.
+BDG	BigDataGrapes Ontology		Ontology, semantic model and semantic data for the H2020 BigDataGrapes EU project. BigDataGrapes ontology is used for representing observations about soil, weather, agriculture, viticulture, wine making, etc. It also contains extra units of measure based on QUDT 2.0.
+BIODIVTHES	Biodiversity Thesaurus	http://www.inist.fr	This bilingual thesaurus organizes the key concepts of biodiversity sciences, in their basic and applied ecological components. It uses polyhierarchy and includes 818 reciprocal associative relationships. The 1654 French and English descriptors (designating 827 concepts) are enriched with a large number of synonyms (1860) and hidden variants (7020) in both languages. Concepts are grouped into 82 collections, by semantic categories, thematic fields and EBV classes (Essential Biodiversity Variables). Definitions are given with their sources. It could be utilized as a controlled vocabulary to enrich metadata of biodiversity data portals, enhancing semantic interoperability. It aims to extend (via narrower concepts, and synonyms) generic environmental science thesauri/ontologies., Ce thésaurus entièrement bilingue organise les concepts clés des sciences de la biodiversité, dans leurs composantes écologiques fondamentales et appliquées. Il utilise la polyhiérarchie et comprend 818 relations associatives réciproques. Les 1654 descripteurs français et anglais (désignant 827 concepts) sont accompagnés d'un grand nombre de synonymes (1860) et de variantes cachées (7020) dans les 2 langues. Les concepts sont regroupés en 82 collections, par catégories sémantiques, domaines thématiques et classes de VEB (variables essentielles de biodiversité). Les définitions sont données avec leurs sources. Cette ressource est alignée sur les thésaurus internationaux AGROVOC, GEMET (GEneral Multilingual Environmental Thesaurus) et EnvThes (Environmental Thesaurus), ainsi que sur l'ontologie ENVO (Environment Ontology)., thematic fields and EBV classes (Essential Biodiversity Variables). Definitions are given with their sources. This resource is aligned with the international thesauri AGROVOC, GEMET (GEneral Multilingual Environmental Thesaurus) and EnvThes (Environmental Thesaurus), as well as with the ontology ENVO (Environment Ontology).
+BIOREFINERY	Biorefinery	https://www6.inra.fr/cati-icat-atweb/Ontologies/Biorefinery	The biorefinery ontology (BIOREFINERY) is dedicated to the description of biomass transformation processes and characterisation of samples.
+BIPOM	Biological interlocked Process Ontology for metabolism		BiPOm is an ontology based on systemic representation of metabolic processes. BiPOm is an ontological model carrying the main biological processes and molecular roles/functions at a high level of genericity where the usual annotated resources are treated as instances. BiPOm, 1) contains biological knowledge as instances and 2) uses automatic reasoning through Semantic Web Rule Language (SWRL) in order to automatically infer, formalize and refine properties of molecules.
+BIPON	Bacterial interlocked Process ONtology		BiPON is an ontology permitting a multi-scale systemic representation of bacterial cellular processes and the coupling to their mathematical models. BiPON is further composed of two sub- ontologies, bioBiPON and modelBiPON. bioBiPON aims at organizing the systemic description of biological information while modelBiPON aims at describing the mathematical models (including parameters) associated to each biological process.
+BOHLMANN	Bohlmann Ontology		An ontology listing the natural substances that occur in the plant family of Compositae (Asteraceae)., An ontology listing the natural substances that occur in the plant family of Compositae (Asteraceae)
+C3PO	Crop Planning and Production Process Ontology	https://www.elzeard.co/ontologies/c3po/	Crop Planning and Production Process Ontology aims at representing vegetable farming crop management knowledge. The ontology is composed of several modules, each one representing specific domain of interest for vegetable agriculture planning
+CASO	Context-Aware System Ontology	https://w3id.org/def/caso	CASO (Context Aware System Observation) is an ontology for context aware system and observation services. Its goal is to describe all the processing of the context.
+CCON	Cerrado Concepts and Plant Community Dynamics	http://cerrado.linkeddata.es/ecology/ccon/	The ontology of Cerrado wood plant dynamics was created in order to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate., The Ccon represents the main concepts about the Cerrado plant communities structure and dynamics. This ontology will be part of the GeoLinked Data Ontology network to enrich the web of data with geospatial information of the Cerrado Biome, especially with regard the wood plant dynamics.
+CD	Crop Disease		A basic ontology for crop-disease-pesticide information, mostly pertaining to Indian Agriculture
+CGO	Common Greenhouse Ontology	https://gitlab.com/ddings/common-greenhouse-ontology	This ontology defines common concepts in the greenhouse domain and covers three main aspects of the greenhouse, namely (1) greenhouse construction concepts, (2) real-time measurements and action concepts and (3) dynamic objects and situation concepts. The construction concepts are defined together with main greenhouse construction companies. The real-time measurements and action concepts are based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group. The dynamic objects and situation concepts are defined based on the DOLCE+DnS Ultralite (DUL) ontology. The definition and usage of units are based on the Ontology of Measurements (OM). This ontology does not describe generic concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.
+CIQUAL	CIQUAL		This ontology contains a OWL representation of Ciqual food terms using Langual thesaurus. Ciqual is the nutritional database managed by ANSES in France.
+CLC	Corine Land Cover Nomenclature	https://www.w3.org/2015/03/corine	This is the human-readable version of the SKOS concept scheme developed from the Corine Land Cover Classes published by the European Environment Agency. In any variance between the EEA documentation and this document, the original documentation is authoritative.
+CO_020	Multi-Crop Passport Ontology	http://www.cropontology.org/	FAO/Bioversity Multi-Crop Passport Descriptors V.2.1 [MCPD V.2.1] standard
+CO_121	Wheat Plant Anatomy and Development Ontology	http://www.cropontology.org/	Defines growth stages of wheat
+CO_125	Banana Anatomy	http://www.cropontology.org/	This ontology is a part of the the Crop Ontology project (http://www.cropontology.org), created in 2008 by the CGIAR, as an essential source of traits and variables to support the standardization of the breeding databases.
+CO_369	Sainfoin Ontology	https://cropontology.org/term/CO_369:ROOT	This ontology describes a standard trait lexicon used in phenotyping the forage and pulse crop, Sainfoin (Onobrychis viciifolia), with the intention of increasing trait consistency across different breeding programs.
+CO_371	Blueberry Ontology	https://cropontology.org/term/CO_371:ROOT	Blueberry (Vaccinium) ontology defines crop traits and variables to support the standardization of phenotypic data collection for blueberry breeding programs in the USA. The ontology provides a description of agronomic, biochemical, morphological, phenological, physiological, quality, abiotic and biotic stress traits with their methods and scales used for each trait.
+CO_715	Crop Research Ontology	http://www.cropontology.org/	Describes experimental design, environmental conditions and methods associated with the crop study/experiment/trail and their evaluation
+CROPUSAGE	French Crop Usage thesaurus (Classification des plantes cultivées en France en fonction des usages)	http://ontology.inrae.fr/pmwiki.php/Site/FrenchCropUsage	"An RDF vocabulary for describing the basic structure and content of concept schemes such as thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', other types of controlled vocabulary, and also concept schemes embedded in glossaries and terminologies., Les sources utilisées sont le registre parcellaire, le larousse agricole, wikipédia, le catalogue officiel des espèces et variétés de plantes cultivées en France du GEVES, les fiches ""les plantes fourragères pour les pairies"" du GNIS, la base Ephy, la liste des cultures à utiliser pour renseigner le descriptif des parcelles et les statistiques agricoles annuelle de l'Agreste, les tables du catalogue de l'Acta publié en 2021. Concernant les légumes et leur classification nous avons cherché les points communs entre plusieurs sources: Wikipedia, Bonduelle, FranceAgriMer, Encyclopedia Universalis, AM Nagelseim, la ferme du Bec Hellouin. A notre qu'il n'existe pas de consensus sur la classification des legumes. Cette classification est utilisée pour organiser les Bulletins de Santé du Végétal (BSV) et les fiches GECO. Cette classification n'est pas complète et aura besoin d'évoluer au cours du temps en fonction des besoins. auteur est catherine roussey de l'INRAE catherine.roussey@inrae.fr, les tables du catalogue de l'Acta publié en 2021. Concernant les légumes et leur classification nous avons cherché les points communs entre plusieurs sources: Wikipedia, la ferme du Bec Hellouin. A notre qu'il n'existe pas de consensus sur la classification des legumes. Cette classification est utilisée pour organiser les Bulletins de Santé du Végétal (BSV) et les fiches GECO. Cette classification n'est pas complète et aura besoin d'évoluer au cours du temps en fonction des besoins. auteur est catherine roussey de l'INRAE catherine.roussey@inrae.fr"
+CSOPRA	Soil organic carbon storage and agricultural practices modeling		This ontology was created to support the development of the csopra libraries and the modelToolBox, which enables the modeling of soil organic changes, as a result of soil management, such as agricultural practices. It also aims at enabling interoperability between various data sources and various crop or biogeochemical models.
+CVO	Crop Vocabulary	http://www.cavoc.org/cvo.php	Crop Vocabulary provides taxonomy of crops in farming. Terms are mainly collected in agricultural documents published by Japanese Government. Crop is basically classified by plant but some are classified by cultivation method, edible parts, and and so on. Links to AGROVOC and NCBI taxonomy are included.
+DATA4CPLUS	Thesaurus to define land management practices in agriculture and forestry for soil carbon storage	http://data4c-plus.net/admin/thesaurus/index	DATA4C+ is a thesaurus classifying and defining land management practices in agriculture and forestry for soil carbon storage. DATA4C+ thesaurus is focussed on land management practices identified in the scientific literature as drivers of soil organic carbon (SOC) changes. DATA4C+ thesaurus aim was to fill the gap of lack of a comprehensive thesaurus for land management practices which directly or indirectly affect SOC dynamics. DATA4C+ thesaurus was developped by Cirad, INRAE and IRD during the ANR DATA4C+ project (https://www.data4c-plus-project.fr/en, Projet ANR- 19-DATA-0005). DATA4C+ thesaurus contains 224 classified and defined terms related to land management practices in agriculture and forestry. DATA4C+ thesaurus is organized as a hierarchical tree reflecting the drivers of SOC storage. To have access to the definition of a given term, the user must click on it in the tree. Then a “pop up” appears with the definition of the term and the source of the definition. A link to the source of the definition (URL or DOI) is given for each term. By clicking on this link, a new web page appears.
+DEMETER-AIM	DEMETER Agriculture Information Model	https://gitlab.com/demeterproject/wp2/agriculturalinformationmodel/domainspecificontologies	The DEMETER Agri Profile is a master profile importing focused specific profiles/modules of DEMETER AIM.
+DSW	Darwin-SW	https://github.com/darwin-sw/	Version 0.4 to 1.0 fixed reversed dsw:locates and dsw:locatedAt. Added labels. Changed comments and descriptions to conform to DC and DwC precedent. Added subClassOf relations to RO hasEvidence and isEvidenceFor. Specified preferred direction for inverse object property pairs., Changes from version 0.2.1 to version 0.3: removal of all functional and inverse function properties of object property terms, use of dwctype classes, deprecation of terms replaced by dwciri: terms, removal of references to TDWG Ontology., Changes from version 0.3 to 0.4 change DwC class namespace from dwctype: to dwc: to follow class proposal, removed references to TDWG TaxonConcept ontology; deprecated terms that now have equivalent terms in Darwin Core., Change from version 1.0 to 1.0.1 Add CC0 license.
+DURUM_WHEAT	Durum Wheat	http://lovinra.inra.fr/	The durum wheat ontology (DURUM_WHEAT) is dedicated to the sustainability analysis of the durum wheat chain.Current data available on this ontology concern durum wheat quality criteria criteria used in different countries (Moisture content rate, chemical content, etc.).
+E-PHY	Catalogue des produits phytopharmaceutiques et de leurs usages, des matières fertilisantes et des supports de culture autorisés en France		Le catalogue des produits phytopharmaceutiques de l’ANSES en une base de connaissances OWL dont le modèle ontologique est celui de la base de données E-Phy (https://ephy.anses.fr/) et les instances sont les produits qui y sont listés, alignées avec d’autres ressources sémantiques tel que le thésaurus French Crop Usage pour les cultures et l’ontologie CHEBI pour les familles chimiques. Cependant considérant que nos organismes ne sont pas des autorités pour ce catalogue, notre modèle de données est volontairement “bridé” pour être complètement rétro-compatible avec la base d’origine de façon à facilement mettre à jour notre ontologie à partir de nouveaux exports de l’ANSES., E-Phy est une base de connaissances (ontologie+instances) tirée de la base de données E-Phy de l'ANSES (https://ephy.anses.fr) qui contient le catalogue des produits phytopharmaceutiques et de leurs usages, des matières fertilisantes et des supports de culture autorisés en France. Cette base de connaissances a été crée dans le cadre du projet ANR D2KAB par le LIRMM et l'INRAE. Elle a vocation à proposer une version RDF de la base de données E-Phy.
+EBO	Environmental Biorefinery Ontology		An ontology for describing environmental biorefinery data for the information system EnviBIS, using the application core ontology OESO and the core ontology PO2.
+FCUO	French Crop Usage Ontology	http://ontology.inrae.fr/pmwiki.php/Site/FrenchCropUsage	"This ontology specialized the skos model to create a new class Crop subclass of skos:Concept. fcuo:Crop is a defined class. Thus a reasoner like Hermit should be used to classify all the instances of skos:Concept that belongs to the scheme fcuo:thesaurus_FrenchCropUsage as an instance of Crop. FCUO contains also new objet properties and annotation properties dedicated to FCU alignement with taxonomy like TAXREF-LD., ontologie associée au thésaurus Usage des plantes cultivées en France et définissant des relations d'alignements entre les usgaes des plantes définies dans ce thésaurus et les taxonomies scientifiques comme NCBI taxon ou TAXREF-LD., ontology related to the thesaurus French Crop Usage. This ontology defines mapping relations between FCU thesaurus and scientific taxonomies like TAXREF-LD or NCBI taxon., Les sources utilisées sont le registre parcellaire, le larousse agricole, wikipédia, le catalogue officiel des espèces et variétés de plantes cultivées en France du GEVES, les fiches ""les plantes fourragères pour les pairies"" du GNIS, la base Ephy, la liste des cultures à utiliser pour renseigner le descriptif des parcelles et les statistiques agricoles annuelle de l'Agreste, les tables du catalogue de l'Acta publié en 2021. Concernant les légumes et leur classification nous avons cherché les points communs entre plusieurs sources: Wikipedia, Bonduelle, FranceAgriMer, Encyclopedia Universalis, AM Nagelseim, la ferme du Bec Hellouin. A notre qu'il n'existe pas de consensus sur la classification des legumes. Cette classification est utilisée pour organiser les Bulletins de Santé du Végétal (BSV) et les fiches GECO. Cette classification n'est pas complète et aura besoin d'évoluer au cours du temps en fonction des besoins. auteur est catherine roussey de l'INRAE catherine.roussey@inrae.fr"
+FLAIR	Wine Descriptors Ontology	https://github.com/XavierDelpuech/flair	Ce fichier au format RDF contient les éléments d'une modélisation de l'analyse sensorielle des vins. Cette ontologie a été construite lors du projet CASDAR VITISDATACROP (France, 2021-2023). Contacter Xavier DELPUECH pour toute modification dans ce fichier.
+FOODIE	FOODIE Core Ontology	http://foodie-cloud.github.io/model/FOODIE.html	This release 4.6.3 added missing crop property; release 4.6.2 fixes model regarding DoseUnit that cannot be a codelist, and is defined as datatype, FOODIE ontology has been generated from FOODIE application schema (UML model), Revision 4.6.1, and translated into an ontology according to ISO/DIS 19150-2 using ShapeChange plus several pre and post processing changes. This is a revision of v4.3.2, manually updated to v4.6.1.
+GACS	Global Agricultural Concept Scheme	http://agrisemantics.org/gacs/	The Global Agricultural Concept Scheme (GACS) is a hub for concepts related to agriculture, in multiple languages, for use in Linked Data. The idea for GACS emerged out of discussions at the World Congress of IAALD, the International Association of Agricultural Information Specialists, in July 2013. The Food and Agricultural Organization of the United Nations (FAO), CAB International (CABI), and the National Agricultural Library of the USA (NAL) agreed in October 2013 to explore the feasibility of developing a shared concept scheme by integrating their three thesauri: the AGROVOC Concept Scheme, the CAB Thesaurus (CABT), and NAL Thesaurus (NALT). In the GACS vision, the integration of these three thesauri is but the first step towards the realization of a hub that links to and from the concept schemes beyond the initial three, and in multiple language areas.
+GAO	Grapevine Anatomy Ontology		Describes a list of organs classified by biological function, Décrit une liste d'organes classé par fonction biologique, Describes a list of organs classified by biological function, Décrit une liste d'organes classé par fonction biologique
+GECO	Agroecology Knowledge Management (GECO ontology)	https://geco.ecophytopic.fr/	Agroecology knowledge management is an application ontology for the description and organization of knowledge to design innovative crop systems. , Gestion des connaissances en agroécologie est une ontologie d’application décrivant et organisant les connaissances permettant de concevoir des systèmes de culture innovants.
+GFVO	Genomic Feature and Variation Ontology	https://github.com/BioInterchange/Ontologies	The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF). It is captures the contents of data files that adhere to the Generic Feature Format Version 3 (GFF3, http://www.sequenceontology.org/resources/gff3.html), the General Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html), the Genome Variation Format Version 1 (GVF, http://www.sequenceontology.org/resources/gvf.html), and the Variant Call Format (VCF, http://vcftools.sourceforge.net/specs.html). The creation of the ontology was inspired by previous work of Robert Hoehndorf on RDF2OWL (http://code.google.com/p/rdf2owl).
+GR-TAX	Gramene Taxonomy Ontology	http://www.gramene.org/	It is a representation of the taxonomy tree in the ontology format. Each term in this ontology can represent subspecies, species, genus, order, class or any rank in the classification. Primarily derived from NCBI Taxonomy, the revisions were made as and when/where required in the rankings. The rank of genome types was added by this project. This taxonomy ontology focuses on the Poaceae (Gramineae) family of plant taxonomy only.
+ICC	Indicative Crop Classification	http://www.fao.org/world-census-agriculture/wcarounds/wca2010/en	The Indicative Crop Classification (ICC) was developed for the 2020 round of agricultural censuses.
+INFRARISK	InfraRisk Ontology	http://vocabs.datagraft.net/infrarisk.html	The InfraRisk Ontology: Enabling Semantic Interoperability for Critical Infrastructures at Risk from Natural Hazards. This InfraRisk ontology may be used for representing relevant information about natural hazard events and their impact on infrastructure components. Earthquakes, landslides, and other natural hazard events have severe negative socio-economic impacts.
+INIA-RDM	INIA Research Datasets	http://data.inia.es/def/	This ontology is used to describe datasets hosted on Spanish National Institute for Agricultural and Food Research and Technology (INIA) Research Data Repository. It combines terms from dataset ontologies such as DCAT, with some specific terms in Agriculture Research, e.g., keywords based on AGROVOC.
+INRAETHES	INRAE Thesaurus	https://thesaurus.inrae.fr	INRAE Thesaurus is the open and shared thesaurus covering INRAE's research fields. It serves as a controled vocabulary within the institute for indexing and annotating documents, web pages, descriptions of activities, datasets, etc. for research or information analysis purposes. It is maintained by an editorial committee under the responsibility of INRAE DipSO.
+IRRIG	Irrigation Ontology	https://w3id.org/def/irrig	IRRIG is an Irrigation Ontology for experimentation in TSCF, Irstea Clermont-Fd.
+LANDVOC	Linked Land Governance Thesaurus	http://landvoc.org	LandVoc is a thesaurus (controlled vocabulary) covering 310 concepts related to all areas of interest to the land community including land administration, land governance, land use and cover etc. It is built by the Land Portal Foundation and relies on a subset of AGROVOC concepts.
+LEXEAU	A stratified lexicon of water related geophysical and textual data		"L'ontologie LEXEAU est la source d'un lexique de l'eau bilingue des services de l'eau et du développement durable. Elle a été conçue et développée dans le cadre d'un projet global (projet Lexeau®) pour améliorer l'intercompréhension des acteurs du domaine : usagers de l'eau publics et privés, élus européens, nationaux et locaux, dirigeants et salariés d'entreprise, ingénieurs et scientifiques, techniciens de maintenance, juristes, fonctionnaires, journalistes, etc. Les entités du lexique sont des unités lexicales, des entités du monde et des acronymes. Les unités lexicales sont spécifiques (propres au domaine de l'eau) ou auxiliaires (partagées avec d'autres domaines de connaissance). Les unités lexicales spécifiques sont préfixées ""1-TS"", ""2-TA"" ou ""3-C"" lorsqu'elles sont utilisées, respectivement, dans la strate discursive spécifique technico-scientifique, technico-administrative ou courante. Les unités lexicales auxiliaires sont préfixées ""A"". Les unités lexicales sont dérivées des libellés des classes de l'ontologie et des entités contrôlées. Les entités du monde du lexique sont des objets concrets, ""référents"" de l'unité lexicale dérivée du libellé de leur classe d'origine dans l'ontologie. Les articles du lexique sont introduits en commentaire (annotation ""comment"") du libellé de l'unité lexicale (sous le libellé de la classe), du libellé de l'entité contrôlée, réputé libellé de l'unité lexicale, ou du libellé de l'entité monde. Les relations lexicales qui suivent chaque article sont dérivées de la hiérarchie des classes, de l'instanciation des classes et des ""assertions de propriété"" associées aux propriétés de l'ontologie. Un graphe conceptuel est édité pour chaque unité lexicale et exporté comme ""image"" (format ""png""). L'édition électronique du lexique avec des liens hypertexte, y compris les graphes conceptuels, est directement issue de l'ontologie. Elle est disponible sur demande. Face à la transition énergétique et à l'adaptation climatique, la structure de l'ontologie est bien adaptée à la mise à jour du lexique des services de l'eau et du développement durable et à son extension à d'autres thèmes tels que le dessalement de l'eau, le recyclage des eaux usées, l'exploitation pérenne des eaux souterraine, la protection du littoral, ainsi que la prévention et la réparation des dommages liés aux sécheresses et aux inondations. Bordeaux, le 7 juin 2024 Jean-Louis Janin"
+LHO	Livestock Health Ontology		The Livestock Health Ontology (LHO) contains information on the health and well-being of livestock animal species such as cattle, pigs, and poultry. Furthermore, it represents the explicit structured and standardized framework for specific domain knowledge and data integration of livestock species. During the development process, knowledge can be retrieved from domain experts, and after the retrieving process, the prototype is designed for reasoning and planning of data related to cattle, pigs, and poultry. Moreover, LHO contains information regarding farms Identifications, their samples, geolocation, breed, diagnostic tests, Pathogen identifications, and Pathogen results for specific bacteria such as Histophilus Somni (HS), Mannheimia Haemolytica (MH), Pasteurella Multocida (PM), Bovine Coronavirus (BCV) bacterial mycoplasma and aerobic culture results for the respiratory diseases in cattle. This information is represented as concepts of classes, subclasses, and their relationship in the form of object and data properties. For pigs, it includes farm type, age, weight, pig stages and pathogens like PRRS, SwineInfluenza, and M_Hyponemoniea. In poultry, LHO incorporates farm type, with specific pathogen names such as Infectious Bronchitis (IB), providing a concise overview of health aspects across livestock species. Incorporating pathogen identification results, whether positive or negative, within the Livestock Health Ontology (LHO), not only enhances data organization but also supports projects like DECIDE EU Horizon 2020. By providing a structured framework for analyzing disease emergence and options for diagnostic confirmation, LHO contributes to the development of robust data-driven decision-support tools in livestock health management.
+MEAT-T	Meat Thesaurus		The meat thesaurus describes different facets of the meat production chain, such as the meat market, breed, slaughtering, culinary preparations, etc. It contains terms and definitions in French and English. It was derived and adapted from the Dictionnaire de la viande, Académie de la viande (France). Publisher, Autres voix, 2012. ISBN, 2918237086, 9782918237082
+MICROFILTRATION	Milk Microfiltration Ontology		The Microfiltration ontology (MICROFILTRATION) is dedicated to the description of milk transformation itineraries for microfiltration purposes and characterisation of associated samples.
+MILKOLIGO	Milk Oligosaccharide Thesaurus - HoloOLIGO project	https://doi.org/10.57745/RA5DAC	This thesaurus gathers milk oligosaccharide synonyms., This dataset is a thesaurus gathering milk oligosaccharide synonyms
+MS2O	Multi-scale Multi-step ontology	http://lovinra.inra.fr/2015/12/16/multi-scale-multi-step-ontology/	The Multi-scale Multi-step ontology (MS²O) is an ontology to describe transformation processes., Multi-scale Multi-step ontology (MS²O) est une ontologie permettant de décrire des processus de transformation.
+NALT	National Agricultural Library Thesaurus	https://agclass.nal.usda.gov/agt.shtml	"The Thesaurus is an online vocabulary of agricultural terms in English and Spanish and is cooperatively produced by the National Agricultural Library, USDA and the Inter-American Institute for Cooperation on Agriculture as well as other Latin American agricultural institutions belonging to the Agriculture Information and Documentation Service of the Americas (SIDALC). The NAL Agricultural Thesaurus (NALT) was first published in 1967 and converted to SKOS in 2019 then released by the National Agricultural Library in 2002, with in-depth coverage of agriculture, biology, and related disciplines. The Spanish language version of NALT was first published in May 2007 under the Spanish language name ""Tesauro Agrícola"", and was created in cooperation with the Inter-American Institute for Cooperation on Agriculture (IICA) and other Latin American agricultural institutions belonging to the Agriculture Information and Documentation Service of the Americas (SIDALC). In 2022 NALT was redesigned as part of the Library's ""NALT for the Machine Age"" initiative, and is a state-of-the-art multischeme concept space with added structural features for enhanced scalability and machine readability. Inaugural schemes included NALT Core, and NALT Full."
+OBOE	The Extensible Observation Ontology	https://github.com/NCEAS/oboe/	The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.
+OEEV	Ontology of Experimental Events		The Ontology of Experimental Events (OEEv), characterises events that occur during an experiment, e.g. dates of sowing, application of a given treatment, harvesting, measurements or sampling for -omic measurements, or any category of technical problem.
+OEPO	Ontology for Experimental Phenotypic Objects		The Ontology for Experimental Phenotypic Objects (OEPO), allows assigning types (e.g. Experimental organization and context, Environment type, Germplasm, Physical Object) to objects involved in phenotyping experiments and defining specialization hierarchy between them according to the specificities of the installations and experiments.
+OESO-CORE	Ontology for Experimental Scientific Objects Core	http://opensilex.org/vocabulary/oeso.owl	The Ontology for Experimental Scientific Objects (OESO), allows assigning types (e.g. Experimental organization and context, Environment type, Germplasm, Physical Object) to objects involved in experiments and defining specialization hierarchy between them according to the specificities of the installations and experiments. OESO core contains the main concept for OpenSILEX application. This core ontology should be extend with the application domain concepts.
+OFPE	Ontology for Food Processing Experiment		OFPE is a generic ontology specialized for food processing experiments, where raw materials are transformed into final products. It includes different classes that represent products and activities during food transformation processes, which can be classified into four main concepts, i.e., Product, Operation, Attribute, and Observation., OFPE is a generic ontology specialized for food processing experiments, where raw ma- terials are transformed into final products. It includes dif- ferent classes that represent products and activities during food transformation processes, which can be classified into four main concepts, and Observation.
+OFSMR	Open Predictive Microbiology Ontology		Food-matrix ontology for Open Food Safety Model Repository
+ONTOAGROHIDRO	OntoAgroHidro		OntoAgroHidro is an ontology that represents knowledge about impacts of agricultural activities and climatic changes on water resources.
+ONTOBIOTOPE	OntoBiotope		OntoBiotope is an ontology of microorganism habitats, phenotypes and use. Its modeling principle and its lexicon reflect the biotope classification used by biologists to describe microorganism isolation sites, phenotypes and uses. OntoBiotope is developed and maintained by the Bibliome group of MaIAGE lab and microbiologists from INRAE (French National Research Institute for Agriculture, Food and Environment) from all fields of applied microbiology. OntoBiotope classes are used in the Bacteria Biotope reference dataset of BioNLP shared task to annotate the habitats and phenotype entities. It is also used to index the data of the Omnicrobe DataBase
+OWSD	Ontology for the management of Wine Sensory analysis Descriptors	http://opendata.inrae.fr/owsd	Les descripteurs d'analyse sensorielle du vin, une nouvelle ontologie, décrit une liste de groupes de descripteurs (classes) utilisés pour classer les descripteurs sensoriels (instances)., The Wine Sensory analysis Descriptors, a new ontology describes a list of descriptors groups (classes) used to classify sensorial descriptors (instances).
+PBO	Plant Breeding Ontology		Plant Breeding Ontology (PBO): an ontology for the plant breeding community which captures more than 2200 entries where 80 represent the core terms. PBO has translations in 8 different languages: English (main language), Spanish, French, Dutch, German, Japanese, Catalan and Thai, as well as their definitions, synonyms, derived terms and samples of their usage. PBO has been built partially manually and semi automatically.
+PDO_CAS	Plant Diversity Ontology		Plant Diversity Ontology (PDO) is the outcome of the construction tasks of domain ontology of science in the project of Scientific & Technological Knowledge Organization Systems (STKOS). The structure of PDO centers on species, including micro level of molecular, cell and tissue, medium level of plant organs, species and population, and macro level of ecosystem. The classes of PDO also capture the habitat, environmental conditions and expand the general characteristics of plants, completing the instances richness for plant species, geographical, classification and morphology. Furthermore, PDO builds the relationships among species, region, morphology, plant organs, developmental stage, revealing the list of species in an area, the morphology and life form of plants, and development process of species. In sum, PDO shows a growth process or development stage of a species and its structure characteristics in particular space and time scale, realizing the description of species diversity, ecosystem diversity and genetic diversity. At present, PDO has been applied to the platform of Go to Selected Open Access Journals (GoOA) developed by National Science Library of Chinese Academy of Sciences, supporting concept retrieval and concept extension for GoOA.
+PEAO	Plant Experimental Assay Ontology	https://bitbucket.org/PlantExpAssay/ontology	The Plant domain has been the subject of several attempts to structure and formally define terms and corresponding relations, such as their anatomical features, developmental stages, and the application of particular experimental procedures to a biological problem. However, a focus on experimental assays in order to describe the whole experimental procedure, to the best of our knowledge, has only been attempted in the context of a very general description based on classical views of the scientific method. In this study, we focus on the development and proposal of an ontology dedicated to the description of these experimental procedures, regardless of the scientific questions that prompted the assays. This ontology includes entities from three distinct realms (biological, physical and data), which include both experimental products, their relations and the protocols describing their manipulation.
+PO2	Process and Observation Ontology	http://lovinra.inra.fr/2016/08/03/process-and-observation-ontology/	A core ontology for modeling transformation processes and their observations. PO2 is part of an interdisciplinary project called Delicious concerning the production and transformation processes in food science. The project combines data from different disciplines like food composition, food structure, sensorial perception and nutrition.
+POLAPGEN_BARLEY	Barley Trait POLAPGEN Ontology	http://www.cropontology.org/	Barley Trait Ontology template v 4, 6 June 2013 submitted by the Institute of Plant Genetics Poznan on behalf of Polapgen Consortium Poland
+PPDO	BBCH-based Plant Phenological Description Ontology	http://ontology.irstea.fr/pmwiki.php/Site/Ppdo	This RDF file contains an extension of the SKOS model to model the development stages (or phenological stages) of cultivated plants. This model defines classes representing the main stages and the secondary stages (2 and 3 digits). The general BBCH scale is represented as an instance of skos:ConceptScheme. A new scale was created, intitled, BBCH global scale, that gather all the stages existing in all BBCh cales. It was built during the ANR D2KAB project., that gather all the stages existing in all BBCh cales. It was built during the ANR D2KAB project. Contact Catherine Roussey (catherine.roussey@inrae.fr) for any modification in this file. This extension of SKOS model was build using 4 versions of BBCH monograph: * Growth stages of mono- and dicotyledonous plants BBCH Monograph edited by Uwe Meier Julius Kühn-Institut (JKI) Quedlinburg 2018 DOI: 10.5073/20180906-074619 ISBN: 978-3-95547-071-5 * Stades phénologiques des mono-et dicotylédones cultivées BBCH Monographie rédigé par Uwe Meier Instituto Julius Kühn (JKI, siglas en alomán) Quedlinburg, 2018 DOI: 10.5073/20180906-075455 ISBN: 978-3-95547-072-2 * Estadios de las plantas mono-y dicotyledóneas BBCH Monografia Elaborado por Uwe Meier Instituto Julius Kühn (JKI, 2018 DOI: 10.5073/20180906-075743 ISBN: 978-3-95547-069-2 * Entwicklungsstadien mono- und dikotyler Pflanzen BBCH Monografie bearbeitet von Uwe Meier Julius Kühn-Institut (JKI) Quedlinburg 2018 DOI: 10.5073/20180906-075119 ISBN: 978-3-95547-070-8 All versions are licensed under a Creative Commons Attribution 4.0 International License., Ce fichier RDF contient une extension du modèle SKOS pour modeliser les stades de développement (ou stades phénologiques) des plantes cultivées. Ce modèle défini des classes représentant les stades principaux et les stades secondaires (à 2 et 3 chiffres). l'échelle BBCH générale est représentée sous forme d'une instance de skos:ConceptScheme. Une nouvelle échelle a été créée, appelée échelle BBCH globale, regroupant tous les stades existant dans toutes les échelles BBCH. L'ontologie a été construite pendant le projet ANR D2KAB. Contacter Catherine Roussey (catherine.roussey@inrae.fr) pour toute modification dans ce fichier. Ce modele skos a été construit en utilisant 4 versions de la monographie BBCH toutes sous licence Creative Commons Attribution 4.0 International: * Growth stages of mono- and dicotyledonous plants BBCH Monograph edited by Uwe Meier Julius Kühn-Institut (JKI) Quedlinburg 2018 DOI: 10.5073/20180906-074619 ISBN: 978-3-95547-071-5 * Stades phénologiques des mono-et dicotylédones cultivées BBCH Monographie rédigé par Uwe Meier Instituto Julius Kühn (JKI, 2018 DOI: 10.5073/20180906-075743 ISBN: 978-3-95547-069-2 * Entwicklungsstadien mono- und dikotyler Pflanzen BBCH Monografie bearbeitet von Uwe Meier Julius Kühn-Institut (JKI) Quedlinburg 2018 DOI: 10.5073/20180906-075119 ISBN: 978-3-95547-070-8, that gather all the stages existing in all BBCh cales. It was built during the ANR D2KAB project. Contact Catherine Roussey (catherine.roussey@inrae.fr) for any modification in this file. This extension of SKOS model was build using 4 versions of BBCH monograph. All versions are licensed under a Creative Commons Attribution 4.0 International License., regroupant tous les stades existant dans toutes les échelles BBCH. L'ontologie a été construite pendant le projet ANR D2KAB. Contacter Catherine Roussey (catherine.roussey@inrae.fr) pour toute modification dans ce fichier. Ce modele skos a été construit en utilisant 4 versions de la monographie BBCH toutes sous licence Creative Commons Attribution 4.0 International.
+PPEO	Plant Phenotype Experiment Ontology	http://purl.org/ppeo	The Plant Phenotyping Experiment Ontology (PPEO) is an implementation of the Minimal Information About Plant Phenotyping Experiment. It lists and organises all the informations necessary to describe and reuse a phenotyping dataset following FAIR principles (Findable Interoperable Accessible Reusable). It has been initiated with experts from Elixir, Emphasis, Bioversity International - CGIAR and RDA.
+SAREF	Smart Applications REFerence ontology	https://saref.etsi.org/	The Smart Applications REFerence ontology (SAREF) is intended to enable interoperability between solutions from different providers and among various activity sectors in the Internet of Things (IoT), thus contributing to the development of the global digital market.
+SAREF4AGRI	SAREF4AGRI: an extension of SAREF for the agriculture and food domain		SAREF4AGRI is an extension of SAREF for the agriculture and food domain. SAREF4AGRI is specified and published by ETSI in the TS 103 410-6 associated to this ontology file. The list of use cases, standards and requirements that guided the creation of SAREF4AGRI are described in the associated ETSI TR 103 511., This ontology extends the SAREF ontology for the Agricultural domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Agricultural domain.
+SAREF4ENVI	SAREF4ENVI: an extension of SAREF for the environment domain	https://saref.etsi.org/saref4envi/	The present document is the technical specification of SAREF4ENVI, an extension of SAREF [1] for the environment domain. The extension was created in collaboration with domain experts in the field of light pollution currently working in the STARS4ALL European H2020 project (http://www.stars4all.eu/index.php/lpi/). The STARS4ALL project is composed by partners such as Universidad Politécnica de Madrid, Universidad Complutense de Madrid, ESCP Europe, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Instituto de Astrofísica de Canarias, University of Southampton, Europan Crowdfunding Network, and CEFRIEL (Società Consortile a Responsabilita Limitata). SAREF4ENVI has two main aims: on the one hand, to be the basis for enabling the use of SAREF in the environment domain and, on the other hand, to exemplify how to enable interoperability between environmental devices in cooperation. SAREF4ENVI is an OWL-DL ontology that extends SAREF with 32 classes (24 defined in SAREF4ENVI and 7 reused from the time, SAREF and geo ontologies), 24 object properties (22 defined in SAREF4ENVI and 2 reused from the SAREF and geo ontologies), 13 data type properties (9 defined in SAREF4ENVI and 4 reused from the SAREF ontology), and 24 individuals (9 defined in SAREF4ENVI and 12 reused from the OM ontology). SAREF4ENVI focuses on extending SAREF for photometers to solve the lack of interoperability between sensors that can measure and share information about light pollution. Such extension involves the following use cases (more details can be found in ETSI TR 103 411 [i.1]): Use case 1: Monitor light pollution in a city, through the data collected by photometers about the magnitude of the light emitted in a given area. Use case 2: Adjust lampposts light intensity due to high pollution, after identifying the most contaminating lampposts and therefore the areas where more energy is being thrown away. Use case 3: Register a photometer, in which a new collection of photometers is incorporated into an existing sensor network., This ontology extends the SAREF ontology for the environment domain, specifically for the light pollution domain, including concepts like photometers, light, etc.
+SEONT	Socio-Economic Ontology	https://github.com/AgriculturalSemantics/SEONT?tab=readme-ov-file	This ontology is the socio-economic ontology developed by CGIAR and partners. Socio-economic ontology team gratefully acknowledges the Platform for big data in agriculture (https://bigdata.cgiar.org) and CGIAR Research program on Policies, Instiutions and Markets(http://pim.cgiar.org/) for their financial support to implement this ontology., None
+SFWO	Soil Food Web Ontology		The Soil Food Web Ontology (SFWO) is a OWL ontology which provides a standardised terminology and a logical formalisation of the domain of soil trophic ecology. It proposes a reference vocabulary to describe information about trophic interactions, feeding-related functional traits, and feeding processes of soil biota. By harmonizing the definitions of trophic groups, SFWO provides a common, logically-sound framework for soil-associated consumers classification across taxonomic groups and trophic levels. The Soil Food Web Ontology aims at being a reference ontology for soil trophic ecology, and a resource for ontology-driven applications in the field, including: trophic trait datasets standardization, trophic data integration and knowledge graph construction, automated soil food web reconstruction using OWL reasoning, and trophic information extraction., The Soil Food Web Ontology (SFWO) describes concepts related to the trophic ecology of soil organisms, including diets, food resources, trophic processes, and trophic groups, across taxonomic groups and trophic levels. SFWO aims at being both a reference ontology -including a standardised vocabulary- for soil trophic ecology, and an application ontology, with a focus on reasoning-based applications.
+SNPO	Single-Nucleotide Polymorphism (SNP) Ontology	https://members.loria.fr/ACoulet/files/snpontology1.6_description.html	SNP-Ontology is a domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name, SNP-Ontology, is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. SNP-Ontology is general enough to enable the representation of variations observed in genome of various species. Latest versions of SNP-Ontology include the representation of haplotype and of CNV. The unambiguous representation of genomic variations provided by SNP-Ontology enables to integrate heterogeneous data related to genomic variations. To achieve this goal SNP-Ontology enables (1) to represent one variation in accordance with various ways that exist for describing it, (2) to represent the equivalence between two distinct descriptions of one variation, and (3) to represent correspondence between a genomic variation and its outcome at the transcriptome and proteome levels.
+SOIL	agINFRA Soil Vocabulary	http://vocabularies.aginfra.eu/soil	This vocabulary is a first formalization of the INSPIRE data model into an RDFs vocabulary.Developed by the Italian Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA) in collaboration with the Global Forum on Agricultural Research (GFAR) and the Food and Agriculture Organization of the United Nations (FAO).
+SOSA	Sensor, Observation, Sample, and Actuator Ontology	https://www.w3.org/TR/vocab-ssn/	This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.
+SOY	Soy Ontology	https://www.soybase.org/	Soybean Growth and Trait Ontology
+SPO-FDM	SmartProducts Network of Ontologies Food Domain Model		SmartProducts Network of Ontologies (SPO) provides a clear specification of the conceptual model underlying the work on the SmartProducts project, and maximises interoperability not just among all SmartProducts applications, but also between these and other applications in related domains. SPO Food ontologies have been designed according to a smart kitchen application scenario. Food Domain Model (FDM) defines concepts and properties specific for the Philips use case (cooking domain)
+SPO-FND	SmartProducts Network of Ontologies Food Nutrition Data		"SmartProducts Network of Ontologies (SPO) provides a clear specification of the conceptual model underlying the work on the SmartProducts project, and maximises interoperability not just among all SmartProducts applications, but also between these and other applications in related domains. SPO Food ontologies have been designed according to a smart kitchen application scenario. Food Nutrition Data (FND) contains nutritional information from Freebase and defines individuals for a ""dummy"" test scenario for Philips"
+SPO-FTM	SmartProducts Network of Ontologies Food Taxonomy Model		SmartProducts Network of Ontologies (SPO) provides a clear specification of the conceptual model underlying the work on the SmartProducts project, and maximises interoperability not just among all SmartProducts applications, but also between these and other applications in related domains. SPO Food ontologies have been designed according to a smart kitchen application scenario. Food Taxonomy Model (FTM) contains food taxonomy constructed using PowerAqua and edited manually
+SPTO	Solanaceae Phenotype Ontology	https://solgenomics.net/	Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.
+SSN	Semantic Sensor Network Ontology	https://www.w3.org/TR/vocab-ssn/	This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.
+TAXREF-LD	TAXREF-LD	https://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref?lg=en	Representation of the TAXREF taxonomic register as linked data. This resource is at the same time an ontology of classes depicting the taxa and a thesaurus (SKOS concept scheme) of the scientific names attached to the taxa., Représentation du référentiel taxonomique TAXREF comme un jeu de données liées. Cette ressource est à la fois une ontologies des classes représentant les taxons, et un thésaurus (SKOS concept scheme) des noms scientifiques désignant ces taxons.
+THESAE	Agroecology Thesaurus		Thésaurus d'Agroécologie is a thesaurus in French containing 556 concepts denoting the issues, levers, indicators and agricultural production systems involved in an agro-ecological approach. This thesaurus, based on the results of a territorial watch on the scale of the Midi-Pyrénées region, is the result of expert work carried out by researchers and specialists in scientific and technical information from the Institut National de la Recherche Agronomique, Le Thésaurus d'Agroécologie est un thésaurus en français présentant 556 concepts dénotant les enjeux, leviers, indicateurs et systèmes de production agricoles impliqués dans une démarche agroécologique. Ce thésaurus, basé sur les résultats d'une veille territoriale à l'échelle de la région Midi-Pyrénées est issu d’un travail d’expertise réalisé par des chercheurs et des spécialistes de l’information scientifique et technique de l’Institut National de la Recherche Agronomique
+TOP	Thesaurus of Plant Characteristics	http://top-thesaurus.org	The Thesaurus Of Plant characteristics (TOP), aims to harmonize and formalize concepts for plant characteristics widely used in ecology. TOP concentrates on two types of plant characteristics: traits and environmental associations. Characteristics are modelled as the ‘Quality’ of an ‘Entity’ used in the context of Open Biological Ontologies. Whenever possible, the Entities and Qualities are taken from existing terminology standards, mainly the Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) ontologies. TOP provides names, definitions, units, synonyms and related terms for about 850 plant characteristics.
+TRANSFORMON	PO2/TransformON		Domain ontology on food and bioproduct processing and characterization. The ontology is a specialization of the PO2 ontology (Process and Observation Ontology).
+TRANSMAT	Matter Transfer Ontology	https://www6.inra.fr/cati-icat-atweb/Ontologies/Transmat	The Matter Transfer ontology is dedicated to matter transfer (e.g. O2, CO2, H2O) and mechanical properties of materials (eg food packaging tensile strength).
+TRIPHASE	Thesaurus for Animal Physiology and Livestock Systems		TODO, TriPhase est un thésaurus couvrant le domaine de la physiologie animale et de l'élevage conçu par l'INRA. , TriPhase is a large thesaurus in the domain of animal physiology and livestock designed by INRA.
+UC_SENSE	Unambiguous Characterization of Sensory Experiences Ontology		uc_Sense is an ontology for unambiguous characterization (UC) of sensory experiences and their descriptive terms. The uc_Sense ontology provides terms gathered from food and beverage flavor wheels in order to provide a vocabulary that will distinguish how a sensory event is perceived and how the same event is processed by an individual.
+USE	Ontobiotope_Use	http://migale.jouy.inra.fr/florilege/#&searchByUse	"The Use ontology is a subpart of the Ontobiotope ontology. It defines the uses and applications of microorganisms. Microorganisms are linked to the classes of the Use ontology by the relationship ""is studied for"". See examples in the Florilege database."
+WCACROPS	FAO WCA Crop	http://stats-class.fao.uniroma2.it/skosmos_demo/WCACrops/en/	The more granular crop classification used in the FAO WCA. Used in the 2010 round of agricultural censuses.
+WHEAT_TAX	Wheat Taxa Gold Standard	http://ontology.irstea.fr/pmwiki.php/Site/AgronomicTaxon	Manually built by Catherine Roussey, inspired by https://fr.wikipedia.org/wiki/Taxonomiedublé. Each species proposed into the wheat species table have been validated with European Wheat data base http://genbank.vurv.cz/ewdb/. The taxon name and its ranking was firstly validated with the use of taxref reference table from INPN. NCBI's taxonomy have been used when not found in taxref. Then links to agrovoc's thesaurus, NAL and CABI Have been added. Links to ITIS database have been added, and also the links to DBpedia. Be warned : DBpedia contains two missing species :triticum zhukovsyi and triticum compactum erinaceum which are not in taxref. triticum zhukovsyi is in European Wheat data base. Links to TAXREF-LD have also been added.
+WHEATPHENOTYPE	Wheat Trait and Phenotype Ontology		WheatPhenotype (also called Wheat Treat Ontology) is an ontology in OBO format that describes the traits of soft wheat (Triticum aestivum) and the environmental factors that affect these traits. Traits include traits of resistance, development, nutritional, baking quality, etc. Environmental factors include biotic and abiotic factors.
+XEO	XEML Environment Ontology	https://xeo.codeplex.com/	XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment.

testbed/biopragmatics__bioregistry/exports/alignment/biocontext.tsv

@@ -0,0 +1,73 @@
+prefix	uri_format
+	https://monarchinitiative.org/$1
+2D-PAGE.PROTEIN	http://identifiers.org/2d-page.protein/$1
+AGD	http://identifiers.org/agd/$1
+APB	http://pb.apf.edu.au/phenbank/strain.html?id=$1
+AQTLPub	https://www.animalgenome.org/cgi-bin/QTLdb/BT/qabstract?PUBMED_ID=$1
+AQTLTrait	http://identifiers.org/animalqtltrait/$1
+BNODE	https://monarchinitiative.org/.well-known/genid/$1
+BT	http://c.biothings.io/#$1
+catfishQTL	https://www.animalgenome.org/cgi-bin/QTLdb/IP/qdetails?QTL_ID=$1
+cattleQTL	https://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_D=$1
+chickenQTL	https://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$1
+CHR	http://purl.obolibrary.org/obo/CHR_$1
+ClinVarSubmitters	http://www.ncbi.nlm.nih.gov/clinvar/submitters/$1
+CLUSTR	http://identifiers.org/clustr/$1
+CMMR	http://www.cmmr.ca/order.php?t=m&id=$1
+CMR.GENE	http://identifiers.org/cmr.gene/$1
+COGS	http://identifiers.org/cogs/$1
+COGS.FUNCTION	http://identifiers.org/cogs.function/$1
+CoriellCollection	https://catalog.coriell.org/1/$1
+CoriellFamily	https://catalog.coriell.org/0/Sections/BrowseCatalog/FamilyTypeSubDetail.aspx?fam=$1
+CoriellIndividual	https://catalog.coriell.org/Search?q=$1
+CYGD	http://identifiers.org/cygd/$1
+DATA	http://edamontology.org/data_$1
+dbSNPIndividual	http://www.ncbi.nlm.nih.gov/SNP/snp_ind.cgi?ind_id=$1
+dbVar	http://www.ncbi.nlm.nih.gov/dbvar/$1
+EBIMETAGENOMICS.PROJ	http://identifiers.org/ebimetagenomics.proj/$1
+EBIMETAGENOMICS.SAMP	http://identifiers.org/ebimetagenomics.samp/$1
+EMMA	https://www.infrafrontier.eu/search?keyword=EM:$1
+EOM	http://purl.obolibrary.org/obo/EOM_$1
+FDADrug	http://www.fda.gov/Drugs/InformationOnDrugs/$1
+FLYSTOCK	http://identifiers.org/flystock/$1
+FUNCAT	http://identifiers.org/funcat/$1
+GeneReviews	http://www.ncbi.nlm.nih.gov/books/$1
+GINAS	http://tripod.nih.gov/ginas/app/substance#$1
+GRO	http://purl.obolibrary.org/obo/GRO_$1
+horseQTL	https://www.animalgenome.org/cgi-bin/QTLdb/EC/qdetails?QTL_ID=$1
+IMPC	http://www.mousephenotype.org/data/genes/$1
+IMPRESS-parameter	https://www.mousephenotype.org/impress/parameterontologies/$1
+IMPRESS-procedure	https://www.mousephenotype.org/impress/procedures/$1
+IMPRESS-protocol	https://www.mousephenotype.org/impress/protocol/$1
+J	http://www.informatics.jax.org/reference/J:$1
+KEGG-ds	http://purl.obolibrary.org/KEGG-ds_$1
+KEGG-hsa	http://www.kegg.jp/dbget-bin/www_bget?hsa:$1
+KEGG-ko	http://www.kegg.jp/dbget-bin/www_bget?ko:$1
+MEROPS	http://identifiers.org/merops/$1
+MONARCH	https://monarchinitiative.org/MONARCH_$1
+MonarchArchive	https://archive.monarchinitiative.org/201806/$1
+MonarchData	https://data.monarchinitiative.org/ttl/$1
+MPD	https://phenome.jax.org/$1
+MPD-assay	https://phenome.jax.org/db/qp?rtn=views/catlines&keymeas=$1
+MPD-strain	http://phenome.jax.org/db/q?rtn=strains/details&strainid=$1
+MUGEN	http://bioit.fleming.gr/mugen/Controller?workflow=ViewModel&expand_all=true&name_begins=model.block&eid=$1
+NCIMR	https://mouse.ncifcrf.gov/available_details.asp?ID=$1
+OMIA-breed	https://monarchinitiative.org/model/OMIA-breed:$1
+PAINT_REF	http://www.geneontology.org/gene-associations/submission/paint/$1
+PANTHER	http://www.pantherdb.org/panther/family.do?clsAccession=$1
+PATHEMA	http://identifiers.org/pathema/$1
+PGN	http://identifiers.org/pgn/$1
+pigQTL	https://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1
+rainbow_troutQTL	https://www.animalgenome.org/cgi-bin/QTLdb/OM/qdetails?QTL_ID=$1
+RBRC	http://www2.brc.riken.jp/lab/animal/detail.php?brc_no=RBRC$1
+RGDRef	http://rgd.mcw.edu/rgdweb/report/reference/main.html?id=$1
+SCIENCESIGNALING.PATH	http://identifiers.org/sciencesignaling.path/$1
+SCIENCESIGNALING.PDC	http://identifiers.org/sciencesignaling.pdc/$1
+SCIENCESIGNALING.PIC	http://identifiers.org/sciencesignaling.pic/$1
+SGD_REF	https://www.yeastgenome.org/reference/$1
+sheepQTL	https://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1
+TAIR	https://www.arabidopsis.org/servlets/TairObject?type=locus&id=$1
+TrEMBL	http://purl.uniprot.org/uniprot/$1
+VIVO	http://vivoweb.org/ontology/core#$1
+ZFIN.EXPRESSION	http://identifiers.org/zfin.expression/$1
+ZFIN.PHENOTYPE	http://identifiers.org/zfin.phenotype/$1

testbed/biopragmatics__bioregistry/exports/alignment/biolink.tsv

@@ -0,0 +1,18 @@
+prefix	uri_format	identifiers	purl
+apollo	https://github.com/GMOD/Apollo$1	False	False
+COAR_RESOURCE	http://purl.org/coar/resource_type/$1	False	False
+CTD	http://ctdbase.org/$1	False	False
+DGIdb	https://www.dgidb.org/interaction_types$1	False	False
+DOID-PROPERTY	http://purl.obolibrary.org/obo/doid#$1	False	True
+gff3	https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#$1	False	False
+GOP	http://purl.obolibrary.org/obo/go#$1	False	True
+gtpo	https://rdf.guidetopharmacology.org/ns/gtpo#$1	False	False
+NBO-PROPERTY	http://purl.obolibrary.org/obo/nbo#$1	False	True
+NCIT-OBO	http://purl.obolibrary.org/obo/ncit#$1	False	True
+PHARMGKB.VARIANT	https://www.pharmgkb.org/variant/$1	False	False
+PHAROS	http://pharos.nih.gov$1	False	False
+SEMMEDDB	https://skr3.nlm.nih.gov/SemMedDB$1	False	False
+UBERGRAPH	http://translator.renci.org/ubergraph-axioms.ofn#$1	False	False
+UBERON_CORE	http://purl.obolibrary.org/obo/uberon/core#$1	False	True
+UBERON_NONAMESPACE	http://purl.obolibrary.org/obo/core#$1	False	True
+UO-PROPERTY	http://purl.obolibrary.org/obo/uo#$1	False	True

testbed/biopragmatics__bioregistry/exports/alignment/cellosaurus.tsv

@@ -0,0 +1,30 @@
+prefix	name	homepage	category	uri_format
+Abeomics	Abeomics cell line products	https://www.abeomics.com/	Cell line collections (Providers)	https://www.abeomics.com/advanced-search-result?keywords=$1
+BioGRID_ORCS_Cell_line	BioGRID Open Repository of CRISPR Screens cell lines	https://orcs.thebiogrid.org/	CRISP screens repositories	https://orcs.thebiogrid.org/Search?searchType=10&search=$1&organism=all
+cancercelllines	cancercelllines.org - cancer cell line oncogenomic online resource	https://cancercelllines.org/	Cell line databases/resources	https://cancercelllines.org/cellline/?id=cellosaurus:$1
+CancerTools	CancerTools.org	https://www.cancertools.org/cell-lines	Cell line collections (Providers)	https://www.cancertools.org/cell-lines/$1
+DSHB	Developmental Studies Hybridoma Bank	https://dshb.biology.uiowa.edu/	Cell line collections (Providers)	https://dshb.biology.uiowa.edu/$1
+EGA	European Genome-Phenome Archive	https://ega-archive.org/	Sequence databases	https://ega-archive.org/studies/$1
+FCDI	FujiFilm Cellular Dynamics, Inc	https://www.fujifilmcdi.com/cirm-ipsc-products/	Cell line collections (Providers)	
+FlyBase_Gene	Drosophila genome database; gene entry	https://flybase.org	Organism-specific databases	https://flybase.org/reports/$1.htm
+FlyBase_Strain	Drosophila genome database; strain entry	https://flybase.org	Organism-specific databases	https://flybase.org/reports/$1.htm
+FPbase	Fluorescent Protein database	https://www.fpbase.org/	Sequence databases	https://www.fpbase.org/protein/$1
+GeneCopoeia	GeneCopoeia cell line products	https://www.genecopoeia.com/	Cell line collections (Providers)	https://www.genecopoeia.com/product/search3/?s=$1
+Genomeditech	Genomeditech cell line products	https://en.genomeditech.com/product?id=9	Cell line collections (Providers)	https://en.genomeditech.com/search?kwd=$1
+Hysigen	Hysigen cell line collection	https://hysigen.com/	Cell line collections (Providers)	https://hysigen.com/$1.html
+IARC_TP53	IARC TP53 Database	https://tp53.isb-cgc.org/explore_cl	Polymorphism and mutation databases	
+IBRC	Iranian Biological Research Center cell line collection	http://www.en.ibrc.ir/	Cell line collections (Providers)	
+Innoprot	Innoprot cell line products	https://innoprot.com/	Cell line collections (Providers)	https://innoprot.com/?s=$1&lang=en
+IZSLER	Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna biobank	http://www.ibvr.org/Services/CellCultures.aspx	Cell line collections (Providers)	
+KCB	Kunming Cell Bank of Type Culture Collection	http://www.kmcellbank.com/	Cell line collections (Providers)	
+LINCS_HMS	Harvard Medical School (HMS) LINCS Center	http://lincs.hms.harvard.edu/db/cells/	Cell line databases/resources	http://lincs.hms.harvard.edu/db/cells/$1
+MCCL	Molecular Connection Cell Line ontology	https://bioportal.bioontology.org/ontologies/MCCL	Cell line databases/resources	
+NCBI_Iran	National Cell Bank of Iran	https://en.pasteur.ac.ir/Department%20of%20Cell%20Bank	Cell line collections (Providers)	
+NCI-DTP	NCI Development Therapeutics Program	https://dtp.cancer.gov/repositories/	Cell line collections (Providers)	
+NISES	National Institute of Sericultural and Entomological Science Cell Database	https://web.archive.org/web/20160709065305/https://www.gene.affrc.go.jp/ex-nises/NISESCells/CellindexE1.html	Cell line collections (Providers)	
+PubChem_Cell_line	PubChem compound database; cell line pages	https://pubchem.ncbi.nlm.nih.gov	Chemistry resources	https://pubchem.ncbi.nlm.nih.gov/cell/$1
+RIKEN_BRC_EPD	RIKEN BRC Experimental Plant Division cell lines	https://epd.brc.riken.jp/en/	Cell line collections (Providers)	https://plant.rtc.riken.jp/resource/cell_line/cell_line_detail.html?brcno=%S
+Rockland	Rockland cell line products	https://www.rockland.com/categories/cell-lines-and-lysates/	Cell line collections (Providers)	https://www.rockland.com/search/?searchString=$1
+RSCB	Royan Stem Cell Bank	https://web.archive.org/web/20201001144644/http://www.royaninstitute.org/cmsen/index.php?option=com_content&task=view&id=205&Itemid=40	Cell line collections (Providers)	
+SKY/M-FISH/CGH	SKY/M-FISH and CGH database	https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd136/	Cell line databases/resources	
+Ubigene	Ubigene Biosciences cell line products	https://www.ubigene.us/	Cell line collections (Providers)	https://www.ubigene.us/product/?cate=0&mykeyword=$1

testbed/biopragmatics__bioregistry/exports/alignment/cheminf.tsv

@@ -0,0 +1,5 @@
+prefix	name	description
+000570	SwissLipids	
+000571	MolMeDB	
+000572	PDB ligand	
+000573	PDB structure	

testbed/biopragmatics__bioregistry/exports/alignment/cropoct.tsv

@@ -0,0 +1,5 @@
+prefix	name	homepage	description
+CO_369	Sainfoin ontology	http://cropontology.org/term/CO_369:ROOT	This ontology describes a standard trait lexicon used in phenotyping the forage and pulse crop, Sainfoin (Onobrychis viciifolia), with the intention of increasing trait consistency across different breeding programs. Submitted on behalf of the Sainfoin Consortium on November 3rd, 2022. Version 1.0.
+CO_371	Blueberry ontology	http://cropontology.org/term/CO_371:ROOT	Blueberry (Vaccinium) ontology defines crop traits and variables to support the standardization of phenotypic data collection for blueberry breeding programs in the USA. The ontology provides a description of agronomic, biochemical, morphological, phenological, physiological, quality, abiotic and biotic stress traits with their methods and scales used for each trait.
+CO_372	Strawberry ontology	http://cropontology.org/term/CO_372:ROOT	Strawberry trait ontology by USDA, GDR, 24 June 2024
+CO_374	Red clover ontology	http://cropontology.org/term/CO_374:ROOT	This red clover (Trifolium pratense) onthology defines variables and traits to support the standardization of phenotypic data collected in the framework of breeding. The ontology describes agronomic traits, productivity traits, traits related to flowering and seed production, and disease and insect pest resistance traits, together with their methods and scales for each traits.

testbed/biopragmatics__bioregistry/exports/alignment/ecoportal.tsv

@@ -0,0 +1,28 @@
+prefix	name	homepage	description
+ACFORMAT	Audubon Core Controlled Vocabulary for Dublin Core format		Audubon Core borrows the Dublin Core terms dc:format and dcterms:format to provide information about the physical or electronic format of a media item. This controlled vocabulary provides values for those two terms.
+ACSUBTYPE	Audubon Core subtype Controlled Vocabulary	http://rs.tdwg.org/ac/doc/subtype/	Audubon Core uses the terms ac:subtype and ac:subtypeLiteral to refine the type of a media item to a level more specific than the Dublin Core Type Vocabulary, http://purl.org/dc/dcmitype/. This controlled vocabulary provides values for ac:subtype and ac:subtypeLiteral.
+ACTRIS_CL	ACTRIS Controlled Lists	https://vocabulary.actris.nilu.no/skosmos/actris_ctrl_lists/en/	Lists of controlled terms used in ACTRIS
+ACTRIS_VOCAB	ACTRIS Vocabulary	https://vocabulary.actris.nilu.no/skosmos/actris_vocab/en/	Controlled vocabulary of terms used in ACTRIS
+ACVARIANT	Audubon Core variant Controlled Vocabulary		Audubon Core uses the terms ac:variant and ac:variantLiteral to provide information about the size, extent, and availability of the Service Access Point of a media item. This controlled vocabulary provides values for those terms.
+ALIENSPECIES	Alien Species Thesaurus		The Alien Species Thesaurus is an initiative to deal with the semantics about alien and invasive species. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). It is developed on the basis of already existing glossaries created within the framework of international initiatives aimed at the study of alien and invasive species. The terms (or concepts) are shared very broadly by the scientific community, and their definitions derive from guidelines prepared by relevant international organizations, and only in few occasions by peer reviewed papers. The Thesaurus currently consists of 157 terms.
+BIODIVTHES	Biodiversity Thesaurus		This bilingual thesaurus organizes the key concepts of biodiversity sciences, in their basic and applied ecological components. It uses polyhierarchy and includes 818 reciprocal associative relationships. The 1654 French and English descriptors (designating 827 concepts) are enriched with a large number of synonyms (1860) and hidden variants (7020) in both languages. Concepts are grouped into 82 collections, by semantic categories, thematic fields and EBV classes (Essential Biodiversity Variables). Definitions are given with their sources. This resource is aligned with the international thesauri AGROVOC, GEMET (GEneral Multilingual Environmental Thesaurus) and EnvThes (Environmental Thesaurus), as well as with the ontology ENVO (Environment Ontology).
+CPMETA	Ontology of Integrated Carbon Observation System (ICOS)	https://github.com/ICOS-Carbon-Portal/meta/blob/master/src/main/resources/owl/cpmeta.owl	OWL vocabulary describing metadata of two environmental research infrastructures: ICOS and SITES, as well as of a pilot project ICOS Cities
+DSW	Darwin-SW	https://github.com/darwin-sw/dsw	Darwin-SW (DSW) is an RDF vocabulary designed to complement the Biodiversity Information Standards (TDWG) Darwin Core Standard. DSW is based on a model derived from a community discussion about the relationships among the main Darwin Core classes.
+DWCDOE	Darwin Core Degree Of Establishment Controlled Vocabulary		The Darwin Core term degreeOfEstablishment provides information about degree to which an Organism survives, reproduces, and expands its range at the given place and time. The Degree of Establishment Controlled Vocabulary provides term that should be used as values for dwc:degreeOfEstablishment and dwciri:degreeOfEstablishment
+DWCEM	Darwin Core Establishment Means Controlled Vocabulary	http://rs.tdwg.org/dwc/doc/em/	The Darwin Core term establishmentMeans provides information about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans. The Establishment Means Controlled Vocabulary provides terms that should be used as values for dwc:establishmentMeans and dwciri:establishmentMeans.
+DWCPW	Darwin Core Pathway Controlled Vocabulary	http://rs.tdwg.org/dwc/doc/pw/	The Darwin Core term pathway provides information about the process by which an Organism came to be in a given place at a given time. The Pathway Controlled Vocabulary provides terms that should be used as values for dwc:pathway and dwciri:pathway.
+ELTER_CL	eLTER Controlled Lists		eLTER_CL is a thesaurus for controlled lists used by the eLTER community
+ENDEMISMS	Endemisms Thesaurus		Thesaurus on endemisms
+ENVTHES	Environmental Thesaurus		EnvThes compiles a set of terms in order to describe in a harmonised way data resulting from observations and measurements of ecosystem processes across different domain specific sciences. It is used by DEIMS-SDR for common keywords for annotation and quering metadata purposes.
+EURIO	eurio	https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/eurio	EURIO (EUropean Research Information Ontology) conceptualises, formally encodes and makes available in an open, structured and machine-readable format data about resarch projects funded by the EU's framework programmes for research and innovation.
+EUROSCIVOC	EuroSciVoc	https://op.europa.eu/s/y4UK	European Science Vocabulary (EuroSciVoc) is the taxonomy of fields of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with fields of science categories extracted from CORDIS content through a semi-automatic process developed with Natural Language Processing (NLP) techniques.
+EUROVOC	EuroVoc Core Concepts	https://op.europa.eu/s/y4TH	EuroVoc is a multilingual, multidisciplinary thesaurus covering the activities of the EU. It contains terms in 24 EU languages, plus in three languages of countries which are candidate for EU accession. EuroVoc is managed by the Publications Office of the European Union, which moved forward to ontology-based thesaurus management and semantic web technologies conformant to W3C recommendations as well as latest trends in thesaurus standards. EuroVoc users include the European Union institutions, the Publications Office of the EU, national and regional parliaments in Europe, plus national governments and private users around the world. EcoPortal is currently hosting the core concepts of EuroVoc, including all their attributes, except alternative labels.
+FISHTRAITS	Fish Traits Thesaurus		The Fish Traits Thesaurus is the first initiative to deal with the semantics of fish functional traits. It has been developed by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). FishTraits reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition, relationships) of approximately 220 concepts.
+I-ADOPT	I-ADOPT Framework ontology		"The I-ADOPT Framework is an ontology designed to facilitate interoperability between existing variable description models (including ontologies, taxonomy, and structured controlled vocabularies). One of the challenges in representing semantic descriptions of variables is getting people to agree about what they mean when describing the components that define the variables. The I-ADOPT ontology addresses this by providing core components and their relations that can be applied to define machine-interpretable variable descriptions that re-use FAIR vocabulary terms. It was developed by a core group of terminology experts and users from the Research Data Alliance (RDA) InteroperAble Descriptions of Observable Property Terminology (I-ADOPT) Working Group. The first published versions of the ontology up to v0.9.1 satisfied the basic cross-domain interoperability requirements. It defines four classes or ""concepts"" (Variable, Property, Entity, Constraint), and six object properties (hasProperty, hasObjectOfInterest, hasContextObject, hasMatrix, hasConstraint, constrains). The Variable is the top concept. It represents the description of something observed or mathematically derived. It minimally consists of one entity (the ObjectOfInterest) and its Property; a Property being a type of characteristic (i.e. a quantity or a quality). More complex variables can involve additional entities, for example an entity may have the role of Matrix and/or of ContextObject(s). The framework does not capture units, instruments, methods, and geographical location information; however its usage recommendation will make explicit reference to these by connecting the I-ADOPT framework to existing and complementary ontologies. This new version of the ontology (v1.0) adds one optional new class (VariableSet) and four optional new object properties (hasApplicableProperty, hasApplicableObjectOfInterest, hasApplicableMatrix, hasApplicableContextObject). This was necessary in order to enable flexibility in assigning optional and user-defined machine-interpretable categorizations of I-ADOPT variables under one or multiple coarser grouping concepts to facilitate dataset discovery and dataset aggregation. With the introduction of these concepts and properties, the framework enables different user communities or product developers to develop their own grouping criteria. While the Variable class must be connected to at least two classes via the mandatory properties hasProperty and hasObjectOIfInterest, the VariableSet class can have either of the new properties. Additionally, the VariableSet class can also be optionally connected to the Variable class using the property [ro:hasMember](http://purl.obolibrary.org/obo/RO_0002351) from the [OBO Relations Ontology](https://obofoundry.org/ontology/ro.html)."
+LUPO	LifeWatch ERIC Upper Ontology		The LifeWatch ERIC Upper Ontology (LUPO) is the model defining the core set of LifeWatch ERIC elements (Actors, Services and Infrastructure) and describing their high-level arrangement. LUPO is extendable and will foster, connect and describe lower level models of its core elements, with the vision to provide functionalities that facilitate the uptake, re-use and enrichment of LifeWatch ERIC resources by an ever broader community.
+MACROALGAETRAITS	Macroalgae Traits Thesaurus		The Macroalgae Traits Thesaurus contains several concepts on demographic and functional traits. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). It reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition) of approximately 100 traits.
+MR	Marine Regions ontology	https://www.marineregions.org/	The Marine Regions ontology provides definitions for the classes and properties used in the Marine Regions dataset.
+MRPTCODELIST	Marine Regions PlaceTypes code list	https://www.marineregions.org/	The Marine Regions PlaceType code list provides definitions for the PlaceTypes used in the Marine Regions dataset.
+OBOE	The Extensible Observation Ontology	https://github.com/NCEAS/oboe/	The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.
+PHYTOTRAITS	Phytoplankton Traits Thesaurus		The Phytoplankton Traits Thesaurus is the first initiative to deal with the semantics of phytoplankton functional traits focusing on morpho-functional traits. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). PhytoTraits reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition) of approximately 120 traits.
+ZOOPLANKTRAITS	Zooplankton Traits Thesaurus		The Zooplankton Traits Thesaurus contains several concepts mainly on zooplankton morpho-functional traits. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). It reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition) of approximately 90 traits.

testbed/biopragmatics__bioregistry/exports/alignment/edam.tsv

@@ -0,0 +1,169 @@
+prefix	name	description
+1031	Gene ID (CGD)	Identifier of a gene or feature from the CGD database.
+1032	Gene ID (DictyBase)	Identifier of a gene from DictyBase.
+1033	Ensembl gene	Unique identifier for a gene (or other feature) from the Ensembl database.
+1034	Gene ID (SGD)	Identifier of an entry from the SGD database.
+1036	TIGR	Identifier of an entry from the TIGR database.
+1037	TAIR accession (gene)	Identifier of an gene from the TAIR database.
+1043	CATH node	A code number identifying a node from the CATH database.
+1066	Sequence alignment	Identifier of a molecular sequence alignment, for example a record from an alignment database.
+1100	PIR	An identifier of PIR sequence database entry.
+1102	Gramene primary	Primary identifier of a Gramene database entry.
+1103	EMBL/GenBank/DDBJ	Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases.
+1104	Sequence cluster ID (UniGene)	A unique identifier of an entry (gene cluster) from the NCBI UniGene database.
+1113	Sequence cluster ID (COG)	Unique identifier of an entry from the COG database.
+1118	HMMER hidden Markov model	Unique identifier or name of a HMMER hidden Markov model.
+1119	JASPAR profile	Unique identifier or name of a profile from the JASPAR database.
+1123	TreeBASE study accession number	Accession number of an entry from the TreeBASE database.
+1124	TreeFam accession number	Accession number of an entry from the TreeFam database.
+1130	IntAct accession number	Accession number of an entry from the IntAct database.
+1134	InterPro secondary	Secondary accession number of an InterPro entry.
+1135	Gene3D	Unique identifier of an entry from the Gene3D database.
+1137	PRINTS code	The unique identifier of an entry in the PRINTS database.
+1139	SMART accession number	Accession number of an entry from the SMART database.
+1140	Superfamily hidden Markov model number	Unique identifier (number) of a hidden Markov model from the Superfamily database.
+1142	ProDom accession number	A ProDom domain family accession number.
+1143	TRANSFAC accession number	Identifier of an entry from the TRANSFAC database.
+1148	GermOnline	Identifier of an entry from the GermOnline database.
+1149	EMAGE	Identifier of an entry from the EMAGE database.
+1151	HGVbase	Identifier of an entry from the HGVbase database.
+1154	KEGG object	Unique identifier of an object from one of the KEGG databases (excluding the GENES division).
+1157	Pathway ID (BioCyc)	Identifier of an pathway from the BioCyc biological pathways database.
+1158	Pathway ID (INOH)	Identifier of an entry from the INOH database.
+1159	Pathway ID (PATIKA)	Identifier of an entry from the PATIKA database.
+1160	Pathway ID (CPDB)	Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.
+1167	Taverna workflow	Unique identifier of a Taverna workflow.
+1171	BioModel	Unique identifier of an entry from the BioModel database.
+1172	PubChem C	Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure.
+1178	HGNC concept	An identifier of a concept from the HGNC controlled vocabulary.
+1183	EMAP concept	An identifier of a concept from the EMAP mouse ontology.
+1184	ChEBI concept	An identifier of a concept from the ChEBI ontology.
+1185	MGED concept	An identifier of a concept from the MGED ontology.
+1186	myGrid concept	An identifier of a concept from the myGrid ontology.
+1189	Medline UI	Medline UI (unique identifier) of an article.
+1794	Gene ID (PlasmoDB)	Identifier of a gene from PlasmoDB Plasmodium Genome Resource.
+1795	Gene ID (EcoGene)	Identifier of a gene from EcoGene Database.
+1796	Gene ID (FlyBase)	Gene identifier from FlyBase database.
+1802	Gene ID (Gramene)	Gene identifier from Gramene database.
+1803	Gene ID (Virginia microbial)	Gene identifier from Virginia Bioinformatics Institute microbial database.
+1804	Gene ID (SGN)	Gene identifier from Sol Genomics Network.
+1873	iHOP organism	A unique identifier for an organism used in the iHOP database.
+1885	Gene ID (GeneFarm)	Identifier of a gene from the GeneFarm database.
+1886	Blattner number	The blattner identifier for a gene.
+1891	iHOP symbol	A unique identifier of a protein or gene used in the iHOP database.
+1895	Locus ID (AGI)	Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases).
+1896	Locus ID (ASPGD)	Identifier for loci from ASPGD (Aspergillus Genome Database).
+1897	Locus ID (MGG)	Identifier for loci from Magnaporthe grisea Database at the Broad Institute.
+1898	Locus ID (CGD)	Identifier for loci from CGD (Candida Genome Database).
+1899	Locus ID (CMR)	Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.
+1900	NCBI locus tag	Identifier for loci from NCBI database.
+1901	Locus ID (SGD)	Identifier for loci from SGD (Saccharomyces Genome Database).
+1902	Locus ID (MMP)	Identifier of loci from Maize Mapping Project.
+1903	Locus ID (DictyBase)	Identifier of locus from DictyBase (Dictyostelium discoideum).
+1904	Locus ID (EntrezGene)	Identifier of a locus from EntrezGene database.
+1905	Locus ID (MaizeGDB)	Identifier of locus from MaizeGDB (Maize genome database).
+1907	Gene ID (KOME)	Identifier of a gene from the KOME database.
+1908	Locus ID (Tropgene)	Identifier of a locus from the Tropgene database.
+2102	KEGG organism code	A three-letter code used in the KEGG databases to uniquely identify organisms.
+2105	Compound ID (BioCyc)	Identifier of a compound from the BioCyc chemical compounds database.
+2106	Reaction ID (BioCyc)	Identifier of a biological reaction from the BioCyc reactions database.
+2107	Enzyme ID (BioCyc)	Identifier of an enzyme from the BioCyc enzymes database.
+2112	FlyBase primary	Primary identifier of an object from the FlyBase database.
+2114	WormBase wormpep	Protein identifier used by WormBase database.
+2174	FlyBase secondary	Secondary identifier of an object from the FlyBase database.
+2209	Mutation	A unique identifier of a specific mutation catalogued in a database.
+2220	Sequence cluster ID (SYSTERS)	Unique identifier of a sequence cluster from the SYSTERS database.
+2285	Gene ID (MIPS)	Identifier for genetic elements in MIPS database.
+2290	EMBL	An accession number of an entry from the EMBL sequence database.
+2293	Gramene secondary	Secondary (internal) identifier of a Gramene database entry.
+2297	Gene ID (ECK)	Identifier of an E. coli K-12 gene from EcoGene Database.
+2315	NCBI version	An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number.
+2327	GI number (protein)	A unique identifier assigned to NCBI protein sequence records.
+2345	Pathway ID (ConsensusPathDB)	Identifier of a pathway from the ConsensusPathDB pathway database.
+2347	Sequence cluster ID (UniRef100)	Unique identifier of an entry from the UniRef100 database.
+2348	Sequence cluster ID (UniRef90)	Unique identifier of an entry from the UniRef90 database.
+2349	Sequence cluster ID (UniRef50)	Unique identifier of an entry from the UniRef50 database.
+2368	ASTD ID (exon)	Identifier of an exon from the ASTD database.
+2369	ASTD ID (intron)	Identifier of an intron from the ASTD database.
+2370	ASTD ID (polya)	Identifier of a polyA signal from the ASTD database.
+2371	ASTD ID (tss)	Identifier of a transcription start site from the ASTD database.
+2374	Spot serial number	Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database.
+2375	Spot ID (HSC-2DPAGE)	Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database.
+2383	EGA	Identifier of an entry from the EGA database.
+2384	IPI protein	Identifier of a protein entry catalogued in the International Protein Index (IPI) database.
+2385	RefSeq accession (protein)	Accession number of a protein from the RefSeq database.
+2387	TAIR	Identifier of an entry from the TAIR database.
+2388	TAIR accession (At gene)	Identifier of an Arabidopsis thaliana gene from the TAIR database.
+2391	UTR	Identifier of an entry from the UTR database.
+2393	mFLJ/mKIAA number	Identifier of an entry from the Rouge or HUGE databases.
+2398	Ensembl protein	Unique identifier for a protein from the Ensembl database.
+2580	BindingDB Monomer	Unique identifier of a monomer from the BindingDB database.
+2588	BlotBase blot	Unique identifier of a blot from a Northern Blot from the BlotBase database.
+2591	Brite hierarchy	Identifier of an entry from the Brite database of biological hierarchies.
+2593	BRENDA organism	A unique identifier for an organism used in the BRENDA database.
+2612	Sequence cluster ID (CluSTr)	Unique identifier of a sequence cluster from the CluSTr database.
+2617	Signaling Gateway protein	Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.
+2621	TAIR accession (protein)	Identifier of a protein sequence from the TAIR database.
+2636	MatrixDB interaction	A unique identifier of an interaction from the MatrixDB database.
+2637	cPath	A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.
+2643	Gene ID (ZFIN)	Identifier for a gene from the Zebrafish information network genome (ZFIN) database.
+2647	LGICdb	Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.
+2648	Reaction kinetics ID (SABIO-RK)	Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database.
+2649	PharmGKB	Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
+2668	iRefIndex	Unique identifier of an entry from the iRefIndex database of protein-protein interactions.
+2670	Pathway ID (DQCS)	Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).
+2701	CATH node ID (family)	A code number identifying a family from the CATH database.
+2702	Enzyme ID (CAZy)	Identifier of an enzyme from the CAZy enzymes database.
+2704	Clone ID (IMAGE)	A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).
+2705	GO concept ID (cellular component)	An identifier of a 'cellular component' concept from the Gene Ontology.
+2709	CleanEx entry name	An identifier of a gene expression profile from the CleanEx database.
+2713	Protein ID (CORUM)	Unique identifier for a protein complex from the CORUM database.
+2714	CDD PSSM-	Unique identifier of a position-specific scoring matrix from the CDD database.
+2715	Protein ID (CuticleDB)	Unique identifier for a protein from the CuticleDB database.
+2721	DiProDB	Identifier of an dinucleotide property from the DiProDB database.
+2725	Ensembl transcript	Unique identifier for a gene transcript from the Ensembl database.
+2729	COGEME EST	Identifier of an EST sequence from the COGEME database.
+2730	COGEME unisequence	Identifier of a unisequence from the COGEME database.
+2731	Protein family ID (GeneFarm)	Accession number of an entry (protein family) from the GeneFarm database.
+2736	Sequence feature ID (SwissRegulon)	A feature identifier as used in the SwissRegulon database.
+2737	FIG	A unique identifier of gene in the NMPDR database.
+2739	Gene ID (Genolist)	A unique identifier of gene in the Genolist database.
+2742	AraC-XylS	Identifier of a transcription factor from the AraC-XylS database.
+2744	Locus ID (PseudoCAP)	Identifier of a locus from the PseudoCAP database.
+2745	Locus ID (UTR)	Identifier of a locus from the UTR database.
+2746	MonosaccharideDB	Unique identifier of a monosaccharide from the MonosaccharideDB database.
+2752	GlycoMap	Identifier of an entry from the GlycoMapsDB (Glycosciences.de) database.
+2759	Gene ID (VectorBase)	Identifier for a gene from the VectorBase database.
+2770	HIT	Identifier of an RNA transcript from the H-InvDB database.
+2771	HIX	A unique identifier of gene cluster in the H-InvDB database.
+2772	HPA antibody id	Identifier of a antibody from the HPA database.
+2774	Gene ID (JCVI)	A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).
+2776	ConsensusPathDB entity	Identifier of a physical entity from the ConsensusPathDB database.
+2778	CCAP strain number	The number of a strain of algae and protozoa from the CCAP database.
+2780	Stock number (TAIR)	A stock number from The Arabidopsis information resource (TAIR).
+2781	REDIdb	Identifier of an entry from the RNA editing database (REDIdb).
+2783	Protein family ID (PANTHER)	Accession number of an entry (family) from the PANTHER database.
+2784	RNAVirusDB	A unique identifier for a virus from the RNAVirusDB database.
+2786	NCBI Genome Project	An identifier of a genome project assigned by NCBI.
+2792	Protein ID (PeroxiBase)	Unique identifier for a peroxidase protein from the PeroxiBase database.
+2793	SISYPHUS	Identifier of an entry from the SISYPHUS database of tertiary structure alignments.
+2794	ORF	Accession of an open reading frame (catalogued in a database).
+2796	LINUCS	Identifier of an entry from the GlycosciencesDB database.
+2797	Protein ID (LGICdb)	Unique identifier for a ligand-gated ion channel protein from the LGICdb database.
+2798	MaizeDB	Identifier of an EST sequence from the MaizeDB database.
+2799	Gene ID (MfunGD)	A unique identifier of gene in the MfunGD database.
+2800	Orpha number	An identifier of a disease from the Orpha database.
+2802	Protein ID (EcID)	Unique identifier for a protein from the EcID database.
+2803	Clone ID (RefSeq)	A unique identifier of a cDNA molecule catalogued in the RefSeq database.
+2804	Protein ID (ConoServer)	Unique identifier for a cone snail toxin protein from the ConoServer database.
+2805	GeneSNP	Identifier of a GeneSNP database entry.
+2835	Gene ID (VBASE2)	Identifier for a gene from the VBASE2 database.
+2836	DPVweb	A unique identifier for a virus from the DPVweb database.
+2837	Pathway ID (BioSystems)	Identifier of a pathway from the BioSystems pathway database.
+2915	Gramene	Identifier of a Gramene database entry.
+2916	DDBJ	An identifier of an entry from the DDBJ sequence database.
+3022	NCBI genetic code	Identifier of a genetic code in the NCBI list of genetic codes.
+3029	Protein ID (EMBL/GenBank/DDBJ)	EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.
+3238	Cell type ontology	Cell type ontology concept ID.
+3270	Ensembl gene tree	Unique identifier for a gene tree from the Ensembl database.
+3769	BRENDA ontology concept	An identifier of a concept from the BRENDA ontology.