Add vo2max module (ported from Generation-I dna-seq/just_vo2max)
Browse files- data/vo2max/annotations.parquet +2 -2
- data/vo2max/clin_sig_authority_calls.parquet +3 -0
- data/vo2max/clin_sig_concordance.parquet +3 -0
- data/vo2max/literature.parquet +2 -2
- data/vo2max/manifest.json +224 -32
- data/vo2max/sources.parquet +2 -2
- data/vo2max/studies.parquet +2 -2
- data/vo2max/weights.parquet +2 -2
data/vo2max/annotations.parquet
CHANGED
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@@ -1,3 +1,3 @@
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size 3624
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data/vo2max/clin_sig_authority_calls.parquet
ADDED
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@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:233b40fd79c7da73a9989ef4f7442886fd11d4495fbab9fe3a8d630855c9a1d4
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size 1138
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data/vo2max/clin_sig_concordance.parquet
ADDED
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@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:0611079ba1ae139bf1b1c3038d0f784a798747436c88275b47e6e986d10fe9a6
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size 919
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data/vo2max/literature.parquet
CHANGED
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@@ -1,3 +1,3 @@
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| 1 |
version https://git-lfs.github.com/spec/v1
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oid sha256:
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size
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version https://git-lfs.github.com/spec/v1
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size 6557
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data/vo2max/manifest.json
CHANGED
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@@ -2,10 +2,11 @@
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"manifest_version": "1.0",
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| 3 |
"schema_version": "1.0",
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"identity": {
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| 5 |
-
"namespace":
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| 6 |
"name": "vo2max",
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-
"version":
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"
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},
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"display": {
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"title": "VO2 Max",
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@@ -19,11 +20,13 @@
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"curator": "just-dna-seq",
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"method": "expert-curated",
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"license": null,
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-
"
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"authors": [],
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"authorship": [],
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"created_at": null,
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-
"published_at":
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"stats": {
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"variant_count": 13,
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| 29 |
"weights_rows": 39,
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@@ -50,26 +53,40 @@
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},
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"compilation": {
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"compile_success": true,
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-
"compiled_by":
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| 54 |
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"compiler_version": "just-dna-compiler 0.
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| 55 |
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"ensembl_reference":
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| 56 |
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"compiled_at": "2026-
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"warnings": [
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"
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"
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"fully_resolved": true,
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"resolution_signature": "sha256:4d42c83d09874f786c307dce786581a40453f2a95ecc524505d28e8fac7d85b1",
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| 63 |
"resolution_sources": [
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| 64 |
"cache"
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| 65 |
],
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| 66 |
"vrs_alleles": 19,
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| 67 |
-
"vrs_alleles_identified": 19
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},
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"frequency": null,
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| 70 |
"gene_metrics": null,
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"literature": {
|
| 72 |
-
"signature": "sha256:
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"sources": [
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"pubmed"
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],
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@@ -79,8 +96,10 @@
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"open_access_count": 3,
|
| 80 |
"abstract_only_count": 0,
|
| 81 |
"quotes_authored": 0,
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| 84 |
"sources": {
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| 85 |
"signature": "sha256:b1c5043ccc97b5c15683fcdc1c63de32c6da8e270295619f2c4954817ed8332f",
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| 86 |
"sources": [
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@@ -107,11 +126,141 @@
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"redistribution": true,
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"row_count": 1
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},
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"inputs": [
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{
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"name": "module_spec.yaml",
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"size":
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{
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"name": "variants.csv",
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@@ -120,46 +269,88 @@
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},
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{
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"name": "studies.csv",
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| 124 |
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"content_signature": "sha256:
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{
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| 132 |
"name": "weights.parquet",
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| 133 |
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"sha256": "sha256:
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| 134 |
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"size":
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| 135 |
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|
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{
|
| 137 |
"name": "annotations.parquet",
|
| 138 |
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"sha256": "sha256:
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| 139 |
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"size":
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| 140 |
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|
| 141 |
{
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"name": "studies.parquet",
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| 143 |
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"sha256": "sha256:
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| 144 |
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"size":
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| 146 |
{
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| 147 |
"name": "literature.parquet",
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| 148 |
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"sha256": "sha256:
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"size":
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{
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"name": "sources.parquet",
|
| 153 |
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"sha256": "sha256:
|
| 154 |
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"size":
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| 155 |
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|
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| 158 |
"logs": [
|
| 159 |
{
|
| 160 |
"name": "v1_port.log",
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| 162 |
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"size":
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"provenance": null,
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@@ -169,5 +360,6 @@
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"manifest_version": "1.0",
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| 3 |
"schema_version": "1.0",
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| 4 |
"identity": {
|
| 5 |
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"namespace": "just-dna-seq",
|
| 6 |
"name": "vo2max",
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| 7 |
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"version": "1.1.0",
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|
| 10 |
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|
| 11 |
"display": {
|
| 12 |
"title": "VO2 Max",
|
|
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|
| 20 |
"curator": "just-dna-seq",
|
| 21 |
"method": "expert-curated",
|
| 22 |
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"owner": "just-dna-seq",
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"published_at": "2026-09-26T23:44:40Z",
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| 30 |
"stats": {
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| 32 |
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| 53 |
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"compilation": {
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"compiled_by": "marketplace-server",
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"compiler_version": "just-dna-compiler 0.7.0",
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"ensembl_reference": "just-dna-seq/ensembl_variations",
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| 59 |
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"compiled_at": "2026-09-26T23:44:40Z",
|
| 60 |
"warnings": [
|
| 61 |
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"This module records no closure: nothing in it states that authoring is finished, so a consumer cannot tell a spec still being edited from one its author considers done. Run `just-dna-compiler close <spec-dir>` when the module is complete — closing is a deliberate act, it is never stamped by a passing check, and editing any authored file afterwards drops the closure again. Compiling without one is a warning today; requiring it is filed for 1.0 (RM73)."
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| 62 |
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|
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|
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|
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"detail": "none of 7 citation(s) carries an authored DOI or PMC id, so there was nothing to compare against PubMed's own",
|
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|
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|
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|
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|
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|
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|
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"skipped": "nothing_to_check",
|
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"detail": "the module records no release, so it makes no claim about where its rows came from",
|
| 175 |
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|
| 176 |
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|
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|
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|
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|
| 184 |
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"skipped": "nothing_to_check",
|
| 185 |
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"detail": "this module records no citation drafted from CIViC's API, so there is no recorded curation status to re-ask about",
|
| 186 |
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"source": "civic",
|
| 187 |
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|
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"checked_at": "2026-09-26T23:44:40Z",
|
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|
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{
|
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|
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|
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|
| 195 |
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"skipped": "offline",
|
| 196 |
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"detail": "the GRCh37 service is the only thing that can tell an old-assembly coordinate from a wrong ref, and there is no local GRCh37 data",
|
| 197 |
+
"source": "ensembl-grch37",
|
| 198 |
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"release": null,
|
| 199 |
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"checked_at": "2026-09-26T23:44:40Z",
|
| 200 |
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"producer": "just-dna-enricher 0.7.0"
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},
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| 202 |
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{
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| 205 |
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"findings": 0,
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| 206 |
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"skipped": "nothing_to_check",
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| 207 |
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"detail": "no provenance quote or regex on any citation, so none of them asked this question",
|
| 208 |
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"source": "europepmc",
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| 209 |
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| 210 |
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"detail": "no row authors both an rsID and a coordinate, so the module makes no pair claim to compare — this is not a comparison that found nothing",
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"source": "ensembl",
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