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Updated development_stage_ontology_term_id (#1173)
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@brianraymor
brianraymor authored Jan 21, 2025
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83 changes: 76 additions & 7 deletions schema/drafts/5.3.0.md
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Expand Up @@ -561,13 +561,77 @@ Curators MUST annotate the following columns in the `obs` dataframe:
</tr>
<tr>
<th>Value</th>
<td>categorical with <code>str</code> categories. If unavailable, this MUST be <code>"unknown"</code>.<br><br>
If <code>organism_ontolology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9606"><code>"NCBITaxon:9606"</code></a> for <i>Homo sapiens</i>, this MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/hsapdv/classes?obo_id=HsapDv%3A0000001"><code>HsapDv:0000001</code></a> for <i>life cycle</i>.<br><br>
If <code>organism_ontolology_term_id</code> is
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A10090"><code>"NCBITaxon:10090"</code></a> for <i>Mus musculus</i>, this MUST be the accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/mmusdv/classes?obo_id=MmusDv%3A0000001"><code>MmusDv:0000001</code></a> for <i>life cycle</i>.<br><br>
Otherwise, for all other organisms this MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/uberon/classes?obo_id=UBERON%3A0000105"<code>UBERON:0000105</code></a> for <i>life cycle stage</i>, excluding <a href="https://www.ebi.ac.uk/ols4/ontologies/uberon/classes?obo_id=UBERON%3A0000071"<code>UBERON:0000071</code></a> for <i>death stage</i>.
</td>
</tr>
<td>
categorical with <code>str</code> categories. If unavailable, this MUST be <code>"unknown"</code>.<br><br>
<table>
<thead>
<tr>
<th>For <code>organism_ontolology_term_id</code></th>
<th>Value</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A6239"><code>"NCBITaxon:6239"</code></a><br>for <i>Caenorhabditis elegans</i>
</td>
<td>
MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/wbls/classes?obo_id=WBls%3A0000075"><code>WBls:0000075</code></a> for <i>worm life stage</i>
</td>
</tr>
<tr>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7955"><code>"NCBITaxon:7955"</code></a><br>for <i>Danio rerio</i>
</td>
<td>
MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/zfs/classes?obo_id=ZFS%3A0100000"><code>ZFS:0100000</code></a><for <i>zebrafish stage</i> and<br>MUST NOT be <a href="https://www.ebi.ac.uk/ols4/ontologies/zfs/classes?obo_id=ZFS%3A0000000"><code>ZFS:0000000</code></a> for <i>Unknown</i>
</td>
</tr>
<tr>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7227"><code>"NCBITaxon:7227"</code></a><br>for <i>Drosophila melanogaster</i>
</td>
<td>
MUST be the most accurate FBdv term
</td>
</tr>
<tr>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9606"><code>"NCBITaxon:9606"</code></a><br>for <i>Homo sapiens</i>
</td>
<td>
MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/hsapdv/classes?obo_id=HsapDv%3A0000001"><code>HsapDv:0000001</code></a> for <i>life cycle</i>
</td>
</tr>
<tr>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A10090"><code>"NCBITaxon:10090"</code></a><br>for <i>Mus musculus</i>
</td>
<td>
MUST be the accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/mmusdv/classes?obo_id=MmusDv%3A0000001"><code>MmusDv:0000001</code></a> for <i>life cycle</i>
</td>
</tr>
<tr>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A8355"><code>"NCBITaxon:8355"</code></a><br>for <i>Xenopus laevis</i>
</td>
<td>
MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/xao/classes?obo_id=XAO%3A1000000"><code>XAO:1000000</code></a><br>for <i>Xenopus developmental stage</i>
</td>
</tr>
<tr>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A8364"><code>"NCBITaxon:8364"</code></a><br>for <i>Xenopus tropicalis</i>
</td>
<td>
MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/xao/classes?obo_id=XAO%3A1000000"><code>XAO:1000000</code></a><br>for <i>Xenopus developmental stage</i>
</td>
</tr>
</tbody>
</table>
<br>Otherwise, for all other organisms this MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/uberon/classes?obo_id=UBERON%3A0000105"<code>UBERON:0000105</code></a> for <i>life cycle stage</i>, excluding <a href="https://www.ebi.ac.uk/ols4/ontologies/uberon/classes?obo_id=UBERON%3A0000071"<code>UBERON:0000071</code></a> for <i>death stage</i>.
</td>
</tr>
</tbody></table>
<br>

Expand Down Expand Up @@ -2156,6 +2220,11 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem
* ZFA for *Danio rerio*
* FBbt for *Drosophila melanogaster*
* XAO for *Xenopus laevis* and *Xenopus tropicalis*
* Updated the ontology requirements for `development_stage_ontology_term_id` to include:
* WBls for *Caenorhabditis elegans*
* ZFS for *Danio rerio*
* FBdv for *Drosophila melanogaster*
* XAO for *Xenopus laevis* and *Xenopus tropicalis*
* Added <code>genetic_ancestry_African</code>
* Added <code>genetic_ancestry_East_Asian</code>
* Added <code>genetic_ancestry_European</code>
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