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Added descendants of (#1242)
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@brianraymor
brianraymor authored Feb 3, 2025
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97 changes: 44 additions & 53 deletions schema/drafts/5.3.0.md
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Expand Up @@ -600,7 +600,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
</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>
<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> or one of its descendants
</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>
Expand Down Expand Up @@ -923,38 +923,38 @@ If <code>organism_ontolology_term_id</code> is <code>"NCBITaxon:9606"</code> for
</td>
</tr>
<tr>
<td><i>Macaca fascicularis</i></td>
<td><i>Macaca fascicularis<br>and its descendants</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9541"><code>"NCBITaxon:9541"</code></a>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9541"><code>"NCBITaxon:9541"</code></a>or one of its descendants
</td>
</tr>
<tr>
<td><i>Macaca mulatta</i></td>
<td><i>Macaca mulatta<br>and its descendants</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9544"><code>"NCBITaxon:9544"</code></a>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9544"><code>"NCBITaxon:9544"</code></a>or one of its descendants
</td>
</tr>
<tr>
<td><i>Microcebus murinus</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A30608"><code>"NCBITaxon:30608"</code></a></td>
</tr>
<tr>
<td><i>Mus musculus</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A10090"><code>"NCBITaxon:10090"</code></a></td>
<td><i>Mus musculus<br>and its descendants</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A10090"><code>"NCBITaxon:10090"</code></a>or one of its descendants</td>
</tr>
<tr>
<td><i>Oryctolagus cuniculus</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9986"><code>"NCBITaxon:9986"</code></a></td>
<td><i>Oryctolagus cuniculus<br>and its descendants</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9986"><code>"NCBITaxon:9986"</code></a>or one of its descendants</td>
</tr>
<tr>
<td><i>Pan troglodytes</i></td>
<td><i>Pan troglodytes<br>and its descendants</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9598"><code>"NCBITaxon:9598"</code></a>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9598"><code>"NCBITaxon:9598"</code></a>or one of its descendants
</td>
</tr>
<tr>
<td><i>Rattus norvegicus</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A10116"><code>"NCBITaxon:10116"</code></a></td>
<td><i>Rattus norvegicus<br>and its descendants</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A10116"><code>"NCBITaxon:10116"</code></a>or one of its descendants</td>
</tr>
<tr>
<td><i>Sus scrofa<br>and its descendants</i></td>
Expand Down Expand Up @@ -1791,6 +1791,12 @@ add the feature length and type.
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A6239"><code>"NCBITaxon:6293"</code></a>
</td>
</tr>
<tr>
<td><i>Callithrix jacchus</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9483"><code>"NCBITaxon:9483"</code></a>
</td>
</tr>
<tr>
<td><i>Danio rerio</i></td>
<td>
Expand All @@ -1802,6 +1808,12 @@ add the feature length and type.
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7227"><code>"NCBITaxon:7227"</code></a>
</td>
</tr>
<tr>
<td><i>Gorilla gorilla gorilla</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9595"><code>"NCBITaxon:9595"</code></a>
</td>
</tr>
<tr>
<td><i>Homo sapiens</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9606"><code>"NCBITaxon:9606"</code></a></td>
Expand All @@ -1812,7 +1824,12 @@ add the feature length and type.
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9541"><code>"NCBITaxon:9541"</code></a>
</td>
</tr>
<tr>
<tr>
<td><i>Macaca mulatta</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9544"><code>"NCBITaxon:9544"</code></a>
</td>
</tr>
<tr>
<td><i>Microcebus murinus</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A30608"><code>"NCBITaxon:30608"</code></a></td>
Expand All @@ -1825,6 +1842,12 @@ add the feature length and type.
<td><i>Oryctolagus cuniculus</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9986"><code>"NCBITaxon:9986"</code></a></td>
</tr>
<tr>
<td><i>Pan troglodytes</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9598"><code>"NCBITaxon:9598"</code></a>
</td>
</tr>
<tr>
<td><i>Rattus norvegicus</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A10116"><code>"NCBITaxon:10116"</code></a></td>
Expand All @@ -1834,48 +1857,15 @@ add the feature length and type.
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A2697049"><code>"NCBITaxon:2697049"</code></a></td>
</tr>
<tr>
<td><i>ERCC Spike-Ins</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A32630"><code>"NCBITaxon:32630"</code></a></td>
</tr>
</tbody></table><br><br><b>Current datasets with features translated into orthologous genes from the <i>Homo sapiens</i> and <i>Mus musculus</i> gene references will not be supported in the next schema release. The following requirements will be updated from STRONGLY RECOMMENDED to MUST:</b><br><br>
<table>
<thead>
<tr>
<th>Reference Organism</th>
<th>STRONGLY RECOMMENDED Use</th>
</tr>
</thead>
<tbody>
<tr>
<td><i>Callithrix jacchus</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9483"><code>"NCBITaxon:9483"</code></a>
<td><i>Sus scrofa</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9823"><code>"NCBITaxon:9823"</code></a>
</td>
</tr>
<tr>
<td><i>Gorilla gorilla gorilla</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9595"><code>"NCBITaxon:9595"</code></a>
</td>
</tr>
<tr>
<td><i>Macaca mulatta</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9544"><code>"NCBITaxon:9544"</code></a>
</td>
</tr>
<tr>
<td><i>Pan troglodytes</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9598"><code>"NCBITaxon:9598"</code></a>
</td>
<td><i>ERCC Spike-Ins</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A32630"><code>"NCBITaxon:32630"</code></a></td>
</tr>
<tr>
<td><i>Sus scrofa<br>and its descendants</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9823"><code>"NCBITaxon:9823"</code></a>or one of its descendants
</td>
</tr>
</tbody></table>
</td>
</tr>
Expand Down Expand Up @@ -2367,7 +2357,7 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem
A Dataset MUST meet all of the following requirements to be eligible for scATAC-seq assets:
* <code>obs['assay_ontology_term_id']</code> values MUST be either all <i>paired assays</i> or <i>unpaired assays</i>
* <code>obs['is_primary_data']</code> values MUST be all <code>True</code>
* <code>obs['organism_ontology_term_id']</code> values MUST be either all <code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i> or <code>"NCBITaxon:10090"</code> for <i>Mus musculus</i>. The value determines the required Chromosome Table.
* <code>obs['organism_ontology_term_id']</code> values MUST be either all <code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i> or <code>"NCBITaxon:10090"</code> for <i>Mus musculus</i> or one of its descendants. The value determines the required Chromosome Table.

If the <code>obs['assay_ontology_term_id']</code> values are all <i>paired assays</i> then the Dataset MAY have a fragments file asset.

Expand Down Expand Up @@ -2889,6 +2879,7 @@ Chromosome Tables are determined by the reference assembly for the gene annotati
* WBls for *Caenorhabditis elegans*
* ZFS for *Danio rerio*
* FBdv for *Drosophila melanogaster*
* Updated `development_stage_ontology_term_id` to include descendants of <i>Mus musclus</i>
* Added <code>genetic_ancestry_African</code>
* Added <code>genetic_ancestry_East_Asian</code>
* Added <code>genetic_ancestry_European</code>
Expand Down

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