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Clarified "na" and "unknown" requirements for organism_*_ontology_ter…
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@brianraymor
brianraymor authored Oct 24, 2024
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56 changes: 37 additions & 19 deletions schema/drafts/5.2.1-experimental.md
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Expand Up @@ -163,39 +163,52 @@ The following gene annotation dependencies are *pinned* for this version of the
<tr>
<th>Value</th>
<td>
categorical with <code>str</code> categories. This MUST be <code>"unknown"</code> when:
<ul>
<li>
no appropriate term can be found (e.g. the cell type is unknown)
</li>
<li>
<code>assay_ontology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0010961"><code>"EFO:0010961"</code></a> for <i>Visium Spatial Gene Expression</i>, <code>uns['spatial']['is_single']</code> is <code>True</code>, and the corresponding value of <code>in_tissue</code> is <code>0</code>
</li>
</ul>
Otherwise:<br>
categorical with <code>str</code> categories.<br><br>
<table>
<thead><tr>
<th>For <code>organism_ontolology_term_id</code></th>
<th>MUST be</th>
<th>Value</th>
</tr></thead>
<tbody>
<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>
the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/zfa/classes?obo_id=ZFA%3A0009000"><code>ZFA:0009000</code></a> for <i>cell</i>
MUST be either the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/zfa/classes?obo_id=ZFA%3A0009000"><code>ZFA:0009000</code></a> for <i>cell</i><br>or <code>"unknown"</code> when:
<ul>
<li>
no appropriate term can be found (e.g. the cell type is unknown)
</li>
<li>
<code>assay_ontology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0010961"><code>"EFO:0010961"</code></a> for<br><i>Visium Spatial Gene Expression</i>, <code>uns['spatial']['is_single']</code> is <code>True</code>,<br>and the corresponding value of <code>in_tissue</code> is <code>0</code>
</li>
</ul>
</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>the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/fbbt/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FFBbt_00007002?lang=en"><code>FBbt:0007002</code></a> for <i>cell</i>
<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 ither the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/fbbt/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FFBbt_00007002?lang=en"><code>FBbt:0007002</code></a> for <i>cell</i><br>or <code>"unknown"</code> when:
<ul>
<li>
no appropriate term can be found (e.g. the cell type is unknown)
</li>
<li>
<code>assay_ontology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0010961"><code>"EFO:0010961"</code></a> for<br><i>Visium Spatial Gene Expression</i>, <code>uns['spatial']['is_single']</code> is <code>True</code>,<br>and the corresponding value of <code>in_tissue</code> is <code>0</code>
</li>
</ul>
</td>
</tr>
<tr>
<td>
All other values of<br><code>organism_ontology_term_id</code>
</td>
<td>MUST be <code>"na"</code></td>
</tr>
</tbody>
</table>
<br>For all other organisms, the value MUST be <code>"na"</code>.
</td>
</tr>
</tbody></table>
Expand Down Expand Up @@ -244,7 +257,7 @@ The following gene annotation dependencies are *pinned* for this version of the
<thead>
<tr>
<th>For <code>organism_ontolology_term_id</code></th>
<th>MUST be</th>
<th>Value</th>
</tr>
</thead>
<tbody>
Expand All @@ -253,20 +266,25 @@ The following gene annotation dependencies are *pinned* for this version of the
<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>
the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/zfa/classes?obo_id=ZFA%3A0100000"><code>ZFA:0100000</code></a> for <i>zebrafish anatomical entity</i><br>and MUST NOT be <a href="https://www.ebi.ac.uk/ols4/ontologies/zfa/classes?obo_id=ZFA%3A0009000"><code>ZFA:0009000</code></a> for <i>cell</i> or any of its descendants
MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/zfa/classes?obo_id=ZFA%3A0100000"><code>ZFA:0100000</code></a> for<br><i>zebrafish anatomical entity</i> and MUST NOT be <a href="https://www.ebi.ac.uk/ols4/ontologies/zfa/classes?obo_id=ZFA%3A0009000"><code>ZFA:0009000</code></a><br>for <i>cell</i> or any of its descendants
</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>
the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/fbbt/classes?obo_id=FBBT%3A10000000"><code>FBbt:10000000</code></a> for <i>anatomical entity</i><br>and MUST NOT be <a href="https://www.ebi.ac.uk/ols4/ontologies/fbbt/classes?obo_id=FBbt%3A00007002"><code>FBbt:00007002</code></a> for <i>cell</i> or any of its descendants.
MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/fbbt/classes?obo_id=FBBT%3A10000000"><code>FBbt:10000000</code></a> for<br><i>anatomical entity</i> and MUST NOT be <a href="https://www.ebi.ac.uk/ols4/ontologies/fbbt/classes?obo_id=FBbt%3A00007002"><code>FBbt:00007002</code></a><br>for <i>cell</i> or any of its descendants.
</td>
</tr>
<tr>
<td>
All other values of<br><code>organism_ontology_term_id</code>
</td>
<td>MUST be <code>"na"</code></td>
</tr>
</tbody>
</table>
<br>For all other organisms, the value MUST be <code>"na"</code>.
</td>
</tr>
</tbody></table>
Expand Down

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