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Updated tissue_ontology_term_id (#1175)
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@brianraymor
brianraymor authored Jan 21, 2025
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Showing 1 changed file with 62 additions and 24 deletions.
86 changes: 62 additions & 24 deletions schema/drafts/5.3.0.md
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Expand Up @@ -501,7 +501,6 @@ Curators MUST annotate the following columns in the `obs` dataframe:
MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/wbbt/classes?obo_id=WBbt%3A0004017"><code>WBbt:0004017</code></a> for <i>Cell</i>
</td>
</tr>
<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>
Expand All @@ -519,14 +518,7 @@ 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%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%3A0003012"><code>XAO:0003012</code></a> for <i>cell</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>
<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> or<br><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%3A0003012"><code>XAO:0003012</code></a> for <i>cell</i>
</td>
Expand Down Expand Up @@ -584,7 +576,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
<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>
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>
Expand Down Expand Up @@ -613,23 +605,15 @@ 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%3A8355"><code>"NCBITaxon:8355"</code></a><br>for <i>Xenopus laevis</i>
<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> or<br><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>
<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>.
<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>
Expand Down Expand Up @@ -1305,10 +1289,60 @@ If <code>organism_ontolology_term_id</code> is <code>"NCBITaxon:9606"</code> for
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<tr>
<th>Value</th>
<td>categorical with <code>str</code> categories. If <code>tissue_type</code> is <code>"tissue"</code> or <code>"organoid"</code>, this MUST be the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/uberon/classes?obo_id=UBERON%3A0001062"><code>UBERON:0001062</code></a> for <i>anatomical entity</i>.<br><br> If <code>tissue_type</code> is <code>"cell culture"</code> this MUST follow the requirements for <code>cell_type_ontology_term_id<code>.</td>
</tr>
<td>
categorical with <code>str</code> categories. If <code>tissue_type</code> is <code>"cell culture"</code> this MUST follow the requirements for <code>cell_type_ontology_term_id</code>.<br><br>If <code>tissue_type</code> is <code>"tissue"</code> or <code>"organoid"</code> then:<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/wbbt/classes?obo_id=WBBT%3A0005766"><code>WBbt:0005766</code></a> for <i>Anatomy</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/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>
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>
<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> or<br><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%3A0000000"><code>XAO:0000000</code></a> for<br><i>Xenopus anatomical entity</i> and MUST NOT be:
<ul>
<li><a href="https://www.ebi.ac.uk/ols4/ontologies/xao/classes?obo_id=XAO%3A0003003"><code>XAO:0003003</code></a> for <i>unspecified</i></li>
<li><a href="https://www.ebi.ac.uk/ols4/ontologies/xao/classes?obo_id=XAO%3A0003012"><code>XAO:0003012</code></a> for <i>cell</i> or any of its descendants</li>
<li><a href="https://www.ebi.ac.uk/ols4/ontologies/xao/classes?obo_id=XAO%3A1000000"><code>XAO:1000000</code></a> for <i>Xenopus developmental stage</i> or any of its descendants</li>
</ul>
</td>
</tr>
</tbody>
</table>
<br>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%3A0001062"><code>UBERON:0001062</code></a> for <i>anatomical entity</i>.
</td>
</tr>
</tbody></table>
<br>

Expand Down Expand Up @@ -2231,11 +2265,15 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem
* Added <code>genetic_ancestry_Indigenous_American</code>
* Added <code>genetic_ancestry_Oceanian</code>
* Added <code>genetic_ancestry_South_Asian</code>

* Updated the requirements for `in_tissue` to include descendants of _Visium Spatial Gene Expression_.
* Updated the requirements for `sex_ontology_term_id`:
* For *Caenorhabditis elegans*, values are limited to <i>hermaphrodite</i>, <i>male</i>, or `"unknown"`
* For all other organisms, values are limited to <i>female</i>, <i>hermaphrodite</i>, <i>male</i>, or `"unknown"`
* Updated the ontology requirements for `tissue_ontology_term_id` ro include:
* WBbt for *Caenorhabditis elegans*
* ZFA for *Danio rerio*
* FBbt for *Drosophila melanogaster*
* XAO for *Xenopus laevis* and *Xenopus tropicalis*
* obsm (Embeddings)
* Updated the requirements for `spatial` to include descendants of _Visium Spatial Gene Expression_ and to prohibit 'Not a Number' values.
* Updated the requirements for `X_{suffix}` to include descendants of _Visium Spatial Gene Expression_.
Expand Down

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