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tidying html (chanzuckerberg#1060)
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@brianraymor
brianraymor authored Oct 23, 2024
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294 changes: 164 additions & 130 deletions schema/drafts/5.2.1-experimental.md
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Expand Up @@ -128,21 +128,22 @@ The following gene annotation dependencies are *pinned* for this version of the
### development_stage_ontology_term_id

<table><tbody>
<tr>
<th>Key</th>
<td>development_stage_ontology_term_id</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</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%3A7955"><code>"NCBITaxon:7955"</code></a> for <i>Danio rerio</i>, then this 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 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>.<br /><br />If <code>organism_ontolology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7227"><code>"NCBITaxon:7227"</code></a> for <i>Drosophila melanogaster</i>, then this MUST be the most accurate FBdv term.
<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>
<tr>
<th>Key</th>
<td>development_stage_ontology_term_id</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</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%3A7955"><code>"NCBITaxon:7955"</code></a> for <i>Danio rerio</i>, then this 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 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>.<br><br>If <code>organism_ontolology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7227"><code>"NCBITaxon:7227"</code></a> for <i>Drosophila melanogaster</i>, then this MUST be the most accurate FBdv term.
<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>
</tbody></table>
<br>

Expand All @@ -151,41 +152,52 @@ The following gene annotation dependencies are *pinned* for this version of the
### organism_cell_type_ontology_term_id

<table><tbody>
<tr>
<th>Key</th>
<td>organism_cell_type_ontology_term_id</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<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>
<br>Otherwise:
<table>
<thead>
<tr>
<tr>
<th>Key</th>
<td>organism_cell_type_ontology_term_id</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<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>
<table>
<thead><tr>
<th>For <code>organism_ontolology_term_id</code></th>
<th>MUST be</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>
</td>
</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>
</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>
<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>
</tr>
</tbody></table>
<br>For all other organisms, the value MUST be <code>"na"</code>.
</td>
</tr>
</td>
</tr>
</tbody>
</table>
<br>For all other organisms, the value MUST be <code>"na"</code>.
</td>
</tr>
</tbody></table>
<br>

Expand All @@ -194,19 +206,20 @@ The following gene annotation dependencies are *pinned* for this version of the
### organism_ontology_term_id

<table><tbody>
<tr>
<th>Key</th>
<td>organism_ontology_term_id</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>categorical with <code>str</code> categories. This MUST be a descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A33208"<code>NCBITaxon:33208</code></a> for <i>Metazoa</i>.<br><br>If <code>organism_ontology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7955"><code>"NCBITaxon:7955"</code></a> for <i>Danio rerio</i> or <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7227"><code>"NCBITaxon:7227"</code></a> for <i>Drosophila melanogaster</i>, then all observations MUST contain the same value.
</td>
</tr>
<tr>
<th>Key</th>
<td>organism_ontology_term_id</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>
categorical with <code>str</code> categories. This MUST be a descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A33208"><code>NCBITaxon:33208</code></a> for <i>Metazoa</i>.<br><br>If <code>organism_ontology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7955"><code>"NCBITaxon:7955"</code></a> for <i>Danio rerio</i> or <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7227"><code>"NCBITaxon:7227"</code></a> for <i>Drosophila melanogaster</i>, then all observations MUST contain the same value.
</td>
</tr>
</tbody></table>
<br>

Expand All @@ -225,28 +238,37 @@ The following gene annotation dependencies are *pinned* for this version of the
</tr>
<tr>
<th>Value</th>
<td>categorical with <code>str</code> categories.<br>
<br>
<table>
<td>
categorical with <code>str</code> categories.<br><br>
<table>
<thead>
<tr>
<th>For <code>organism_ontolology_term_id</code></th>
<th>MUST be</th>
</tr>
<tr>
<th>For <code>organism_ontolology_term_id</code></th>
<th>MUST be</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%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
<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%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
</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.</code>
<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.
</td>
</tr>
</tbody></table>
<br>For all other organisms, the value 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>
<br>

Expand All @@ -255,18 +277,20 @@ The following gene annotation dependencies are *pinned* for this version of the
### tissue_type

<table><tbody>
<tr>
<th>Key</th>
<td>tissue_type</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>categorical with <code>str</code> categories.<br><br>If <code>organism_ontology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7955"><code>"NCBITaxon:7955"</code></a> for <i>Danio rerio</i> or <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7227"><code>"NCBITaxon:7227"</code></a> for <i>Drosophila melanogaster</i>, then the value MUST be <code>"tissue"</code>.<br><br>Otherwise, the value MUST be <code>"tissue"</code>, <code>"organoid"</code>, or <code>"cell culture"</code>.
</tr>
<tr>
<th>Key</th>
<td>tissue_type</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>
categorical with <code>str</code> categories.<br><br>If <code>organism_ontology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7955"><code>"NCBITaxon:7955"</code></a> for <i>Danio rerio</i> or <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7227"><code>"NCBITaxon:7227"</code></a> for <i>Drosophila melanogaster</i>, then the value MUST be <code>"tissue"</code>.<br><br>Otherwise, the value MUST be <code>"tissue"</code>, <code>"organoid"</code>, or <code>"cell culture"</code>.
</td>
</tr>
</tbody></table>
<br>

Expand All @@ -277,53 +301,63 @@ The following gene annotation dependencies are *pinned* for this version of the
### feature_reference

<table><tbody>
<tr>
<th>Key</th>
<td>feature_reference</td>
</tr>
<tr>
<th>Annotator</th>
<td>CELLxGENE Discover MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td><code>str</code>. This MUST be the reference organism for a feature:
<br><br>
<table>
<thead>
<tr>
<tr>
<th>Key</th>
<td>feature_reference</td>
</tr>
<tr>
<th>Annotator</th>
<td>CELLxGENE Discover MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>
<code>str</code>. This MUST be the reference organism for a feature:<br><br>
<table>
<thead><tr>
<th>Reference Organism</th>
<th>MUST Use</th>
</tr></thead>
<tbody>
<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>
</tr>
</thead>
<tbody>
<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>
</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>
</tr>
<tr>
<td><i>SARS-CoV-2</i></td>
<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>Danio rerio</i></td>
<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7955"><code>"NCBITaxon:7955"</code></a></td>
</tr>
<tr>
<td><i>Drosophila melanogaster</i></td>
<td><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>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>
</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>
</tr>
<tr>
<td><i>SARS-CoV-2</i></td>
<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>Danio rerio</i></td>
<td>
<a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A7955"><code>"NCBITaxon:7955"</code></a></td>
</tr>
<tr>
<td><i>Drosophila melanogaster</i></td>
<td>
<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>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>
</td>
</tr>
</tbody></table>
<br>

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