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removed strongly recommended from development stage #1110

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Nov 16, 2024
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removed strongly recommended from development stage #1110

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removed strongly recommended from development stage
brianraymor Nov 16, 2024
d104994
editorial
brianraymor Nov 16, 2024
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2 changes: 1 addition & 1 deletion schema/drafts/5.2.1-experimental.md
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Expand Up @@ -190,7 +190,7 @@ The following gene annotation dependencies are *pinned* for this version of the
<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 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:00007002</code></a> for <i>cell</i><br>or <code>"unknown"</code> when:
<td>MUST be either 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:00007002</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)
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54 changes: 5 additions & 49 deletions schema/drafts/5.3.0.md
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Expand Up @@ -503,55 +503,11 @@ 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> with the following STRONGLY RECOMMENDED:
<br><br>
<table>
<thead>
<tr>
<th>For</th>
<th>Use</th>
</tr>
</thead>
<tbody>
<tr>
<td>Embryonic stage</td>
<td>A term from the set of <a href="http://www.ontobee.org/search?ontology=HSAPDV&keywords=carnegie&submit=Search+terms">Carnegie stages 1-23</a><br>(up to 8 weeks after conception; e.g. <a href="https://www.ebi.ac.uk/ols4/ontologies/hsapdv/classes?obo_id=HsapDv%3A0000003">HsapDv:0000003</a>)</td>
</tr>
<tr>
<td>Fetal development</td>
<td>A term from the set of <a href="http://www.ontobee.org/search?ontology=HSAPDV&keywords=post-fertilization&submit=Search+terms">9 to 38 week post-fertilization human stages</a><br>(9 weeks after conception and before birth; e.g. <a href="https://www.ebi.ac.uk/ols4/ontologies/hsapdv/classes?obo_id=HsapDv%3A0000046">HsapDv:0000046</a>)</td>
</tr>
<tr>
<td>After birth for the<br>first 12 months</td>
<td>A term from the set of <a href="http://www.ontobee.org/search?ontology=HSAPDV&keywords=month-old&submit=Search+terms">1 to 12 month-old human stages</a><br>(e.g. <a href="https://www.ebi.ac.uk/ols4/ontologies/hsapdv/classes?obo_id=HsapDv%3A0000273">HsapDv:0000273)</a></td>
</tr>
<tr>
<td>After the first 12<br>months post-birth</td>
<td>A term from the set of <a href="http://www.ontobee.org/search?ontology=HSAPDV&keywords=year-old&submit=Search+terms">year-old human stages</a><br>(e.g. <a href="https://www.ebi.ac.uk/ols4/ontologies/hsapdv/classes?obo_id=HsapDv%3A0000246">HsapDv:0000246)</a></td>
</tr>
</tbody></table>
<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> with the following STRONGLY RECOMMENDED:
<br><br>
<table>
<thead>
<tr>
<th>For</th>
<th>Use</th>
</tr>
</thead>
<tbody>
<tr>
<td>From the time of conception<br>to 1 month after birth</td>
<td>A term from the set of <a href="http://www.ontobee.org/search?ontology=MMUSDV&keywords=theiler+stage&submit=Search+terms">Theiler stages</a><br>(e.g. <a href="https://www.ebi.ac.uk/ols4/ontologies/mmusdv/classes?obo_id=MmusDv%3A0000003">MmusDv:0000003</a>)</td>
</tr>
<tr>
<td>From 2 months after birth</td>
<td>A term from the set of <a href="http://www.ontobee.org/search?ontology=MMUSDV&keywords=month-old&submit=Search+terms"> month-old stages</a><br>(e.g. <a href="https://www.ebi.ac.uk/ols4/ontologies/mmusdv/classes?obo_id=MmusDv%3A0000062">MmusDv:0000062)</a></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>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>
</tbody></table>
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