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Updated requirements for assay_ontology_term_id (#872)
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brianraymor authored May 1, 2024
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Expand Up @@ -367,6 +367,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
<li>
the most accurate descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0010183"><code>"EFO:0010183"</code></a> for <i>single cell library construction</i>
</li></ul>
If <code>assay_ontology_term_id</code> is either <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> or <a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0030062"><code>"EFO:0030062"</code></a> for <i>Slide-seqV2</i>. then all observations MUST contain the same value.<br><br>
An assay based on 10X Genomics products SHOULD either be <a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0008995"><code>"EFO:0008995"</code></a> for <i>10x technology</i> or <b>preferably</b> its most accurate descendant. An assay based on <i>SMART (Switching Mechanism at the 5' end of the RNA Template) or SMARTer technology</i> SHOULD either be <a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0010184"><code>"EFO:0010184"</code></a> for <i>Smart-like</i> or preferably its most accurate descendant.<br><br>
<br>Recommended values for specific assays:
<br><br>
Expand Down Expand Up @@ -1872,6 +1873,7 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem
* obs (Cell metadata)
* Added `array_col` for _Visium Spatial Gene Expression_ when <code>uns['spatial']['is_single']</code> is <code>True</code>
* Added `array_row` for _Visium Spatial Gene Expression_ when <code>uns['spatial']['is_single']</code> is <code>True</code>
* Updated the requirements for `assay_ontology_term_id` for _Visium Spatial Gene Expression_ and _Slide-seqV2_. All observations must contain the same value.
* Updated the requirements for `cell_type_ontology_term_id` for _Visium Spatial Gene Expression_ when <code>uns['spatial']['is_single']</code> is <code>True</code>. The value must be `"unknown"` if the corresponding value of `in_tissue` is `0`.
* Added `in_tissue` for _Visium Spatial Gene Expression_ when <code>uns['spatial']['is_single']</code> is <code>True</code>
* Updated the requirements for `is_primary_data` for _Visium Spatial Gene Expression_. The value must be <code>False</code>when <code>uns['spatial']['is_single']</code> is <code>False</code>.
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