Added experimental species draft (#1038)

chanzuckerberg · Oct 21, 2024 · de92e0b · de92e0b
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+# Schema
+
+Contact: [email protected]
+
+Document Status: _Draft_
+
+Version: 5.2.0+experimental
+
+The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "NOT RECOMMENDED" "MAY", and "OPTIONAL" in this document are to be interpreted as described in [BCP 14](https://tools.ietf.org/html/bcp14), [RFC2119](https://www.rfc-editor.org/rfc/rfc2119.txt), and [RFC8174](https://www.rfc-editor.org/rfc/rfc8174.txt) when, and only when, they appear in all capitals, as shown here.
+
+This draft is limited to **additions** or **modifications** to [schema 5.2.0](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.2.0/schema.md). If a 5.2.0 reference does not appear in this document, then no schema change is required. The following **temporary** constraints for *Danio rerio* and *Drosophila melanogaster* are specified:
+
+* The `organism_ontology_term_id` MUST be the same for all observations.
+* The `tissue_type` MUST be `'tissue'` for all observations.
+
+## General Requirements
+
+**Organisms**. Supported organisms MUST be documented in [Required Gene Annotations](#required-gene-annotations). 
+
+
+### Required Ontologies
+
+The following ontology dependencies are *pinned* for this version of the schema.
+
+| Ontology | OBO Prefix | Release | Download |
+|:--|:--|:--|:--|
+| [Cell Ontology] | CL |  [2024-08-16] | [cl.owl]|
+| [Drosophila Anatomy Ontology] | FBbt | [2024-08-08](https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/releases/tag/v2024-08-08) | [fbbt.owl] |
+| [Drosophila Development Ontology] | FBdv | [2024-08-07](https://github.com/FlyBase/drosophila-developmental-ontology/releases/tag/v2024-08-07) | [fbdv.owl] |
+| [Experimental Factor Ontology] | EFO | [2024-08-15 EFO 3.69.0] | [efo.owl]
+| [Human Ancestry Ontology] | HANCESTRO | [3.0] | [hancestro-base.owl] |
+| [Human Developmental Stages] |  HsapDv | [2024-05-28] | [hsapdv.owl] |
+| [Mondo Disease Ontology] | MONDO | [2024-08-06] | [mondo.owl] |
+| [Mouse Developmental Stages]| MmusDv | [2024-05-28] | [mmusdv.owl] |
+| [NCBI organismal classification] |  NCBITaxon | [2023-06-20] | [ncbitaxon.owl] |
+| [Phenotype And Trait Ontology] | PATO | [2023-05-18] | [pato.owl]  |
+| [Uberon multi-species anatomy ontology] |  UBERON | [2024-08-07] | [uberon.owl] |
+| [Zebrafish Anatomy Ontology] | ZFA<br>ZFS | [2022-12-09] | [zfa.owl] |
+| | | | |
+
+[Cell Ontology]: http://obofoundry.org/ontology/cl.html
+[2024-08-16]: https://github.com/obophenotype/cell-ontology/releases/tag/v2024-08-16
+[cl.owl]: https://github.com/obophenotype/cell-ontology/releases/download/v2024-08-16/cl.owl
+
+[Drosophila Anatomy Ontology]: https://obofoundry.org/ontology/fbbt.html
+[2024-08-08]: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/releases/tag/v2024-08-08
+[fbbt.owl]: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/releases/download/v2024-08-08/fbbt.owl
+
+[Drosophila Development Ontology]: https://obofoundry.org/ontology/fbdv.html
+[fbdv.owl]: https://github.com/FlyBase/drosophila-developmental-ontology/releases/download/v2024-08-07/fbdv.owl
+
+[Experimental Factor Ontology]: http://www.ebi.ac.uk/efo
+[2024-08-15 EFO 3.69.0]: https://github.com/EBISPOT/efo/releases/tag/v3.69.0
+[efo.owl]: https://github.com/EBISPOT/efo/releases/download/v3.69.0/efo.owl
+
+[Human Ancestry Ontology]: http://www.obofoundry.org/ontology/hancestro.html
+[3.0]: https://github.com/EBISPOT/hancestro/releases/tag/3.0
+[hancestro-base.owl]: https://github.com/EBISPOT/hancestro/blob/3.0/hancestro-base.owl
+
+[Human Developmental Stages]: http://obofoundry.org/ontology/hsapdv.html
+[2024-05-28]: https://github.com/obophenotype/developmental-stage-ontologies/releases/tag/v2024-05-28
+[hsapdv.owl]: https://github.com/obophenotype/developmental-stage-ontologies/releases/download/v2024-05-28/hsapdv.owl
+
+[Mondo Disease Ontology]: http://obofoundry.org/ontology/mondo.html
+[2024-08-06]: https://github.com/monarch-initiative/mondo/releases/tag/v2024-08-06
+[mondo.owl]: https://github.com/monarch-initiative/mondo/releases/download/v2024-08-06/mondo.owl
+
+[Mouse Developmental Stages]: http://obofoundry.org/ontology/mmusdv.html
+[mmusdv.owl]: https://github.com/obophenotype/developmental-stage-ontologies/releases/download/v2024-05-28/mmusdv.owl
+
+[NCBI organismal classification]: http://obofoundry.org/ontology/ncbitaxon.html
+[2023-06-20]: https://github.com/obophenotype/ncbitaxon/releases/tag/v2023-06-20
+[ncbitaxon.owl]: https://github.com/obophenotype/ncbitaxon/releases/download/v2023-06-20/ncbitaxon.owl.gz
+
+[Phenotype And Trait Ontology]: http://www.obofoundry.org/ontology/pato.html
+[2023-05-18]: https://github.com/pato-ontology/pato/releases/tag/v2023-05-18
+[pato.owl]: https://github.com/pato-ontology/pato/blob/v2023-05-18/pato.owl
+
+[Uberon multi-species anatomy ontology]: http://www.obofoundry.org/ontology/uberon.html
+[2024-08-07]: https://github.com/obophenotype/uberon/releases/tag/v2024-08-07
+[uberon.owl]: https://github.com/obophenotype/uberon/releases/download/v2024-08-07/uberon.owl
+
+[Zebrafish Anatomy Ontology]: https://obofoundry.org/ontology/zfa.html
+[2022-12-09]: https://github.com/ZFIN/zebrafish-anatomical-ontology/releases/tag/v2022-12-09
+[zfa.owl]: https://github.com/ZFIN/zebrafish-anatomical-ontology/blob/v2022-12-09/zfa.owl
+
+---
+
+### Required Gene Annotations
+
+ENSEMBL identifiers are required for genes and [External RNA Controls Consortium (ERCC)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978944/) identifiers for [RNA Spike-In Control Mixes] to ensure that all datasets measure the same features and can therefore be integrated.
+
+The following gene annotation dependencies are *pinned* for this version of the schema. For multi-organism experiments, cells from any Metazoan organism are allowed as long as orthologs from the following organism annotations are used.
+
+| Organism | Source | Required version | Download |
+|:--|:--|:--|:--|
+| <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9606"><code>NCBITaxon:9606</code></a><br>for <i>Homo sapiens</i> | [GENCODE (Human)] | Human reference GRCh38.p14<br>(GENCODE v44/Ensembl 110) | [gencode.v44.primary_assembly.annotation.gtf] |
+| <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A10090"><code>NCBITaxon:10090</code></a><br>for <i>Mus musculus</i> | [GENCODE (Mouse)] | Mouse reference GRCm39<br>(GENCODE vM33/Ensembl 110) | [gencode.vM33.primary_assembly.annotation.gtf] |
+| <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A2697049"><code>NCBITaxon:2697049</code></a><br>for <i>SARS-CoV-2</i>  | [ENSEMBL (COVID-19)] | SARS-CoV-2 reference (ENSEMBL assembly: ASM985889v3) | [Sars\_cov\_2.ASM985889v3.101.gtf] |
+| <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> |  [ENSEMBL (Zebrafish)] | GRCz11.112 (Ensembl 112) | [Danio_rerio.GRCz11.112.gtf] |
+| <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>| [ENSEMBL (Fruit fly)] | BDGP6.46 (Ensembl 112) | [Drosophila_melanogaster.BDGP6.46.112.gtf] | 
+| | [ThermoFisher ERCC Spike-Ins] | ThermoFisher ERCC RNA Spike-In Control Mixes (Cat # 4456740, 4456739) | [cms_095047.txt] |
+
+[RNA Spike-In Control Mixes]: https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2Fcms_086340.pdf&title=VXNlciBHdWlkZTogRVJDQyBSTkEgU3Bpa2UtSW4gQ29udHJvbCBNaXhlcyAoRW5nbGlzaCAp
+
+[GENCODE (Human)]: https://www.gencodegenes.org/human/
+[gencode.v44.primary_assembly.annotation.gtf]: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.primary_assembly.annotation.gtf.gz
+
+[GENCODE (Mouse)]: https://www.gencodegenes.org/mouse/
+[gencode.vM33.primary_assembly.annotation.gtf]: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M33/gencode.vM33.primary_assembly.annotation.gtf.gz
+
+[ENSEMBL (COVID-19)]: https://covid-19.ensembl.org/index.html
+[Sars\_cov\_2.ASM985889v3.101.gtf]: https://ftp.ensemblgenomes.org/pub/viruses/gtf/sars_cov_2/Sars_cov_2.ASM985889v3.101.gtf.gz
+
+[ENSEMBL (Zebrafish)]: https://useast.ensembl.org/Danio_rerio/Info/Index
+[Danio_rerio.GRCz11.112.gtf]: https://ftp.ensembl.org/pub/release-112/gtf/danio_rerio/Danio_rerio.GRCz11.112.gtf.gz
+
+[ENSEMBL (Fruit fly)]: https://www.ensembl.org/Drosophila_melanogaster/Info/Index
+[Drosophila_melanogaster.BDGP6.46.112.gtf]: https://ftp.ensembl.org/pub/release-112/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.112.gtf.gz
+
+[ThermoFisher ERCC Spike-Ins]: https://www.thermofisher.com/order/catalog/product/4456740#/4456740
+[cms_095047.txt]: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095047.txt
+
+---
+
+## `obs` (Cell Metadata)
+
+### 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>
+</tbody></table>
+<br>
+
+---
+
+### 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>
+          <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>
+            </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>
+            </tr>
+          </tbody></table>
+        </td>
+    </tr>
+</tbody></table>
+<br>
+
+---
+
+### 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>
+</tbody></table>
+<br>
+
+---
+
+### organism_tissue_ontology_term_id
+
+<table><tbody>
+    <tr>
+      <th>Key</th>
+      <td>organism_tissue_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.<br>
+          <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%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
+            </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>
+            </tr>
+          </tbody></table>
+        </td>
+    </tr>
+</tbody></table>
+<br>
+
+---
+
+### 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>
+</tbody></table>
+<br>
+
+---
+
+## var and raw.var (Gene Metadata)
+
+### 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>
+          <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>
+            <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>
+
+---
+
+## Appendix A. Changelog
+
+### schema v5.2.0+experimental
+
+* General Requirements
+  * Updated requirements for supported organisms
+* Required Ontologies
+  * Added Drosophila Anatomy Ontology (FBbt) release 2024-08-08
+  * Added Drosophila Development Ontology (FBdv) release 2024-08-07
+  * Added Zebrafish Anatomy Ontology (ZFA+ZFS) release 2022-12-09
+* Required Gene Annotations
+  * Refactored table to include NCBI Taxon for supported organisms
+  * Added  *Danio rerio* Reference GRCz11.112 (Ensembl 112)
+  * Added  *Drosophila melanogaster* Reference BDGP6.46 (Ensembl 112)
+* obs (Cell metadata)
+  * Updated `development_stage_ontology_term_id` to support *Danio rerio* and *Drosophila melanogaster* 
+  * Added `organism_cell_type_ontology_term_id`
+  * Updated `organism_ontology_term_id` for *Danio rerio* and *Drosophila melanogaster* to require all observations to contain the same value
+  * Added `organism_tissue_ontology_term_id`
+  * Updated `tissue_type` to require `"tissue"` for *Danio rerio* and *Drosophila melanogaster* 
+* var and raw.var (Gene Metadata)
+  * Updated `feature_reference` to support *Danio rerio* and *Drosophila melanogaster*