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feat: add function to fetch curated ontology term lists #141

Merged
merged 3 commits into from
Mar 22, 2024
Merged

feat: add function to fetch curated ontology term lists #141

merged 3 commits into from
Mar 22, 2024

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nayib-jose-gloria
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Reason for Change

Changes

  • added uberon_development_stage_list.json ontology asset from https://github.com/chanzuckerberg/single-cell-curation/blob/main/scripts/compute_mappings/compute_ancestor_mapping.py#L107. Used in FE filters to narrow scope of development stage ancestors to look at. No such curated equivalent exists for other ontologies that define development stages (HsapDv, MmusDv) so named it to specify uberon development stage terms.
  • added function to load into memory curated list JSONs packaged with the library, and an Enum to limit the input to this function to only those curated lists we support
  • updated is_valid_term_id function to optionally take an ontology name to check for the term ID in. By default, checks for the term in the ontology parsed from the term ID. cellxgene-schema CLI does a few "is this term both valid and in this specific ontology" checks, so this is a small util for that consumer

Testing steps

  • Integration with FE Filters in a PR

@nayib-jose-gloria nayib-jose-gloria mentioned this pull request Mar 22, 2024
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Bento007
Bento007 reviewed Mar 22, 2024
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Are the lists packaged with API. If we update the list, would that be a patch updates?

@nayib-jose-gloria
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Are the lists packaged with API. If we update the list, would that be a patch updates?

We had agreed not to update unless there was a schema version update to go with it, so it'd be a minor bump to include the new schema version ontologies

@nayib-jose-gloria nayib-jose-gloria merged commit 5c7db62 into main Mar 22, 2024
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@nayib-jose-gloria nayib-jose-gloria deleted the nayib/add-integration-utils branch March 22, 2024 20:39
This was referenced Mar 22, 2024
Closed
Closed
Merged
Bento007 pushed a commit that referenced this pull request Mar 25, 2024
@github-actions
chore: release main (#146)
4ca76f0 
🤖 I have created a release *beep* *boop*
---


<details><summary>python-api: 0.2.0</summary>

##
[0.2.0](python-api-v0.1.2...python-api-v0.2.0)
(2024-03-25)


### Features

* add function to fetch curated ontology term lists
([#141](#141))
([5c7db62](5c7db62))
* set-up docsite
([#99](#99))
([b7591bc](b7591bc))


### Misc

* enable code coverage
([#143](#143))
([c52c436](c52c436))
* use trusted publisher to publish pypi package.
([#137](#137))
([5fc917b](5fc917b))


### BugFixes

* make constant.py private
([46d04a4](46d04a4))
* typos
([76ae9fa](76ae9fa))
</details>

<details><summary>ontology-assets: 0.2.0</summary>

##
[0.2.0](ontology-assets-v0.1.0...ontology-assets-v0.2.0)
(2024-03-25)


### Features

* add function to fetch curated ontology term lists
([#141](#141))
([5c7db62](5c7db62))


### Misc

* update ontology decendant mappings
([#142](#142))
([fb23618](fb23618))
</details>

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
This was referenced Apr 5, 2024
Closed
Merged
Bento007 pushed a commit that referenced this pull request Apr 9, 2024
@github-actions
chore: release tsmith/release-docs (#190)
41215a4 
🤖 I have created a release *beep* *boop*
---


<details><summary>assets: 0.4.0</summary>

##
[0.4.0](assets-v0.3.0...assets-v0.4.0)
(2024-04-09)


### Features

* add function to fetch curated ontology term lists
([#141](#141))
([5c7db62](5c7db62))
* fetch ontology term descriptions, if available
([#181](#181))
([0120377](0120377))
* load GH Release Assets for schema version in memory
([#72](#72))
([58bad0a](58bad0a))
* refactor ancestry mapping to include distance from descendant node +
implement functions to support curated list term mapping
([#96](#96))
([7fc3562](7fc3562))
* refer to ontology source filenames in ontology_info and return that in
get_ontology_download_url
([#106](#106))
([ff9d826](ff9d826))
* **release:** generate descendant mapping for tissues and cells
([#100](#100))
([841fddf](841fddf))
* remove all-ontology.json.gz
([83fefd6](83fefd6))
* split all_ontology into individual files.
([#93](#93))
([ead59e5](ead59e5))
* upload assets on release
([#56](#56))
([84a1c5d](84a1c5d))


### Misc

* deprecate older version of cellxgene schema
([#172](#172))
([186e762](186e762))
* move curated lists to ontology-assets
([#48](#48))
([77916df](77916df))
* moving the generated artifacts
([c03c8e3](c03c8e3))
* release main
([#130](#130))
([0b37dc8](0b37dc8))
* release main
([#146](#146))
([4ca76f0](4ca76f0))
* release main
([#185](#185))
([9b2fe53](9b2fe53))
* release main
([#74](#74))
([e748fe9](e748fe9))
* release tsmith/release-assets
([63b782d](63b782d))
* release tsmith/release-assets
([#57](#57))
([6a6b02a](6a6b02a))
* update ontology decendant mappings
([#117](#117))
([48451af](48451af))
* update ontology decendant mappings
([#142](#142))
([fb23618](fb23618))
* update ontology decendant mappings
([#162](#162))
([12def74](12def74))
* update ontology descendant mappings
([#167](#167))
([5d3d097](5d3d097))
* update ontology descendant mappings
([#180](#180))
([65ca10f](65ca10f))


### BugFixes

* lint errors
([f5e4583](f5e4583))
* Schema format and validation fixes.
([#113](#113))
([0465ee7](0465ee7))
</details>

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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@Bento007 Bento007 Bento007 approved these changes

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@nayib-jose-gloria @Bento007