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feat: fetch ontology term descriptions, if available #181

Merged
merged 4 commits into from
Apr 9, 2024
Merged

feat: fetch ontology term descriptions, if available #181

merged 4 commits into from
Apr 9, 2024

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nayib-jose-gloria
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Reason for Change

  • Feedback from downstream consumer integration that term descriptions are required by Cell Guide

Changes

  • fetch description (coded as IAO_0000115 in owl format) when building ontology JSONs in all_ontology builder. Leave optional, as some terms do not have descriptions
  • surface functions to get term descriptions by term ID (and term ID list) in ontology_parser
  • update all_ontology JSON schema accordingly

Testing steps

  • unit tests and running builder locally + validating resulting artifacts

Notes for Reviewer

@nayib-jose-gloria nayib-jose-gloria merged commit 0120377 into main Apr 9, 2024
6 checks passed
@nayib-jose-gloria nayib-jose-gloria deleted the nayib/add-term-description branch April 9, 2024 17:09
This was referenced Apr 9, 2024
Closed
Merged
Bento007 pushed a commit that referenced this pull request Apr 9, 2024
@github-actions
chore: release main (#185)
9b2fe53 
🤖 I have created a release *beep* *boop*
---


<details><summary>python-api: 0.5.0</summary>

##
[0.5.0](python-api-v0.4.0...python-api-v0.5.0)
(2024-04-09)


### Features

* add term label to OntologyNode
([#182](#182))
([326185c](326185c))
* fetch ontology term descriptions, if available
([#181](#181))
([0120377](0120377))


### Misc

* add doctesting to API
([#176](#176))
([c0aec23](c0aec23))
* deprecate older version of cellxgene schema
([#172](#172))
([186e762](186e762))
* move pytest configs to pyproject.toml
([#175](#175))
([a90341b](a90341b))
</details>

<details><summary>ontology-assets: 0.3.0</summary>

##
[0.3.0](ontology-assets-v0.2.0...ontology-assets-v0.3.0)
(2024-04-09)


### Features

* fetch ontology term descriptions, if available
([#181](#181))
([0120377](0120377))


### Misc

* deprecate older version of cellxgene schema
([#172](#172))
([186e762](186e762))
* update ontology decendant mappings
([#162](#162))
([12def74](12def74))
* update ontology descendant mappings
([#167](#167))
([5d3d097](5d3d097))
* update ontology descendant mappings
([#180](#180))
([65ca10f](65ca10f))
</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>
@github-actions github-actions bot mentioned this pull request Apr 9, 2024
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