cellxgene_ontology_guide

cellxgene-ontology-guide

A Python package to help with ontology term mapping in for projects in the cellxgene ecosystem.

Installation

pip install cellxgene-ontology-guide

Notebooks

Notebooks on how to use the ontology guide can be found in the notebooks directory of the repository.

Changelog

1.9.0 (2025-10-03)

Features

Add AfPO ontology (#312) (1e65457)
implement Zstandard compression for ontology files (#307) (2e13e6d)

1.8.0 (2025-09-30)

Features

Add API ontology querying module (68f3168)
Add API ontology querying module (#39) (239ef2b)
add data to the python package (#87) (0eb6831)
add experimental release + cl terms in efo (#263) (#267) (508dc12)
add function to fetch curated ontology term lists (#141) (5c7db62)
add get_term_children and get_term_parents (#186) (dfcd2c2)
add is_valid_term_id method to OntologyParser (#115) (72c2073)
add term label to OntologyNode (#182) (326185c)
additional species-specific ontologies for cxg 5.3 multispecies schema (#255) (64c32fe)
API: setup python library (211a099)
API: setup python library (f60f897)
API: Setup the library for development (1f7ce03)
build subgraph from term ID (#156) (3f4cd4b)
bump CL, EFO, HsapDv, MmusDv, MONDO, UBERON ontology versions for CxG schema 5.2.0 (#217) (5bb43b9)
bump ontology assets for 6.0 (#281) (96d17de)
cellxgene schema 7.0.0 update Hancestor to v2025-04-01 (#296) (96cf8a3)
fetch ontology term descriptions, if available (#181) (0120377)
fetch ontology term synonyms (#200) (89c1725)
fetch term ID by term label (#212) (11c671d)
fix string error in python release (#244) (1587423)
implement stubbed query functions (334deb5)
include license file with python package (#85) (2be3d81)
load GH Release Assets for schema version in memory (#72) (58bad0a)
pinned ontologies for schema 5.3.0 (#275) (cd6a15e)
put out alpha release of 7.0.0 (#297) (46e22e8)
query cross-ontology terms imported into a supported ontology (#232) (2e1a834)
refactor ancestry mapping to include distance from descendant node + implement functions to support curated list term mapping (#96) (7fc3562)
refer to ontology source filenames in ontology_info and return that in get_ontology_download_url (#106) (ff9d826)
remove v from ontology_info.json (#196) (a1292a3)
set up new github workflow for only ontologies that have changed (#264) (45d0fce)
set version regex for pyton api (3720dab)
set-up docsite (#99) (b7591bc)
split all_ontology into individual files. (#93) (ead59e5)
support cellosauras ontology (#294) (93972f1)
Support getting download link for ontology from source repo (#86) (fd55b76)
update EFO to 3.71.0 (#242) (7a92c0f)
update ontologies and add punning term removal for CL (#302) (99d5309)
update ontology_info.json for 5.1 (#207) (d5c8ae3)
write python API demo notebook (#101) (bfae292)

Misc

add doctesting to API (#176) (c0aec23)
add test to ensure all supported ontologies are supported by COG API (#236) (56051f9)
automate testpypi releases (#118) (b5a1a66)
clean-up ontology_parser single fetch and bulk fetch methods + account for acceptable non-ontology terms (#112) (2ef7435)
deploy api when ontology_info.json changes (#194) (40d58f6)
deprecate older version of cellxgene schema (#172) (186e762)
deps-dev: bump semantic-version from 2.8.5 to 2.10.0 in /api/python (#98) (dfe0b39)
enable code coverage (#143) (c52c436)
Fix typo in python readme (#216) (30a6ba8)
move pytest configs to pyproject.toml (#175) (a90341b)
reformat examples in docstrings (#157) (e5528e1)
release 1.0.0 (60eef67)
release 1.8.0 (#305) (089029b)
release main (#130) (0b37dc8)
release main (#132) (8509bbf)
release main (#134) (5f876cc)
release main (#146) (4ca76f0)
release main (#147) (3eacdd2)
release main (#160) (cdb8faf)
release main (#161) (f0066a5)
release main (#185) (9b2fe53)
release main (#187) (986342a)
release main (#193) (e9a4ab5)
release main (#195) (2f36845)
release main (#199) (cac2a12)
release main (#201) (a8f5991)
release main (#204) (dfc8d8e)
release main (#211) (77d6d7d)
release main (#224) (133167c)
release main (#243) (7c2ff4d)
release main (#245) (2f1b91b)
release main (#256) (bd48472)
release main (#258) (d56f1f4)
release main (#260) (9edebfd)
release main (#268) (0ac2219)
release main (#274) (06fbda3)
release main (#282) (919a083)
release main (#284) (0facc1e)
release main (#288) (89eb058)
release main (#290) (4a9dcdb)
release main (#295) (799bd08)
release main (#74) (e748fe9)
release tsmith/release-assets (63b782d)
release tsmith/release-assets (#57) (6a6b02a)
remove 5.3.1-alpha (#273) (a930332)
trigger another release please PR (#283) (ac9436a)
update readmes (#171) (d38ba65)
use trusted publisher to publish pypi package. (#137) (5fc917b)

BugFixes

idempotency issue (#247) (0eebc68)
imports for api (4cd3386)
lint errors (f5e4583)
make constant.py private (46d04a4)
move get_ontology_download_url. (#152) (8365411)
ontology_parser.py defaults to latest (#153) (5b94d6e)
parse through NCBITaxon ancestors (#259) (c461251)
Preserve order of high_level_terms when matching against an input curated list of terms (#189) (8dca5f3)
python api releases (bf0477e)
python-api release version (#131) (3237651)
README.md (1eae21d)
remove setuptools-scm (#197) (254b981)
typos (76ae9fa)
update notebooks (96c7213)
update README.md for API (f606073)
update requirements (#114) (9888f3d)
upgrade EFO from 3.69 to 3.74 (#257) (c38e905)

1.8.0-alpha (2025-09-09)

Features

cellxgene schema 7.0.0 update Hancestor to v2025-04-01 (#296) (96cf8a3)
put out alpha release of 7.0.0 (#297) (46e22e8)
support cellosauras ontology (#294) (93972f1)

1.7.2 (2025-06-02)

Features

pinned ontologies for schema 6.0.0 (#279) (96d17de)

1.6.0-alpha (2025-03-05)

Features

pinned ontologies for schema 5.3.0 (#275) (cd6a15e)
set up new github workflow for only ontologies that have changed (#264) (45d0fce)

Misc

remove 5.3.1-alpha (#273) (a930332)

1.5.0-alpha (2025-02-13)

Features

add experimental release + cl terms in efo (#263) (#267) (508dc12)

1.4.2 (2025-02-06)

BugFixes

parse through NCBITaxon ancestors (#259) (c461251)

1.4.1 (2025-01-28)

BugFixes

upgrade EFO from 3.69 to 3.74 (#257) (c38e905)

1.4.0 (2025-01-28)

Features

additional species-specific ontologies for cxg 5.3 multispecies schema (#255) (64c32fe)

1.3.1 (2024-11-21)

Features

fix string error in python release (#244) (1587423)

BugFixes

idempotency issue (#247) (0eebc68)

1.3.0 (2024-11-14)

Features

query cross-ontology terms imported into a supported ontology (#232) (2e1a834)
update EFO to 3.71.0 (#242) (7a92c0f)

Misc

add test to ensure all supported ontologies are supported by COG API (#236) (56051f9)

1.2.0 (2024-09-04)

Features

bump CL, EFO, HsapDv, MmusDv, MONDO, UBERON ontology versions for CxG schema 5.2.0 (#217) (5bb43b9)

Misc

Fix typo in python readme (#216) (30a6ba8)

1.1.0 (2024-07-08)

Features

fetch term ID by term label (#212) (11c671d)

1.0.0 (2024-05-15)

Features

update ontology_info.json for 5.1 (#207) (d5c8ae3)

Misc

release 1.0.0 (60eef67)

0.8.0 (2024-04-15)

Features

fetch ontology term synonyms (#200) (89c1725)

0.7.1 (2024-04-12)

BugFixes

remove setuptools-scm (#197) (254b981)

0.7.0 (2024-04-11)

Features

remove v from ontology_info.json (#196) (a1292a3)

Misc

deploy api when ontology_info.json changes (#194) (40d58f6)
update readmes (#171) (d38ba65)

BugFixes

update notebooks (96c7213)

0.6.1 (2024-04-10)

BugFixes

Preserve order of high_level_terms when matching against an input curated list of terms (#189) (8dca5f3)

0.6.0 (2024-04-09)

Features

add get_term_children and get_term_parents (#186) (dfcd2c2)

0.5.0 (2024-04-09)

Features

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

Misc

add doctesting to API (#176) (c0aec23)
deprecate older version of cellxgene schema (#172) (186e762)
move pytest configs to pyproject.toml (#175) (a90341b)

0.4.0 (2024-03-29)

Features

build subgraph from term ID (#156) (3f4cd4b)

0.3.1 (2024-03-27)

Misc

reformat examples in docstrings (#157) (e5528e1)

BugFixes

move get_ontology_download_url. (#152) (8365411)
ontology_parser.py defaults to latest (#153) (5b94d6e)

0.3.0 (2024-03-25)

Features

write python API demo notebook (#101) (bfae292)

0.2.0 (2024-03-25)

Features

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

Misc

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

BugFixes

make constant.py private (46d04a4)
typos (76ae9fa)

0.1.2 (2024-03-18)

BugFixes

update README.md for API (f606073)

0.1.1 (2024-03-18)

BugFixes

python-api release version (#131) (3237651)

0.1.0 (2024-03-15)

Features

add data to the python package (#87) (0eb6831)
add is_valid_term_id method to OntologyParser (#115) (72c2073)
include license file with python package (#85) (2be3d81)
refactor ancestry mapping to include distance from descendant node + implement functions to support curated list term mapping (#96) (7fc3562)
refer to ontology source filenames in ontology_info and return that in get_ontology_download_url (#106) (ff9d826)
split all_ontology into individual files. (#93) (ead59e5)
Support getting download link for ontology from source repo (#86) (fd55b76)

Misc

automate testpypi releases (#118) (b5a1a66)
clean-up ontology_parser single fetch and bulk fetch methods + account for acceptable non-ontology terms (#112) (2ef7435)
deps-dev: bump semantic-version from 2.8.5 to 2.10.0 in /api/python (#98) (dfe0b39)

BugFixes

imports for api (4cd3386)
update requirements (#114) (9888f3d)

0.0.1 (2024-02-26)

Features

Add API ontology querying module (68f3168)
Add API ontology querying module (#39) (239ef2b)
API: setup python library (211a099)
API: setup python library (f60f897)
API: Setup the library for development (1f7ce03)
implement stubbed query functions (334deb5)
set version regex for pyton api (3720dab)

Misc

release tsmith/release-assets (63b782d)
release tsmith/release-assets (#57) (6a6b02a)

BugFixes

README.md (1eae21d)

View Source

 1"""
 2[![PyPI](https://img.shields.io/pypi/v/cellxgene-ontology-guide?label=pypi%20package)](https://pypi.org/project/cellxgene-ontology-guide/)
 3[![PyPI - Downloads](https://img.shields.io/pypi/dm/cellxgene-ontology-guide)](<(https://pypi.org/project/cellxgene-ontology-guide/)>)
 4[![codecov](https://codecov.io/gh/chanzuckerberg/cellxgene-ontology-guide/graph/badge.svg?token=ceXxNPx22I)](https://codecov.io/gh/chanzuckerberg/cellxgene-ontology-guide)
 5![example workflow](https://github.com/chanzuckerberg/cellxgene-ontology-guide/actions/workflows/push-tests.yml/badge.svg?branch=main)
 6[![GitHub](https://img.shields.io/github/license/chanzuckerberg/cellxgene-ontology-guide)](./LICENSE)
 7
 8# cellxgene-ontology-guide
 9A Python package to help with ontology term mapping in for projects in the [cellxgene](https://cellxgene.cziscience.com/) ecosystem.
10
11## Installation
12```bash
13pip install cellxgene-ontology-guide
14```
15## Notebooks
16Notebooks on how to use the ontology guide can be found in the
17[notebooks directory](https://github.com/chanzuckerberg/cellxgene-ontology-guide/tree/main/api/python/notebooks) of the
18repository.
19.. include:: ../../CHANGELOG.md
20"""
21
22__version__ = "1.9.0"
23__all__ = ["curated_ontology_term_lists", "entities", "ontology_parser", "supported_versions"]