https://github.com/obophenotype/provisional_cell_ontology
Draft cell type definitions from data - candidates for inclusion in CL
https://github.com/obophenotype/provisional_cell_ontology
cell-ontology cell-types obofoundry ontology single-cell-analysis single-cell-rna-seq transcriptomics
Last synced: about 1 month ago
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Draft cell type definitions from data - candidates for inclusion in CL
- Host: GitHub
- URL: https://github.com/obophenotype/provisional_cell_ontology
- Owner: obophenotype
- License: cc-by-4.0
- Created: 2019-02-19T22:11:05.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2025-07-08T07:55:53.000Z (11 months ago)
- Last Synced: 2026-01-29T21:16:13.675Z (4 months ago)
- Topics: cell-ontology, cell-types, obofoundry, ontology, single-cell-analysis, single-cell-rna-seq, transcriptomics
- Language: Makefile
- Homepage:
- Size: 112 MB
- Stars: 12
- Watchers: 8
- Forks: 1
- Open Issues: 19
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# Provisional Cell Ontology
Description: Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties. All terms subclass conventionally defined terms in CL. If more data emerges that allows more conventional definitions, terms may migrate to CL.
More information can be found at http://obofoundry.org/ontology/pcl
Browse the ontology using OLS
https://www.ebi.ac.uk/ols4/ontologies/pcl
## Versions
Latest PCL release files
https://github.com/obophenotype/provisional_cell_ontology/releases/latest
### Stable release versions
The latest version of the ontology can always be found at:
http://purl.obolibrary.org/obo/pcl-base.owl
http://purl.obolibrary.org/obo/pcl-full.owl
http://purl.obolibrary.org/obo/pcl.owl
See the [latest release](https://github.com/obophenotype/provisional_cell_ontology/releases/latest/)
### Editors' version
Currently PCL works by importing components that should be created seperated, with a base file (an ontology file that only contains axioms belonging to the ontology, excluding any axioms from imported ontologies). To request inclusion of your ontology into PCL, please create a ticket in our [Issue tracker](https://github.com/obophenotype/provisional_cell_ontology/issues).
## Contact
Please use this GitHub repository's [Issue tracker](https://github.com/obophenotype/provisional_cell_ontology/issues) to request new terms/classes or report errors or specific concerns related to the ontology.
## Acknowledgements
This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit).
## Ontology Components
[Brain Data Standards Ontology](https://github.com/obophenotype/brain_data_standards_ontologies)
[Whole Human Brain Ontology](https://github.com/Cellular-Semantics/whole_human_brain_ontology)
[Whole Mouse Brain Ontology](https://github.com/Cellular-Semantics/whole_mouse_brain_ontology)
## Contributors
- David Osumi-Sutherland
- Huseyin Kir
- Richard Scheuermann
- Brian Aevermann
- Jeremy A Miller
- Tom Gillespie
- Yun (Renee) Zhang
- Nicolas Matentzoglu
- Shawn Zheng Kai Tan
## For Editors
Currently, for the release to be prepared correctly, we need to force bdso-ext.owl component to be built first - this can be done by using `sh run.sh make components/bdso-pcl-comp.owl prepare_release`
PCL uses a "base file import system" that merges before incorporating. To update imports, use `sh run.sh make no-mirror-refresh-merged`
## Cite
- Brain Data Standards: https://www.biorxiv.org/content/10.1101/2021.10.10.463703v1
- PCL usage: [PMID:34616062](https://pubmed.ncbi.nlm.nih.gov/34616062/), [PMID:31435019](https://pubmed.ncbi.nlm.nih.gov/31435019/), [PMID:29322913](https://pubmed.ncbi.nlm.nih.gov/29322913/)
## Ontology Metadata
```
id: pcl
mirror_from: https://raw.githubusercontent.com/obophenotype/provisional_cell_ontology/master/pcl-base.owl
title: "Provisional Cell Ontology"
contact:
email: davidos@ebi.ac.uk
label: David Osumi-Sutherland
github: dosumis
description: Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties.
domain: phenotype
homepage: https://github.com/obophenotype/provisional_cell_ontology
products:
- id: pcl.owl
- id: pcl.obo
- id: pcl.json
- id: pcl-base.owl
- id: pcl-base.obo
- id: pcl-base.json
- id: pcl-full.owl
- id: pcl-full.obo
- id: pcl-full.json
- id: pcl-simple.owl
- id: pcl-simple.obo
- id: pcl-simple.json
dependencies:
- id: pr
- id: go
- id: uberon
- id: ro
- id: pato
- id: ncbitaxon
- id: bfo
- id: cl
- id: omo
- id: nbo
- id: chebi
- id: so
tracker: https://github.com/obophenotype/provisional_cell_ontology/issues
license:
url: http://creativecommons.org/licenses/by/4.0/
label: CC BY 4.0
usages:
- user: https://biccn.org/
description: This ontology will be used to annotate cell types in single cell transcriptomics data, with an initial focus on the brain. It is also used to drive search and navigation in a cell type data explorer web application.
repository: https://github.com/obophenotype/provisional_cell_ontology
preferredPrefix: PCL
```