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.owl

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.

Contact

Please use this GitHub repository's Issue tracker 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).

Ontology Components

Brain Data Standards Ontology

Whole Human 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, PMID:31435019, PMID: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