{"id":48879432,"url":"https://github.com/obophenotype/provisional_cell_ontology","last_synced_at":"2026-04-16T02:04:51.891Z","repository":{"id":41817675,"uuid":"171558104","full_name":"obophenotype/provisional_cell_ontology","owner":"obophenotype","description":"Draft cell type definitions from data - candidates for inclusion in CL","archived":false,"fork":false,"pushed_at":"2025-07-08T07:55:53.000Z","size":117726,"stargazers_count":12,"open_issues_count":19,"forks_count":1,"subscribers_count":8,"default_branch":"master","last_synced_at":"2026-01-29T21:16:13.675Z","etag":null,"topics":["cell-ontology","cell-types","obofoundry","ontology","single-cell-analysis","single-cell-rna-seq","transcriptomics"],"latest_commit_sha":null,"homepage":"","language":"Makefile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/obophenotype.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2019-02-19T22:11:05.000Z","updated_at":"2025-07-08T07:53:48.000Z","dependencies_parsed_at":"2023-01-20T01:48:47.739Z","dependency_job_id":"fcebd537-0854-4130-9f19-c30324edc4cb","html_url":"https://github.com/obophenotype/provisional_cell_ontology","commit_stats":{"total_commits":95,"total_committers":6,"mean_commits":"15.833333333333334","dds":0.3263157894736842,"last_synced_commit":"69aeaa0f72ef4e968c66749ca271886d037ede6e"},"previous_names":[],"tags_count":19,"template":false,"template_full_name":null,"purl":"pkg:github/obophenotype/provisional_cell_ontology","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fprovisional_cell_ontology","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fprovisional_cell_ontology/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fprovisional_cell_ontology/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fprovisional_cell_ontology/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/obophenotype","download_url":"https://codeload.github.com/obophenotype/provisional_cell_ontology/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fprovisional_cell_ontology/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31867716,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-15T15:24:51.572Z","status":"online","status_checked_at":"2026-04-16T02:00:06.042Z","response_time":69,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cell-ontology","cell-types","obofoundry","ontology","single-cell-analysis","single-cell-rna-seq","transcriptomics"],"created_at":"2026-04-16T02:04:39.410Z","updated_at":"2026-04-16T02:04:51.886Z","avatar_url":"https://github.com/obophenotype.png","language":"Makefile","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n![Build Status](https://github.com/obophenotype/provisional_cell_ontology/workflows/CI/badge.svg)\n# Provisional Cell Ontology\n\nDescription: Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward \u0026 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.\n\nMore information can be found at http://obofoundry.org/ontology/pcl\n\nBrowse the ontology using OLS\nhttps://www.ebi.ac.uk/ols4/ontologies/pcl\n\n## Versions\n\nLatest PCL release files\nhttps://github.com/obophenotype/provisional_cell_ontology/releases/latest\n\n### Stable release versions\n\nThe latest version of the ontology can always be found at:\n\nhttp://purl.obolibrary.org/obo/pcl-base.owl\nhttp://purl.obolibrary.org/obo/pcl-full.owl\nhttp://purl.obolibrary.org/obo/pcl.owl\n\nSee the [latest release](https://github.com/obophenotype/provisional_cell_ontology/releases/latest/)\n\n### Editors' version\n\nCurrently 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).\n\n## Contact\n\nPlease 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.\n\n## Acknowledgements\n\nThis ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit).\n\n## Ontology Components\n\n[Brain Data Standards Ontology](https://github.com/obophenotype/brain_data_standards_ontologies)\n\n[Whole Human Brain Ontology](https://github.com/Cellular-Semantics/whole_human_brain_ontology)\n\n[Whole Mouse Brain Ontology](https://github.com/Cellular-Semantics/whole_mouse_brain_ontology)\n\n## Contributors\n\n- David Osumi-Sutherland\n- Huseyin Kir\n- Richard Scheuermann\n- Brian Aevermann\n- Jeremy A Miller\n- Tom Gillespie\n- Yun (Renee) Zhang\n- Nicolas Matentzoglu\n- Shawn Zheng Kai Tan\n\n\n## For Editors\n\nCurrently, 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`\n\nPCL uses a \"base file import system\" that merges before incorporating. To update imports, use  `sh run.sh make no-mirror-refresh-merged`\n\n## Cite\n\n- Brain Data Standards: https://www.biorxiv.org/content/10.1101/2021.10.10.463703v1\n- 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/)\n\n## Ontology Metadata\n```\nid: pcl\nmirror_from: https://raw.githubusercontent.com/obophenotype/provisional_cell_ontology/master/pcl-base.owl\ntitle: \"Provisional Cell Ontology\"\ncontact:\n  email: davidos@ebi.ac.uk\n  label: David Osumi-Sutherland\n  github: dosumis\ndescription: Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward \u0026 coherent set of properties.\ndomain: phenotype\nhomepage: https://github.com/obophenotype/provisional_cell_ontology\nproducts:\n  - id: pcl.owl\n  - id: pcl.obo\n  - id: pcl.json\n  - id: pcl-base.owl\n  - id: pcl-base.obo\n  - id: pcl-base.json\n  - id: pcl-full.owl\n  - id: pcl-full.obo\n  - id: pcl-full.json\n  - id: pcl-simple.owl\n  - id: pcl-simple.obo\n  - id: pcl-simple.json\ndependencies:\n  - id: pr\n  - id: go\n  - id: uberon\n  - id: ro\n  - id: pato\n  - id: ncbitaxon\n  - id: bfo\n  - id: cl\n  - id: omo\n  - id: nbo\n  - id: chebi\n  - id: so\ntracker: https://github.com/obophenotype/provisional_cell_ontology/issues\nlicense:\n  url: http://creativecommons.org/licenses/by/4.0/\n  label: CC BY 4.0\nusages:\n  - user: https://biccn.org/\n    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.\nrepository: https://github.com/obophenotype/provisional_cell_ontology\npreferredPrefix: PCL\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fobophenotype%2Fprovisional_cell_ontology","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fobophenotype%2Fprovisional_cell_ontology","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fobophenotype%2Fprovisional_cell_ontology/lists"}