Ontology

CL

Cell Ontology

The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.

anatomyannotationcellcell biologyimmunogeneticsimmunologylife sciencemorphology
A99

FAIR 48/48

Version 2026-06-08

Evaluated 26 Oct 2026

How scores work

Source & access

Homepageobophenotype.github.io Repositorygithub.com DownloadCanonical file / PURL Browse in OLSEMBL-EBI Ontology Lookup ServiceBrowse in BioPortalNCBO BioPortalBrowse in OBO FoundryOBO Foundry registry

Portals & registries

SourceIDVersionClassesPropertiesIndividualsLoaded
OLS (EMBL-EBI)cl2026-06-0819,16747321725 Oct 2026
OBO Dashboardcl2026-06-085,248——11 Jun 2026

Ontology IRI http://purl.obolibrary.org/obo/cl.owl
Version IRI http://purl.obolibrary.org/obo/cl/releases/2026-06-08/cl.owl

Languages en

Imports from (15)
BFO BSPO CHEBI COB GO IAO NCBITaxon OMO PATO PCL PR RO SO STATO UBERON

Reused by (93)
AISM AMPHX CLO CLYH CTENO DIDEO DOID DPO FBbt FYPO GSSO HP IDO INO MAXO MONDO MP OBA OBI OBIB OHPI OPL PATO PCL PHIPO PORO PREFER RO TXPO UBERON UPHENO WBPhenotype ADO AEO BCGO BCO BMONT CARO CCF CEPH CHMO CIDO CMPO COB COLAO COVOC ECAO ECO ECOCORE EFO EHDAA2 ENM EUPATH FLOPO FOODON FOVT GENEPIO GENO GO HCAO HRA ICO IDOCOVID19 IDOMAL LEPAO MCO MFMO MICRO MSIO NGBO OBCS OHMI OMIABIS ONE ONS ONTONEO OPMI ORNASEQ PAIN PBPKO PLANP PR PRIDE PSDO RBO SLSO STATO TAO VBO VO VSAO WIKIPATHWAYS XPO

Logical consistency
consistent · 0 unsatisfiable
OWL 2 DL
yes
ROBOT report
0 errors · 109 warnings · 6 info
OBO principles
FP01FP02FP03FP04FP05FP06FP07FP08FP09FP11FP12FP16FP20
Axioms
39,422 · 34.08% entities reused

Also registered as
aberowl: CL agroportal: CL biodivportal: CL bioportal: CL fairsharing: FAIRsharing.j9y503 obofoundry: cl ols: cl ontobee: CL wikidata.entity: Q55118285

Automated evaluation

F Findable FAIR12/12
  • Persistent identifier (F1)purl.obolibrary.org+4
  • Indexed in services (F4)5: OLS, BioPortal, OBO Foundry, Bioregistry, FAIRsharing+5
  • Citable reference (F2)doi:10.1186/s13326-016-0088-7+3
A Accessible FAIR12/12
  • Homepage reachableHTTP 200+3
  • Artefact retrievable over HTTP(S) (A1)download HTTP 200+6
  • Metadata persists in a registry (A2)OBO Foundry, Bioregistry+3
I Interoperable FAIR12/12
  • Formal machine-readable format (I1)OWL, OBO+5
  • Semantic-web IRIs (I2)OWL, OBO+3
  • References other vocabularies (I3)imports 15: bfo, bspo, chebi, cob, go, iao, ncbitaxon, omo…+4
R Reusable FAIR12/12
  • Clear license (R1.1)CC BY 4.0+5
  • Release provenance (R1.2)2026-06-08 (version IRI in the artefact)+4
  • Community standards (R1.3)OBO principles: 11/13 checks pass+3
Q Ontology consistency & quality20/20
  • Logical consistencyconsistent, 0 unsatisfiable classes (OBO Dashboard)+10
  • OWL 2 DL profilein OWL 2 DL+2
  • Upper-ontology alignmentimports BFO, COB+3
  • Standard relations (RO)imports RO+1
  • ROBOT report: no errors0 errors+2
  • ROBOT report: warning density109 warnings / 5248 classes = 0.02+1
  • Pitfall scan: no critical pitfallsno pitfall scan yet; ROBOT report has 0 errors+1
M Maintenance16/16
  • Recency2026-10-23 → 0.1 months (≤ 3 months)+10
  • Release cadence (12 months)6 releases (GitHub releases)+6
U Community adoption15/16
  • Documented adopting projects8 projects+7
  • Reused by other ontologies93: aism, amphx, clo, clyh, cteno, dideo…+4
  • Community signalmax(stars 217 → 4, citations 361 → 4)+4
P Penalties (inactivity & inconsistency)0
  • Time since last activity0.0 years → 4 × max(0, 0.0 − 1)0
  • Inactive statusnot archived, legacy or inactive0
  • Consistencyconsistent, no unsatisfiable classes0

FAIR subtotal 48/48 · earned 99/100 = 99/100 → grade A

Community adoption 8

  • CELLxGENE

    Cell type annotation standard

    Curated by SchemaScope
  • Human Cell Atlas

    Cell type annotation

    Curated by SchemaScope
  • BICAN

    Brain cell types

    Curated by SchemaScope
  • biccn.org

    The BICCN created a high-resolution atlas of cell types in the primary motor based on single cell transcriptomics. These cell types are represented in the brain data standards ontology which anchors to cell types in the cell ontology.

    Source: OBO Foundry registry
  • hubmapconsortium.org

    HuBMAP develops tools to create an open, global atlas of the human body at the cellular level. The Cell Ontology is used in annotating cell types in the tools developed.

    Source: OBO Foundry registry
  • ebi.ac.uk

    The EBI single cell expression atlas is an extension to EBI expression atlas that displays gene expression in single cells. Cell types in the single cell expression atlas linked with terms from the Cell Ontology.

    Source: OBO Foundry registry
  • encodeproject.org

    The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome …

    Source: OBO Foundry registry
  • fantom5-collaboration.gsc.riken.jp

    FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity.

    Source: OBO Foundry registry

Know a project that uses CL? Suggest it.

History & changes 1 run

History starts with the first archived run; changes appear after the next evaluation.

RunScoreFAIRVersion evaluatedTermsSnapshot
26 Oct 2026, 03:31 UTC99 A482026-06-0819,167JSON

Provenance

Every fact on this page was fetched automatically. Each row shows where it came from and when. If a source fails, the last good value is kept and marked “carried forward”.

FactSourceRetrieved
Homepage link check (HTTP 200)obophenotype.github.io26 Oct 2026, 02:43 UTC
Repository link check (HTTP 200)github.com26 Oct 2026, 02:43 UTC
Download link check (HTTP 200)purl.obolibrary.org26 Oct 2026, 02:43 UTC
Artefact header (version IRI)release-assets.githubusercontent.com26 Oct 2026, 02:43 UTC
Git refs (commit ba92ab5, latest tag v2026-06-08)github.com26 Oct 2026, 02:43 UTC
GitHub repository statisticsapi.github.com26 Oct 2026, 02:43 UTC
OLS classes, imports, version & releaseebi.ac.uk26 Oct 2026, 02:43 UTC
OBO Foundry status, license & usagesobofoundry.org26 Oct 2026, 02:37 UTC
Bioregistry mappings, dependencies & reusebioregistry.io26 Oct 2026, 02:43 UTC
OBO Dashboard (checked 11 Jun 2026)dashboard.obofoundry.org26 Oct 2026, 02:37 UTC
Crossref citations (doi:10.1186/s13326-016-0088-7)api.crossref.org26 Oct 2026, 02:43 UTC
Crossref citations (doi:10.1186/1471-2105-12-6)api.crossref.org26 Oct 2026, 02:43 UTC

Run 2026-10-26T02-37-38Z · evaluator v2.0.0 · rubric v3.4 · entry.json · run snapshot

How to cite