Ontology
CL
Cell Ontology
The reference ontology of cell types across organisms, with a large and growing branch of neuron and glial types.
Source & access
- homepage obophenotype.github.io HTTP 200
- repository github.com HTTP 200
- download purl.obolibrary.org HTTP 200
Portals & registries
| Source | ID | Version | Classes | Properties | Individuals | Loaded |
|---|---|---|---|---|---|---|
| OLS (EMBL-EBI) | cl | 2026-06-08 | 19,167 | 473 | 217 | 27 Oct 2026 |
| OBO Dashboard | cl | 2026-06-08 | 5,248 | — | — | 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 HPO 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
OOPS!: 1 critical · 1 important · 2 minor pitfall types
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
- 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
- Homepage reachableHTTP 200+3
- Artefact retrievable over HTTP(S) (A1)download HTTP 200+6
- Metadata persists in a registry (A2)OBO Foundry, Bioregistry+3
- 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
- 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
- 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 pitfalls1 critical, 1 important, 2 minor pitfall types (SchemaScope Python scan (OOPS! pitfall subset))0
- Recency2026-10-27 → 0.0 months (≤ 3 months)+10
- Release cadence (12 months)6 releases (GitHub releases)+6
- Documented adopting projects9 projects+7
- Reused by other ontologies93: aism, amphx, clo, clyh, cteno, dideo…+4
- Community signalmax(stars 218 → 4, citations 361 → 4)+4
- Time since last activity0.0 years → 4 × max(0, 0.0 − 1)0
- Inactive statusnot archived, legacy or inactive0
- Consistencyconsistent, no unsatisfiable classes0
- Critical pitfalls1 critical pitfall type (P19) × 3-3
FAIR subtotal 48/48 · earned 98/100 − 3 inactivity = 95/100 → grade A
Community adoption 9
- CELLxGENE
Cell type annotation standard
Curated by SchemaScope - Human Cell Atlas
Cell type annotation
Curated by SchemaScope - BICAN
Brain cell types
Curated by SchemaScope - BIDS
Recommended vocabulary for the CellType metadata field
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 2 runs
Metrics across runs
| 27 Oct 2026 rubric v3.5 | 26 Oct 2026 rubric v3.4 | |
|---|---|---|
| Score | 95 | 99 |
| Findable | 12 | 12 |
| Accessible | 12 | 12 |
| Interoperable | 12 | 12 |
| Reusable | 12 | 12 |
| Quality | 19 | 20 |
| Maintenance | 16 | 16 |
| Adoption | 15 | 15 |
| Penalty | -3 | 0 |
| Logically consistent | yes | yes |
| Unsatisfiable classes | 0 | 0 |
| In OWL 2 DL | yes | yes |
| ROBOT errors | 0 | 0 |
| ROBOT warnings | 109 | 109 |
| Critical pitfalls | 1 | — |
| Imported vocabularies | 15 | 15 |
| Reused by | 93 | 93 |
Newest run first. Highlighted cells changed since the run before; hover to see the earlier value. A rubric change alone can move points.
- Penalty: 0 → -3
- Quality: 20 → 19 (-1)
- Documented adopters: 8 → 9
- Score: 99 → 95 · rubric v3.4 → v3.5
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”.
| Fact | Source | Retrieved |
|---|---|---|
| Homepage link check (HTTP 200) | obophenotype.github.io | 27 Oct 2026, 21:58 UTC |
| Repository link check (HTTP 200) | github.com | 27 Oct 2026, 21:58 UTC |
| Download link check (HTTP 200) | purl.obolibrary.org | 27 Oct 2026, 21:58 UTC |
| Artefact header (version IRI) | release-assets.githubusercontent.com | 27 Oct 2026, 21:58 UTC |
| Git refs (commit d1b2fbd, latest tag v2026-06-08) | github.com | 27 Oct 2026, 21:58 UTC |
| GitHub repository statistics | api.github.com | 27 Oct 2026, 21:58 UTC |
| OLS classes, imports, version & release | ebi.ac.uk | 27 Oct 2026, 21:58 UTC |
| OBO Foundry status, license & usages | obofoundry.org | 27 Oct 2026, 21:58 UTC |
| Bioregistry mappings, dependencies & reuse | bioregistry.io | 27 Oct 2026, 21:58 UTC |
| OBO Dashboard (checked 11 Jun 2026) | dashboard.obofoundry.org | 27 Oct 2026, 21:58 UTC |
| OOPS! pitfall scan | oops.linkeddata.es | 27 Oct 2026, 21:58 UTC |
| Crossref citations (doi:10.1186/s13326-016-0088-7) | api.crossref.org | 26 Oct 2026, 02:43 UTC carried forward |
Run 2026-10-27T21-58-30Z · evaluator v2.0.0 · rubric v3.5 · entry.json · run snapshot
How to cite
- The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability (2016) · doi:10.1186/s13326-016-0088-7 · 361 citations