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cello: rdf:type owl:Ontology
dcterms:created 2025-03-30
dcterms:modified 2026-03-25
rdfs:label Cellosaurus ontology
owl:versionInfo 1.0 - 2026-03-25 15:44:33.246236 - prod
rdfs:seeAlso help:rdf-ontology
widoco:ntSerialization help:ontology.nt
sh:declare _:vb2396161
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widoco:introduction **Links with other ontologies** Most of the classes and properties defined within the Cellosaurus ontology (prefix cello:) are derived from existing terms defined in general purpose or domain specific OWL ontologies. In this version (revision 1.0): * Out of 131 classes, 126 are rdfs:subClassOf+ or / and owl:equivalentClass of an external term. * Out of 108 properties, 90 are rdfs:subPropertyOf+ or / and owl:equivalentProperty of an external term. More details about the subsuming / equivalency term relationships are available in the SPARQL query examples at [sparql-editor](/sparql-editor). Since Cellosaurus is an extensive description of cell lines, multiple ontologies were required to cover its conceptual field, among which : * [IAO is_about](http://purl.obolibrary.org/ontology/IAO_0000136) to define [cello:hasAnnotation](#hasAnnotation) as its inverse property (owl:inverseOf) * [IAO DataItem](http://purl.obolibrary.org/ontology/IAO_0000027) as a superclass of several topic comments in conjunction with EDAM concepts topic and has_topic. See for example [cello:DonorInfoComment](#DonorInfoComment) * [BFO has_part](http://purl.obolibrary.org/obo/BFO_0000051) as a super property for [cello:hasAntibodyLightChain](#hasAntibodyLightChain) and others * Multiple [schema.org concepts](https://schema.org/) concepts for person, organization, location, and observation entities * Some [dcterms](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-2) properties are used as super properties for many of our terms, see [dcterms:source](#httppurlorgdctermssource) and [dcterms:identifier](#httppurlorgdctermsidentifier). * For publication citations, our terms are mostly derived from dcterms and from [FaBiO](http://purl.org/spar/fabio) which extends dcterms and provides with a classification of bibliographic entities and more attributes. * We use [OBI Genetic transformation](http://purl.obolibrary.org/obo/OBI_0600043) as a superclass for [cello:GenomeModificationMethod](#GenomeModificationMethod) subclasses and [OBI Genetic characteristics information](http://purl.obolibrary.org/obo/OBI_0001404) and other OBI terms to root and organize multiple cell line annotations types as seen [here](#httppurlobolibraryorgoboOBI_0001404) * Root biological concepts like disease, gene, marker, sequence variations from [NCIt](https://ncithesaurus.nci.nih.gov) are used as subsuming or equivalent to our terms. See for example [cello:Sequencevariation](#SequenceVariation) * [UBERON](https://obophenotype.github.io/uberon/) and [CL](https://obophenotype.github.io/cell-ontology/) which describe anatomical terms and cell types respectively. * [ChEBI](https://www.ebi.ac.uk/chebi/) serves as a root to define chemical compounds and [cello:Protein](#Protein) * [cello:CellLine](#CellLine) sub-classes have an owl:equivalentClass in [Wikidata](https://www.wikidata.org/wiki/Wikidata:Main_Page) and 5 cell line properties have owl:equivalentProperty as well. Note that every cell line of Cellosaurus is also described in Wikidata. The content of Wikidata regarding cellosaurus cell lines is synchronized with a bot running on each new Cellosaurus release. * [skos](https://www.w3.org/2004/02/skos/) terms are used to define local [concept schemes](#CelloConceptScheme) and to link related concepts within concept schemes. It is also used to add informal semantic links between terms across ontologies, for example between [cello:PrivaDocentThesis](#PrivaDocentThesis) and [up:ThesisCitation](https://purl.uniprot.org/html/index-en.html#Thesis_Citation). Note that skos properties linking our terms to other ontology terms are displayed in the _has relation_ section of the term. **Cross-references** [Xref](#Xref) instances are widely used in Cellosaurus. They have their own namespace and IRIs. A cross-reference instance provides information about its database, its identifier within the database (accession) and an URL pointing to a Web page. It may also come with an optional _rdfs:label_ property or _discontinued_ property depending on the context. The most common use cases are: * with [cello:seeAlsoXref](#seeAlsoXref) property to propose additional information about a cell line * with [cello:originatesFrom](#originatesFrom) property for indicate the origin of a source of information * with [cello:isIdentifiedByXref](#isIdentifiedByXref) property where it plays the role of an identifier for some instance of Gene, Species, Anatomical, Chemical or other kind of entity. **Concept schemes and concepts** Sub-classes of [cello:Database](#Database) may have instances (named individuals) which also belong to [cello:CelloConceptScheme](#CelloConceptScheme), see for example [db:ORDO](#httplocalhostrdfdbORDO). This occurs when the cross-references of a database can also be seen as concepts linked to each other to form a hierachy of concepts, that is an ontology. Such cross-references are also declared as instances of [skos:Concept](#httpwwww3org200402skoscoreConcept) and linked to each other within their CelloConceptScheme with [cello:more_specific_than](#more_specific_than) properties. For any cross-reference used in Cellosaurus to somehow describe a cell line and which belongs to either db:CL, db:ChEBI, db:NCBI_TaxID, db:NCIt, db:ORDO, db:RS, db:UBERON, or db:VBO, we provide with: * all the parent concepts up to the root concept in the original ontology * the hierarchical structure with property _cello:more_specific_than_ properties linking concepts Making the hierarchy of concepts available within Cellosaurus makes it possible to build SPARQL queries using a criterion like > ?any_concept cello:more_specific_than* ?some_concept . See also SPARQL query examples at [sparql-editor](/sparql-editor) **Names for instances** The instances of many classes have names. And to give a thing a name we use many different properties: rdfs:label, skos:prefLabel, cello:recommendedName, cello:alternativeName, cello:registeredName, etc. used in different contexts. All these properties have a specific function but sometimes you just don't know whether the name you have in mind is a recommended or an alternative name or whatever. To solve this problem, we provide a so-called materialization of triples that can be inferred from the hierarchy of naming properties. As an example, if you're looking for 'He-La' cell line ('He-La' is an cello:alternativeName of cvcl:CVCL_0030), you can simply use the cello:name property in the basic graph pattern: > select ... where { > ?cl cello:name 'He-La'^^xsd:string . > } This is because cello:alternativeName is defined as a rdfs:subPropertyOf cello:name See also the usage of name properties for instances of each class in SPARQL query examples at [sparql-editor](/sparql-editor). **Named individuals** The ontology defines a number of so-called named individuals (owl:NamedIndividual). They belong to a few classes: * [cello:CelloConceptScheme](#CelloConceptScheme) class and [cello:Database](#Database) sub-classes are populated with named individuals, example [db:ATCC](#httplocalhostrdfdbATCC) * [cello:GenomeModificationMethod](#GenomeModificationMethod) class and its sub-classes are populated with named individuals, example: [cello:CrisprCas9](#CrisprCas9) * [Sex](#Sex) class is defined as a set of named individuals, example [cello:MixedSex](#MixedSex). **Main namespaces** | Prefix | IRI | Name | |------------|------------|------| | cello: | https://purl.expasy.org/cellosaurus/rdf/ontology/ | Cellosaurus ontology classes and properties | | cvcl: | https://purl.expasy.org/cellosaurus/rdf/cvcl/ | Cellosaurus cell line instances | | orga: | https://purl.expasy.org/cellosaurus/rdf/orga/ | Cellosaurus organization instances | | db: | https://purl.expasy.org/cellosaurus/rdf/db/ | Cellosaurus online database and concept scheme named individuals | | xref: | https://purl.expasy.org/cellosaurus/rdf/xref/ | Cellosaurus cross-reference and concept instances | | BFO: | http://purl.obolibrary.org/obo/BFO_ | Basic Formal Ontology | | CHEBI: | http://purl.obolibrary.org/obo/CHEBI_ | Chemical Entities of Biological Interest | | EDAM: | http://edamontology.org/ | The ontology of data analysis and management | | IAO: | http://purl.org/ontology/IAO_ | Information Artifact Ontology | | fabio: | http://purl.org/spar/fabio/ | FaBiO, the FRBR-aligned Bibliographic Ontology | | dcterms: | http://purl.org/dc/terms/ | DCMI Metadata Terms | | NCIt: | http://purl.obolibrary.org/obo/NCIT_ | NCI Thesaurus OBO Edition | | OBI: | http://purl.obolibrary.org/obo/OBI_ | Ontology for Biomedical Investigations | | owl: | http://www.w3.org/2002/07/owl# | The OWL 2 Schema vocabulary | | rdf: | http://www.w3.org/1999/02/22-rdf-syntax-ns# | The RDF Concepts Vocabulary | | rdfs: | http://www.w3.org/2000/01/rdf-schema# | The RDF Schema vocabulary | | schema: | https://schema.org/ | Schemas for structured data on the Internet | | skos: | http://www.w3.org/2004/02/skos/core# | Simple Knowledge Organization System | | wd: | http://www.wikidata.org/entity/ | Wikidata entities |
widoco:jsonldSerialization help:ontology.jsonld
widoco:rdfxmlSerialization help:ontology.owl
widoco:turtleSerialization help:ontology.ttl
dcterms:abstract Cellosaurus is a manually curated resource that attempts to extensively describe all cell lines used in biomedical research. The OWL Cellosaurus ontology serves as the semantic model for all the diverse information contained in the Cellosaurus RDF. Cellosaurus is a comprehensive knowledge resource on cell lines used in biomedical research, encompassing both vertebrate and invertebrate species. It provides detailed information for over 170,000 cell lines, including recommended names, synonyms, unique accession numbers, species of origin, and structured comments. The database contains crucial details such as contamination status, genetic modifications, disease associations, STR profiles, and cell line categorization. Delivering a RDF version of Cellosaurus is an important step towards FAIRification. Making it available from our [SPARQL endpoint](https://sparql.cellosaurus.org/sparql) is key to Linked Open Data (LOD) perspective and for improving interoperability in particular thanks to federated queries. The OWL Cellosaurus ontology was developed to serve as the semantic model for all the diverse information contained in the Cellosaurus RDF. Two key principles guided its construction: * Anchorage and reuse. A common vocabulary is essential for RDF to allow good interoperability so reusing terms from standard ontologies was a priority. * Practicalities. Readability and documentation are important for us humans. Local equivalent classes and / or properties with human readable IRIs as well as sub-properties with documented domains and ranges were defined in order to take advantage of the [SPARQL-editor](/sparql-editor) (autocompletion functionality) and of the [widoco](https://github.com/dgarijo/Widoco) documentation tool which generated this page. The [EMBL-EBI Ontology Lookup Service](https://www.ebi.ac.uk/ols4/) (OLS) was the main tool used to search for existing terms relevant to our ontology. In addition to their formal OWL definition, some of our classes and properties are also described using the SKOS ontology. It adds some very informative links between our concepts and those from other ontologies for both humans and search algorithms. When available, the SKOS links also appear in this widoco documentation in the _has relation_ section of the terms.
dcterms:bibliographicCitation (to be defined)
dcterms:contributor n13:0000-0002-7023-1045
n13:0000-0002-0819-0473
n13:0000-0003-2826-6444
dcterms:creator n13:0000-0002-7023-1045
dcterms:description See https://api.cellosaurus.org/rdf-ontology
dcterms:hasVersion 1.0 - 2026-03-25 15:44:33.246236 - prod
dcterms:license n14:4.0
dcterms:publisher n7:www.sib.swiss
dcterms:title Cellosaurus ontology
bibo:status n12:draft
vann:preferredNamespacePrefix cello
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sh:prefix cello
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sh:prefix cvcl
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sh:prefix xref
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sh:prefix orga
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sh:prefix xsd
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sh:prefix rdf
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sh:prefix rdfs
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sh:prefix skos
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sh:prefix owl
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sh:prefix dcterms
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sh:prefix fabio
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sh:prefix up
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sh:prefix bibo
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sh:prefix widoco
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sh:prefix vann
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sh:prefix oa
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sh:prefix wdt
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sh:prefix wd
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sh:prefix sh
_:vb2396182 sh:namespace https://schema.org/
sh:prefix schema
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sh:prefix help
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sh:prefix pubmed
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sh:prefix BAO
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sh:prefix BTO
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sh:prefix CLO
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sh:prefix NCIt
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sh:prefix OBI
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sh:prefix OMIT
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sh:prefix FBcv
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sh:prefix GENO
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sh:prefix CARO
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sh:prefix CL
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sh:prefix CHEBI
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sh:prefix ORDO
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sh:prefix IAO
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sh:prefix EDAM
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sh:prefix prism
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sh:prefix BFO
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sh:prefix OLS