This HTML5 document contains 102 embedded RDF statements represented using HTML5+Microdata notation.
The embedded RDF content will be recognized by any processor of HTML5 Microdata.
| Subject | Predicate | Object |
|---|---|---|
| sibilo: | rdf:type | owl:Ontology |
| dcterms:created | 2025-08-07 | |
| dcterms:modified | 2025-10-20 | |
| rdfs:label | SIBiLS ontology | |
| owl:versionInfo | dev version - 2025-10-20 16:47:59.315600 - prod | |
| rdfs:seeAlso | help:rdf-ontology | |
| dcterms:hasVersion | dev version - 2025-10-20 16:47:59.315600 - prod | |
| dcterms:abstract | SIBiLS (Swiss Institute of Bioinformatics Literature Services) is a resource that enables personalized retrieval of biomedical literature through REST APIs, utilizing semantically enriched content to support curation workflows. A subset of the SIBiLS content is represented as RDF and made available via a SPARQL endpoint. The OWL SIBiLS ontology serves as the semantic model for the diverse information contained within the SIBiLS RDF. The SIBiLS RDF includes a collection of full-text publications from PubMed Central as well as a collection of MedLine records, all semantically enriched with annotations. Publications in the RDF are annotated to identify and localize biological concepts both within the full text and metadata. These concepts are extracted from a curated set of terminologies and ontologies relevant to the biological domain. The terminologies, ontologies, their concepts, and some of their semantic relationships are also represented in the RDF, enabling powerful and precise SPARQL queries. The subset of scientific publications included in SIBiLS RDF is the union of those cited in other curated [SIB](https://www.sib.swiss/) resources such as [UniProtKB](https://www.uniprot.org/), [Rhea](https://www.rhea-db.org/), [SwissLipids](https://www.swisslipids.org/), and [Cellosaurus](https://www.cellosaurus.org/). When the full text of a publication is freely available from [PubMed Central](https://pmc.ncbi.nlm.nih.gov/), it is included; otherwise, only the [MedLine](https://www.nlm.nih.gov/medline/medline_home.html) record is used. Each publication’s RDF representation contains metadata (including publication year, title, abstract, journal, and identifiers), as well as a hierarchical structure of the publication’s content. This structure is broken down into sections and subsections, which include paragraphs, tables, and figures, and further into leaf components such as titles, sentences, and list items where the actual textual content is found. Delivering a RDF version of SIBiLS is an important step towards FAIRification. Making it available from our [SPARQL endpoint](https://sparql.sibils.org/sparql) is key to Linked Open Data (LOD) perspective and for improving interoperability in particular thanks to federated queries. Two key principles guided the construction of the SIBiLS ontology: * Anchorage and reuse. A common vocabulary is essential for RDF to allow good interoperability so reusing terms from standard ontologies was a priority. Most of the classes and properties used in our ontology are terms defined in standard preexisting ontologies. * 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. | |
| dcterms:creator | n10:0000-0002-7023-1045 | |
| dcterms:title | SIBiLS ontology | |
| sh:declare | _:vb355361106 | |
| _:vb355361107 | ||
| _:vb355361104 | ||
| _:vb355361105 | ||
| _:vb355361110 | ||
| _:vb355361111 | ||
| _:vb355361108 | ||
| _:vb355361109 | ||
| _:vb355361114 | ||
| _:vb355361115 | ||
| _:vb355361112 | ||
| _:vb355361113 | ||
| _:vb355361090 | ||
| _:vb355361091 | ||
| _:vb355361094 | ||
| _:vb355361095 | ||
| _:vb355361092 | ||
| _:vb355361093 | ||
| _:vb355361098 | ||
| _:vb355361099 | ||
| _:vb355361096 | ||
| _:vb355361097 | ||
| _:vb355361102 | ||
| _:vb355361103 | ||
| _:vb355361100 | ||
| _:vb355361101 | ||
| widoco:turtleSerialization | help:ontology.ttl | |
| widoco:introduction | **Links with other ontologies** Most of the classes and properties defined within the SIBiLS ontology (prefix sibilo:) are derived from existing terms defined in general purpose or domain specific OWL ontologies: * [fabio:](https://sparontologies.github.io/fabio/current/fabio.html) which extends dcterms and provides with a classification of bibliographic entities and more attributes (e.g. fabio:JournalArticle, ConferencePaper, ...) * [prism:](https://www.w3.org/submissions/prism/) and [dcterms:](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/) which allow to describe most of publication metadata (e.g. dcterms:title, prism:year prism:doi, etc.) * [deo:](https://sparontologies.github.io/deo/current/deo.html) and [doco:](https://sparontologies.github.io/doco/current/doco.html) terms are used to describe the structure of the publication which breaks into connected discourse elements (e.g. doco:Section, doco:Sentence, etc.) * [oa:](https://www.w3.org/ns/oa#) terms are used to describe annotations linked to a publication, specifying which concept is identified and its exact location (e.g., the position within a sentence). * [schema:](https://schema.org/) provides concepts for persons, organizations, membership and affiliation * [skos](https://www.w3.org/2004/02/skos/) terms are used to define concept schems (terminologies, ontologies) and to link related concepts within concept schemes. It is also used to add informal semantic links between terms across ontologies, for example between fabio:Thesis and up:ThesisCitation. Note that skos properties linking our terms to other ontology terms are displayed in the _has relation_ section of the term. **Concept schemes and concepts** In SIBiLS RDF, publications are annotated with concepts derived from standard terminologies or ontologies: * each terminology is represented as an owl:NamedIndividual and also as an instance of sibilo:SibilsConceptScheme. * each concept is represented as an instance of skos:Concept and linked to its terminology using the skos:inScheme property. When a terminology defines a subsumption relationship between two concepts within the same terminology, it is represented by the sibilo:more_specific_than property, which is a sub-property of skos:broader. For any concept used in SIBiLS to annotate a publication, the RDF provide with: * all the parent concepts up to the root concept in the original terminology (when subsuming relationships exist) * the hierarchical structure with property _sibilo:more_specific_than_ properties linking concepts Making the hierarchy of concepts available within SIBiLS makes it possible to build SPARQL queries using a criterion like > ?any_concept sibilo:more_specific_than* ?some_concept . See also SPARQL query examples at [sparql-editor](/sparql-editor) **Named individuals** The SIBiLS ontology defines a number of so-called named individuals (owl:NamedIndividual) for terminologies. They belong to the class sibilo:SibilsConceptScheme and their IRIs are in the _sibilt:_ namespace (e.g. sibilt:uniprot, sibilt:ECO, sibilt:NCBI_TaxID, sibilt:CHEBI, etc.). See [Named Individuals](#namedindividuals) for the full list. **Main namespaces** Here is a list of the most important namespaces used in the SIBiLS RDF. | Prefix | IRI | Name | |------------|------------|------| | sibils: | https://purl.expasy.org/sibils/rdf/data/ | SIBiLS data | | sibilo: | https://purl.expasy.org/sibils/rdf/ontology/ | SIBiLS ontology classes and properties | | sibilt: | https://purl.expasy.org/sibils/rdf/scheme/ | SIBiLS terminologies | | sibilc: | https://purl.expasy.org/sibils/rdf/concept/ | SIBiLS concepts | | fabio: | http://purl.org/spar/fabio/ | FaBiO, the FRBR-aligned Bibliographic Ontology | | prism: | (http://prismstandard.org/namespaces/basic/2.0/) | PRISM Specification Package - W3C Member Submission 10 September 2020 | | dcterms: | http://purl.org/dc/terms/ | DCMI Metadata Terms | | deo: | http://purl.org/spar/deo/ | The Discourse Elements Ontology | | doco: | http://purl.org/spar/doco/ | DoCO, the Document Components Ontology | | oa: | http://www.w3.org/ns/oa# | Web Annotation Ontology (W3C) | | schema: | https://schema.org/ | Schemas for structured data on the Internet | | skos: | http://www.w3.org/2004/02/skos/core# | Simple Knowledge Organization System | | 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 | | |
| widoco:jsonldSerialization | help:ontology.jsonld | |
| widoco:ntSerialization | help:ontology.nt | |
| widoco:rdfxmlSerialization | help:ontology.owl | |
| dcterms:bibliographicCitation | (to be defined) | |
| dcterms:contributor | n10:0000-0003-2209-5218 | |
| n10:0000-0002-3374-2962 | ||
| n10:0000-0002-7023-1045 | ||
| dcterms:description | See https://sparql.sibils.org/rdf-ontology | |
| dcterms:license | n12:4.0 | |
| dcterms:publisher | n7:www.sib.swiss | |
| bibo:status | n6:draft | |
| vann:preferredNamespacePrefix | sibils | |
| _:vb355361090 | sh:namespace | https://purl.expasy.org/sibils/rdf/ontology/ |
| sh:prefix | sibilo | |
| _:vb355361091 | sh:namespace | https://purl.expasy.org/sibils/rdf/concept/ |
| sh:prefix | sibilc | |
| _:vb355361092 | sh:namespace | https://purl.expasy.org/sibils/rdf/data/ |
| sh:prefix | sibils | |
| _:vb355361093 | sh:namespace | https://purl.expasy.org/sibils/rdf/scheme/ |
| sh:prefix | sibilt | |
| _:vb355361094 | sh:namespace | http://purl.org/spar/deo/ |
| sh:prefix | deo | |
| _:vb355361095 | sh:namespace | http://purl.org/spar/doco/ |
| sh:prefix | doco | |
| _:vb355361096 | sh:namespace | http://www.essepuntato.it/2008/12/pattern# |
| sh:prefix | po | |
| _:vb355361097 | sh:namespace | http://www.w3.org/2011/content# |
| sh:prefix | cnt | |
| _:vb355361098 | sh:namespace | http://www.w3.org/2001/XMLSchema# |
| sh:prefix | xsd | |
| _:vb355361099 | sh:namespace | http://www.w3.org/1999/02/22-rdf-syntax-ns# |
| sh:prefix | rdf | |
| _:vb355361100 | sh:namespace | http://www.w3.org/2000/01/rdf-schema# |
| sh:prefix | rdfs | |
| _:vb355361101 | sh:namespace | http://www.w3.org/2004/02/skos/core# |
| sh:prefix | skos | |
| _:vb355361102 | sh:namespace | http://www.w3.org/2002/07/owl# |
| sh:prefix | owl | |
| _:vb355361103 | sh:namespace | http://purl.org/dc/terms/ |
| sh:prefix | dcterms | |
| _:vb355361104 | sh:namespace | http://purl.org/spar/fabio/ |
| sh:prefix | fabio | |
| _:vb355361105 | sh:namespace | http://purl.org/vocab/frbr/core# |
| sh:prefix | frbr | |
| _:vb355361106 | sh:namespace | http://purl.obolibrary.org/obo/IAO_ |
| sh:prefix | IAO | |
| _:vb355361107 | sh:namespace | http://purl.uniprot.org/core/ |
| sh:prefix | up | |
| _:vb355361108 | sh:namespace | http://purl.org/ontology/bibo/ |
| sh:prefix | bibo | |
| _:vb355361109 | sh:namespace | https://w3id.org/widoco/vocab# |
| sh:prefix | widoco | |
| _:vb355361110 | sh:namespace | http://purl.org/vocab/vann/ |
| sh:prefix | vann | |
| _:vb355361111 | sh:namespace | http://www.w3.org/ns/oa# |
| sh:prefix | oa | |
| _:vb355361112 | sh:namespace | http://www.w3.org/ns/shacl# |
| sh:prefix | sh | |
| _:vb355361113 | sh:namespace | https://schema.org/ |
| sh:prefix | schema | |
| _:vb355361114 | sh:namespace | http://prismstandard.org/namespaces/basic/2.0/ |
| sh:prefix | prism | |
| _:vb355361115 | sh:namespace | https://sparql.sibils.org/ |
| sh:prefix | help |