SIBiLS ontology
language en

SIBiLS ontology

Release: 2025-08-07

Modified on: 2025-10-03
Revision:
dev version - 2025-10-03 19:01:33.733572 - prod
Authors:
Pierre-André Michel (SIB)
Contributors:
Pierre-André Michel (SIB)
Alexandre Flament (HES-SO Genève)
Patrick Ruch (SIB)
Publisher:
SIB Swiss Institute of Bioinformatics
See also:
https://sparql.sibils.org/rdf-ontology
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
http://creativecommons.org/licenses/by/4.0
Visualization:
Visualize with WebVowl
Cite as:
(to be defined)
Provenance of this page
draft

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.

Introduction back to ToC

**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 |

SIBiLS ontology: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Annotation Properties

Named Individuals

SIBiLS ontology: Description back to ToC

See https://sparql.sibils.org/rdf-ontology

Cross-reference for SIBiLS ontology classes, object properties and data properties back to ToC

This section provides details for each class and property defined by SIBiLS ontology.

Classes

Abstractc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/Abstract

Abstract as a part of a publication (or fabio:Expression). A brief summary of a book, a research article, thesis, review, conference proceeding or any in-depth analysis of a particular subject or discipline, the purpose of which is to help the reader quickly ascertain the publication's purpose.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Abstractc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Abstract

Abstract as a publication in itself (more precisely a subclass of fabio:Expression). A brief summary of a work on a particular subject, designed to act as the point-of-entry that will help the reader quickly to obtain an overview of the work's contents. The abstract may be an integral part of the work itself, written by the same author(s) and appearing at the beginning of a work such as a research paper, report, review or thesis. Alternatively it may be separate from the published work itself, and written by someone other than the author(s) of the published work, for example by a member of a professional abstracting service such as CAB Abstracts.
Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c

Addendumc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Addendum

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c

Annotationc back to ToC or Class ToC

IRI: http://www.w3.org/ns/oa#Annotation

The class for Web Annotations.
Is defined by
http://www.w3.org/ns/oa#
has sub-classes
Named Entity Extraction Annotation c

Annotation targetc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/AnnotationTarget

Target of an annotation: a text selection within a subpart of a publication
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Specific resource c

Appendixc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/Appendix

A supplemental addition to the main work. It may contain data, more detailed information about methods and materials, or provide additional detail concerning the information found in the main work.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Articlec back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Article

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c
has sub-classes
Journal article c, Review article c

Bachelor's thesisc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/BachelorsThesis

<dt>has relation</td><dd>skos:broadMatch <b>with</b> <a href="#http://purl.uniprot.org/core/Thesis_Citation" title="http://purl.uniprot.org/core/Thesis_Citation">Thesis citation</a></dd>
Is defined by
http://purl.org/spar/fabio/
has super-classes
Thesis c

Back matterc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/BackMatter

The final principle part of a document, in which is usually found the bibliography, index, appendixes, etc.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Biographyc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Biography

Is defined by
http://purl.org/spar/fabio/
has super-classes
Work c

Block quotationc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/BlockQuotation

A block quotation (also known as a long quotation or extract) is a quotation in a written document which is set off from the main text as a container for distinct paragraphs, which is typically distinguished visually using indentation, a different font, or smaller size. Block quotations are used for longer passages than run-in quotations (which are set off with quotation marks).
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Body matterc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/BodyMatter

The central principle part of a document, that contains the real content. It may be subdivided hierarchically by the use of chapters and sections.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Bookc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Book

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c
has sub-classes
Thesis c

Book chapterc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/BookChapter

<dt>has relation</td><dd>skos:closeMatch <b>with</b> <a href="#http://purl.uniprot.org/core/Book_Citation" title="http://purl.uniprot.org/core/Book_Citation">Book chapter citation</a></dd>
Is defined by
http://purl.org/spar/fabio/
has super-classes
Chapter c

Book chapter citationc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Book_Citation

Is defined by
http://purl.uniprot.org/core/

Book reviewc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/BookReview

Is defined by
http://purl.org/spar/fabio/
has super-classes
Review c

Brief reportc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/BriefReport

Is defined by
http://purl.org/spar/fabio/
has super-classes
Report document c

Captionc back to ToC or Class ToC

IRI: http://purl.org/spar/deo/Caption

Caption of a text box.
Is defined by
http://purl.org/spar/deo/
has super-classes
Discourse element c

Captioned boxc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/CaptionedBox

A rectangle space within a page that contains an object and its related caption.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Case reportc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/CaseReport

Is defined by
http://purl.org/spar/fabio/
has super-classes
Report c

Chapterc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Chapter

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c
has sub-classes
Book chapter c

Citing sourcec back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/CitingSource

A knowledge base, repository, or database that cites publications to support its statements.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has members
Cellosaurus ni, Rhea ni, SwissLipids ni, UniProtKB ni

Clinical trial reportc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/ClinicalTrialReport

Is defined by
http://purl.org/spar/fabio/
has super-classes
Trial report c

Commentc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Comment

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c

Conceptc back to ToC or Class ToC

IRI: http://www.w3.org/2004/02/skos/core#Concept

Is defined by
http://www.w3.org/2004/02/skos/core#
is in domain of
more specific than op
is in range of
more specific than op

Concept schemec back to ToC or Class ToC

IRI: http://www.w3.org/2004/02/skos/core#ConceptScheme

Is defined by
http://www.w3.org/2004/02/skos/core#
has sub-classes
Sibils concept scheme c

Conference paperc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/ConferencePaper

Is defined by
http://purl.org/spar/fabio/
has super-classes
Proceedings paper c

Correctionc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Correction

Is defined by
http://purl.org/spar/fabio/
has super-classes
Work c

Discourse elementc back to ToC or Class ToC

IRI: http://purl.org/spar/deo/DiscourseElement

An element of a document that carries out a rhetorical function.
Is defined by
http://purl.org/spar/deo/
has sub-classes
Abstract c, Appendix c, Back matter c, Block quotation c, Body matter c, Caption c, Captioned box c, Figure box c, Float matter c, Front matter c, Glossary c, Label c, List c, List item block c, Media block c, Object id block c, Paragraph c, Section c, Section label c, Speech block c, Statement block c, Table c, Table box c, Table footer c, Text box c, Title c, Verse group block c, Word sequence c
is in domain of
ordinal dp

Doctoral thesisc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/DoctoralThesis

<dt>has relation</td><dd>skos:broadMatch <b>with</b> <a href="#http://purl.uniprot.org/core/Thesis_Citation" title="http://purl.uniprot.org/core/Thesis_Citation">Thesis citation</a></dd>
Is defined by
http://purl.org/spar/fabio/
has super-classes
Thesis c

Editorialc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Editorial

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c

Expressionc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Expression

Is defined by
http://purl.org/spar/fabio/
has sub-classes
Abstract c, Addendum c, Article c, Book c, Chapter c, Comment c, Editorial c, Lecture notes c, Letter c, News item c, Proceedings paper c, Rapid communication c, Report document c, Specification document c
is in domain of
has annotation op, in collection dp, see also annotated ap

Figure boxc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/FigureBox

A space within a document that contains a figure and its caption.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Float matterc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/FloatMatter

Floating part of a document related to some aspect of the body section. Usually in a box with its own body with some title and / or caption.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Discourse element c

Front matterc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/FrontMatter

The initial principle part of a document, usually containing self-referential metadata. In a book, this typically includes its title, authors, publisher, publication date, ISBN and copyright declaration, together with the preface, foreword, table of content, etc. In a journal article, the front matter is normally restricted to the title, authors and the authors' affiliation details, although the latter may alternatively be included in a footnote or the back matter. In books, the front matter pages may be numbered in lowercase Roman numerals.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Glossaryc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/Glossary

A set of definitions of words or phrases of importance to the work, normally alphabetized. In longer works of fiction, the entries may contains places and characters.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Journal articlec back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/JournalArticle

<dt>has relation</td><dd>skos:closeMatch <b>with</b> <a href="#http://purl.uniprot.org/core/Journal_Citation" title="http://purl.uniprot.org/core/Journal_Citation">Journal article citation</a></dd>
Is defined by
http://purl.org/spar/fabio/
has super-classes
Article c

Journal article citationc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Journal_Citation

Is defined by
http://purl.uniprot.org/core/

Labelc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/Label

A block containing text, that may include a number (e.g., "Chapter Three", "3.2", "Figure 1", "Table"), used to identify an item within the document, for example a chapter, a figure, a section or a table.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Lecture notesc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/LectureNotes

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c

Letterc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Letter

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c

Listc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/List

List of items
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c
has sub-classes
List of agents c, List of references c

List item blockc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/ListItemBlock

A list item part of a document. Usually appears multiple time in a sequence. May be prefixed with a bullet or a number.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Discourse element c

List of agentsc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/ListOfAgents

Is defined by
http://purl.org/spar/doco/
has super-classes
List c
has sub-classes
List of authors c, List of organizations c

List of authorsc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/ListOfAuthors

Is defined by
http://purl.org/spar/doco/
has super-classes
List of agents c

List of organizationsc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/ListOfOrganizations

A list of items each denoting an agent, such as an author, a contributor or an organization, related to a particular publication.
Is defined by
http://purl.org/spar/doco/
has super-classes
List of agents c

List of referencesc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/ListOfReferences

A list of items each representing a reference to a specific part of the same document, or to another publication.
Is defined by
http://purl.org/spar/doco/
has super-classes
List c

Manifestationc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Manifestation

A subclass of FRBR manifestation, restricted to manifestations of fabio:Expressions. fabio:Manifestation specifically applies to electronic (digital) as well as to physical manifestations of expressions.
Is defined by
http://purl.org/spar/fabio/

Master's thesisc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/MastersThesis

<dt>has relation</td><dd>skos:broadMatch <b>with</b> <a href="#http://purl.uniprot.org/core/Thesis_Citation" title="http://purl.uniprot.org/core/Thesis_Citation">Thesis citation</a></dd>
Is defined by
http://purl.org/spar/fabio/
has super-classes
Thesis c

Media blockc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/MediaBlock

A reference or link to some media (audio, video) part of a document.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Discourse element c

Meeting reportc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/MeetingReport

Is defined by
http://purl.org/spar/fabio/
has super-classes
Report c

Methods paperc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/MethodsPaper

Is defined by
http://purl.org/spar/fabio/
has super-classes
Scholarly work c

Named Entity Extraction Annotationc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/NexAnnotation

A concept identified at a specific position in a discourse element of a publication by a named entity extraction process.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Annotation c
is in range of
has annotation op

News itemc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/NewsItem

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c

Object id blockc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/ObjectIdBlock

An identifier appearing as a distinct part of a document.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Discourse element c

Organizationc back to ToC or Class ToC

IRI: https://schema.org/Organization

Is defined by
https://schema.org/

Paragraphc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/Paragraph

A self-contained unit of discourse that deals with a particular point or idea. Paragraphs contains one or more sentences. The start of a paragraph is indicated by beginning on a new line, which may be indented or separated by a small vertical space by the preceding paragraph.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Patent citationc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Patent_Citation

Is defined by
http://purl.uniprot.org/core/

Patent documentc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/PatentDocument

<dt>has relation</td><dd>skos:closeMatch <b>with</b> <a href="#http://purl.uniprot.org/core/Patent_Citation" title="http://purl.uniprot.org/core/Patent_Citation">Patent citation</a></dd>
Is defined by
http://purl.org/spar/fabio/
has super-classes
Specification document c

Personc back to ToC or Class ToC

IRI: https://schema.org/Person

Is defined by
https://schema.org/

Proceedings paperc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/ProceedingsPaper

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c
has sub-classes
Conference paper c

Product reviewc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/ProductReview

Is defined by
http://purl.org/spar/fabio/
has super-classes
Review c

Rapid communicationc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/RapidCommunication

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c

Reportc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Report

Is defined by
http://purl.org/spar/fabio/
has super-classes
Work c
has sub-classes
Case report c, Meeting report c, Technical report c, Trial report c

Report documentc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/ReportDocument

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c
has sub-classes
Brief report c

Reviewc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Review

Is defined by
http://purl.org/spar/fabio/
has super-classes
Work c
has sub-classes
Book review c, Product review c, Systematic review c

Review articlec back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/ReviewArticle

Is defined by
http://purl.org/spar/fabio/
has super-classes
Article c

Scholarly workc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/ScholarlyWork

Is defined by
http://purl.org/spar/fabio/
has super-classes
Work c
has sub-classes
Methods paper c

Sectionc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/Section

A logical division of the text, usually numbered and/or titled, which may contain subsections.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Section labelc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/SectionLabel

A block containing a label for the section, that may include the section number.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Sentencec back to ToC or Class ToC

IRI: http://purl.org/spar/doco/Sentence

An expression in natural language forming a single grammatical unit. A sentence minimally consists of a subject and an intransitive verb, or a subject, a transitive verb and an object, and may include additional dependent clauses. In written text, a sentence is always terminated by a full stop. A sentence can include words grouped meaningfully to express a statement, a question, an exclamation, a request or a command.
Is defined by
http://purl.org/spar/doco/
has super-classes
Word sequence c

Specific resourcec back to ToC or Class ToC

IRI: http://www.w3.org/ns/oa#SpecificResource

Instances of the SpecificResource class identify part of another resource (referenced with oa:hasSource), a particular representation of a resource, a resource with styling hints for renders, or any combination of these, as used within an Annotation.
Is defined by
http://www.w3.org/ns/oa#
has sub-classes
Annotation target c

Specification documentc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/SpecificationDocument

Is defined by
http://purl.org/spar/fabio/
has super-classes
Expression c
has sub-classes
Patent document c

Speech blockc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/SpeechBlock

A dialog or part of dialog appearing as a distinct part of a document.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Discourse element c

Statement blockc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/StatementBlock

A statement appearing as a distinct part of a document.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Discourse element c

Systematic reviewc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/SystematicReview

Is defined by
http://purl.org/spar/fabio/
has super-classes
Review c

Tablec back to ToC or Class ToC

IRI: http://purl.org/spar/doco/Table

A set of data arranged in cells within rows and columns.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Table boxc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/TableBox

A space within a document that contains a table and its caption.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Table cell valuesc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/TableCellValues

A concatenation of the values found in the cells of a table separated with a space.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Word sequence c

Table column namec back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/TableColumnName

The name given to of a column in a table.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Word sequence c

Table footerc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/TableFooter

Text appearing at the bottom of a table.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Discourse element c

Technical reportc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/TechnicalReport

Is defined by
http://purl.org/spar/fabio/
has super-classes
Report c

Text boxc back to ToC or Class ToC

IRI: http://purl.org/spar/doco/TextBox

A space within a document that contains textual content relating to, quoting from or expanding upon the main text. Usually a textbox is delimited by a border or use of a background colour distinct from that of the main text.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Text position selectorc back to ToC or Class ToC

IRI: http://www.w3.org/ns/oa#TextPositionSelector

The TextPositionSelector describes a range of text by recording the start and end positions of the selection in the stream. Position 0 would be immediately before the first character, position 1 would be immediately before the second character, and so on.
Is defined by
http://www.w3.org/ns/oa#

Thesisc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Thesis

<dt>has relation</td><dd>skos:closeMatch <b>with</b> <a href="#http://purl.uniprot.org/core/Thesis_Citation" title="http://purl.uniprot.org/core/Thesis_Citation">Thesis citation</a></dd>
Is defined by
http://purl.org/spar/fabio/
has super-classes
Book c
has sub-classes
Bachelor's thesis c, Doctoral thesis c, Master's thesis c

Thesis citationc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Thesis_Citation

Is defined by
http://purl.uniprot.org/core/

Titlec back to ToC or Class ToC

IRI: http://purl.org/spar/doco/Title

A word, phrase or sentence that precedes and indicates the subject of a document or a document component - e.g., a book, a report, a news article, a chapter, a section or a table.
Is defined by
http://purl.org/spar/doco/
has super-classes
Discourse element c

Trial reportc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/TrialReport

Is defined by
http://purl.org/spar/fabio/
has super-classes
Report c
has sub-classes
Clinical trial report c

Verse group blockc back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/VerseGroupBlock

A block containing one or several verses appearing as a distinct part of a document.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Discourse element c

Word sequencec back to ToC or Class ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/WordSequence

A super class for sentences, table column names, table cell values or any textual item that is part of a list
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-classes
Discourse element c
has sub-classes
Sentence c, Table cell values c, Table column name c

Workc back to ToC or Class ToC

IRI: http://purl.org/spar/fabio/Work

Is defined by
http://purl.org/spar/fabio/
has sub-classes
Biography c, Correction c, Report c, Review c, Scholarly work c

Object Properties

affiliationop back to ToC or Object Property ToC

IRI: https://schema.org/affiliation

An organization that this person is affiliated with. For example, a school/university, a club, or a team.
Is defined by
https://schema.org/
has super-properties
member of op

containsop back to ToC or Object Property ToC

IRI: http://www.essepuntato.it/2008/12/pattern#contains

A structured element contains another generic element.
Is defined by
http://www.essepuntato.it/2008/12/pattern#

contributorop back to ToC or Object Property ToC

IRI: http://purl.org/dc/terms/contributor

Is defined by
http://purl.org/dc/terms/
has sub-properties
creator op

creatorop back to ToC or Object Property ToC

IRI: http://purl.org/dc/terms/creator

Is defined by
http://purl.org/dc/terms/
has super-properties
contributor op

embodimentop back to ToC or Object Property ToC

IRI: http://purl.org/vocab/frbr/core#embodiment

Having a frbr:embodiment implies being something that, amongst other things, is a frbr:Expression
Is defined by
http://purl.org/vocab/frbr/core#

has annotationop back to ToC or Object Property ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/hasAnnotation

Links a publication to an annotation generated by named entity extraction.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has domain
Expression c
has range
Named Entity Extraction Annotation c
is inverse of
is about op

has broaderop back to ToC or Object Property ToC

IRI: http://www.w3.org/2004/02/skos/core#broader

Is defined by
http://www.w3.org/2004/02/skos/core#
has sub-properties
more specific than op

has broader transitiveop back to ToC or Object Property ToC

IRI: http://www.w3.org/2004/02/skos/core#broaderTransitive

Is defined by
http://www.w3.org/2004/02/skos/core#
has sub-properties
more specific than transitive op

has partop back to ToC or Object Property ToC

IRI: http://purl.org/dc/terms/hasPart

Links a resource that is included either physically or logically in the described resource.
Is defined by
http://purl.org/dc/terms/

is aboutop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000136

A (currently) primitive relation that relates an information artifact to an entity.
Is defined by
http://purl.obolibrary.org/obo/IAO_
is inverse of
has annotation op

member ofop back to ToC or Object Property ToC

IRI: https://schema.org/memberOf

Is defined by
https://schema.org/
has sub-properties
affiliation op

more specific thanop back to ToC or Object Property ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/more_specific_than

Links two concepts. The subject concept is more specific than the object concept. The semantics is the similar to the skos:broader property but its label less ambiguous.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-properties
has broader op
has domain
Concept c
has range
Concept c

more specific than transitiveop back to ToC or Object Property ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/more_specific_than_transitive

Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-properties
has broader transitive op

realization ofop back to ToC or Object Property ToC

IRI: http://purl.org/vocab/frbr/core#realizationOf

Having a frbr:realizationOf implies being something that, amongst other things, is a frbr:Expression
Is defined by
http://purl.org/vocab/frbr/core#

Data Properties

abstractdp back to ToC or Data Property ToC

IRI: http://purl.org/dc/terms/abstract

Is defined by
http://purl.org/dc/terms/

categorydp back to ToC or Data Property ToC

IRI: https://schema.org/category

Is defined by
https://schema.org/
has sub-properties
in collection dp

Character sequencedp back to ToC or Data Property ToC

IRI: http://www.w3.org/2011/content#chars

The character sequence of the text content.
Is defined by
http://www.w3.org/2011/content#

enddp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/oa#end

Position of the last character of a range of text in a discourse element.
Is defined by
http://www.w3.org/ns/oa#

ending pagedp back to ToC or Data Property ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/endingPage

Identifies the last page of an entity such as a journal article.
Is defined by
http://prismstandard.org/namespaces/basic/2.0/

exactdp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/oa#exact

Text representing the annotated concept as found in the discourse element.
Is defined by
http://www.w3.org/ns/oa#

has bodydp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/oa#hasBody

The object of the relationship is a resource that is a body of the Annotation.
Is defined by
http://www.w3.org/ns/oa#

has DOIdp back to ToC or Data Property ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/doi

Is defined by
http://prismstandard.org/namespaces/basic/2.0/
has super-properties
identifier dp

has National Library of Medicine journal title abbreviationdp back to ToC or Data Property ToC

IRI: http://purl.org/spar/fabio/hasNLMJournalTitleAbbreviation

An internal identifier for the abbreviation of the title of journals available from the National Library of Medicine repository.
Is defined by
http://purl.org/spar/fabio/
has super-properties
identifier dp

has PMC identifierdp back to ToC or Data Property ToC

IRI: http://purl.org/spar/fabio/hasPubMedCentralId

PubMedCentral identifier for the resource.
Is defined by
http://purl.org/spar/fabio/
has super-properties
identifier dp

has publication datedp back to ToC or Data Property ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/publicationDate

The date on which a resource is published or disclosed.
Is defined by
http://prismstandard.org/namespaces/basic/2.0/

has publication yeardp back to ToC or Data Property ToC

IRI: http://purl.org/spar/fabio/hasPublicationYear

Is defined by
http://purl.org/spar/fabio/

has PubMed identifierdp back to ToC or Data Property ToC

IRI: http://purl.org/spar/fabio/hasPubMedId

PubMed identifier for the resource.
Is defined by
http://purl.org/spar/fabio/
has super-properties
identifier dp

has selectordp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/oa#hasSelector

The object of the relationship is a Selector that describes the segment or region of interest within the source resource. Please note that the domain ( oa:ResourceSelection ) is not used directly in the Web Annotation model.
Is defined by
http://www.w3.org/ns/oa#

has sourcedp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/oa#hasSource

The resource that the ResourceSelection, or its subclass SpecificResource, is refined from, or more specific than. Please note that the domain ( oa:ResourceSelection ) is not used directly in the Web Annotation model.
Is defined by
http://www.w3.org/ns/oa#

has targetdp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/oa#hasTarget

The relationship between an Annotation and its Target.
Is defined by
http://www.w3.org/ns/oa#

has versiondp back to ToC or Data Property ToC

IRI: http://purl.org/dc/terms/hasVersion

Is defined by
http://purl.org/dc/terms/

identifierdp back to ToC or Data Property ToC

IRI: http://purl.org/dc/terms/identifier

Is defined by
http://purl.org/dc/terms/
has sub-properties
has DOI dp, has National Library of Medicine journal title abbreviation dp, has PMC identifier dp, has PubMed identifier dp, issue identifier dp, volume dp

in collectiondp back to ToC or Data Property ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/inCollection

Within the SIBiLS RDF dataset, publications are grouped into two distinct collections, each reflecting the source from which they were obtained: 'pmc' or 'medline'.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-properties
category dp
has domain
Expression c
has range
string

is referenced bydp back to ToC or Data Property ToC

IRI: http://purl.org/dc/terms/isReferencedBy

Is defined by
http://purl.org/dc/terms/

issue identifierdp back to ToC or Data Property ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/issueIdentifier

Is defined by
http://prismstandard.org/namespaces/basic/2.0/
has super-properties
identifier dp

keyworddp back to ToC or Data Property ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/keyword

Is defined by
http://prismstandard.org/namespaces/basic/2.0/

namedp back to ToC or Data Property ToC

IRI: https://schema.org/name

Is defined by
https://schema.org/
has equivalent properties
title dp

notationdp back to ToC or Data Property ToC

IRI: http://www.w3.org/2004/02/skos/core#notation

Notations are symbols which are not normally recognizable as words or sequences of words in any natural language and are thus usable independently of natural-language contexts. They are typically composed of digits, complemented with punctuation signs and other characters.
Is defined by
http://www.w3.org/2004/02/skos/core#

ordinaldp back to ToC or Data Property ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/ordinal

Relative order of appearance of a sentence in the publication. A sentence right after another one usually have an ordinal incremented by 1 but the orginal value can sometimes be arbitrary, for instance between body contents and some floating content.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has domain
Discourse element c
has range
integer

page rangedp back to ToC or Data Property ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/pageRange

Is defined by
http://prismstandard.org/namespaces/basic/2.0/

startdp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/oa#start

Position of the first character of a range of text in a discourse element.
Is defined by
http://www.w3.org/ns/oa#

starting pagedp back to ToC or Data Property ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/startingPage

Identifies the first page of an entity such as a journal article.
Is defined by
http://prismstandard.org/namespaces/basic/2.0/

titledp back to ToC or Data Property ToC

IRI: http://purl.org/dc/terms/title

Is defined by
http://purl.org/dc/terms/
has equivalent properties
name dp

volumedp back to ToC or Data Property ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/volume

An identifier for a particular volume of a resource, such as a journal or a multi-volume book.
Is defined by
http://prismstandard.org/namespaces/basic/2.0/
has super-properties
identifier dp

Annotation Properties

alt labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#altLabel

Is defined by
http://www.w3.org/2004/02/skos/core#
has super-properties
label

bibliographic Citationap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/bibliographicCitation

broad matchap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#broadMatch

Is defined by
http://www.w3.org/2004/02/skos/core#

close matchap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#closeMatch

Is defined by
http://www.w3.org/2004/02/skos/core#

createdap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/created

declareap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/ns/shacl#declare

descriptionap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/description

introductionap back to ToC or Annotation Property ToC

IRI: https://w3id.org/widoco/vocab#introduction

jsonld Serializationap back to ToC or Annotation Property ToC

IRI: https://w3id.org/widoco/vocab#jsonldSerialization

licenseap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/license

modifiedap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/modified

namespaceap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/ns/shacl#namespace

nt Serializationap back to ToC or Annotation Property ToC

IRI: https://w3id.org/widoco/vocab#ntSerialization

pref labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#prefLabel

Is defined by
http://www.w3.org/2004/02/skos/core#
has super-properties
label

preferred Namespace Prefixap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocab/vann/preferredNamespacePrefix

prefixap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/ns/shacl#prefix

publisherap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/publisher

rdfxml Serializationap back to ToC or Annotation Property ToC

IRI: https://w3id.org/widoco/vocab#rdfxmlSerialization

see also annotatedap back to ToC or Annotation Property ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/seeAlsoAnnotated

Provides a link to a URI where the annotated publication can be viewed.
Is defined by
https://purl.expasy.org/sibils/rdf/ontology/
has super-properties
see Also
has domain
Expression c
has range
Resource

statusap back to ToC or Annotation Property ToC

IRI: http://purl.org/ontology/bibo/status

turtle Serializationap back to ToC or Annotation Property ToC

IRI: https://w3id.org/widoco/vocab#turtleSerialization

Named Individuals

Affiliationsni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/ROR

A list of international research institutes.
belongs to
Sibils concept scheme c
has facts
has version dp "v2025-01-23"

Agrovocni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/AGROVOC

AGROVOC covers all areas of interest to FAO, such as food, nutrition, agriculture, forestry, fisheries, names of animals and plants, environment, biological notions, techniques of plant cultivation, etc. The thesaurus is hierarchically organized under 25 top concepts.
belongs to
Sibils concept scheme c
has facts
has version dp "v2024-06-04"

ATCni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/ATC

This ontology is a representation of the ATC classification used for the classification of drugs and provided by WHO (World Health Organization). Based on the ATC code of the main ingredient of a product, this medical product can be classified in the ATC system.
belongs to
Sibils concept scheme c
has facts
has version dp "v2024AB"

Cell Ontologyni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/CL

The Cell Ontology is a structured controlled vocabulary for cell types in animals.
belongs to
Sibils concept scheme c
has facts
has version dp "2025-01-07"

Cellosaurusni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/data/Cellosaurus

belongs to
Citing source c

Cellosaurusni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/CVCL

The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; Naturally immortal cell lines (example: stem cell lines); Finite life cell lines when those are distributed and used widely; Vertebrate cell line with an emphasis on human, mouse and rat cell lines; Invertebrate (insects and ticks) cell lines. Its scope does not include: Primary cell lines (with the exception of the finite life cell lines described above); Plant cell lines
belongs to
Sibils concept scheme c
has facts
has version dp "51.0"

ChEBIni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/CHEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. ChEBI incorporates an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified.
belongs to
Sibils concept scheme c
has facts
has version dp "v239"

COVOC BioMedical Vocabularyni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/COVocBMV

The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

COVOC Cell Linesni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/COVocCL

The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

COVOC Chemicalsni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/COVocDG

The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
belongs to
Sibils concept scheme c
has facts
has version dp "v2.0"

COVOC Clinical trialsni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/COVocCT

The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

COVOC Conceptual Entitiesni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/COVocCE

The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

COVOC Disease and Syndromeni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/COVocDIS

The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

COVOC Geographic Locationni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/COVocLOC

The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

COVOC Organismni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/COVocSP

The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
belongs to
Sibils concept scheme c
has facts
has version dp "v2.0"

COVOC Protein and Genomeni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/COVocPG

The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
belongs to
Sibils concept scheme c
has facts
has version dp "v2.0"

Detection methodsni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/DM

List of methods used to detect or study viruses in a corpus of scientific texts.
belongs to
Sibils concept scheme c
has facts
has version dp "v2022"

Disprotni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/DisProtType4

belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

Disprot_type1ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/DisProtType1

belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

Disprot_type2ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/DisProtType2

belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

Disprot_type3ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/DisProtType3

belongs to
Sibils concept scheme c
has facts
has version dp "v1.0"

Drugbankni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/DrugBank

The Drugbank database is a freely accessible resource which includes more than 13,000 records (version 5.1.4, released 2019-07-20). It contains information on drugs and drug targets, synonyms and product names.
belongs to
Sibils concept scheme c
has facts
has version dp "v5.1.13"

ECO - Evidence & Conclusion Ontologyni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/ECO

The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means.
belongs to
Sibils concept scheme c
has facts
has version dp "v2024-07-19"

ENVO - Environment Ontologyni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/ENVO

ENVO is an expressive, community ontology which helps humans, machines, and semantic web applications understand environmental entities of all kinds, from microscopic to intergalactic scales.
belongs to
Sibils concept scheme c
has facts
has version dp "v2024-07-01"

Floponi back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/FLOPO

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.
belongs to
Sibils concept scheme c
has facts
has version dp "2025-01-28"

GO Biological Processni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/GO_BP

The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research. Specific type: Biological process.
belongs to
Sibils concept scheme c
has facts
has version dp "v2024-11-03"

GO Cellular Componentni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/GO_CC

The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research. Specific type: Molecular function.
belongs to
Sibils concept scheme c
has facts
has version dp "v2024-11-03"

GO Molecular Functionni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/GO_MF

The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research. Specific type: Cellular component.
belongs to
Sibils concept scheme c
has facts
has version dp "v2024-11-03"

ICD-O-3ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/ICDO3

The International Classification of Diseases Oncology (ICD-O) is a biomedical ontology for logical representation of the terms and relations related to the International Classification of Diseases (ICD).
belongs to
Sibils concept scheme c
has facts
has version dp "unknown"

ICTV (International Committee on Taxonomy of Viruses)ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/ICTV

The task of the International Committee on Taxonomy of Viruses (ICTV) is to develop a single, universal taxonomic scheme for all the viruses infecting animals (vertebrates, invertebrates and protozoa), plants (higher plants and algae), fungi, bacteria and archaea.
belongs to
Sibils concept scheme c
has facts
has version dp "MSL39v4"

Ictv_subsetni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/ICTV_subset

belongs to
Sibils concept scheme c
has facts
has version dp "MSL39v4"

Licenseni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/License

The SPDX License List itself is a list of commonly found licenses and exceptions used in free and open or collaborative software, data, hardware, or documentation.
belongs to
Sibils concept scheme c
has facts
has version dp "v3.26"

LOTUS Natural Productsni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/LOTUS

LOTUS, one of the biggest and best annotated resources for Natural Products occurrences available free of charge and without any restriction.
belongs to
Sibils concept scheme c
has facts
has version dp "v10"

MDD (Mammal Diversity Database)ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/MDD

Mammal species list with synonyms. An initial taxonomy of accepted names + synonyms based on v1.7 of the Mammal Diversity Database (MDD)
belongs to
Sibils concept scheme c
has facts
has version dp "v1.13"

MeSHni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/MeSH

The Medical Subject Headings (MeSH), provided by the U.S. National Library of Medicine (NLM), is a controlled vocabulary thesaurus used for indexing articles for PubMed. In comparison with specialzed ontologies like the NCIt, MeSH is less granular and easily identified by Natural Language Processing thanks to synonyms.
belongs to
Sibils concept scheme c
has facts
has version dp "v2025"

NCBI Taxonomy Fullni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/NCBI_TaxID

The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.
belongs to
Sibils concept scheme c
has facts
has version dp "v.2025-02-11"

NCBI Taxonomy Modelsni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/NCBI_Model

This terminology was created by the team and includes many species of clinical interest and related code from NCBI taxonomy collection.
belongs to
Sibils concept scheme c
has facts
has version dp "v.2025-02-11"

Ncbitaxon_virusesni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/NCBI_Virus

belongs to
Sibils concept scheme c
has facts
has version dp "v.2025-02-11"

NCI Thesaurusni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/NCIt

The NCI Thesaurus (NCIt) is used for disease mapping. It covers clinical care, translational and basic research, public information and administrative activities. Provided by the National Cancer Institute, this terminology is a standard for biomedical coding and reference, used both by public and private scientific partners worldwide. This NCI's reference terminology contains the NCI_CUI, the semantic type, a prefered term, some NCI and MeSH synonyms.
belongs to
Sibils concept scheme c
has facts
has version dp "v24.12e"

neXtProtni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/nextprot

Developed by the SIB (Swiss Institute of Bioinformatics) in 2008, the neXtProt human protein knowledgebase is a comprehensive human-centric discovery platform. More than 20,000 proteins were manually annotated and still updated. The provides to researchers a high-quality synonym for both protein and gene names.
belongs to
Sibils concept scheme c
has facts
has version dp "v2023-09-11"

OTT (Open Tree of Life)ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/OTT

Open Tree of Life aims to construct a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data. https://doi.org/10.5281/zenodo.3937750
belongs to
Sibils concept scheme c
has facts
has version dp "v3.7.2"

PO (Plant Ontology)ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/PO

The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
belongs to
Sibils concept scheme c
has facts
has version dp "04-18-2024"

PPI-PTMni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/ppiptm

belongs to
Sibils concept scheme c
has facts
has version dp "unknown"

PSI-MIni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/MI

A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.
belongs to
Sibils concept scheme c
has facts
has version dp "v1.2"

Pubchem (Mesh subset)ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/PubChem

Pubchem database, only coumpounds with mesh terms associated. Reconstitution pipeline from FTP, Extras files.
belongs to
Sibils concept scheme c
has facts
has version dp "unknown"

Rheani back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/data/Rhea

belongs to
Citing source c

ROBI (Relation Ontology - Biotic Interactions)ni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/ROBIext

RO is a collection of relations intended primarily for standardization across ontologies in the OBO Foundry and wider OBO library. It incorporates ROCore upper-level relations such as part of as well as biology-specific relationship types such as develops from. We extracted a subset of terms of interest for biotic interactions.
belongs to
Sibils concept scheme c
has facts
has version dp "v2025"

SIBiLS ontologyni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/ontology/

has facts
contributor op 0000 0002 3374 2962 ni
contributor op 0000 0002 7023 1045 ni
contributor op 0000 0003 2209 5218 ni
creator op 0000 0002 7023 1045 ni
abstract dp "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. "
has version dp "dev version - 2025-10-03 19:01:33.733572 - prod"
title dp "SIBiLS ontology"

SwissLipidsni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/data/SwissLipids

belongs to
Citing source c

UniProtKBni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/data/UniProtKB

belongs to
Citing source c

UniProtKB/SwissProtni back to ToC or Named Individual ToC

IRI: https://purl.expasy.org/sibils/rdf/scheme/uniprot

The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. We used a large fraction of the reviewed subset UinProtKB/Swiss-Prot which includes records with information extracted from literature and curator-evaluated computational analysis.
belongs to
Sibils concept scheme c
has facts
has version dp "v11"

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.