SIBiLS ontology
type: Ontology
bibliographic citation: (to be defined)
created: 2025-08-07
description: See https://sparql.sibils.org/rdf-ontology
license: http://creativecommons.org/licenses/by/4.0
modified: 2025-10-03
publisher: www.sib.swiss
status: draft
preferred namespace prefix: sibils
version info: dev version - 2025-10-03 19:01:33.733572 - prod
declare:
  namespace: SIBiLS ontology
  prefix: sibilo
declare:
  namespace: http://local.sibils.org/rdf/concept/
  prefix: sibilc
declare:
  namespace: http://local.sibils.org/rdf/data/
  prefix: sibils
declare:
  namespace: http://local.sibils.org/rdf/scheme/
  prefix: sibilt
declare:
  namespace: http://purl.org/spar/deo/
  prefix: deo
declare:
  namespace: http://purl.org/spar/doco/
  prefix: doco
declare:
  namespace: http://www.essepuntato.it/2008/12/pattern#
  prefix: po
declare:
  namespace: http://www.w3.org/2011/content#
  prefix: cnt
declare:
  namespace: http://www.w3.org/2001/XMLSchema#
  prefix: xsd
declare:
  namespace: http://www.w3.org/1999/02/22-rdf-syntax-ns#
  prefix: rdf
declare:
  namespace: http://www.w3.org/2000/01/rdf-schema#
  prefix: rdfs
declare:
  namespace: http://www.w3.org/2004/02/skos/core#
  prefix: skos
declare:
  namespace: http://www.w3.org/2002/07/owl#
  prefix: owl
declare:
  namespace: http://purl.org/dc/terms/
  prefix: dcterms
declare:
  namespace: http://purl.org/spar/fabio/
  prefix: fabio
declare:
  namespace: http://purl.org/vocab/frbr/core#
  prefix: frbr
declare:
  namespace: http://purl.obolibrary.org/obo/IAO_
  prefix: IAO
declare:
  namespace: http://purl.uniprot.org/core/
  prefix: up
declare:
  namespace: http://purl.org/ontology/bibo/
  prefix: bibo
declare:
  namespace: https://w3id.org/widoco/vocab#
  prefix: widoco
declare:
  namespace: http://purl.org/vocab/vann/
  prefix: vann
declare:
  namespace: http://www.w3.org/ns/oa#
  prefix: oa
declare:
  namespace: http://www.w3.org/ns/shacl#
  prefix: sh
declare:
  namespace: https://schema.org/
  prefix: schema
declare:
  namespace: http://prismstandard.org/namespaces/basic/2.0/
  prefix: prism
declare:
  namespace: https://sparql.sibils.org/
  prefix: help
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 a…
jsonld serialization: ontology.jsonld
nt serialization: ontology.nt
rdfxml serialization: ontology.owl
turtle serialization: ontology.ttl
type: NamedIndividual
contributor: https://orcid.org/0000-0002-3374-2962
contributor: https://orcid.org/0000-0002-7023-1045
contributor: https://orcid.org/0000-0003-2209-5218
creator: https://orcid.org/0000-0002-7023-1045
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 versi…
has version: dev version - 2025-10-03 19:01:33.733572 - prod

see also annotated
type: AnnotationProperty
comment: Provides a link to a URI where the annotated publication can be viewed.
sub property of: seeAlso
range: Resource
domain: Expression

alt label
type: AnnotationProperty
sub property of: label

broad match
type: AnnotationProperty

close match
type: AnnotationProperty

pref label
type: AnnotationProperty
sub property of: label

has annotation
type: ObjectProperty
inverse of: is about
domain: Expression
range: Named Entity Extraction Annotation
comment: Links a publication to an annotation generated by named entity extraction.

more specific than
type: ObjectProperty
sub property of: has broader
domain: Concept
range: Concept
comment: 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.

more specific than transitive
type: ObjectProperty
sub property of: has broader transitive

is about
type: ObjectProperty
comment: A (currently) primitive relation that relates an information artifact to an entity.

contributor
type: ObjectProperty

creator
type: ObjectProperty
sub property of: contributor

has part
type: ObjectProperty
comment: Links a resource that is included either physically or logically in the described resource.

embodiment
type: ObjectProperty
comment: Having a frbr:embodiment implies being something that, amongst other things, is a frbr:Expression

realization of
type: ObjectProperty
comment: Having a frbr:realizationOf implies being something that, amongst other things, is a frbr:Expression

contains
type: ObjectProperty
comment: A structured element contains another generic element.

has broader
type: ObjectProperty

has broader transitive
type: ObjectProperty

affiliation
type: ObjectProperty
sub property of: member of
comment: An organization that this person is affiliated with. For example, a school/university, a club, or a team.

member of
type: ObjectProperty

in collection
type: DatatypeProperty
sub property of: category
domain: Expression
range: string
comment: Within the SIBiLS RDF dataset, publications are grouped into two distinct collections, each reflecting the source from which they were obtained: 'pmc' or 'medline'.

ordinal
type: DatatypeProperty
domain: Discourse element
range: integer
comment: 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.

has DOI
type: DatatypeProperty
sub property of: identifier

ending page
type: DatatypeProperty
comment: Identifies the last page of an entity such as a journal article.

issue identifier
type: DatatypeProperty
sub property of: identifier

keyword
type: DatatypeProperty

page range
type: DatatypeProperty

has publication date
type: DatatypeProperty
comment: The date on which a resource is published or disclosed.

starting page
type: DatatypeProperty
comment: Identifies the first page of an entity such as a journal article.

volume
type: DatatypeProperty
sub property of: identifier
comment: An identifier for a particular volume of a resource, such as a journal or a multi-volume book.

abstract
type: DatatypeProperty

has version
type: DatatypeProperty

identifier
type: DatatypeProperty

is referenced by
type: DatatypeProperty

title
type: DatatypeProperty
equivalent property: name

has National Library of Medicine journal title abbreviation
type: DatatypeProperty
sub property of: identifier
comment: An internal identifier for the abbreviation of the title of journals available from the National Library of Medicine repository.

has PMC identifier
type: DatatypeProperty
sub property of: identifier
comment: PubMedCentral identifier for the resource.

has PubMed identifier
type: DatatypeProperty
sub property of: identifier
comment: PubMed identifier for the resource.

has publication year
type: DatatypeProperty

notation
type: DatatypeProperty
comment: 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.

Character sequence
type: DatatypeProperty
comment: The character sequence of the text content.

end
type: DatatypeProperty
comment: Position of the last character of a range of text in a discourse element.

exact
type: DatatypeProperty
comment: Text representing the annotated concept as found in the discourse element.

has body
type: DatatypeProperty
comment: The object of the relationship is a resource that is a body of the Annotation.

has selector
type: DatatypeProperty
comment: 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.

has source
type: DatatypeProperty
comment: 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.

has target
type: DatatypeProperty
comment: The relationship between an Annotation and its Target.

start
type: DatatypeProperty
comment: Position of the first character of a range of text in a discourse element.

category
type: DatatypeProperty

name
type: DatatypeProperty

Annotation target
type: Class
subclass of: Specific resource
comment: Target of an annotation: a text selection within a subpart of a publication

Citing source
type: Class
comment: A knowledge base, repository, or database that cites publications to support its statements.

Float matter
type: Class
subclass of: Discourse element
comment: 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.

List item block
type: Class
subclass of: Discourse element
comment: A list item part of a document. Usually appears multiple time in a sequence. May be prefixed with a bullet or a number.

Media block
type: Class
subclass of: Discourse element
comment: A reference or link to some media (audio, video) part of a document.

Named Entity Extraction Annotation
type: Class
subclass of: Annotation
comment: A concept identified at a specific position in a discourse element of a publication by a named entity extraction process.

Object id block
type: Class
subclass of: Discourse element
comment: An identifier appearing as a distinct part of a document.

Sibils concept scheme
type: Class
subclass of: Concept scheme
comment: A subclass of skos:ConceptScheme defined as the list of terminologies used to annotate the publications

Speech block
type: Class
subclass of: Discourse element
comment: A dialog or part of dialog appearing as a distinct part of a document.

Statement block
type: Class
subclass of: Discourse element
comment: A statement appearing as a distinct part of a document.

Table cell values
type: Class
subclass of: Word sequence
comment: A concatenation of the values found in the cells of a table separated with a space.

Table column name
type: Class
subclass of: Word sequence
comment: The name given to of a column in a table.

Table footer
type: Class
subclass of: Discourse element
comment: Text appearing at the bottom of a table.

Verse group block
type: Class
subclass of: Discourse element
comment: A block containing one or several verses appearing as a distinct part of a document.

Word sequence
type: Class
subclass of: Discourse element
comment: A super class for sentences, table column names, table cell values or any textual item that is part of a list

Caption
type: Class
subclass of: Discourse element
comment: Caption of a text box.

Discourse element
type: Class
comment: An element of a document that carries out a rhetorical function.

Abstract
type: Class
subclass of: Discourse element
comment: 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.

Appendix
type: Class
subclass of: Discourse element
comment: 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.

Back matter
type: Class
subclass of: Discourse element
comment: The final principle part of a document, in which is usually found the bibliography, index, appendixes, etc.

Block quotation
type: Class
subclass of: Discourse element
comment: 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).

Body matter
type: Class
subclass of: Discourse element
comment: The central principle part of a document, that contains the real content. It may be subdivided hierarchically by the use of chapters and sections.

Captioned box
type: Class
subclass of: Discourse element
comment: A rectangle space within a page that contains an object and its related caption.

Figure box
type: Class
subclass of: Discourse element
comment: A space within a document that contains a figure and its caption.

Front matter
type: Class
subclass of: Discourse element
comment: 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.

Glossary
type: Class
subclass of: Discourse element
comment: 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.

Label
type: Class
subclass of: Discourse element
comment: 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.

List
type: Class
subclass of: Discourse element
comment: List of items

List of agents
type: Class
subclass of: List

List of authors
type: Class
subclass of: List of agents

List of organizations
type: Class
subclass of: List of agents
comment: A list of items each denoting an agent, such as an author, a contributor or an organization, related to a particular publication.

List of references
type: Class
subclass of: List
comment: A list of items each representing a reference to a specific part of the same document, or to another publication.

Paragraph
type: Class
subclass of: Discourse element
comment: 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.

Section
type: Class
subclass of: Discourse element
comment: A logical division of the text, usually numbered and/or titled, which may contain subsections.

Section label
type: Class
subclass of: Discourse element
comment: A block containing a label for the section, that may include the section number.

Sentence
type: Class
subclass of: Word sequence
comment: 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.

Table
type: Class
subclass of: Discourse element
comment: A set of data arranged in cells within rows and columns.

Table box
type: Class
subclass of: Discourse element
comment: A space within a document that contains a table and its caption.

Text box
type: Class
subclass of: Discourse element
comment: 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.

Title
type: Class
subclass of: Discourse element
comment: 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.

Abstract
type: Class
subclass of: Expression
comment: 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.

Addendum
type: Class
subclass of: Expression

Article
type: Class
subclass of: Expression

Bachelor's thesis
type: Class
subclass of: Thesis
comment: has relation skos:broadMatch with Thesis citation
broad match: Thesis citation

Biography
type: Class
subclass of: Work

Book
type: Class
subclass of: Expression

Book chapter
type: Class
subclass of: Chapter
comment: has relation skos:closeMatch with Book chapter citation

Book review
type: Class
subclass of: Review

Brief report
type: Class
subclass of: Report document

Case report
type: Class
subclass of: Report

Chapter
type: Class
subclass of: Expression

Clinical trial report
type: Class
subclass of: Trial report

Comment
type: Class
subclass of: Expression

Conference paper
type: Class
subclass of: Proceedings paper

Correction
type: Class
subclass of: Work

Doctoral thesis
type: Class
subclass of: Thesis
comment: has relation skos:broadMatch with Thesis citation
broad match: Thesis citation

Editorial
type: Class
subclass of: Expression

Expression
type: Class

Journal article
type: Class
subclass of: Article
comment: has relation skos:closeMatch with Journal article citation

Lecture notes
type: Class
subclass of: Expression

Letter
type: Class
subclass of: Expression

Manifestation
type: Class
comment: 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.

Master's thesis
type: Class
subclass of: Thesis
comment: has relation skos:broadMatch with Thesis citation
broad match: Thesis citation

Meeting report
type: Class
subclass of: Report

Methods paper
type: Class
subclass of: Scholarly work

News item
type: Class
subclass of: Expression

Patent document
type: Class
subclass of: Specification document
comment: has relation skos:closeMatch with Patent citation

Proceedings paper
type: Class
subclass of: Expression

Product review
type: Class
subclass of: Review

Rapid communication
type: Class
subclass of: Expression

Report
type: Class
subclass of: Work

Report document
type: Class
subclass of: Expression

Review
type: Class
subclass of: Work

Review article
type: Class
subclass of: Article

Scholarly work
type: Class
subclass of: Work

Specification document
type: Class
subclass of: Expression

Systematic review
type: Class
subclass of: Review

Technical report
type: Class
subclass of: Report

Thesis
type: Class
subclass of: Book
comment: has relation skos:closeMatch with Thesis citation

Trial report
type: Class
subclass of: Report

Work
type: Class

Book chapter citation
type: Class

Journal article citation
type: Class

Patent citation
type: Class

Thesis citation
type: Class

Concept
type: Class

Concept scheme
type: Class

Annotation
type: Class
comment: The class for Web Annotations.

Specific resource
type: Class
comment: 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.

Text position selector
type: Class
comment: 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.

Organization
type: Class

Person
type: Class

Cellosaurus
type: NamedIndividual
type: Citing source

Rhea
type: NamedIndividual
type: Citing source

SwissLipids
type: NamedIndividual
type: Citing source

UniProtKB
type: NamedIndividual
type: Citing source

Agrovoc
type: NamedIndividual
type: Sibils concept scheme
has version: v2024-06-04
comment: 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.

ATC
type: NamedIndividual
type: Sibils concept scheme
has version: v2024AB
comment: 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.

ChEBI
type: NamedIndividual
type: Sibils concept scheme
has version: v239
comment: 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.

Cell Ontology
type: NamedIndividual
type: Sibils concept scheme
has version: 2025-01-07
comment: The Cell Ontology is a structured controlled vocabulary for cell types in animals.

COVOC BioMedical Vocabulary
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0
comment: 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.

COVOC Conceptual Entities
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0
comment: 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.

COVOC Cell Lines
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0
comment: 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.

COVOC Clinical trials
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0
comment: 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.

COVOC Chemicals
type: NamedIndividual
type: Sibils concept scheme
has version: v2.0
comment: 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.

COVOC Disease and Syndrome
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0
comment: 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.

COVOC Geographic Location
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0
comment: 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.

COVOC Protein and Genome
type: NamedIndividual
type: Sibils concept scheme
has version: v2.0
comment: 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.

COVOC Organism
type: NamedIndividual
type: Sibils concept scheme
has version: v2.0
comment: 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.

Cellosaurus
type: NamedIndividual
type: Sibils concept scheme
has version: 51.0
comment: 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

Detection methods
type: NamedIndividual
type: Sibils concept scheme
has version: v2022
comment: List of methods used to detect or study viruses in a corpus of scientific texts.

Disprot_type1
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0

Disprot_type2
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0

Disprot_type3
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0

Disprot
type: NamedIndividual
type: Sibils concept scheme
has version: v1.0

Drugbank
type: NamedIndividual
type: Sibils concept scheme
has version: v5.1.13
comment: 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.

ECO - Evidence & Conclusion Ontology
type: NamedIndividual
type: Sibils concept scheme
has version: v2024-07-19
comment: 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.

ENVO - Environment Ontology
type: NamedIndividual
type: Sibils concept scheme
has version: v2024-07-01
comment: 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.

Flopo
type: NamedIndividual
type: Sibils concept scheme
has version: 2025-01-28
comment: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.

GO Biological Process
type: NamedIndividual
type: Sibils concept scheme
has version: v2024-11-03
comment: 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.

GO Cellular Component
type: NamedIndividual
type: Sibils concept scheme
has version: v2024-11-03
comment: 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.

GO Molecular Function
type: NamedIndividual
type: Sibils concept scheme
has version: v2024-11-03
comment: 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.

ICD-O-3
type: NamedIndividual
type: Sibils concept scheme
has version: unknown
comment: 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).

ICTV (International Committee on Taxonomy of Viruses)
type: NamedIndividual
type: Sibils concept scheme
has version: MSL39v4
comment: 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.

Ictv_subset
type: NamedIndividual
type: Sibils concept scheme
has version: MSL39v4

LOTUS Natural Products
type: NamedIndividual
type: Sibils concept scheme
has version: v10
comment: LOTUS, one of the biggest and best annotated resources for Natural Products occurrences available free of charge and without any restriction.

License
type: NamedIndividual
type: Sibils concept scheme
has version: v3.26
comment: 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.

MDD (Mammal Diversity Database)
type: NamedIndividual
type: Sibils concept scheme
has version: v1.13
comment: Mammal species list with synonyms. An initial taxonomy of accepted names + synonyms based on v1.7 of the Mammal Diversity Database (MDD)

PSI-MI
type: NamedIndividual
type: Sibils concept scheme
has version: v1.2
comment: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.

MeSH
type: NamedIndividual
type: Sibils concept scheme
has version: v2025
comment: 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.

NCBI Taxonomy Models
type: NamedIndividual
type: Sibils concept scheme
has version: v.2025-02-11
comment: This terminology was created by the team and includes many species of clinical interest and related code from NCBI taxonomy collection.

NCBI Taxonomy Full
type: NamedIndividual
type: Sibils concept scheme
has version: v.2025-02-11
comment: The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.

Ncbitaxon_viruses
type: NamedIndividual
type: Sibils concept scheme
has version: v.2025-02-11

NCI Thesaurus
type: NamedIndividual
type: Sibils concept scheme
has version: v24.12e
comment: 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.

OTT (Open Tree of Life)
type: NamedIndividual
type: Sibils concept scheme
has version: v3.7.2
comment: 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

PO (Plant Ontology)
type: NamedIndividual
type: Sibils concept scheme
has version: 04-18-2024
comment: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.

Pubchem (Mesh subset)
type: NamedIndividual
type: Sibils concept scheme
has version: unknown
comment: Pubchem database, only coumpounds with mesh terms associated. Reconstitution pipeline from FTP, Extras files.

ROBI (Relation Ontology - Biotic Interactions)
type: NamedIndividual
type: Sibils concept scheme
has version: v2025
comment: 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.

Affiliations
type: NamedIndividual
type: Sibils concept scheme
has version: v2025-01-23
comment: A list of international research institutes.

neXtProt
type: NamedIndividual
type: Sibils concept scheme
has version: v2023-09-11
comment: 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.

PPI-PTM
type: NamedIndividual
type: Sibils concept scheme
has version: unknown

UniProtKB/SwissProt
type: NamedIndividual
type: Sibils concept scheme
has version: v11
comment: 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.

exact match

in scheme