See https://sparql.sibils.org/rdf-ontology
**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: | http://local.sibils.org/rdf/data/ | SIBiLS data | | sibilo: | http://local.sibils.org/rdf/ontology/ | SIBiLS ontology classes and properties | | sibilt: | http://local.sibils.org/rdf/scheme/ | SIBiLS terminologies | | sibilc: | http://local.sibils.org/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 |
Provides a link to a URI where the annotated publication can be viewed.
Links a publication to an annotation generated by named entity extraction.
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.
A (currently) primitive relation that relates an information artifact to an entity.
Links a resource that is included either physically or logically in the described resource.
Having a frbr:embodiment implies being something that, amongst other things, is a frbr:Expression
Having a frbr:realizationOf implies being something that, amongst other things, is a frbr:Expression
A structured element contains another generic element.
An organization that this person is affiliated with. For example, a school/university, a club, or a team.
Within the SIBiLS RDF dataset, publications are grouped into two distinct collections, each reflecting the source from which they were obtained: 'pmc' or 'medline'.
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.
Identifies the last page of an entity such as a journal article.
The date on which a resource is published or disclosed.
Identifies the first page of an entity such as a journal article.
An identifier for a particular volume of a resource, such as a journal or a multi-volume book.
An internal identifier for the abbreviation of the title of journals available from the National Library of Medicine repository.
has National Library of Medicine journal title abbreviation
PubMedCentral identifier for the resource.
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.
The character sequence of the text content.
Position of the last character of a range of text in a discourse element.
Text representing the annotated concept as found in the discourse element.
The object of the relationship is a resource that is a body of the Annotation.
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.
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.
The relationship between an Annotation and its Target.
Position of the first character of a range of text in a discourse element.
Target of an annotation: a text selection within a subpart of a publication
A knowledge base, repository, or database that cites publications to support its statements.
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.
A list item part of a document. Usually appears multiple time in a sequence. May be prefixed with a bullet or a number.
A reference or link to some media (audio, video) part of a document.
A concept identified at a specific position in a discourse element of a publication by a named entity extraction process.
An identifier appearing as a distinct part of a document.
A subclass of skos:ConceptScheme defined as the list of terminologies used to annotate the publications
A dialog or part of dialog appearing as a distinct part of a document.
A statement appearing as a distinct part of a document.
A concatenation of the values found in the cells of a table separated with a space.
The name given to of a column in a table.
Text appearing at the bottom of a table.
A block containing one or several verses appearing as a distinct part of a document.
A super class for sentences, table column names, table cell values or any textual item that is part of a list
An element of a document that carries out a rhetorical function.
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.
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.
The final principle part of a document, in which is usually found the bibliography, index, appendixes, etc.
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).
The central principle part of a document, that contains the real content. It may be subdivided hierarchically by the use of chapters and sections.
A rectangle space within a page that contains an object and its related caption.
A space within a document that contains a figure and its caption.
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.
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.
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.
A list of items each denoting an agent, such as an author, a contributor or an organization, related to a particular publication.
A list of items each representing a reference to a specific part of the same document, or to another publication.
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.
A logical division of the text, usually numbered and/or titled, which may contain subsections.
A block containing a label for the section, that may include the section number.
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.
A set of data arranged in cells within rows and columns.
A space within a document that contains a table and its caption.
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.
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 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.
has relation skos:broadMatch with Thesis citation
has relation skos:closeMatch with Book chapter citation
has relation skos:closeMatch with Journal article citation
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.
has relation skos:closeMatch with Patent citation
has relation skos:closeMatch with Thesis citation
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.
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.
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.
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.
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.
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.
The Cell Ontology is a structured controlled vocabulary for cell types in animals.
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.
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
List of methods used to detect or study viruses in a corpus of scientific texts.
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.
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 is an expressive, community ontology which helps humans, machines, and semantic web applications understand environmental entities of all kinds, from microscopic to intergalactic scales.
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.
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.
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.
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.
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).
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 (International Committee on Taxonomy of Viruses)
LOTUS, one of the biggest and best annotated resources for Natural Products occurrences available free of charge and without any restriction.
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.
Mammal species list with synonyms. An initial taxonomy of accepted names + synonyms based on v1.7 of the Mammal Diversity Database (MDD)
A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.
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.
This terminology was created by the team and includes many species of clinical interest and related code from NCBI taxonomy collection.
The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.
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.
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
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
Pubchem database, only coumpounds with mesh terms associated. Reconstitution pipeline from FTP, Extras files.
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.
ROBI (Relation Ontology - Biotic Interactions)
A list of international research institutes.
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.
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.