made by pyLODE 2.13.2

SIBiLS ontology

Metadata

URI
http://sibils.org/rdf
Created
2022-11-01
Modified
2023-07-11
Version Information
Current release
Imports
deo:
doco:
fabio:
po:
skos:
License
http://creativecommons.org/licenses/by/4.0
Ontology RDF
RDF (turtle)

Description

The SIBiLS ontology is used to represent annotated scientific publications

Table of Contents

  1. Classes
  2. Object Properties
  3. Datatype Properties
  4. Named Individuals
  5. Namespaces
  6. Legend

Overview

Pictures say 1,000 words
Figure 1: Ontology overview

Classes

Abstractc # Classes

URI http://sibils.org/rdf#Abstract
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes doco:Abstractc
Discourse elementc

Annotationc # Classes

URI http://sibils.org/rdf#Annotation
Is Defined By http://sibils.org/rdf
Description

A concept identified at a specific position in a discourse element of a publication by a named entity extraction process.

Super-classes oa:Annotationc
In domain of has bodyop
has targetop
In range of has annotationop

Annotation targetc # Classes

URI http://sibils.org/rdf#AnnotationTarget
Is Defined By http://sibils.org/rdf
Description

Location of the annotation in a discourse element.

In domain of has selectorop
has sourceop
In range of has targetop

Appendixc # Classes

URI http://sibils.org/rdf#Appendix
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes doco:Appendixc
Discourse elementc

Back matterc # Classes

URI http://sibils.org/rdf#BackMatter
Is Defined By http://sibils.org/rdf
Description

The final principle part of a document, in which is usually found the bibliography, index, appendixes, etc.

Super-classes doco:BackMatterc
Discourse elementc

Blockc # Classes

URI http://sibils.org/rdf#Block
Is Defined By http://sibils.org/rdf
Description
Super-classes po:Blockc
Sub-classes Object id blockc
Block quotationc
Statement blockc
Figure boxc
Tablec
Verse group blockc
List item blockc
Table boxc
Speech blockc
Paragraphc
Glossaryc
List of referencesc
Media blockc

Block quotationc # Classes

URI http://sibils.org/rdf#BlockQuotation
Is Defined By http://sibils.org/rdf
Description

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).

Super-classes Blockc
Discourse elementc
doco:BlockQuotationc

Body matterc # Classes

URI http://sibils.org/rdf#BodyMatter
Is Defined By http://sibils.org/rdf
Description

The central principle part of a document, that contains the real content. It may be subdivided hierarchically by the use of chapters and sections.

Super-classes doco:BodyMatterc
Discourse elementc

Brief reportc # Classes

URI http://sibils.org/rdf#BriefReport
Is Defined By http://sibils.org/rdf
Description

A brief report document. This term may also be used synonymously with Rapid Communication to mean 'A short rapidly published research article or conference paper, typically reporting significant research results that have been recently discovered, or a brief news item reporting such discoveries.'

Super-classes fabio:BriefReportc
Publicationc

Captionc # Classes

URI http://sibils.org/rdf#Caption
Is Defined By http://sibils.org/rdf
Description

Caption of a text box.

Super-classes deo:Captionc
Discourse elementc

Captioned boxc # Classes

URI http://sibils.org/rdf#CaptionedBox
Is Defined By http://sibils.org/rdf
Description

A rectangle space within a page that contains an object and its related caption.

Super-classes doco:CaptionedBoxc
Discourse elementc

Case reportc # Classes

URI http://sibils.org/rdf#CaseReport
Is Defined By http://sibils.org/rdf
Description

A report about a particular case or situation.

Super-classes fabio:CaseReportc
Publicationc

Discourse elementc # Classes

URI http://sibils.org/rdf#DiscourseElement
Is Defined By http://sibils.org/rdf
Description

An element of a document that carries out a rhetorical function.

Super-classes deo:DiscourseElementc
Sub-classes Front matterc
Float matterc
Sentencec
Sequence of wordsc
Table cell valuesc
Text boxc
Table boxc
Media blockc
Speech blockc
Paragraphc
Glossaryc
Sectionc
Statement blockc
Figure boxc
List of referencesc
Section labelc
Titlec
Captioned boxc
Labelc
Object id blockc
Captionc
Appendixc
Verse group blockc
Block quotationc
Back matterc
Abstractc
List item blockc
Body matterc
Table column namec
Tablec
In domain of containsop
charsop
creatorop
In range of containsop
has sourceop
creatorop

Editorialc # Classes

URI http://sibils.org/rdf#Editorial
Is Defined By http://sibils.org/rdf
Description

The realization of an opinion written by an editor.

Super-classes Publicationc
fabio:Editorialc

Figure boxc # Classes

URI http://sibils.org/rdf#FigureBox
Is Defined By http://sibils.org/rdf
Description

A space within a document that contains a figure and its caption.

Super-classes Blockc
doco:FigureBoxc
Discourse elementc

Float matterc # Classes

URI http://sibils.org/rdf#FloatMatter
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes Discourse elementc

Front matterc # Classes

URI http://sibils.org/rdf#FrontMatter
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes Discourse elementc
doco:FrontMatterc

Glossaryc # Classes

URI http://sibils.org/rdf#Glossary
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes doco:Glossaryc
Discourse elementc
Blockc

Journal articlec # Classes

URI http://sibils.org/rdf#JournalArticle
Is Defined By http://sibils.org/rdf
Description

An article, typically the realization of a research paper reporting original research findings, published in a journal issue.

Super-classes Publicationc
fabio:c

Labelc # Classes

URI http://sibils.org/rdf#Label
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes doco:Labelc
Discourse elementc

Letterc # Classes

URI http://sibils.org/rdf#Letter
Is Defined By http://sibils.org/rdf
Description

A written or printed communication of a personal or professional nature between individuals and/or representatives of corporate bodies, usually transmitted by the postal service or published in a periodical. In the latter case, the letter is typically addressed to the editor and comments on or discussed an item previously published by that periodical, or of interest to its readership.

Super-classes Publicationc
fabio:JournalArticlec

List item blockc # Classes

URI http://sibils.org/rdf#ListItemBlock
Is Defined By http://sibils.org/rdf
Description

A list item part of a document. Usually appears multiple time in a sequence. May be prefixed with a bullet or a number.

Super-classes Blockc
Discourse elementc

List of referencesc # Classes

URI http://sibils.org/rdf#ListOfReferences
Is Defined By http://sibils.org/rdf
Description

A list of items each representing a reference to a specific part of the same document, or to another publication.

Super-classes doco:ListOfReferencesc
Discourse elementc
Blockc

Manifestationc # Classes

URI http://sibils.org/rdf#Manifestation
Is Defined By http://sibils.org/rdf
Description

A subclass of fabio manifestation. Specifically applies to electronic (digital) as well as to physical manifestations of expressions.

Super-classes fabio:Manifestationc
In range of embodimentop

Media blockc # Classes

URI http://sibils.org/rdf#MediaBlock
Is Defined By http://sibils.org/rdf
Description

A reference or link to some media (audio, video) part of a document.

Super-classes Discourse elementc
Blockc

Meeting reportc # Classes

URI http://sibils.org/rdf#MeetingReport
Is Defined By http://sibils.org/rdf
Description

A report of a meeting of some kind.

Super-classes fabio:MeetingReportc
Publicationc

Object id blockc # Classes

URI http://sibils.org/rdf#ObjectIdBlock
Is Defined By http://sibils.org/rdf
Description

An identifier appearing as a distinct part of a document.

Super-classes Blockc
Discourse elementc

Paragraphc # Classes

URI http://sibils.org/rdf#Paragraph
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes doco:Paragraphc
Discourse elementc
Blockc

Publicationc # Classes

URI http://sibils.org/rdf#Publication
Is Defined By http://sibils.org/rdf
Description

A subclass of fabio expression, restricted to publications in SIBiLS.

Super-classes fabio:Expressionc
Sub-classes Letterc
Journal articlec
Editorialc
Review articlec
Brief reportc
Meeting reportc
Case reportc
In domain of issue identifier pagedp
titledp
keyworddp
has publication yeardp
ending pagedp
abstractdp
has NLM journal title abbreviationdp
creatorop
page rangedp
doidp
starting pagedp
has PubMed iddp
volumedp
publication datedp
embodimentop
has annotationop
has PubMed Central iddp

Review articlec # Classes

URI http://sibils.org/rdf#ReviewArticle
Is Defined By http://sibils.org/rdf
Description

An article that contains a review.

Super-classes fabio:ReviewArticlec
Publicationc

Sectionc # Classes

URI http://sibils.org/rdf#Section
Is Defined By http://sibils.org/rdf
Description

A logical division of the text, usually numbered and/or titled, which may contain subsections.

Super-classes doco:Sectionc
Discourse elementc

Section labelc # Classes

URI http://sibils.org/rdf#SectionLabel
Is Defined By http://sibils.org/rdf
Description

A block containing a label for the section, that may include the section number.

Super-classes doco:SectionLabelc
Discourse elementc

Sentencec # Classes

URI http://sibils.org/rdf#Sentence
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes Discourse elementc
Sequence of wordsc
doco:Sentencec

SIBiLS Terminologyc # Classes

URI http://sibils.org/rdf#SibilsTerminology
Is Defined By http://sibils.org/rdf#
Description

SIBiLS Terminology scheme containing the concepts used for annotating the publications.

Super-classes skos:ConceptSchemec
Members http://sibils.org/rdf#cellosaurus
http://sibils.org/rdf#covocdiseaseandsyndrom
http://sibils.org/rdf#covocbiomed
http://sibils.org/rdf#nextprot
http://sibils.org/rdf#drugbank
http://sibils.org/rdf#covocgeographicloc
http://sibils.org/rdf#ictv
http://sibils.org/rdf#covoccelllines
http://sibils.org/rdf#icdo3
http://sibils.org/rdf#disprot_type3
http://sibils.org/rdf#covocproteinsgenomes
http://sibils.org/rdf#robi
http://sibils.org/rdf#covocchemicals
http://sibils.org/rdf#go_mf
http://sibils.org/rdf#envo
http://sibils.org/rdf#disprot_type2
http://sibils.org/rdf#ncbitaxon_clinic
http://sibils.org/rdf#atc
http://sibils.org/rdf#covocconceptualentities
http://sibils.org/rdf#go_cc
http://sibils.org/rdf#detectionmethods
http://sibils.org/rdf#go_bp
http://sibils.org/rdf#mdd
http://sibils.org/rdf#covocorganism
http://sibils.org/rdf#eco
http://sibils.org/rdf#ppiptm
http://sibils.org/rdf#disprot_type1
http://sibils.org/rdf#ncbitaxon_full
http://sibils.org/rdf#disprot_type4
http://sibils.org/rdf#chebi
http://sibils.org/rdf#mesh
http://sibils.org/rdf#uniprot_small
http://sibils.org/rdf#covocclinicaltrials
http://sibils.org/rdf#ncit
http://sibils.org/rdf#ott

Speech blockc # Classes

URI http://sibils.org/rdf#SpeechBlock
Is Defined By http://sibils.org/rdf
Description

A dialog or part of dialog appearing as a distinct part of a document.

Super-classes Discourse elementc
Blockc

Statement blockc # Classes

URI http://sibils.org/rdf#StatementBlock
Is Defined By http://sibils.org/rdf
Description

A statement appearing as a distinct part of a document.

Super-classes Blockc
Discourse elementc

Tablec # Classes

URI http://sibils.org/rdf#Table
Is Defined By http://sibils.org/rdf
Description

A set of data arranged in cells within rows and columns.

Super-classes Blockc
doco:Tablec
Discourse elementc

Table boxc # Classes

URI http://sibils.org/rdf#TableBox
Is Defined By http://sibils.org/rdf
Description

A space within a document that contains a table and its caption.

Super-classes Discourse elementc
Blockc
doco:TableBoxc

Table cell valuesc # Classes

URI http://sibils.org/rdf#TableCellValues
Is Defined By http://sibils.org/rdf
Description

A concatenation of the values found in the cells of a table separated with a space.

Super-classes Discourse elementc
Sequence of wordsc

Table column namec # Classes

URI http://sibils.org/rdf#TableColumnName
Is Defined By http://sibils.org/rdf
Description

The name given to of a column in a table.

Super-classes Sequence of wordsc
Discourse elementc

Text boxc # Classes

URI http://sibils.org/rdf#TextBox
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes Discourse elementc
doco:TextBoxc

Text position selectorc # Classes

URI http://sibils.org/rdf#TextPositionSelector
Is Defined By http://sibils.org/rdf
Description

A range ot text in a discourse element defined by a start and end position.

Super-classes http://sibils.org/rdf#oa:TextPositionSelectorc
In domain of enddp
startdp
enddp
In range of has selectorop

Titlec # Classes

URI http://sibils.org/rdf#Title
Is Defined By http://sibils.org/rdf
Description

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.

Super-classes doco:Titlec
Discourse elementc

Verse group blockc # Classes

URI http://sibils.org/rdf#VerseGroupBlock
Is Defined By http://sibils.org/rdf
Description

A block containing one or several verses appearing as a distinct part of a document.

Super-classes Blockc
Discourse elementc

Sequence of wordsc # Classes

URI http://sibils.org/rdf#WordSequence
Is Defined By http://sibils.org/rdf
Description

A super class for sentences, table column names and table cell values

Super-classes Discourse elementc
Sub-classes Table column namec
Sentencec
Table cell valuesc
In domain of ordinaldp

Object Properties

charsop # OPs

URI http://sibils.org/rdf#chars
Is Defined By http://sibils.org/rdf
Description

The character sequence of a discourse element.

Super-properties cnt:chars
Domain(s) Discourse elementc
Range(s) xsd:stringc

containsop # OPs

URI http://sibils.org/rdf#contains
Is Defined By http://sibils.org/rdf
Description

Relationships between a discourse element containing another one.

Super-properties po:contains
Domain(s) Discourse elementc
Range(s) http://sibils.org/rdf#DiscourseElementc

creatorop # OPs

URI http://sibils.org/rdf#creator
Is Defined By http://sibils.org/rdf
Description

Links a publication to a person involved in its creation.

Super-properties dcterms:creator
Domain(s) Publicationc
Range(s) foaf:Personc

embodimentop # OPs

URI http://sibils.org/rdf#embodiment
Is Defined By http://sibils.org/rdf
Description

Links a publication to its manifestation.

Super-properties frbr:embodiment
Domain(s) Publicationc
Range(s) http://sibils.org/rdf#Manifestationc

has annotationop # OPs

URI http://sibils.org/rdf#hasAnnotation
Is Defined By http://sibils.org/rdf
Description

Links a publication to an annotation generated by named entity extraction.

Domain(s) Publicationc
Range(s) http://sibils.org/rdf#Annotationc

has bodyop # OPs

URI http://sibils.org/rdf#hasBody
Is Defined By http://sibils.org/rdf
Description

Annotation body. The property object is a concept.

Super-properties oa:hasBody
Domain(s) Annotationc
Range(s) skos:Conceptc

creatorop # OPs

URI http://sibils.org/rdf#hasPart
Is Defined By http://sibils.org/rdf
Description

Links a resource that is included either physically or logically in the described resource.

Super-properties dcterms:hasPart
Domain(s) Discourse elementc
Range(s) http://sibils.org/rdf#DiscourseElementc

has selectorop # OPs

URI http://sibils.org/rdf#hasSelector
Is Defined By http://sibils.org/rdf
Description

Annotation selector. The property object is a selector defining a range of text in a discourse element.

Super-properties oa:hasSelector
Domain(s) Annotation targetc
Range(s) http://sibils.org/rdf#TextPositionSelectorc

has sourceop # OPs

URI http://sibils.org/rdf#hasSource
Is Defined By http://sibils.org/rdf
Description

Source of the annotation. The property object is a discourse element.

Super-properties oa:hasSource
Domain(s) Annotation targetc
Range(s) http://sibils.org/rdf#DiscourseElementc

has targetop # OPs

URI http://sibils.org/rdf#hasTarget
Is Defined By http://sibils.org/rdf
Description

Annotation target. The property object defines the positional coordinates of the annotation concept in a discourse element.

Super-properties oa:hasTarget
Domain(s) Annotationc
Range(s) http://sibils.org/rdf#AnnotationTargetc

Datatype Properties

abstractdp # DPs

URI http://sibils.org/rdf#abstract
Is Defined By http://sibils.org/rdf
Description

Links a publication to its abstract as a string.

Super-properties dcterms:abstract
Domain(s) Publicationc
Range(s) xsd:stringc

affiliationdp # DPs

URI http://sibils.org/rdf#affiliation
Is Defined By http://sibils.org/rdf
Description

Links a person, usually an author, to an organization they are affiliated to.

Domain(s) foaf:Personc
Range(s) xsd:stringc

doidp # DPs

URI http://sibils.org/rdf#doi
Is Defined By http://sibils.org/rdf
Description

Links a publication to its Digital Object Identifier.

Super-properties prism:doi
Domain(s) Publicationc
Range(s) xsd:stringc

enddp # DPs

URI http://sibils.org/rdf#end
Is Defined By http://sibils.org/rdf
Description

Position of the last character of a range of text in a discourse element.

Super-properties oa:end
Domain(s) Text position selectorc
Range(s) xsd:integerc

ending pagedp # DPs

URI http://sibils.org/rdf#endingPage
Is Defined By http://sibils.org/rdf
Description

Links a publication to the last page of the journal containing it.

Super-properties prism:endingPage
Domain(s) Publicationc
Range(s) xsd:stringc

enddp # DPs

URI http://sibils.org/rdf#exact
Is Defined By http://sibils.org/rdf
Description

Text representing the annotated concept as found in the discourse element.

Super-properties oa:exact
Domain(s) Text position selectorc
Range(s) xsd:stringc

has NLM journal title abbreviationdp # DPs

URI http://sibils.org/rdf#hasNLMJournalTitleAbbreviation
Is Defined By http://sibils.org/rdf
Description

Links a publication to an internal identifier for the abbreviation of the title of journals available from the National Library of Medicine repositoryn.

Super-properties fabio:hasNLMJournalTitleAbbreviation
Domain(s) Publicationc
Range(s) xsd:stringc

has PubMed Central iddp # DPs

URI http://sibils.org/rdf#hasPubMedCentralId
Is Defined By http://sibils.org/rdf
Description

Links a publication to an identifier for bibliographic entities hosted by the PubMed Central repository.

Super-properties fabio:hasPubMedCentralId
Domain(s) Publicationc
Range(s) xsd:stringc

has PubMed iddp # DPs

URI http://sibils.org/rdf#hasPubMedId
Is Defined By http://sibils.org/rdf
Description

Links a publication to an identifier for bibliographic records held by the PubMed repository.

Super-properties fabio:hasPubMedId
Domain(s) Publicationc
Range(s) xsd:stringc

has publication yeardp # DPs

URI http://sibils.org/rdf#hasPublicationYear
Is Defined By http://sibils.org/rdf
Description

Links a publication to the year in which it was published.

Super-properties fabio:hasPublicationYear
Domain(s) Publicationc
Range(s) xsd:integerc

issue identifier pagedp # DPs

URI http://sibils.org/rdf#issueIdentifier
Is Defined By http://sibils.org/rdf
Description

Links a publication to an identifier used to identify a specific issue of a magazine, a journal or other resource.

Super-properties prism:issueIdentifier
Domain(s) Publicationc
Range(s) xsd:stringc

keyworddp # DPs

URI http://sibils.org/rdf#keyword
Is Defined By http://sibils.org/rdf
Description

Links a publication with a keyword that is likely to be used in search queries.

Super-properties prism:endingkeywordPage
Domain(s) Publicationc
Range(s) xsd:stringc

ordinaldp # DPs

URI http://sibils.org/rdf#ordinal
Is Defined By http://sibils.org/rdf
Description

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.

Domain(s) Sequence of wordsc
Range(s) xsd:integerc

page rangedp # DPs

URI http://sibils.org/rdf#pageRange
Is Defined By http://sibils.org/rdf
Description

Links a publication to the pages of a journal where it appears.

Super-properties prism:pageRange
Domain(s) Publicationc
Range(s) xsd:stringc

publication datedp # DPs

URI http://sibils.org/rdf#publicationDate
Is Defined By http://sibils.org/rdf
Description

Links a publication to its publication date.

Super-properties prism:publicationDate
Domain(s) Publicationc
Range(s) xsd:datec

startdp # DPs

URI http://sibils.org/rdf#start
Is Defined By http://sibils.org/rdf
Description

Position of the first character of a range of text in a discourse element.

Super-properties oa:start
Domain(s) Text position selectorc
Range(s) xsd:integerc

starting pagedp # DPs

URI http://sibils.org/rdf#startingPage
Is Defined By http://sibils.org/rdf
Description

Links a publication to the first page of the journal containing it

Super-properties prism:startingPage
Domain(s) Publicationc
Range(s) xsd:stringc

titledp # DPs

URI http://sibils.org/rdf#title
Is Defined By http://sibils.org/rdf
Description

Links a publication to its title.

Super-properties dcterms:title
Domain(s) Publicationc
Range(s) xsd:stringc

volumedp # DPs

URI http://sibils.org/rdf#volume
Is Defined By http://sibils.org/rdf
Description

Links a publication to an identifier for a particular volume of a resource, such as a journal or a multi-volume book.

Super-properties prism:volume
Domain(s) Publicationc
Range(s) xsd:stringc

Named Individuals

ATCni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#atc
Is Defined By http://sibils.org/rdf#
Description 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 classify in the ATC system.

Cellosaurusni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#cellosaurus
Is Defined By http://sibils.org/rdf#
Description xxx

CheBI (Chemical Entities of Biological Interest)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#chebi
Is Defined By http://sibils.org/rdf#
Description 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.

COVoc Biomedicalni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#covocbiomed
Is Defined By http://sibils.org/rdf#
Description 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 linesni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#covoccelllines
Is Defined By http://sibils.org/rdf#
Description 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 Chemicalsni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#covocchemicals
Is Defined By http://sibils.org/rdf#
Description 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 Trialsni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#covocclinicaltrials
Is Defined By http://sibils.org/rdf#
Description 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 Entitiesni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#covocconceptualentities
Is Defined By http://sibils.org/rdf#
Description 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 Syndromeni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#covocdiseaseandsyndrom
Is Defined By http://sibils.org/rdf#
Description 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 Locationni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#covocgeographicloc
Is Defined By http://sibils.org/rdf#
Description 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 Organismni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#covocorganism
Is Defined By http://sibils.org/rdf#
Description 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 Genomeni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#covocproteinsgenomes
Is Defined By http://sibils.org/rdf#
Description 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.

Detection methodsni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#detectionmethods
Is Defined By http://sibils.org/rdf#
Description List of methods used to detect or study viruses in a corpus of scientific texts.

Disprotni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#disprot_type1
Is Defined By http://sibils.org/rdf#
Description xxx

Disprotni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#disprot_type2
Is Defined By http://sibils.org/rdf#
Description xxx

Disprotni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#disprot_type3
Is Defined By http://sibils.org/rdf#
Description xxx

Disprotni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#disprot_type4
Is Defined By http://sibils.org/rdf#
Description xxx

Drugbankni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#drugbank
Is Defined By http://sibils.org/rdf#
Description 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 and Conclusion Ontology)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#eco
Is Defined By http://sibils.org/rdf#
Description 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)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#envo
Is Defined By http://sibils.org/rdf#
Description 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.

GO (Gene Ontology)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#go_bp
Is Defined By http://sibils.org/rdf#
Description 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 (Gene Ontology)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#go_cc
Is Defined By http://sibils.org/rdf#
Description 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.

GO (Gene Ontology)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#go_mf
Is Defined By http://sibils.org/rdf#
Description 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.

ICD-O-3ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#icdo3
Is Defined By http://sibils.org/rdf#
Description 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)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#ictv
Is Defined By http://sibils.org/rdf#
Description 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.

MDD (Mammal Diversity Database)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#mdd
Is Defined By http://sibils.org/rdf#
Description Mammal species list with synonyms. An initial taxonomy of accepted names + synonyms based on v1.7 of the Mammal Diversity Database (MDD)

MeSHni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#mesh
Is Defined By http://sibils.org/rdf#
Description 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 Clinicni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#ncbitaxon_clinic
Is Defined By http://sibils.org/rdf#
Description This terminology was created by the team and includes many species of clinical interest and related code from NCBI taxonomy collection.

NCBI Taxonomy Fullni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#ncbitaxon_full
Is Defined By http://sibils.org/rdf#
Description The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.

NCI Thesaurusni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#ncit
Is Defined By http://sibils.org/rdf#
Description 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.

neXtProtni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#nextprot
Is Defined By http://sibils.org/rdf#
Description 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.

OTT (Open Tree of Life)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#ott
Is Defined By http://sibils.org/rdf#
Description 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

PPI-PTMni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#ppiptm
Is Defined By http://sibils.org/rdf#
Description xxx

ROBI (Relation Ontology - Biotic Interactions)ni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#robi
Is Defined By http://sibils.org/rdf#
Description 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.

UniProtKB/SwissProtni

Class(es)
http://sibils.org/rdf#SibilsTerminology
URI http://sibils.org/rdf#uniprot_small
Is Defined By http://sibils.org/rdf#
Description 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.

Namespaces

default (:)
http://sibils.org/rdf
brick
https://brickschema.org/schema/Brick#
cnt
http://www.w3.org/2011/content#
csvw
http://www.w3.org/ns/csvw#
dc
http://purl.org/dc/elements/1.1/
dcam
http://purl.org/dc/dcam/
dcat
http://www.w3.org/ns/dcat#
dcmitype
http://purl.org/dc/dcmitype/
dcterms
http://purl.org/dc/terms/
deo
http://purl.org/spar/deo/
doap
http://usefulinc.com/ns/doap#
doco
http://purl.org/spar/doco/
fabio
http://purl.org/spar/fabio/
foaf
http://xmlns.com/foaf/0.1/
frbr
http://purl.org/vocab/frbr/core#
oa
http://www.w3.org/ns/oa#
odrl
http://www.w3.org/ns/odrl/2/
org
http://www.w3.org/ns/org#
owl
http://www.w3.org/2002/07/owl#
po
http://www.essepuntato.it/2008/12/pattern#
prism
http://prismstandard.org/namespaces/basic/2.0/
prof
http://www.w3.org/ns/dx/prof/
prov
http://www.w3.org/ns/prov#
qb
http://purl.org/linked-data/cube#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
sdo
https://schema.org/
sh
http://www.w3.org/ns/shacl#
skos
http://www.w3.org/2004/02/skos/core#
sosa
http://www.w3.org/ns/sosa/
ssn
http://www.w3.org/ns/ssn/
time
http://www.w3.org/2006/time#
vann
http://purl.org/vocab/vann/
void
http://rdfs.org/ns/void#
xsd
http://www.w3.org/2001/XMLSchema#

Legend

cClasses
opObject Properties
fpFunctional Properties
dpData Properties
apAnnotation Properties
pProperties
niNamed Individuals