SIBiLS Vocabularies - version 3.2 (2023)

Mapped vocabularies

"An ontology is a formal representation of a body of knowledges within a given domain. Ontologies usually consist of a set of classes (or terms or concepts) with relations that operate between them."

These are the various terminologies used to create annotations.

Name	Code	Type	Update / Version	Description	Link
ATC	atc	drug	2022-11-07	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.	ATC
Cellosaurus	cell	cell line	v45.0	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	Cellosaurus
CheBI (Chemical Entities of Biological Interest)	chebi	chemical	v222	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.	ChEBI
COVoc			2022	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. Several axis are detailed below and accessible via SIBiLS.	COVoc
COVoc Biomedical	cov	biomedical_vocab	v1.0	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
COVoc Cell lines	cov	cell_lines	v1.0	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
COVoc Chemicals	cov	chemical	v2.0	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
COVoc Clinical Trials	cov	clinical_trial	v1.0	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
COVoc Conceptual Entities	cov	conceptual_entity	v1.0	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
COVoc Disease and Syndrome	cov	disease_syndrome	v1.0	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
COVoc Geographic Location	cov	geographic_location	v1.0	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
COVoc Organism	cov	species	v2.0	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
COVoc Protein and Genome	cov	protein_genome	v2.0	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
Detection methods	vdm	method	2022	List of methods used to detect or study viruses in a corpus of scientific texts.	[Private]
Disprot	disprot	disprot_type1	v1.0	xxx	xxx
Disprot	disprot	disprot_type2	v1.0	xxx	xxx
Disprot	disprot	disprot_type3	v1.0	xxx	xxx
Disprot	disprot	disprot_type4	v1.0	xxx	xxx
Drugbank	drugbank	drug	v5.1.5	The Drugbank database is a freely accessible resource that 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.	Drugbank
ECO (Evidence and Conclusion Ontology)	eco	evidence	2022/08/05	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.	ECO
ENVO (Environment Ontology)	envo	environment	2023/02/13	ENVO is an expressive, community ontology that helps humans, machines, and semantic web applications understand environmental entities of all kinds, from microscopic to intergalactic scales.	ENVO
GO (Gene Ontology)	go	biological_process	2023/06/11	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.	Gene Ontology
GO (Gene Ontology)	go	cellular_component	2023/06/11	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.	Gene Ontology
GO (Gene Ontology)	go	molecular_function	2023/06/11	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.	Gene Ontology
ICD-O-3	icdo3	disease	unknown (2023)	The International Classification of Diseases Oncology (ICD-O) is a biomedical ontology for the logical representation of the terms and relations related to the International Classification of Diseases (ICD).	ICD-O-3
ICTV (International Committee on Taxonomy of Viruses)	ictv	virus	v3	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
MDD (Mammal Diversity Database)	mdd	species	v1.7	Mammal species list with synonyms. An initial taxonomy of accepted names + synonyms based on v1.7 of the Mammal Diversity Database (MDD)	MDD
MeSH	mesh	mesh	v2023	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 specialized ontologies like the NCIt, MeSH is less granular and easily identified by Natural Language Processing thanks to synonyms.	MeSH
NCBI Taxonomy Clinic	ncbi	Species	2023/06/29	This terminology was created by the team and includes many species of clinical interest and related code from NCBI taxonomy collection.	NCBI Taxonomy
NCBI Taxonomy Full	ncbi	Species	2023/06/29	The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.	NCBI Taxonomy
NCI Thesaurus	ncit	disease	v23.05e	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 preferred term, some NCI and MeSH synonyms.	NCIt
neXtProt	nextprot	gene	v2.52.0	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. It provides to researchers with a high-quality synonym for both protein and gene names.	neXtProt
OTT (Open Tree of Life)	ott	species	v3.3	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	OTT
PPI-PTM	ppiptm	ppi-ptm	unknown	xxx	[Manual]
ROBI (Relation Ontology - Biotic Interactions)	robi	biotic_interaction	unknown	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.	RO
UniProtKB/SwissProt	uniprot	gene	2022-04	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.	UniProtKB/SwissProt

Planed for v3.3 : pubchem (subset), license (spdx), lotus (natural chemical products)