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SIBiLS Vocabularies - version 4.2.5.6 (2025)

Name Code Type Update / Version Description Link Concept_source
Accession numbers identifiers accession_numbers v01-2025 A list of patterns based on the registry of identifiers.org and enriched manually. Identifiers.org accessionnumbers
Affiliations ror affiliation v2025-01-23 A list of international research institutes. ROR ror
ATC atc drug v2024AB 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. ATC atc
Agrovoc agrovoc agriculture v2024-06-04 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. Agrovoc agrovoc
Cell Ontology celltype cell type 2025-01-07 The Cell Ontology is a structured controlled vocabulary for cell types in animals. Cell Ontology cellontology
Cellosaurus cellosaurus cell line 51.0 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 cellosaurus
CheBI (Chemical Entities of Biological Interest) chebi chemical v239 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 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 covocbiomed
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 covoccelllines
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 covocchemicals
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 covocclinicaltrials
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 covocconceptualentities
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 covocdiseaseandsyndrom
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 covocgeographicloc
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 covocorganism
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 covocproteinsgenomes
Detection methods vdm method v2022 List of methods used to detect or study viruses in a corpus of scientific texts. [Private] detectionmethods
Disprot disprot disprot_type1 v1.0 xxx xxx disprot_type1
Disprot disprot disprot_type2 v1.0 xxx xxx disprot_type2
Disprot disprot disprot_type3 v1.0 xxx xxx disprot_type3
Disprot disprot disprot_type4 v1.0 xxx xxx disprot_type4
Drugbank drugbank drug v5.1.13 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. Drugbank drugbank
ECO (Evidence and Conclusion Ontology) eco evidence v2024-07-19 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 eco
ENVO (Environment Ontology) envo environment v2024-07-01 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. ENVO envo
Flopo flopo plant 2025-01-28 The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.. Flopo flopo
GO (Gene Ontology) go biological_process v2024-11-03 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_bp
GO (Gene Ontology) go cellular_component v2024-11-03 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_cc
GO (Gene Ontology) go molecular_function v2024-11-03 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 go_mf
ICD-O-3 icdo3 disease unknown 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). ICD-O-3 icdo3
ICTV (International Committee on Taxonomy of Viruses) ictv virus MSL39v4 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 ictv
License license license v3.26 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. Licenses (SPDX) license
LOTUS lotus chemical v10 LOTUS, one of the biggest and best annotated resources for Natural Products occurrences available free of charge and without any restriction. LOTUS lotus
MDD (Mammal Diversity Database) mdd species v1.13 Mammal species list with synonyms. An initial taxonomy of accepted names + synonyms based on v1.7 of the Mammal Diversity Database (MDD) MDD mdd
MeSH mesh mesh v2025 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. MeSH mesh
NCBI Taxonomy Full ncbi species v.2025-02-11 The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. NCBI Taxonomy ncbitaxon_full
NCBI Taxonomy Models ncbi species v.2025-02-11 This terminology was created by the team and includes many species of clinical interest and related code from NCBI taxonomy collection. NCBI Taxonomy ncbitaxon_models
NCI Thesaurus ncit disease v24.12e 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. NCIt ncit
neXtProt nextprot gene v2023-09-12 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. neXtProt nextprot
OTT (Open Tree of Life) ott species v3.7.2 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 ott
PO (Plant Ontology) po plant 04-18-2024 The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. PO po
PPI-PTM ppiptm ppi-ptm unknown [Manual] ppiptm
PSI-MI psimi molecular_interaction v1.2 A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. psi-mi psimi
Pubchem (Mesh subset) pubchemmesh chemical unknown Pubchem database, only coumpounds with mesh terms associated. Reconstitution pipeline from FTP, Extras files. pubchem pubchemmesh
ROBI (Relation Ontology - Biotic Interactions) robiext biotic_interaction v2025 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 robiext
UniProtKB/SwissProt uniprot gene v11 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 uniprot_swissprot

Correspondance between definition, json_field and annotation_field:

definition json_field annotation_field
terminology name terminology concept_source
terminology version version version
release date date null
terminology type type type

Correspondance between type and concept_source

type concept_source
accession_numbers accessionnumbers
affiliation ror
agriculture agrovoc
biological_process go_bp
biomedical_vocab covocbiomed
biotic_interaction robiext
cell_lines covoccelllines
cell line cellosaurus
cell type cellontology
cellular_component go_cc
chemical chebi, covocchemicals, lotus, pubchemmesh
clinical_trial covocclinicaltrials
conceptual_entity covocconceptualentities
disease icdo3, ncit
disease_syndrome covocdiseaseandsyndrom
disprot_type1 disprot_type1
disprot_type2 disprot_type2
disprot_type3 disprot_type3
disprot_type4 disprot_type4
drug atc, drugbank
evidence eco
environment envo
geographic_location covocgeographicloc
gene nextprot, uniprot_swissprot
license license
mesh mesh
method detectionmethods
molecular_function go_mf
molecular_interaction psi-mi
plant flopo, po
ppi-ptm ppi-ptm
protein_genome covocproteinsgenomes
species mdd, ott, covocorganism, ncbitaxon_full, ncbitaxon_models
virus ictv