Tag: ontology and terminology

Found 54 sources
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Gene Ontology

The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from hu ...

Comparative Toxicogenomics Database

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

Disease Ontology

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. Releases: https://githu ...

DisGeNET: a knowledge base for disease genomics

DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific liter ...

HUGO Gene Nomenclature Committee

HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.

PRotein Ontology

Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms ...


SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.

Xenopus laevis and tropicalis biology and genomics resource

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. It includes gene expression patterns that incorporate image data from the li ...

Gene Ontology Annotation Database

The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotati ...


ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.

BRENDA tissue / enzyme source

A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

Comprehensive Antibiotic Resistance Database

A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.

Protein Data Bank Japan

The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

Progenetix - genomic copy number aberrations in cancer

The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With 30817 cases from 1016 publications (Oct 2013), Progenetix is the largest curated database for who ...

ArachnoServer: Spider toxin database

ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom.

International Classification of Diseases Version 10

ICD-10 is the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD), a medical classification list by the World Health Organization. It contains codes for diseases, signs and symptoms, abnormal fi ...


The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. It can be used for clinical diagnostics in human genetics, bioinformatics research on the relationships between hum ...

Ascidian Network for In Situ Expression and Embryological Data

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...

Orphanet Rare Diseases Ontology

Orphanet Rare Diseases Ontology (ORDO) provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.


The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or t ...


ParameciumDB is a new model organism database for Paramecium, built using components of the Generic Model Organism Database (http://www.gmod.org) construction set (Chado relational database schema, Turnkey generic web framework and Gbrowse). The data ...

Genome Biology Ontology Language

To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated stack (GBOL stack). GBOL is provenance centered and provides a consistent representation of genome derived automated predic ...


FlyTF (v2) is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified T ...

Alliance of Genome Resources

The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biol ...


Experimental annotations of localization for Homo sapiens and Arabidopsis thaliana


Experimentally Characterized Protein annotations


Mutant mouse lines held at MRC Harwell


A database for systems biology of DNA dynamics during the cell life.

RIKEN mammals

Integrated database of mammalian genomes, phenotypes, strains and cell lines


Framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies.


GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.

NBRP resources

System for collecting, preserving and providing bioresources for use as experimental materials for life science research.

Protein Naming Utility

Repository of protein names and naming rules


Semantic web application network that combines a set of algorithms to streamline the creation of new semantic web-based knowledge management systems. In a single package, it provides the tools to create new applications, including advanced integratio ...

HL7 FHIR and SSN ontology based Type 1 Diabetes Mellitus Ontology

FHIR And SSN based Type 1 diabetes Ontology (FASTO) is an OWL 2 ontology for real time management of insulin for diabetes patients especially type 1 diabetics. The ontology is based on BFO as the top-level ontology, SSN sensor ontology, and HL7 FHIR ...

Ontology of Drug Adverse Events

The Ontology of Drug Adverse Events (ODAE) is a biomedical ontology in the area of drug adverse events, developed by following OBO Foundry principles (e.g., openness, collaboration).


PlantCircNet is a database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. It provides convenient search functions for circRNA-associated regulatory networks and enables user ...

Clinical MetaData Ontology

The Clinical MetaData Ontology is designed to be used to classify Common Data Elements (CDEs) from different studies and clinical documents. CDEs can be efficiently searched, shared and reused by using our ontology.


Collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user-selected terms.

Plant Experimental Assay Ontology

The Plant Experimental Assay Ontology (PEAO) was created to describe experimental procedures within plant research, regardless of the scientific questions that prompted the assays. This ontology models entities from three distinct realms (biological, ...


ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources.


the small RNA Expression Atlas web application. Sign in with Google or with you SEA account below. If you have not created an account yet, then please register first. If you have received an eMail from Oasis 2 that the classification or DE analysis ...


Genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches.


The Colorado Richly Annotated Full Text Corpus (CRAFT) is a manually annotated corpus consisting of 67 full-text biomedical journal articles from the PubMed Central Open Access Subset.


A manually curated database of polycystic ovarian syndrome. Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein, PCOSBase: a manually curated database of polycystic ovarian syndrome, Datab ...


Orphadata provides the scientific community with comprehensive, quality datasets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats.


The community registry of computational tools and data resources for biosciences.

Genome Trax

A search tool for finding variants from specific chromosome coordinates. It is possible to integrate the results in NGS pipeline.


Methods for broad-scale plant phenology assessments using citizen scientists’ photographs | iNaturalist.org is a joint initiative of the California Academy of Sciences and the National Geographic Society | Explore and share your observations from the ...


Biomedical Research Software as a Service that enables biomedical & translational researchers to securely manage and combine datasets, typically for patient cohorts. A suite of cloud enabled & integrated open source applications can be accessed in a ...

Bibliome Variant Database

The Bibliome Variant Database is a collection of variants mined from open-access primary literature. All variants included in the database have been mapped to the human genome and are presented in a manner ordered by genomic location. The goal of thi ...


A toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. GOMCL is a tool to cluster and extract summarized associations of Gene Ontology based functions in omics data. It clusters GO terms using MCL ba ...


Gene Ontology Meta Annotator for Plants. Lawrence-Dill Plant Informatics and Computation Lab. Welcome to GOMAP-singularity’s documentation! — GOMAP-Singularity 1.3.2 documentation. All publications and products by the team at Lawrence-Dill Plant I ...

Avian Immunome DB

Avian Immunome DB is a user-friendly interface for extracting genetic information about the avian immune system. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes.

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