Registry

The registry contains metadata about ontologies, controlled vocabularies, and resources including their preferred prefix, name, description, homepage, mappings to other registries, and more.

Anyone can suggest improvements or make pull requests to update the underlying database, which is stored in JSON on GitHub where the community can engage in an open review process.

Name Prefix Description
3D Metabolites 3dmet 3DMET is a database collecting three-dimensional structures of natural metabolites.
4D Nucleome Data Portal Biosource 4dn.biosource The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets.
4D Nucleome Data Portal Experiment Replicate 4dn.replicate Database portal containing replicate experiments of different assays and samples.
AAindex aaindex Identifier of an entry from the AAindex database.
Amphibian gross anatomy aao A structured controlled vocabulary of the anatomy of Amphibians.
AntiBodies Chemically Defined database abcd The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies.
Applied Biological Materials cell line products abm Cell line collections.
Annotated Regulatory Binding Sites abs The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.
Activity Streams ac Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's.
Aceview Worm aceview.worm AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace).
AddexBio cell line products addexbio Cell line collections.
Addgene Plasmid Repository addgene Addgene is a non-profit plasmid repository.
Alzheimer's Disease Ontology ado Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO).
Animal natural history and life history adw Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.
Anatomical Entity Ontology aeo AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology.
Academic Event Ontology aeon The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series.
Adverse Event Reporting Ontology aero The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.
Affymetrix Probeset affy.probeset An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit.
Allotrope Merged Ontology Suite afo Allotrope Merged Ontology Suite.
Assembling the Fungal Tree of Life - Taxonomy aftol.taxonomy The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life.
Agilent Probe agilent.probe This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628.
Agricultural Online Access agricola AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information.
Alliance of Genome Resources Knowledge Base agrkb The Alliance of Genome Resources creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.

The Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:

Agronomy Ontology agro AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities.
Agronomy Vocabulary agrovoc AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest.
Animal Genome Size Database agsd The Animal Genome Size Database (AGSD) is a comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.
Ontology for the Anatomy of the Insect SkeletoMuscular system aism The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.
The ALlele FREquency Database alfred ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases.
Allergome allergome Allergome is a repository of data related to all IgE-binding compounds.
Alzforum Mutations alzforum.mutation Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease.
Alzheimer Gene Database alzgene The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease.
AmoebaDB amoebadb AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
The Amphioxus Development and Anatomy Ontology amphx An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).
Antibody Registry antibodyregistry The Antibody Registry provides identifiers for antibodies used in publications.
AntWeb antweb AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.
AOPWiki aop International repository of Adverse Outcome Pathways.
AOPWiki (Key Event) aop.events International repository of Adverse Outcome Pathways.
AOPWiki (Key Event Relationship) aop.relationships International repository of Adverse Outcome Pathways.
AOPWiki (Stressor) aop.stressor International repository of Adverse Outcome Pathways.
Psychology Ontology apaonto An ontology developed by the American Psychological Association (APA).
Antimicrobial Peptide Database apd The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.
AphidBase Transcript aphidbase.transcript AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC).
APID Interactomes apid.interactions APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs).
Ascomycete phenotype ontology apo A structured controlled vocabulary for the phenotypes of Ascomycete fungi.
Apollo Structured Vocabulary apollosv Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models.
ArachnoServer arachnoserver ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms.
Arabidopsis Information Portal araport Website with general information about Arabidopsis and functionalities such as a genomic viewer.
ArchDB archdb ArchDB is a compilation of structural classifications of loops extracted from known protein structures.
Antibiotic Resistance Genes Database ardb The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance.
Archival Resource Key ark An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type.
Antibiotic Resistance Ontology aro Antibiotic resistance genes and mutations.
ArrayExpress arrayexpress ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.
ArrayExpress Platform arrayexpress.platform ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results.
ArrayMap arraymap arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles.
arXiv ID arxiv arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.
A Systematic Annotation Package for Community Analysis of Genomes asap ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data.
Astrophysics Source Code Library ascl The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications.
Amazon Standard Identification Number asin Almost every product on our site has its own ASIN, a unique code we use to identify it.
Aspergillus Genome Database aspgd.locus The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance.
AspGD Protein aspgd.protein The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance.
Arabidopsis Small RNA Project asrp Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes.
ASTD astd Identifier of an object from the ASTD database.
Anatomical Therapeutic Chemical Classification System atc The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties.
American Type Culture Collection atcc The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.
Anatomical Therapeutic Chemical Vetinary atcvet The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine.
Animal TFDB Family atfdb.family The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes.
Amphibian taxonomy ato Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres.
Animal Trait Ontology for Livestock atol ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL).
AutDB autdb AutDB is a curated database for autism research.
Bacterial Diversity Metadatabase bacdive BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.
BacMap Biography bacmap.biog BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes.
BacMap Map bacmap.map BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes.
Bactibase bactibase Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.
Brain Architecture Knowledge Management System Neuroanatomical Ontology bams BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.
BioAssay Ontology bao The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.
Basic Register of Thesauri, Ontologies & Classifications bartoc The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries. The main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing.
Blue Brain Project Knowledge Graph bbkg Blue Brain Project's published data as knowledge graphs and Web Studios.
Blue Brain Project Topological sampling Knowledge Graph bbtp Input data and analysis results for the paper "Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).
Beta Cell Genomics Ontology bcgo An application ontology built for beta cell genomics studies.
The Behaviour Change Intervention Ontology bcio The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.
Biological Collections Ontology bco An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
BCRC Strain Collection Catalog bcrc Cell line collections.
Banco de Celulas do Rio de Janeiro bcrj Cell line collections.
Berkeley Drosophila Genome Project EST database bdgp.est The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster.
BDGP insertion DB bdgp.insertion BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.
Bloomington Drosophila Stock Center bdsc The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.
Tribolium Genome Database -- Insertion beetlebase BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology.
Benchmark Energy & Geometry Database begdb The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties.
BEI Resources beiresources Cell line collections.
Biological Expression Language bel The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents.
Basic Formal Ontology bfo The upper level ontology upon which OBO Foundry ontologies are built.
Bgee family bgee.family Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species.
Bgee gene bgee.gene Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data).
Bgee organ bgee.organ Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species.
Bgee stage bgee.stage Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species.
The Bibliographic Ontology bibo The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e.
Bibliometric Data Ontology bido An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF.
BiGG Compartment bigg.compartment BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions.
BiGG Metabolite bigg.metabolite BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions.
BiGG Model bigg.model BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions.
BiGG Reaction bigg.reaction BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions.
Bilateria anatomy bila This is a record of the Bilateria anatomy terminology and ontology.
BIND accession number bind Accession number of an entry from the BIND database.
BindingDB bindingdb BindingDB is the first public database of protein-small molecule affinity data.
BioCarta Pathway biocarta.pathway BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research.
BioCatalogue Service biocatalogue.service The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community.
BioCyc collection of metabolic pathway databases biocyc BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.
BioGRID biogrid BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.
BioGRID Interactions biogrid.interaction BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.
BioLegend biolegend BioLegend is a life sciences supply vendor.
Biolink Model biolink A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations.
BioMagResBank biomagresbank A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids.
Bio-MINDER Tissue Database biominder Database of the dielectric properties of biological tissues.
BioModels Database biomodels.db BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.
Kinetic Simulation Algorithm Ontology biomodels.kisao The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them.
Terminology for Description of Dynamics biomodels.teddy The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.
SBML RDF Vocabulary biomodels.vocabulary Vocabulary used in the RDF representation of SBML models.
BioNumbers bionumbers BioNumbers is a database of key numberical information that may be used in molecular biology.
biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology biopixie bioPIXIE is a novel system for biological data integration and visualization.
BioPortal bioportal BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames.
BioProject bioproject BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases.
Bioregistry bioregistry The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database.
Bioregistry Collections bioregistry.collection Manually curated collections of resources stored in the bioregistry.
Bioregistry Metaregistry bioregistry.registry The Bioregistry's meta-registry.
Bioregistry Schema bioregistry.schema Schema for the export of the Bioregistry as RDF.
bioRxiv biorxiv The bioRxiv is a preprint server for biology.
BioSample biosample The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics.
biosimulations biosimulations BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results.
BioSimulators biosimulators BioSimulators is a registry of containerized simulation tools that support a common interface.
BioStudies database biostudies The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI.
BioSystems biosystems The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.
BioTools biotools BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.
BIOZIL biozil Redistributor of bilogics and biomedical supplies.
Biomedical Informatics Research Network Lexicon birnlex The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.
Bibliographic Reference Ontology biro An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.
Bitbucket bitbucket Bitbucket is a Git-based source code repository hosting service owned by Atlassian.
BitterDB Compound bitterdb.cpd BitterDB is a database of compounds reported to taste bitter to humans.
BitterDB Receptor bitterdb.rec BitterDB is a database of compounds reported to taste bitter to humans.
SBGN Bricks data and ontology bko SBGN bricks represent biomolecular or biological concepts.
Biological Magnetic Resonance Data Bank bmrb BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites.
NMR Restraints Grid bmrb.restraint The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries.
BOLD Systems taxon ID bold.taxonomy The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records.
Gene Regulation Ontology bootstrep
Bio-Pesticides DataBase bpdb Database of biopesticides maintained by the University of Hertfordshire .
BRENDA, The Comprehensive Enzyme Information System brenda BRENDA is a collection of enzyme functional data available to the scientific community.
BRENDA Ligand brenda.ligand Information for ligands in the BRENDA database.
BRENDA Ligand Group brenda.ligandgroup Information for ligand groups (chemical classes).
Broad Fungal Genome Initiative broad Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions.
Biosapiens Protein Feature Ontology bs SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation.
Biological Spatial Ontology bspo An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces.
BRENDA tissue / enzyme source bto The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database.
BugBase Expt bugbase.expt BugBase is a MIAME-compliant microbial gene expression and comparative genomic database.
BugBase Protocol bugbase.protocol BugBase is a MIAME-compliant microbial gene expression and comparative genomic database.
Bacterial Tyrosine Kinase Database bykdb The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.
Citation Counting and Context Characterisation Ontology c4o An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date.
Common Access to Biological Resources and Information Project cabri CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues.
Cancer Data Standards Registry and Repository cadsr The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR.
CALIPHO Group Ontology of Human Anatomy caloha This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data.
Continuous Automated Model Evaluation cameo The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner.
CAPS-DB caps CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures.
Common Anatomy Reference Ontology caro None.
CAS Registry Number cas CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.
Eschmeyer's Catalog of Fishes casspc
CATH Protein Structural Domain Superfamily cath CATH is a classification of protein structural domains.
CATH domain cath.domain The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank.
CATH superfamily cath.superfamily The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank.
Animal Genome Cattle QTL cattleqtldb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species.
Carbohydrate Active EnZYmes cazy The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates.
Chinese Biological Abstracts cba CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.
The cBioPortal for Cancer Genomics cbioportal The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.
CCDC Number ccdc The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data.
Consensus CDS ccds The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality.
Cancer Cell Line Encyclopedia Cells ccle Datasets around different cancer cell lines generated by the Broad Institute and Novartis.
Cell Cycle Ontology cco The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.
National Experimental Cell Resource Sharing Platform ccrid Cell line databases/resources.
Comparative Data Analysis Ontology cdao The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis.
Conserved Domain Database at NCBI cdd The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.
Compositional Dietary Nutrition Ontology cdno None.
Canadian Drug Product Database cdpd The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products.
Current Dental Terminology cdt The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.
Cell Biolabs cell line products cell_biolabs Cell line collections.
Sanger Cell Model Passports cell_model_passport Cell line databases/resources.
CellBank Australia cellbank.australia CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world.
Cell Image Library cellimage The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.
Cellosaurus Publication cellopub Cellosaurus identifeirs for publications, like Pubmed.
Cellosaurus cellosaurus The Cellosaurus is a knowledge resource on cell lines.
Cellosaurus Registry cellosaurus.resource The set of prefixes used in the Cellosaurus resource.
Cell Version Control Repository cellrepo The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines.
The COVID-19 epidemiology and monitoring ontology cemo The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response.
Cephalopod Ontology ceph An anatomical and developmental ontology for cephalopods.
Candida Genome Database cgd The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans.
CGH Data Base cghdb Cell line databases/resources.
Chicken Gene Nomenclature Consortium cgnc Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans).
Coli Genetic Stock Center cgsc The CGSC Database of E.
CharProt charprot CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines.
Chemical Entities of Biological Interest chebi Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.
ChemBank chembank ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG).
ChEMBL chembl ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc).
ChEMBL database of bioactive drug-like small molecules - Cell lines section chembl.cell Chemistry resources.
ChEMBL chembl.compound ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc).
ChEMBL target chembl.target ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc).
ChemDB chemdb ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.
ChemIDplus chemidplus ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases.
Chemical Information Ontology cheminf Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.
Chemical Entity Materials and Reactions Ontological Framework chemrof CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework.
ChemSpider chemspider ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry.
Animal Genome Chicken QTL chickenqtldb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species.
ChEBI Integrated Role Ontology chiro CHEBI provides a distinct role hierarchy.
Chemical Methods Ontology chmo CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns.
Coronavirus Infectious Disease Ontology cido The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease.
Confidence Information Ontology cio An ontology to capture confidence information about annotations.
CiteXplore citexplore One of the precursors to the EuropePMC project.
Citation Typing Ontology cito An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.
CIViC Assertion civic.aid A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines.
CIViC Disease civic.did Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant.
CIViC Evidence civic.eid Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase.
CIViC Gene civic.gid A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene.
CIViC Source civic.sid In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims.
CIViC Therapy civic.tid Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present.
CIViC variant ID civic.vid CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome.
Cell Ontology cl The Cell Ontology is designed as a structured controlled vocabulary for cell types.
Collembola Anatomy Ontology clao CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).
ClassyFire classyfire ClassyFire is a web-based application for automated structural classification of chemical entities.
Cell Line Database cldb The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines.
ClinGen Allele Registry clingene The allele registry provides and maintains identifiers for genetic variants.
ClinicalTrials.gov ID clinicaltrials ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions.
ClinVar Variation clinvar ClinVar archives reports of relationships among medically important variants and phenotypes.
ClinVar Record clinvar.record ClinVar archives reports of relationships among medically important variants and phenotypes.
ClinVar Submission clinvar.submission ClinVar archives reports of relationships among medically important variants and phenotypes.
ClinVar Submitter clinvar.submitter ClinVar archives reports of relationships among medically important variants and phenotypes.
Cell Line Ontology clo The Cell Line Ontology (CLO) is a community-based ontology of cell lines.
Cell Lines Service cls Cell line collections.
Clytia hemisphaerica Development and Anatomy Ontology clyh Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.
Costal and Marine Ecological Classification Standard cmecs Use this database to browse the CMECS classification and to get definitions for individual CMECS Units.
CranioMaxilloFacial ontology cmf This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain.
Clinical measurement ontology cmo Morphological and physiological measurement records generated from clinical and model organism research and health programs.
Cellular Microscopy Phenotype Ontology cmpo CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.
Rice ontology co_320 Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables.
Wheat ontology co_321 July 2018.
Maize ontology co_322 Maize Trait Dictionary in template 5 - CIMMYT- September 2016.
Barley ontology co_323 ICARDA - TDv5 - Sept 2018.
Sorghum ontology co_324 Sorghum TDv5 - Oct 2019.
Banana ontology co_325 Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019.
Coconut ontology co_326 Draft version.
Pearl millet ontology co_327 Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016.
Potato ontology co_330 CIP - potato ontology - december 2018.
Sweet Potato ontology co_331 Sweet Potato Trait Dictionary in template v5 - CIP - November 2019.
Beet Ontology ontology co_333 This ontology was built as part of the AKER project.
Cassava ontology co_334 Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016.
Common Bean ontology co_335 CIAT Common bean trait dictionary - version August 2014.
Soybean ontology co_336 Soybean Trait Dictionary in template v5 - IITA - July 2015.
Groundnut ontology co_337 Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015.
Chickpea ontology co_338 Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015.
Lentil ontology co_339 Lentil Trait Dictionary in template v5 - ICARDA - July 2015.
Cowpea ontology co_340 Cowpea Trait Dictionary in template v5 - IITA - August 2015.
Pigeonpea ontology co_341 Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015.
Yam ontology co_343 version 2019 - pvs.
Brachiaria ontology co_345 Brachiaria (forages) ontology TD v5 - Version Oct 2016.
Mungbean ontology co_346 oct 2016.
Castor bean ontology co_347 March 2017 version .
Brassica ontology co_348 Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data.
Oat ontology co_350 Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo.
Vitis ontology co_356 Grape Ontology including OIV and bioversity descriptors.
Woody Plant Ontology ontology co_357 This ontology lists all variables used for woody plant observations.
Cotton ontology co_358 Cotton ontology from CottonGen database - June 2019.
Sunflower ontology co_359 December 2019.
Sugar Kelp trait ontology co_360 Sugar Kelp trait ontology.
Fababean ontology co_365 developed by ICARDA - Dec 2018.
Bambara groundnut ontology co_366 version Dec 2019.
Quinoa Ontology ontology co_367 Curator name: Clara S.
Apple ontology co_370 Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales.
Core Ontology for Biology and Biomedicine cob COB brings together key terms from a wide range of OBO projects to improve interoperability.
COlleCtion of Open Natural ProdUcTs coconut COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis.
GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray codelink GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain.
Cluster of orthologous genes cog COGs stands for Clusters of Orthologous Genes.
COG Categories cog.category Higher-level classifications of COG Pathways.
COG Pathways cog.pathway Database of Clusters of Orthologous Genes grouped by pathways and functional systems.
MIMIC III Database cohd MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012.
Catalogue of Life in Taiwan col.taiwan Identifier (name code) for a taxon in the catalogue of life in taiwan.
Coleoptera Anatomy Ontology colao The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.
Collagen Mutation Database collagenmutdb This database aims to record all published accounts of variants resulting in osteogenesis imperfecta.
Colorectal Cancer Atlas colonatlas Cell line databases/resources.
COMBINE specifications combine.specifications The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields.
The Bioinorganic Motif Database come COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif.
Common Core Ontologies commoncoreontology The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.

CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015).

Complex Portal complexportal A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.
DSSTox substance ID comptox The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program.
Compluyeast-2D-DB compulyeast Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database.
ConfIDent Event confident.event Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.
ConfIDent Event Series confident.series Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.
ConoServer conoserver ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.
Curation of Neurodegeneration Supporting Ontology conso An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases.
CORDIS Article cordis.article The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
CORDIS Project cordis.project The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
Coriell Institute for Medical Research coriell The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures.
CorrDB corrdb A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population.
Comprehensive Resource of Mammalian protein complexes corum The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms.
COSMIC Gene cosmic COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K.
COSMIC Cell Lines cosmic.cell COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer.
COVID-19 Surveillance Ontology covid19 Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease.
CoVoc Coronavirus Vocabulary covoc The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic.
Cellular Phenotypes cp
Cooperative Patent Classification cpc The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO).
Current Procedural Terminology cpt Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform.
CASRAI Contributor Roles Taxonomy credit CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output.
CRISPRdb crisprdb Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation.
Contributor Role Ontology cro A classification of the diverse roles performed in the work leading to a published research output in the sciences.
CropMRepository crop2ml CropMRespository is a database of soil and crop biophysical process models.
Cryo Electron Microscopy ontology cryoem Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles.
CryptoDB cryptodb CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
Catalytic Site Atlas csa The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
Cambridge Structural Database csd The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures.
Computer Retrieval of Information on Science Projects Thesaurus csp Computer Retrieval of Information on Scientific Projects (CRISP).
Cell Signaling Technology Pathways cst Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products.
Cell Signaling Technology Antibody cst.ab Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products.
Common Terminology Criteria for Adverse Events ctcae The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy.
CTD Chemical ctd.chemical The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates.
CTD Disease ctd.disease The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates.
CTD Gene ctd.gene The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates.
Ctenophore Ontology cteno An anatomical and developmental ontology for ctenophores (Comb Jellies).
Clinical Trials Ontology cto The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials.
Cube db cubedb Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families.
Codon Usage Tabulated from GenBank cutg Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database.
Cardiovascular Disease Ontology cvdo An ontology to describe entities related to cardiovascular diseases.
Vaccine administered code set cvx The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set.
DataONE d1id DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.
DailyMed dailymed DailyMed provides information about marketed drugs.
Distributed Archives for Neurophysiology Data Integration dandi DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. These data will help scientists uncover and understand cellular level mechanisms of brain function.
Database of Aligned Ribosomal Complexes darc DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system.
Database of small human noncoding RNAs dashr DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types.
DASHR expression dashr.expression DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types.
DataCite Ontology datacite An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.
Datanator Gene datanator.gene Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models.
Datanator Metabolite datanator.metabolite Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models.
Datanator Reaction datanator.reaction
Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models.
Database of Arabidopsis Transcription Factors datf DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.
Transcription Factor Database dbd The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life.
EST database maintained at the NCBI. dbest The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
DBG2 Introns dbg2introns The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.
Database of Genotypes and Phenotypes dbgap The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.
Database of human Major Histocompatibility Complex dbmhc Cell line databases/resources.
DBPedia Ontology dbo This ontology is generated from the manually created specifications in the dbpedia mappings wiki.
NCBI Probe database Public registry of nucleic acid reagents dbprobe The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.
dbSNP Reference SNP number dbsnp The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.
Database of Genomic Structural Variation - Study dbvar.study Studies in dbVar.
Database of Genomic Structural Variation - Variant dbvar.variant Variants in dbVar.
Dublin Core dc Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.
Dendritic cell dc_cl
Data Catalog dcat DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.
Dublin Core Metadata Vocabulary dcterms This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.
Dublin Core Types dctypes This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.
Dictyostelium discoideum anatomy ddanat A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum.
Curated Drug-Drug Interactions Database - Drug ddinter.drug Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions.
Curated Drug-Drug Interactions Database - Interaction ddinter.interaction Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions.
Dictyostelium discoideum phenotype ontology ddpheno A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.
Decentralized Biomedical Ontology debio A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON.
DECIPHER CNV Syndromes decipher CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms.
Degradome Database degradome The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing.
Discourse Elements Ontology deo An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix).
DepMap Cell Lines depmap Cell lines used in the Dependency Map (DepMap).
Human Dephosphorylation Database depod The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates.
Human Dermatological Disease Ontology dermo DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders.
Development Data Object Service dev.ga4ghdos Assists in resolving data across cloud resources.
BioData Catalyst dg.4503 Full implementation of the DRS 1.1 standard with support for persistent identifiers.
NCI Data Commons Framework Services dg.4dfc DRS server that follows the Gen3 implementation.
JCOIN dg.6vts Full implementation of the DRS 1.1 standard with support for persistent identifiers.
Anvil dg.anv0 DRS server that follows the Gen3 implementation.
Kids First dg.f82a1a Full implementation of the DRS 1.1 standard with support for persistent identifiers.
BloodPAC dg5b0d The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention.
Drosophila Genomics Resource Center dgrc Cell line collections.
Developing Human Brain Atlas dhba A controlled vocabulary to support the study of transcription in the developing human brain.
DICOM Controlled Terminology dicom DICOM Controlled Terminology.
dictyBase dictybase A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics.
dictyBase Expressed Sequence Tag dictybase.est The dictyBase database provides data on the model organism Dictyostelium discoideum and related species.
Dictybase Gene dictybase.gene The dictyBase database provides data on the model organism Dictyostelium discoideum and related species.
Decentralized Identifier did DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary.
Drug-drug Interaction and Drug-drug Interaction Evidence Ontology dideo The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology.
The Drug-Drug Interactions Ontology dinto A formal represention for drug-drug interactions knowledge.
Database of Interacting Proteins dip The database of interacting protein (DIP) database stores experimentally determined interactions between proteins.
DiscoverX cell line products discoverx Cell line collections.
Disease Drivers Ontology disdriv Drivers of human diseases including environmental, maternal and social exposures.
Disease Class diseaseclass Legacy disease classes that later became MONDO.
Diseases Database diseasesdb The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc.
DisProt disprot DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature.
DisProt region disprot.region DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature.
Linear double stranded DNA sequences dlxb DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences.
Circular double stranded DNA sequences composed dlxc DOULIX lab-tested standard biological parts, in this case, full length constructs.
Developing Mouse Brain Atlas dmba A controlled vocabulary to support the study of transcription in the developing mouse brain.
Description of a Project doap DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects.
Document Components Ontology doco An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix).
Digital Object Identifier doi The Digital Object Identifier System is for identifying content objects in the digital environment.
Human Disease Ontology doid The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.
Database of Macromolecular Interactions dommino DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.
Database for Prokaryotic Operons door DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes.
Database of Quantitative Cellular Signaling: Model doqcs.model The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways.
Database of Quantitative Cellular Signaling: Pathway doqcs.pathway The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways.
Drosophila Phenotype Ontology dpo An ontology for the description of Drosophila melanogaster phenotypes.
Description of Plant Viruses dpv Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa.
DragonDB Allele dragondb.allele DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
DragonDB DNA dragondb.dna DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
DragonDB Locus dragondb.locus DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
DragonDB Protein dragondb.protein DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
Dr. Duke's Phytochemical and Ethnobotanical Databases chemical ID drduke identifier for chemicals linked to information on occurrence in plants.
The Drug Ontology dron We built this ontology primarily to support comparative effectiveness researchers studying claims data.
Drosophila RNAi Screening Center drsc The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results.
DrugBank drugbank The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e.
DrugBank Drug Category drugbank.category Close to 5K Categorizations for drugs, similar to ATCC.
DrugBank Salts drugbank.salt DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.
DrugBank Target v4 drugbankv4.target The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e.
Drug Central drugcentral DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.
Diagnostic and Statistical Manual of Mental Disorders (4th Edition) dsm4 A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria.
Diagnostic and Statistical Manual of Mental Disorders (5th Edition) dsm5 A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria.
Deutsche Sammlung von Mikroorganismen und Zellkulturen dsmz The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines).
Data Science Ontology dso The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics.
Drug Target Ontology dto DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.
Data Use Ontology duo DUO is an ontology which represent data use conditions.
eagle-i eaglei Discovery tool for biomedical research resources available at institutions throughout the U.S.
EasyChair Call for Paper easychair.cfp Conferences in EasyChair.
EasyChair Topic easychair.topic Call for paper topics in EasyChair.
European Bank for induced pluripotent Stem Cells ebisc Cell line collections.
European Collection of Authenticated Cell Culture ecacc The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England.
The Echinoderm Anatomy and Development Ontology ecao None.
Enzyme Commission Code eccode The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.
Electrocardiogram Ontology ecg The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO.
EchoBASE post-genomic database for Escherichia coli echobase EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12.
E. coli Metabolite Database ecmdb The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655).
EC number ecn identifier for a chemical compound per EINECS or ELINCS.
Evidence ontology eco Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge.
An ontology of core ecological entities ecocore Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.
EcoCyc ecocyc EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655.
Database of Escherichia coli Sequence and Function ecogene The EcoGene database contains updated information about the E.
EcoLexicon ecolexicon EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus.
EcoliWiki from EcoliHub ecoliwiki EcoliWiki is a wiki-based resource to store information related to non-pathogenic E.
Environmental conditions, treatments and exposures ontology ecto ECTO describes exposures to experimental treatments of plants and model organisms (e.g.
E-cyanobacterium entity ecyano.entity E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria.
E-cyanobacterium Experimental Data ecyano.experiment E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria.
E-cyanobacterium model ecyano.model E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria.
E-cyanobacterium rule ecyano.rule E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria.
Bioinformatics operations, data types, formats, identifiers and topics edam EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations.
EDAM Data edam.data Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.
EDAM Format edam.format A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.
EDAM Operation edam.operation A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs).
EDAM Topic edam.topic A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology.
EDDA Study Designs Taxonomy edda Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis.
Experimental Factor Ontology efo The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases.
European Genome-phenome Archive Dataset ega.dataset The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.
European Genome-phenome Archive Study ega.study The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.
eggNOG eggnog eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes.
Human developmental anatomy, timed version ehda A structured controlled vocabulary of stage-specific anatomical structures of the human.
Human developmental anatomy, abstract version ehdaa A structured controlled vocabulary of stage-specific anatomical structures of the human.
Human developmental anatomy, abstract ehdaa2 A structured controlled vocabulary of stage-specific anatomical structures of the developing human.
Eukaryotic Linear Motif Resource elm Linear motifs are short, evolutionarily plastic components of regulatory proteins.
Mouse gross anatomy and development, timed emap A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).
Mouse Developmental Anatomy Ontology emapa An ontology for mouse anatomy covering embryonic development and postnatal stages.
Electron Microscopy Data Bank emdb The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures.
Reaxys eMolecules emolecules Catalog of purchasable reagents and building blocks.
Electron Microscopy Public Image Archive empiar EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images.
European Nucleotide Archive ena.embl The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing.
Encyclopedia of DNA Elements encode The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.
eNanoMapper Ontology enm The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies.
Ensembl Gene ensembl Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.
Ensembl Bacteria ensembl.bacteria Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl.
Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi. ensembl.fungi Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl.
Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa. ensembl.metazoa Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl.
Ensembl Plants ensembl.plant Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl.
Ensembl Protists ensembl.protist Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl.
Ensembl Glossary ensemblglossary The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used.
enviPath envipath enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants.
Environment Ontology envo The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities.
Enzo Life Sciences enzo Enzo Life Sciences is an antibody vendor.
Plant Environment Ontology eo The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure.
Environment Ontology for Livestock eol The EOL ontology describes environmental conditions of livestock farms.
Encyclopedia of Life eolife A collaborative project intended to create an encyclopedia documenting all living species known to science.
European Paediatric Cardiac Codes epcc Collection of European paediatric cardiac coding files.
Eukaryotic Promoter Database epd The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
Epilepsy Ontology epio A application driven Epilepsy Ontology with official terms from the ILAE.
Epidemiology Ontology epo An ontology designed to support the semantic annotation of epidemiology resources.
Epilepsy and Seizure Ontology epso The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research.
European Registry of Materials erm The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.
eagle-i resource ontology ero An ontology of research resources such as instruments.
Endogenous Regulatory OligoPeptide knowledgebase-Moscow eropmoscow EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.).
Human Endogenous Retrovirus Database erv Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements.
eukaryotic Subcellular Localization database esldb eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms.
European Searchable Tumour Line Database estdab Cell line databases/resources.
JRC Data Catalogue eu89h The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.
EU Clinical Trials euclinicaltrials The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.
Eukaryotic Genes eugenes euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.
VEuPathDB ontology eupath The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org).
European Food Information Resource Network eurofir EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries.
eVOC (Expressed Sequence Annotation for Humans) ev Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.
eVOC mouse development stage evm
ExAC Gene exac.gene The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community.
ExAC Transcript exac.transcript The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community.
ExAC Variant exac.variant The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community.
Exposure ontology exo ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.
FaBiO, the FRBR-aligned Bibliographic Ontology fabio The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.
FaceBase Data Repository facebase FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation.
FAIRsharing fairsharing The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals.
Feature Annotation Location Description Ontology faldo It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources.
Fungal gross anatomy fao A structured controlled vocabulary for the anatomy of fungi.
Biological Imaging Methods Ontology fbbi A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
Drosophila gross anatomy fbbt An ontology of Drosophila melanogaster anatomy.
FlyBase Controlled Vocabulary fbcv A miscellaneous ontology of terms used for curation in FlyBase, including the DPO.
Drosophila development fbdv An ontology of Drosophila melanogaster developmental stages.
International Fungal Working Group Fungal Barcoding. fbol DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life.
FlyBase Qualifiers fbql
FlyBase Reference Report fbrf FlyBase internal citation identifiers.
Fly taxonomy fbsp The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
Flybase Cell Line fbtc The cell line vocabulary inside FlyBase.
the FAIR Cookbook fcb Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).

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Fetal Calf Serum-Free Database fcsfree Cell line databases/resources.
FHIR United States Implementation Guides fhir.implementation A set of guides on implementing various processes within hospitals or healthcare systems.
Food Interactions with Drugs Evidence Ontology fideo The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia.
FishBase fishbase.species Global biodiversity database on finfishes.
Five Stars of Online Research Articles Ontology fivestars An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata.
Physico-chemical methods and properties fix An ontology of physico-chemical methods and properties.
Flora Phenotype Ontology flopo Traits and phenotypes of flowering plants occurring in digitized Floras.
FlowRepository flowrepository FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard.
Influenza Ontology flu Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology.
FlyBase Gene flybase FlyBase is the database of the Drosophila Genome Projects and of associated literature.
FlyBrain Neuron Database flybrain.ndb A database of fly neurons and pathways with an associated 3D viewer.
FlyMine Chromosome Band flymine.chromosome FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C.
Foundational Model of Anatomy fma The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology.
Friend of a Friend foaf FOAF is a project devoted to linking people and information using the Web.
Food-Biomarker Ontology fobi FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data.
FooDB compound ID foodb.compound FooDB is resource on food and its constituent compounds.
FooDB Food foodb.food Foods in FooDB.
Food classification and description system foodex2 FoodEx2 is a comprehensive food classification and description system aimed at covering the need to describe food in data collections across different food safety domains.
The Food Ontology foodon FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world.
Fossilworks Journal fossilworks.journal Identifier for a journal article in the fossilworks website.
Fossilworks Taxon fossilworks.taxon Identifier for an animal, plant, or microorganism from the fossilworks website.
FuTRES Ontology of Vertebrate Traits fovt None.
FamPlex fplx FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.
FAIR* Reviews Ontology fr An ontology that enables the description of reviews of scientific articles and other scholarly resources.
Funding, Research Administration and Projects Ontology frapo An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.
Functional Requirements for Bibliographic Records frbr The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary.
F-SNP fsnp The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs.
Feature Type Thesaurus ftt Types of named geographic features.
FuncBase Fly funcbase.fly Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks.
FuncBase Human funcbase.human Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks.
FuncBase Mouse funcbase.mouse Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks.
FuncBase Yeast funcbase.yeast Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks.
DOI funderregistry The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.
FungiDB fungidb FungiDB is a genomic resource for fungal genomes.
Index Fungorum fungorum identifier for a fungus taxon in Index Fungorum.
Fission Yeast Experimental Conditions Ontology fyeco PomBase manages gene and phenotype data related to Fission Yeast.
Fyler fyler A hierarchical classification of congenital heart disease .
Fission Yeast Phenotype Ontology fypo A formal ontology of phenotypes observed in fission yeast.
Data Object Service ga4ghdos Assists in resolving data across cloud resources.
Network of Different Plant Genomic Research Projects gabi GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species.
GALEN galen A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.
Genetic and Rare Diseases Information Center gard Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.
Health Data Research Innovation Gateway gateway The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation.
Gazetteer gaz A gazetteer constructed on ontological principles.
Global Biodiversity Information Facility gbif Database of living organisms, taxonomic.
Genetic Code gc Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.
GWAS Catalog gcst The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.
Genomic Data Commons Data Portal gdc The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.
Genomics of Drug Sensitivity in Cancer gdsc The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.
Genomics Cohorts Knowledge Ontology gecko An ontology to represent genomics cohort attributes.
General Multilingual Environmental Thesaurus gemet The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries.
Genatlas genatlas GenAtlas is a database containing information on human genes, markers and phenotypes.
GenBank genbank GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).
Genomic Distribution of structural Superfamilies gendis Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases.
GeneCards genecards The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information.
Gene Location genecards.geneloc GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm.
GeneDB genedb GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.
GeneFarm genefarm GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.
Genomic Epidemiology Ontology genepio The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.
GeneTree genetree Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes.
Gene Wiki genewiki The Gene Wiki is project which seeks to provide detailed information on human genes.
Genotype Ontology geno GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities.
GenPept genpept The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.
Genome Properties genprop Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome.
NCBI Gene Expression Omnibus geo The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.
Geographical Entity Ontology geogeo An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction.
GeoNames geonames The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.
GeoNames Feature Code geonames.feature All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes.
Gene Expression Ontology gexo Gene Expression Ontology.
General Formal Ontology gfo The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med.
Genetics Home Reference ghr MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA).
GiardiaDB giardiadb GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
github github GitHub is an online host of Git source code repositories.
GitHub Issue github.issue An issue in any public repository on GitHub.
GitHub Pull Request github.pull A pull request in any public repository on GitHub.
GitLab gitlab GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance.
GLIDA GPCR glida.gpcr The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands.
GLIDA Ligand glida.ligand The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands.
GlycoEpitope glycoepitope GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression.
GlycoMapsDB glycomapsdb A database of GlycoMaps containing 2585 conformational maps.
GlycomeDB glycomedb GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.
GlycoNAVI glyconavi GlycoNAVI is a website for carbohydrate research.
GlycoPOST glycopost GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics.
Glycosciences.DB glycosciencesdb A database to support glycobiology and glycomics research.
Computational and Informatics Resources for Glycoscience glygen GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.
GlyTouCan glytoucan GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.
Golm Metabolome Database gmd Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools.
Golm Metabolome Database Analyte gmd.analyte Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools.
Golm Metabolome Database GC-MS spectra gmd.gcms Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools.
Golm Metabolome Database Profile gmd.profile Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools.
Golm Metabolome Database Reference Substance gmd.ref Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools.
Gmelins Handbuch der anorganischen Chemie gmelin The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly.
Glycan Naming and Subsumption Ontology gno An ontology for glycans based on GlyTouCan, but organized by subsumption.
GnpIS gnpis GnpIS is an integrative information system focused on plants and fungal pests.
Gene Ontology go The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
Gene Ontology Causal Assembly Model go.model GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner.
Gene Ontology Database references go.ref The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g.
Gene Ontology Registry go.resource A database-specific registry supporting curation in the Gene Ontology.
Gene Ontology Annotation Database goa The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI).
GO Chemicals goche Represent chemical entities having particular CHEBI roles.
GO Evidence Code goeco A GO annotation is a statement about the function of a particular gene.
Genomes Online Database gold The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata.
GOLD genome gold.genome
  • DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.

The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide.

GOLD metadata gold.meta
  • DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.
IUPAC Gold Book Compendium of Chemical Terminology goldbook The Compendium is popularly referred to as the "Gold Book", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition.
Google Books google.book Search the world's most comprehensive index of full-text books.
Google Patents google.patent Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO.
Google Scholar Researcher google.scholar Google Scholar provides a simple way to broadly search for scholarly literature.
GO Relations gorel Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.
G protein-coupled receptor database gpcrdb The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs.
Global Proteome Machine Database gpmdb The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.
GrainGenes graingenes.reference A database for Triticeae and Avena references.
GrainGenes graingenes.symbol A database for Triticeae and Avena gene symbols.
Gramene Gene gramene.gene Gramene is a comparative genome mapping database for grasses and crop plants.
Gramene Growth Stage Ontology gramene.growthstage Gramene is a comparative genome mapping database for grasses and crop plants.
Gramene protein gramene.protein Gramene is a comparative genome mapping database for grasses and crop plants.
Gramene QTL gramene.qtl Gramene is a comparative genome mapping database for grasses and crop plants.
Gramene Reference gramene.reference Literature references in Gramene.
Gramene Taxonomy gramene.taxonomy Gramene is a comparative genome mapping database for grasses and crop plants.
GrassBase grassbase GrassBase provides an interactive guide to nomenclature for the whole grass family.
16S rRNA gene database greengenes A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.
Global Research Identifier Database grid International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.
Germplasm Resources Information Network grin GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.
GRIN URL grin.taxonomy GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.
Gene Regulation Ontology gro The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation.
G-Rich Sequences Database grsdb GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated).
General Standard for Food Additives Online Database gsfa The "Codex General Standard for Food Additives" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex.
Gender, Sex, and Sexual Orientation Ontology gsso The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment.
Genotype-Tissue Expression gtex The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.
Genetic Testing Registry gtr The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers.
Genitourinary Development Molecular Anatomy Project gudmap The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.
GWAS Central Marker gwascentral.marker GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small.
GWAS Central Phenotype gwascentral.phenotype GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small.
GWAS Central Study gwascentral.study GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small.
GXA Expt gxa.expt The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.
GXA Gene gxa.gene The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.
Habronattus courtship habronattus
The Ageing Gene Database hagr.genage GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.
The Dietary Restriction Gene Database hagr.gendr GenDR is a database of genes associated with dietary restriction (DR).
High-quality Automated and Manual Annotation of microbial Proteomes hamap HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies.
Human Ancestry Ontology hancestro Human ancestry ontology for the NHGRI GWAS Catalog.
Hymenoptera Anatomy Ontology hao A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants).
Hathi Trust Digital Library hathitrust Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world.
Human Brain Atlas hba A controlled vocabulary to support the study of transcription in the human brain.
A Database of Human Hemoglobin Variants and Thalassemias hbvar This is a relational database of information about hemoglobin variants and mutations that cause thalassemia.
Health Canada Drug Identification Number hc.din A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada.
Health Canada Natural Product Number hc.npn The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada.
Human Cell Atlas Ontology hcao Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.
Healthcare Common Procedure Coding System hcpcs HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services.
Hepatitis C Virus Database hcvdb the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.
Homeodomain Research hdr The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family.
Human Gene Mutation Database hgmd The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease.
HUGO Gene Nomenclature Committee hgnc The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene.
HGNC gene family hgnc.genefamily The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene.
HGNC Gene Group hgnc.genegroup The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene.
HGNC gene symbol hgnc.symbol The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene.
H-InvDb Locus hinv.locus H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts.
H-InvDb Protein hinv.protein H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts.
H-InvDb Transcript hinv.transcript H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts.
Human Induced Pluripotent Stem Cells Initiative hipsci Cell line databases/resources.
NIH HIV Reagent Program hivreagentprogram Cell line collections.
HL7 V2 Code Systems hl7.v2codesystem A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.
HL7 V2 Code Systems hl7.v3codesystem A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.
Human Metabolome Database hmdb The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.
HMS LINCS Compound hms.lincs.compound Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.
Homologous Organ Groups hog Documentation of HOGS (Homologous Organs Groups).
Database of Complete Genome Homologous Genes Families hogenom HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya).
Homeostasis imbalance process ontology hoip An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.
Homology Ontology hom This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.
HOMD Sequence Metainformation homd.seq The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity.
Human Oral Microbiome Database homd.taxon The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity.
HomoloGene homologene HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
Horizon Discovery cell line collection horizon_discovery Cell line collections.
Homologous Vertebrate Genes Database hovergen HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.
Human Phenotype Ontology hp The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease.
Human Protein Atlas tissue profile information hpa The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines.
Histopathology Ontology hpath An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies.
Human Proteome Map Peptide hpm.peptide The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project.
Human Proteome Map hpm.protein The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project.
Human Protein Reference Database hprd The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
Human Pluripotent Stem Cell Registry hpscreg hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).
Human Developmental Stages hsapdv Life cycle stages for Human.
Hazardous Substances Data Bank hsdb The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals.
Health Surveillance Ontology hso The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc.
Database of homology-derived secondary structure of proteins hssp HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D).
Hypertension Ontology htn An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines.
Human Unidentified Gene-Encoded huge The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
Information Artifact Ontology iao An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.
International Classification of Diseases, 10th Revision icd10 The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO).
International Classification of Diseases, 10th Revision, Clinical Modification icd10cm ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS).
International Classification of Diseases, 10th Revision, Procedure Coding System icd10pcs ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM).
International Classification of Diseases, 11th Revision icd11 Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO).
International Classification of Diseases, 9th Revision icd9 The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.
International Classification of Diseases, 9th Revision, Clinical Modification icd9cm ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.
Integrated Canine Data Commons icdc The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data.
International Classification of Diseases for Oncology icdo The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases.
ICEberg cis-integrative and mobilizable element iceberg.cime ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc.
ICEberg integrative and conjugative element iceberg.element ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria.
ICEberg family iceberg.family ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria.
ICEberg integrative and mobilizable element iceberg.ime ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc.
Integrative and Conjugative Element Ontology iceo A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.
Ion Channel Electrophysiology Ontology icepo The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools.
International Classification of Functioning, Disability and Health icf The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains.
Interlab Cell Line Collection iclc Cell line collections.
Informed Consent Ontology ico The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.
Intrinsically Disordered proteins with Extensive Annotations and Literature ideal IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins.
Infectious Disease Ontology ido Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.
The COVID-19 Infectious Disease Ontology idocovid19 The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO).
Dengue Fever Ontology idoden An ontology for dengue fever.
Malaria Ontology idomal An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.
Identifiers.org Ontology idoo Identifiers.org Ontology.
Identifiers.org Terms idot Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.
Intrinsically Disordered Proteins Ontology idpo IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state.
Image Data Resource idr Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies.
Immune Epitope Database iedb The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID.
Internet Engineering Task Force Language Tag ietf.language Shorthand representations of languages and their subtypes.
Event (INOH pathway ontology) iev The Event Ontology is an ontology of pathways.
Integrated Genomic Resources of human Cell Lines for Identification igrhcellid Cell line databases/resources.
International Geo Sample Number igsn IGSN is a globally unique and persistent identifier for material samples and specimens.
International Genome Sample Resource igsr The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set.
International Histocompatibility Workshop cell lines ihw The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics.
Illumina Probe Identifier illumina.probe Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.
Imanis Life Sciences cell line products imanis Cell line collections.
International Medical Device Regulators Forum imdrf The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence.
International Molecular Exchange imex The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.
Integrated Microbial Genomes Gene img.gene The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes.
Integrated Microbial Genomes Taxon img.taxon The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes.
IMGT/HLA human major histocompatibility complex sequence database imgt.hla IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species.
ImMunoGeneTics database covering immunoglobulins and T-cell receptors imgt.ligm IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species.
Database of Spatially Interacting Motifs in Proteins imotdb The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB.
Molecule role (INOH Protein name/family name ontology) imr MoleculeRole Ontology is an ontology for proteins/chemicals.
iNaturalist Observation inaturalist.observation The identifier for an observation in iNaturalist.
iNaturalist Place inaturalist.place Identifier for a place in iNaturalist.
iNaturalist Taxonomy inaturalist.taxon Identifier for a species in iNaturalist.
iNaturalist User inaturalist.user Identifier for a user in iNaturalist.
InChI inchi The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources.
InChIKey inchikey The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance.
The International Harmonization of Nomenclature and Diagnostic criteria inhand The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.
International Nonproprietary Names inn Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.
A Knowledge Resource for Innate Immunity Interactions and Pathways innatedb InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection.
Interaction Network Ontology ino he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks.
Nucleotide Sequence Database insdc The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.
INSDC CDS insdc.cds The coding sequence or protein identifiers as maintained in INSDC.
Genome assembly database insdc.gca The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea.
International Nucleotide Sequence Database Collaboration (INSDC) Run insdc.run An experimental run, served thrugh the ENA.
Sequence Read Archive insdc.sra The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA.
IntAct protein interaction database intact IntAct provides a freely available, open source database system and analysis tools for protein interaction data.
IntAct Molecule intact.molecule IntAct provides a freely available, open source database system and analysis tools for protein interaction data.
Human Intermediate Filament Database interfil The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis.
InterLex interlex InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets.
InterPro interpro InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
International Protein Index ipi IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms.
IRD Segment Sequence ird.segment Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information.
iRefWeb irefweb iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.
Database of experimentally verified IRES structures iresite The IRESite database presents information about the experimentally studied IRES (Internal Ribosome Entry Site) segments.
Insect Resistance Ontology iro
International Standard Book Number isbn The International Standard Book Number (ISBN) is for identifying printed books.
Insertion sequence elements database isfinder ISfinder is a database of bacterial insertion sequences (IS).
International Standard Name Identifier isni ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more.
ISO 3166-1 Country Code iso.3166 An identifier for a country in numeric format per ISO 3166-1.
International Standard Serial Number issn The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books.
Integrated Taxonomic Information System itis Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world.
Intelligence Task Ontology ito The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks.
IUPHAR family iuphar.family The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels.
Guide to Pharmacology Ligand iuphar.ligand The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels.
Guide to Pharmacology Target iuphar.receptor The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels.
Jackson Laboratories Strain jax Information about the C57BL/6J.
JAX Mice jaxmice JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory.
Japan Consortium for Glycobiology and Glycotechnology Database jcggdb JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan.
Japan Collection of Microorganisms jcm The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.
JRBC Cell Bank jcrb Cell line collections.
Japan Chemical Substance Dictionary jcsd The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).
Digital archive of scholarly articles jstor JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals.
JWS Online jws JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.
Kaggle kaggle Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.
Korean Cell Line Bank kclb Cell line collections.
Kyoto Encyclopedia of Genes and Genomes kegg Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
KEGG BRITE kegg.brite KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems.
KEGG Compound kegg.compound KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.
KEGG Drug Group kegg.dgroup KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG.
KEGG Disease kegg.disease The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations.
KEGG Drug kegg.drug KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.
KEGG Environ kegg.environ KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants.
KEGG Enzyme kegg.enzyme KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee.
KEGG Genes kegg.genes KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.
KEGG Genome kegg.genome KEGG Genome is a collection of organisms whose genomes have been completely sequenced.
KEGG Glycan kegg.glycan KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures.
KEGG LIGAND kegg.ligand
KEGG Metagenome kegg.metagenome The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.
KEGG Module kegg.module KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes.
KEGG Orthology kegg.orthology KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.
KEGG Pathways Database kegg.pathway KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
KEGG Reaction Class kegg.rclass KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns.
KEGG Reaction kegg.reaction KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.
Kerafast cell lines kerafast Cell line collections.
KNApSAcK knapsack KNApSAcK provides information on metabolites and the taxonomic class with which they are associated.
Kidney and Urinary Pathway Ontology kupo
KYinno cell lines kyinno Cell line collections.
clinical LABoratory Ontology labo LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.
Langua aLimentaria Thesaurus langual Langual stands for "langua alimentaria" or "language of food".
Livestock Breed Ontology lbo A vocabulary for cattle, chicken, horse, pig, and sheep breeds.
Leafsnap ID leafsnap identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide.
Global LEI Index lei Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI).
Lepidoptera Anatomy Ontology lepao The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.
LG Chemical Entity Detection Dataset (LGCEDe) lgai.cede LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e.
Ligand-Gated Ion Channel database lgic The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels.
LiceBase licebase Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry.
LigandBook ligandbook Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins.
LigandBox ligandbox LigandBox is a database of 3D compound structures.
Ligand Expo ligandexpo Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.
Cancer cell LInes GEne fusions portAl ligea Polymorphism and mutation databases.
Liver Cancer Model Repository limore Cell line databases/resources.
LINCS Cell lincs.cell The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents.
LINCS Data lincs.data The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents.
LINCS Protein lincs.protein The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins).
LINCS Small Molecule lincs.smallmolecule The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents.
Linguist linguist Registry of programming languages for the Linguist program for detecting and highlighting programming languages.
LinkML linkml Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data.
LipidBank lipidbank LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
LIPID MAPS ID lipidmaps The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy.
Lipid Ontology lipro An ontology representation of the LIPIDMAPS nomenclature classification.
LNCipedia lncipedia A comprehensive compendium of human long non-coding RNAs.
Loggerhead nesting loggerhead
Logical Observation Identifiers Names and Codes loinc The international standard for identifying health measurements, observations, and documents.
Lonza lonza Contains information about cells and data sheets related to transfection.
The localization and quantitation atlas of the yeast proteome loqate The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library.
LOTUS Initiative for Open Natural Products Research lotus LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs.
Livestock Product Trait Ontology lpt The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.
Locus Reference Genomic lrg A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants.
Laboratory of Systems Pharmacology Compound lspci Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions).
Long Term Ecological Research Controlled Vocabulary lter Ecological terms.
Mouse adult gross anatomy ma A structured controlled vocabulary of the adult anatomy of the mouse (Mus).
Mechanism, Annotation and Classification in Enzymes macie MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms.
MaizeGDB Locus maizegdb.locus MaizeGDB is the maize research community's central repository for genetics and genomics information.
Mathematical modeling ontology mamo The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.
Mammalia Polymorphism Database mampol The Mammalia Polymorphism Database is a secondary database designed to provide a collection of all the existing polymorphic sequences in the MammaliaOnline query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches).
Multiple alignment mao An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.
MassBank accession ID massbank MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).
MassIVE massive MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data.
Minimal Anatomical Terminology mat Minimal set of terms for anatomy.
MatrixDB matrixdb MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides.
MatrixDB Association matrixdb.association MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule.
Medical Action Ontology maxo An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.
Mouse Brain Atlas mba A controlled vocabulary to support the study of transcription in the mouse brain.
Cell Line Ontology [derivative] mcc Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them.
Microbial Conditions Ontology mco Microbial Conditions Ontology is an ontology.
Medical Data Models mdm The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms.
Medical Dictionary for Regulatory Activities Terminology meddra The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans.
Human Medical Genetics medgen MedGen is a portal for information about conditions and phenotypes related to Medical Genetics.
MedlinePlus Health Topics medlineplus MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends.
MEROPS Clan merops.clan The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
MEROPS Entry merops.entry The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
MEROPS Family merops.family The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
Medical Subject Headings mesh MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus.
MeSH 2012 mesh.2012 MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus.
MeSH 2013 mesh.2013 MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus.
MetaboLights Compound metabolights MetaboLights is a database for Metabolomics experiments and derived information.
Metabolic Encyclopedia of metabolic and other pathways metacyc.compound MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life.
MetaCyc Reaction metacyc.reaction MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life.
MetaNetX chemical metanetx.chemical MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments.
MetaNetX compartment metanetx.compartment MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments.
MetaNetX reaction metanetx.reaction MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments.
Metabolic Atlas metatlas A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis.
Metabolic Atlas Metabolite metatlas.metabolite A subspace of Metabolic Atlas for compartment-specific records for metabolites.
Metabolic Atlas Reaction metatlas.reaction A subspace of Metabolic Atlas for reactions.
Metabolite and Tandem Mass Spectrometry Database metlin The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data.
Metabolic Network Exchange Database metnetdb The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis.
Metabolome Express mex A public place to process, interpret and share GC/MS metabolomics datasets.
Mental Functioning Ontology mf The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.
Mammalian Feeding Muscle Ontology mfmo The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.
Medaka fish anatomy and development mfo A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.
Emotion Ontology mfoem An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.
Mental Disease Ontology mfomd The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease.
Aclame mge ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.
Mouse Genome Informatics mgi The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
MGnify Analysis mgnify.analysis Analyses of microbiome data within MGnify.
MGnify Project mgnify.proj MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples.
MGnify Sample mgnify.samp The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample.
Molecular Interactions Controlled Vocabulary mi The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.
Minimal Information About Anatomy ontology miaa
Minimum Anformation About a Phylogenetic Analysis Ontology miapa The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard.
Ontology of Prokaryotic Phenotypic and Metabolic Characters micro An ontology of prokaryotic phenotypic and metabolic characters.
MicroScope microscope MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.
MicrosporidiaDB microsporidia MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
Merck Millipore (EMD Millipore) millipore Cell line collections.
MimoDB mimodb MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs.
Minimal Viable Identifier minid Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.
MINID Test minid.test Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.
Molecular Interaction Database mint The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.
MIPModDB mipmod MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence.
Identifiers.org Registry mir The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections.
miRBase pre-miRNA mirbase The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation.
miRBase Families mirbase.family The miRBase database is a searchable database of published miRNA sequences and annotation.
miRBase mature miRNA mirbase.mature The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation.
mirEX mirex mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis.
Identifiers.org namespace miriam Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain.
MIRIAM Registry collection miriam.collection MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections.
MIRIAM Legacy Registry Identifier miriam.resource MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.
microRNA Ontology mirnao An application ontology for use with miRNA databases.
miRNEST mirnest miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.
Mosquito insecticide resistance miro Application ontology for entities related to insecticide resistance in mosquitos.
mirTarBase ID mirtarbase miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs.
miRNA Target Prediction at EMBL mirte This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs.
GSC Minimal Information about any Sequence mixs The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS).
MLCommons Association mlc MLCommons Association artifacts, including benchmark results, datasets, and saved models.
Molecular Modeling Database mmdb The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB).
Melanoma Molecular Map Project Biomaps mmmp.biomaps A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.
Measurement method ontology mmo A representation of the variety of methods used to make clinical and phenotype measurements.
MarCat mmp.cat MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.
MarDB mmp.db MarDB includes all sequenced marine microbial genomes regardless of level of completeness.
MarFun mmp.fun MarFun is manually curated database for marine fungi which is a part of the MAR databases.
MarRef mmp.ref MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.
Mutant Mouse Resource and Research Centers mmrrc The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.
MMsINC mmsinc MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications.
Multum MediSource Lexicon mmsl The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information.
Mouse Developmental Stages mmusdv Life cycle stages for Mus Musculus.
Microarray experimental conditions mo The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.
MobiDB mobidb MobiDB is a database of protein disorder and mobility annotations.
Protein modification mod The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.
ModelDB modeldb ModelDB is a curated, searchable database of published models in the computational neuroscience domain.
ModelDB concept modeldb.concept Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models.
Molbase molbase Molbase provides compound data information for researchers as well as listing suppliers and price information.
MolBase molbase.sheffield An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students.
MolMeDB molmedb MolMeDB is an open chemistry database about interactions of molecules with membranes.
Database of Macromolecular Movements molmovdb The Molecular Movements Database lists motions in proteins and other macromolecules.
Monarch Disease Ontology mondo A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.
Molecular Process Ontology mop MOP is the molecular process ontology.
Morpheus model repository morpheus The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software. .
MOSAiC Ontology mosaic An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io).
Mammalian Phenotype Ontology mp The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species.
Mouse pathology ontology mpath A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes.
Microbial Protein Interaction Database mpid The microbial protein interaction database (MPIDB) provides physical microbial interaction data.
Minimum PDDI Information Ontology mpio An ontology of minimum information regarding potential drug-drug interaction information.
MHC Restriction Ontology mro The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.
Mass spectrometry ontology ms The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards.
Molecular Signatures Database msigdb The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software.
Metabolomics Standards Initiative Ontology msio an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.
Mouse Tumor Biology Database mtbd The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors.
MultiCellDS multicellds MultiCellDS is data standard for multicellular simulation, experimental, and clinical data.
MultiCellDS Digital Cell Line multicellds.cell_line MultiCellDS is data standard for multicellular simulation, experimental, and clinical data.
MultiCellDS collection multicellds.collection MultiCellDS is data standard for multicellular simulation, experimental, and clinical data.
MultiCellDS Digital snapshot multicellds.snapshot MultiCellDS is data standard for multicellular simulation, experimental, and clinical data.
Metabolomics Workbench Project mw.project Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).
Metabolomics Workbench Study mw.study Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).
MycoBrowser leprae myco.lepra Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis.
MycoBrowser marinum myco.marinum Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis.
MycoBrowser smegmatis myco.smeg Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis.
TubercuList knowledge base myco.tuber Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis.
Fungal Nomenclature and Species Bank mycobank MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.
Universal Spectrum Identifier mzspec The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it.
Name-to-Thing n2t An ARK resolver as well as resolver built with common prefixes as in Identifiers.org.
NameRXN namerxn The nomenclature used for named reactions in text mining software from NextMove.
Natural Product-Drug Interaction Research Data Repository napdi The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).
Nucleic Acids Phylogenetic Profiling napp NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes.
National Academic Research and Collaborations Information System narcis NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases.
NASC code nasc The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
National Bibliography Number nbn The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland.
Neuro Behavior Ontology nbo An ontology of human and animal behaviours and behavioural phenotypes.
NITE Biological Resource Center nbrc NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications.
National Center for Advancing Translation Sciences BioPlanet ncats.bioplanet The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them.
NCATS Drugs ncats.drug The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information.
Assembly ncbi.assembly A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.
NCBI Genome ncbi.genome This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.
NCBI Registry ncbi.resource A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources.
NCBI Bookshelf ncbibook The NCBI Bookshelf provides free online access to books and documents in life science and healthcare.
Entrez Gene ncbigene Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis.
GenInfo Identifier ncbigi A GI number (for GenInfo Identifier, sometimes written in lower case, gi) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI.
NCBI Protein ncbiprotein The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
NCBI Taxonomy ncbitaxon The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.
NCI Metathesaurus ncim NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities.
NCI Thesaurus ncit NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code.
Non-Coding RNA Ontology ncro An ontology for non-coding RNA, both of biological origin, and engineered.
National Drug Code ndc The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use.
National Drug Data File nddf FDB MedKnowledge encompasses medications approved by the U.S.
Network Data Exchange ndex The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge.
National Drug File - Reference Terminology ndfrt NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model.
Nematode & Neglected Genomics nembase NEMBASE is a comprehensive Nematode Transcriptome Database.
Neural ElectroMagnetic Ontology nemo This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects.
NIF Standard Ontology: Neurolex neurolex The NeuroLex project is a dynamic lexicon of terms used in neuroscience.
NeuroMorpho neuromorpho NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons.
NeuroNames neuronames BrainInfo is designed to help you identify structures in the brain.
NeuronDB neurondb NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances.
NeuroVault Collection neurovault.collection Neurovault is an online repository for statistical maps, parcellations and atlases of the brain.
NeuroVault Image neurovault.image Neurovault is an online repository for statistical maps, parcellations and atlases of the brain.
Nematode Expression Pattern DataBase nextdb NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans.
nextProt nextprot neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases.
neXtProt family nextprot.family NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.
NASA GeneLab ngl NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.
NINDS Human Cell and Data Repository nhcdr Cell line collections.
NIA Mouse cDNA Project niaest A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.
NIF Cell nif.cell Neuronal cell types.
NIF Dysfunction nif.dysfunction
NIF Standard Ontology: External nif.ext NIFEXT covers IRIs that were "external" identifiers that were brought into the ontology at some point in time.
NIF Gross Anatomy nif.grossanatomy
NIF Standard Ontology nif.std NIFSTD is a base namespace (like obo:) which houses many other prefixes.
NIH RePORTER nihreporter.project RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding.
NIST Chemistry WebBook nist The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet.
National Library of Medicine Catalog nlm Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings.
NeuroLex Anatomy nlx.anat NLXANAT covers anatomy terms.
NIF Standard Ontology: Brain Regions nlx.br NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).
NIF Standard Ontology: Cell Types nlx.cell NLXCELL conatins cell types with a focus on neuron types.
NIF Standard Ontology: Chemical nlx.chem NLXCHEM covers chemicals.
NeuroLex Dysfunction nlx.dys NLXDYS covers dysfunction, diseases, and disorders.
NIF Standard Ontology: Cognitive Function nlx.func NLXFUNC covers terms for cognitive function.
NIF Standard Ontology: Investigations nlx.inv NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.
NIF Standard Ontology: Molecules nlx.mol NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system.
NIF Standard Ontology: OEN Terms in Neurolex nlx.oen NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results).
NIF Standard Ontology: Organisms nlx.org NLXORG covers organisms.
NIF Standard Ontology: Qualities nlx.qual NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).
NIF Standard Ontology: Digital Resources nlx.res NLXRES covers digital resources.
NIF Standard Ontology: Subcellular Entities nlx.sub NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO).
National Microbiome Data Collaborative nmdc An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.
National Microbial Pathogen Data Resource nmpdr The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.
NMR-instrument specific component of metabolomics investigations nmr nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.
NMRShiftDB structure ID nmrshiftdb2 NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra.
NOAA Fisheries Species Directory noaa Identifier for a species on the noaa fisheries website.
A nomenclatural ontology for biological names nomen NOMEN is a nomenclatural ontology for biological names (not concepts).
NONCODE v3 noncodev3 NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies.
NONCODE v4 Gene noncodev4.gene NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies.
NONCODE v4 Transcript noncodev4.rna NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies.
Nonribosomal Peptides Database norine Norine is a database dedicated to nonribosomal peptides (NRPs).
Novus Biologicals novus A vendor of antibodies and other biologics.
Natural Product Activity and Species Source Database npass Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data. .
NanoParticle Ontology npo An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.
USA National Service Center Number nsc Identifier used by the Cancer Chemotherapy National Service Center.
National Science Foundation Award nsf.award Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database.
National Uniform Claim Committee Characteristic nucc.characteristic The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses.
National Uniform Claim Committee Taxonomy nucc.taxonomy The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions.
NucleaRDB nuclearbd NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs).
Nucleotide nucleotide The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB.
Web Annotation Ontology oa The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture.
Ontology of Adverse Events oae The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events.
Ontology of Arthropod Circulatory Systems oarcs OArCS is an ontology describing the Arthropod ciruclatory system.
Ontology of Biological Attributes oba A collection of biological attributes (traits) covering all kingdoms of life.
Ontology of Biological and Clinical Statistics obcs OBCS stands for the Ontology of Biological and Clinical Statistics.
Ontology for Biomedical Investigations obi The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations.
Ontology for Biobanking obib The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank.
Open Biological and Biomedical Ontologies obo The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.
OBO in OWL oboinowl This meta-ontology is self-describing.
OpenCitations Corpus occ The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.
Open Citation Identifier oci Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.

OCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash.

Ontology Concept Identifiers ocid 'ocid' stands for "Ontology Concept Identifiers" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.
Online Computer Library Center WorldCat oclc The global library cooperative OCLC maintains WorldCat.
Open Data for Access and Mining odam Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider.
Open Data Commons for Spinal Cord Injury odc.sci The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data.
Open Data Commons for Traumatic Brain Injury odc.tbi The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data.
Odor Molecules DataBase odor OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors.
The Ontology of Genes and Genomes ogg OGG is a biological ontology in the area of genes and genomes.
Ontology for genetic interval ogi OGI formalized the genomic element by defining an upper class 'genetic interval'.

The definition of 'genetic interval' is "the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture."

Related paper:

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Ontology for General Medical Science ogms The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter.
Ontology of Genetic Susceptibility Factor ogsf An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.
Oral Health and Disease Ontology ohd The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.
Ontology of Host-Microbiome Interactions ohmi OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.
Ontology of Host Pathogen Interactions ohpi OHPI is a biomedical ontology in the area of host-pathogen interactions.
ISO Object Identifier oid OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.
Medaka Developmental Stages olatdv Life cycle stages for Medaka.
Ontology of units of Measure om The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units.
OMA Group oma.grp OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences.
OMA HOGs oma.hog Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database.
OMA Protein oma.protein OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences.
Online Mendelian Inheritance in Animals omia Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).
Ontologized MIABIS omiabis An ontological version of MIABIS (Minimum Information About BIobank data Sharing).
Online Mendelian Inheritance in Man omim Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.
OMIM Phenotypic Series omim.ps A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.
Ontology for MicroRNA Target omit The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain.
OBO Metadata Ontology omo An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies.
Observational Medical Outcomes Partnership omop The OMOP Common Data Model allows for the systematic analysis of disparate observational databases.
Ontology of Microbial Phenotypes omp An ontology of phenotypes covering microbes.
Ontology of Medically Related Social Entities omrse This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations.
OncoTree oncotree OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.
Ontology for Nutritional Epidemiology one An ontology to standardize research output of nutritional epidemiologic studies.
Ontology for Nutritional Studies ons The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies.
Ontology for Avida digital evolution platform ontoavida The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).

The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution.

Obstetric and Neonatal Ontology ontoneo The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.
Ontology of Organizational Structures of Trauma centers and Trauma systems oostt An ontology built for representating the organizational components of trauma centers and trauma systems.
Ontology of Physics for Biology opb The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems.
OpenAlex openalex OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other.
Ontology for Parasite LifeCycle opl The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.
Orientations of Proteins in Membranes Database opm The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.
Ontology of Precision Medicine and Investigation opmi OPMI is a biomedical ontology in the area of precision medicine and its related investigations.
Open Researcher and Contributor orcid ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers.
Olfactory Receptor Database ordb The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs).
OriDB Saccharomyces oridb.sacch OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe.
OriDB Schizosaccharomyces oridb.schizo OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe.
Ontology of RNA Sequencing ornaseq An application ontology designed to annotate next-generation sequencing experiments performed on RNA.
Orphanet orphanet Orphanet is a reference portal for information on rare diseases and orphan drugs.
Orphanet Rare Disease Ontology orphanet.ordo The Orphanet Rare Disease ontology (ORDO) is 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. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).
Orthology Ontology orth The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH).
OrthoDB orthodb OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi.
Oryzabase Gene oryzabase.gene Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information.
Oryzabase Mutant oryzabase.mutant Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information.
Oryzabase Reference oryzabase.reference The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.
Oryzabase Stage oryzabase.stage Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information.
Oryzabase Strain oryzabase.strain Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information.
OASIS Open Services for Lifecycle Collaboration Core Vocabulary oslc Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains.
Oryza Tag Line otl Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv.
Open Tree of Life otol Identifier for an entity in open tree of life.
Ontology of Vaccine Adverse Events ovae OVAE is a biomedical ontology in the area of vaccine adverse events.
Web Ontology Language owl Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages.
P3DB Protein p3db.protein Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species.
P3DB Site p3db.site Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species.
Paleobiology Database paleodb The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record.
Protein and Associated NucleotideDomains with Inferred Trees pandit PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.
Panorama Public panorama Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow.
Protein ANalysis THrough Evolutionary Relationships Classification System panther.family The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
PANTHER Node panther.node The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
PANTHER Pathway panther.pathway The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
PANTHER Pathway Component panther.pthcmp The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
Plant Anatomy Ontology pao
Protein Alignment organised as Structural Superfamily pass2 The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.
PathBank pathbank PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E.
Pathguide pathguide Pathguide contains information about 325 biological related resources and molecular interaction related resources.
PathoPlant® pathoplant PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis.
Pathway Commons pathwaycommons Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search.
Phenotype And Trait Ontology pato PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.
Provenance, Authoring, and Versioning Vocabulary pav PAV is a lightweight ontology for tracking provenance, authorship, and versioning.
PaxDb Organism paxdb.organism PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms.
PaxDb Protein paxdb.protein PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms.
Pazar Transcription Factor pazar The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation.
Primate Brain Atlas pba A controlled vocabulary to support the study of transcription in the primate brain.
Provisional Cell Ontology pcl Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.
Population and Community Ontology pco The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities.
Platynereis stage ontology pd_st
PDB Structure pdb The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.
Chemical Component Dictionary pdb-ccd The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries.
PDB ligand ID pdb.ligand The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.
PDBsum; at-a-glance overview of macromolecular structures pdbsum PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
Proteomic Data Commons pdc.study The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public.
The Prescription of Drugs Ontology pdro An ontology to describe entities related to prescription of drugs.
Platynereis Developmental Stages pdumdv Life cycle stages for Platynereis dumerilii.
Plant Experimental Conditions Ontology peco A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.
Protein Ensemble Database ped The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.
Protein Ensemble Database ensemble ped.ensemble The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.
PSI Extended File Format peff
Pennsieve pennsieve Pennsieve is a publicly accessible Scientific Data Management and publication platform.
PepBank Peptide Database pepbank PepBank is a database of peptides based on sequence text mining and public peptide data sources.
PeptideAtlas peptideatlas The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.
PeptideAtlas Dataset peptideatlas.dataset Experiment details about PeptideAtlas entries.
PerkinElmer cell line collection perkinelmer Cell line collections.
Peroxibase peroxibase Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.
Alan Wood's Pesticides pesticides The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients.
Pfam pfam The Pfam database contains information about protein domains and families.
Pfam Clans pfam.clan Higher order grouping of Pfam families.
Proteoform Atlas pfr Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets.
Plant Growth and Development Stage pgdso
Polygenic Score Catalog pgs The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation.
Progenetix pgx The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies.
PharmacoDB Cells pharmacodb.cell Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date.
PharmacoDB Datasets pharmacodb.dataset Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date.
PharmacoDB Tissues pharmacodb.tissue Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date.
PharmGKB Disease pharmgkb.disease The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies.
PharmGKB Drug pharmgkb.drug The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies.
Pharmacogenetics and Pharmacogenomics Knowledge Base pharmgkb.gene The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies.
PharmGKB pharmgkb.pathways The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies.
Pharmacogene Variation Consortium pharmvar The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository.
Phenol-Explorer phenolexplorer Phenol-Explorer is an electronic database on polyphenol content in foods.
PhenX Toolkit phenx A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants.
Pathogen Host Interaction Phenotype Ontology phipo Ontology of species-neutral phenotypes observed in pathogen-host interactions.
PhosphoPoint Kinase phosphopoint.kinase PhosphoPOINT is a database of the human kinase and phospho-protein interactome.
PhosphoPoint Phosphoprotein phosphopoint.protein PhosphoPOINT is a database of the human kinase and phospho-protein interactome.
PhosphoSite Protein phosphosite.protein PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites.
PhosphoSite Residue phosphosite.residue PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites.
PhosphoSite Site Group phosphosite.sitegroup Site groups are orthologous positions in human, mouse, rat, etc.
PhylomeDB phylomedb PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range.
Plant Genome Network phytozome.locus Phytozome is a project to facilitate comparative genomic studies amongst green plants.
Database of structurally defined protein interfaces pibase PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases.
PicTar pictar
NCI Pathway Interaction Database: Pathway pid.pathway The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways.
Animal Genome Pig QTL pigqtldb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species.
Protein Interaction Network Analysis pina Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management.
PiroplasmaDB piroplasma PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
PIR Superfamily Classification System pirsf The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.
PK-DB pkdb PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research.
Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology plana PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.
Planarian Phenotype Ontology planp Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.
Plant Transcription Factor Database planttfdb The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species.
PlasmoDB plasmodb AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
Plasmodium Life Cycle plo
CutDB pmap.cutdb The Proteolysis MAP is a resource for proteolytic networks and pathways.
SubstrateDB pmap.substratedb The Proteolysis MAP is a resource for proteolytic networks and pathways.
PMCID pmc PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature.
Protein Model Database pmdb The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.
Protein Model Portal pmp The number of known protein sequences exceeds those of experimentally solved protein structures.
Physical Medicine and Rehabilitation pmr Resource for the community to store, retrieve, search, reference, and reuse CellML models.
Physiome Model Repository workspace pmr.workspace Workspace (Git repository) for modeling projects managed by the Physiome Model Repository.
Plant Ontology po The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
Pocketome pocketome Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank.
PolBase polbase Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity.
PomBase pombase PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe.
Porifera Ontology poro An ontology describing the anatomical structures and characteristics of Porifera (sponges).
Pesticide Properties DataBase ppdb PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties.
Plant Phenology Ontology ppo An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.
Europe PMC Preprints ppr Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000.
Protein Ontology pr The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies.
Prefix Commons prefixcommons A registry of life science prefxes.
PRIDE Controlled Vocabulary pride The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.
PRIDE Project pride.project The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.
PRINTS compendium of protein fingerprints prints PRINTS is a compendium of protein fingerprints.
Probes and Drugs probesanddrugs The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison.
Probability Distribution Ontology probonto ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae.
Process Chemistry Ontology proco PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.
ProDom prodom ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.
ProGlycProt proglyc ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue).
Proteomics data and process provenance propreo A comprehensive proteomics data and process provenance ontology.
PROSITE prosite PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
ProtClustDB protclustdb ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes.
Database of protein-protein complexes protcom This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures.
ProteomicsDB Peptide proteomicsdb.peptide ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community.
ProteomicsDB Protein proteomicsdb.protein ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community.
ProtoNet Cluster protonet.cluster ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins.
ProtoNet ProteinCard protonet.proteincard ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins.
PROV Namespace prov The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.
Protein Structural Change Database pscdb The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding.
Performance Summary Display Ontology psdo Performance Summary Display Ontology (PSDO) (pronounced "pseudo" or "sudo") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations.
PseudoGene pseudogene This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.
Pseudomonas Genome Database pseudomonas The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species.
Protein Affinity Reagents psipar Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods.
Plant Stress Ontology pso The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.
Phenoscape Publication pspub Documentation of the Phenoscape Curation Workflow.
NCBI PubChem database of bioassay records pubchem.bioassay PubChem provides information on the biological activities of small molecules.
PubChem Cell Line pubchem.cell Cell Lines in PubChem.
PubChem Classification pubchem.classification The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data.
PubChem CID pubchem.compound PubChem provides information on the biological activities of small molecules.
PubChem Element pubchem.element PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number.
PubChem Substance ID (SID) pubchem.substance PubChem provides information on the biological activities of small molecules.
Publons publication ID publons.publication identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID).
Publons Researcher publons.researcher Database of researchers to track publications, citation metrics, peer reviews, and journal editing work.
PubMed ID pubmed PubMed is a service of the U.S.
Publishing Roles Ontology puro An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process.
Pathway ontology pw The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure.
Publishing Workflow Ontology pwo An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity.
ProteomeXchange px The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.
PyPI pypi The Python Package Index (PyPI) is a repository for Python packages.
The data cube vocabulary qb This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF.
Animal Genome QTL qtldb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species.
Quantities, Units, Dimensions, and Types Ontology qudt Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.
Radiomics Ontology radiomics The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features.
RSNA Informatics RadLex radlex A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research.

RadLex provides the foundation for vital data resources used in radiology:

  • The LOINC/RSNA Radiology Playbook
  • RadElement Common Data Elements -RadReport Radiology Reporting Templates

The development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.

RAP-DB Locus rapdb.locus Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp.
Rice annotation Project database rapdb.transcript Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp.
Rat Genome Database ratmap The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome.
Rebuilding a Kidney rbk (Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function.
Radiation Biology Ontology rbo RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.
RIKEN Bioresource Center Cell Bank rcb Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center.
Resource Description Framework rdf This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts.
RDF Schema rdfs RDF Schema provides a data-modelling vocabulary for RDF data.
RGD Disease Ontology rdo Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms.
re3data re3data Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.
Reactome reactome The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.
Reaxys reaxys Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents.
REBASE Enzyme Number rebase REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M).
Human Plasma Membrane Receptome Families receptome.family The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database.
Regulatory Elements Database for Drosophila redfly REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).
Reference Sequence Collection refseq The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.
Reagent Ontology reo The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials.
RepeatsDB Protein repeatsdb.protein RepeatsDB is a database of annotated tandem repeat protein structures.
RepeatsDB Structure repeatsdb.structure RepeatsDB is a database of annotated tandem repeat protein structures.
REPRODUCE-ME Ontology reproduceme The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment.
Protein covalent bond resid The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
Regulation of Transcription Ontology reto Regulation of Transcription.
Physico-chemical process rex An ontology of physico-chemical processes, i.e.
Regulation of Gene Expression Ontology rexo Regulation of Gene Expression.
Rfam database of RNA families rfam The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).
Internet Standard -- IETF Request for Comments rfc Legacy site for IETF RFC proposals.
Rice Genome Annotation Project rgap This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes.
Rat Genome Database rgd Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community.
Rat Genome Database qTL rgd.qtl Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community.
Rat Genome Database strain rgd.strain Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community.
Rhea, the Annotated Reactions Database rhea Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest.
Ribocentre ribocentre Ribocentre is designed to contain comprehensive information of all natural ribozymes.
Rice Metabolic Pathways ricecyc RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa).
Rice Genome Annotation Project ricegap The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare.
RiceNetDB Compound ricenetdb.compound RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation.
RiceNetDB Gene ricenetdb.gene RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation.
RiceNetDB miRNA ricenetdb.mirna RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation.
RiceNetDB Protein ricenetdb.protein RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation.
RiceNetDB Reaction ricenetdb.reaction RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation.
RISM Online rism RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project.
RNA SSTRAND rna_sstrand RNA STRAND contains known RNA secondary structures of any type and organism.
RNACentral ID rnacentral RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.
Database of RNA Junctions and Kissing loop Structures rnajunction Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each.
RNAloops rnaloops Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank.
The RNA Modification Database rnamod A comprehensive listing of post-transcriptionally modified nucleosides from RNA -.
RNA Modification Database rnamods The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA.
RNA ontology rnao Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.
Relation Ontology ro The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.
Role Ontology roleo The Role Ontology (RoleO) is a ontology in the domain of role classification.
Research Organization Registry ror ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations.
Rodent Unidentified Gene-Encoded Large Proteins rouge The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
Research Resource Identification rrid The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections.
Rat Strain Ontology rs Ontology of rat strains.
Registry of Toxic Effects of Chemical Substances rtecs RTECS is a compendium of data extracted from the open scientific literature.
runBioSimulations runbiosimulations runBioSimulations is a platform for sharing simulation experiments and their results.
Name Reaction Ontology rxno RXNO is the name reaction ontology.
RxNorm rxnorm RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database.
The S/MAR transaction DataBase s_mart_db S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix.
SABIO-RK Compound sabiork.compound SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
SABIO-RK EC Record sabiork.ec SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
SABIO Reaction Kinetics sabiork.kineticrecord SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
SABIO-RK Reaction sabiork.reaction SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List sael
Salk Institute for Biological Studies salk Scientific research institute for neuroscience, genetics, immunology, plant biology and more.
Subcellular Anatomy Ontology sao SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.
Small Angle Scattering Biological Data Bank sasbdb Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models.
Systems Biology Ontology sbo The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling.
Sickle Cell Disease Ontology scdo An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease.
Selventa Chemicals schem Selventa legacy chemical namespace used with the Biological Expression Language.
Schema.org schema Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond.
Scholia Registry scholia.resource A frontend to Wikidata.
Selventa Complexes scomp Selventa legacy complex namespace used with the Biological Expression Language.
Structural Classification of Protein scop The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships.
Scopus Researcher scopus Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings.
Scholarly Contributions and Roles Ontology scoro An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g.
Saccharomyces cerevisiae promoter database scpd Database containing promotor sequences found in Saccharomyces cerevisiae.
SciCrunch Registry scr The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services.
ScerTF scretf ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species.
Structural Database of Allergenic Proteins sdap SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes.
Spectral Database for Organic Compounds sdbs The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds.
Sustainable Development Goals Interface Ontology sdgio An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators.
Selventa Diseases sdis Selventa legacy disease namespace used with the Biological Expression Language.
SED-ML data format sedml.format Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).
SED-ML model format sedml.language Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).
The SEED; seed This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED.
SEED Compound seed.compound This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED.
SEED Reactions seed.reaction ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants.
Southwestern Environmental Information Network seinet A vocabulary about species to support the environmental research community in Arizona and New Mexico.
Sample processing and separation techniques sep A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.
Scientific Evidence and Provenance Information Ontology sepio An ontology for representing the provenance of scientific claims and the evidence that supports them.
Selventa Families sfam Selventa legacy protein family namespace used with the Biological Expression Language.
Saccharomyces Genome Database sgd The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.
Saccharomyces genome database pathways sgd.pathways Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).
Sol Genomics Network sgn The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.
Shapes Constraint Language shacl A language for validating RDF graphs against a set of conditions.
ShareLoc shareloc ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc.
Sharkipedia Species sharkipedia.species Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone.
Sharkipedia Trait sharkipedia.trait Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone.
Sharkipedia Trend sharkipedia.trend Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone.
Animal Genome Sheep QTL sheepqtldb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species.
Shape Expression Vocabulary shex The Shape Expressions (ShEx) language describes RDF nodes and graph structures.
ShiBASE shibase The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format.
Social Insect Behavior Ontology sibo Social Behavior in insects.
SIDER Drug sider.drug SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms.
SIDER Side Effect sider.effect SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms.
Sigma Aldrich sigmaaldrich Sigma Aldrich is a life sciences supply vendor.
Signaling Gateway signaling-gateway The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.
Signaling Network Open Resource signor SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.
SIGNOR Relation signor.relation Identifiers for relationships between proteins and complexes, along with their type and provenance.
Semanticscience Integrated Ontology sio The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.
Sequencing Initiative Suomi sisu The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians.
SitEx sitex SitEx is a database containing information on eukaryotic protein functional sites.
Stemcell Knowledge and Information Portal skip SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine.
Simple Knowledge Organization System skos SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web.
Simple Knowledge Organization System eXtension for Labels skosxl The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web.
SUM Breast Cancer Cell Line Knowledge Base slkbase Cell line databases/resources.
Simple Modular Architecture Research Tool smart The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.
C. elegans Small Molecule Identifier Database smid SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C.
Simplified molecular-input line-entry system smiles Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.
Small Molecule Pathway Database smpdb The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually.
Snapshot snap Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality.
SNOMED CT (International Edition) snomedct SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.
snoRNABase snornabase A comprehensive database of

human H/ACA and C/D box snoRNAs.

SNP to Transcription Factor Binding Sites snp2tfbs SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome.
SNP500Cancer snp500cancer The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.
Sequence types and features ontology so The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation.
Suggested Ontology for Pharmacogenomics sopharm SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge.
Glycine max Genome Database soybase SoyBase is a repository for curated genetics, genomics and related data resources for soybean.
Span span Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality.
SpBase spbase SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin.
Spider Ontology spd An ontology for spider comparative biology including anatomical parts (e.g.
Software Package Data Exchange License spdx The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation.
Swiss Personalized Health Network Schema sphn The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland.
SPIKE Map spike.map SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community.
Spectra Hash Code splash The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed.
SpliceNest splicenest SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome.
Signaling Pathways Project spp The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors.
Search PRINTS-S sprint SPRINT (Search PRINTS-S) provides an interface to the PRINTS-S database.
FAIRsharing Subject Ontology srao The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences.
System Science of Biological Dynamics dataset ssbd.dataset Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics.
System Science of Biological Dynamics project ssbd.project Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics.
Sequence-Structural Templates of Single-member Superfamilies sstoss SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2.
Statistical Torsional Angles Potentials stap STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures.
The Statistical Methods Ontology stato STATO is the statistical methods ontology.
Search Tool for Interactions of Chemicals stitch STITCH is a resource to explore known and predicted interactions of chemicals and proteins.
Store DB storedb STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation.
STOREDB at University of Cambridge storedb.dataset Datasets inside StoreDB.
STOREDB at University of Cambridge storedb.file File inside StoreDB.
STOREDB at University of Cambridge storedb.study Study inside StoreDB.
Search Tool for Retrieval of Interacting Genes/Proteins string STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge.
UMLS Semantic Types Ontology sty UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types.
Bacillus subtilis genome sequencing project subtilist SubtiList serves to collate and integrate various aspects of the genomic information from B.
SubtiWiki subtiwiki SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis.
SugarBind sugarbind The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference.
SUPERFAMILY supfam SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt.
Semantic Web for Earth and Environment Technology Ontology sweetrealm The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL.
Software Heritage swh Software Heritage is the universal archive of software source code.
SWISS-MODEL Repository swiss-model The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences.
SwissLipid swisslipid SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization.
SwissRegulon swissregulon A database of genome-wide annotations of regulatory sites.
Software ontology swo The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data.
A Semantic Web Rule Language Combining OWL and RuleML swrl SWRL enables Horn-like rules to be combined with an OWL knowledge base.
Symptom Ontology symp The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases.
Gemina Symptom Ontology syoid
Toxin and Toxin Target Database t3db Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.
Tick Anatomy Ontology tads The anatomy of the Tick, Families: Ixodidae, Argassidae.
Terminology of Anatomy of Human Embryology tahe
Terminology of Anatomy of Human Histology tahh
TAIR Gene tair.gene The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
The Arabidopsis Information Resource tair.locus The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
TAIR Protein tair.protein The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
Teleost Anatomy Ontology tao Multispecies fish anatomy ontology.
TarBase tarbase TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.
Taxonomic rank vocabulary taxrank A vocabulary of taxonomic ranks (species, family, phylum, etc).
Tick Cell Biobank tcb Cell line collections.
The Cell Cycle DB tccd Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle.
Transporter Classification Database tcdb The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system.
Terminologia Embryologica te The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures.
Classification of Transcription Factors in Mammalia tfclass TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains.
Tetrahymena Genome Database tgd The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence.
Mosquito gross anatomy ontology tgma A structured controlled vocabulary of the anatomy of mosquitoes.
Getty Thesaurus of Geographic Names tgn
Terminologia Histologica th The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology.
Thermo Fisher Scientific thermofisher ThermoFisher is a life sciences supply vendor.
TIGR protein families tigrfam TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.
Time Ontology in OWL time Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages.
Tohoku University cell line catalog tkg Collection of cell lines by Tohoku University.
Telethon Network of Genetic Biobanks tngb Cell line collections.
Plant Trait Ontology to A controlled vocabulary to describe phenotypic traits in plants.
TOKU-E Cell-culture Database tokue Cell line databases/resources.
Tree of Life Web Project tol The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world.
Topology Data Bank of Transmembrane Proteins topdb The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information.
TopFind topfind TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.
ToxoDB toxoplasma ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
Pathogen Transmission Ontology trans The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host.
TransportDB transportdb TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.
Transport Systems Tracker transyt The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes.
Transcriptional Regulatory Element Database tred Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present.
TreeBASE treebase TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships.
TreeFam treefam TreeFam is a database of phylogenetic trees of gene families found in animals.
TrichDB trichdb TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
TriTrypDB tritrypdb TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma.
tRNA Gene Database trnadbce The tRNA Gene DataBase Curated by Experts "tRNADB-CE" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones.
TTD Drug ttd.drug The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets.
TTD Target ttd.target The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets.
Teleost taxonomy ontology tto An ontology covering the taxonomy of teleosts (bony fish).
Toxic Process Ontology txpo Elucidating the mechanism of toxicity is crucial in drug safety evaluations.
Uber Anatomy Ontology uberon Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage.
uBio NameBank ubio.namebank NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes.
Uberon Property ubprop
UCSC Genome Browser ucsc The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.
Unified Code for Units of Measure ucum Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business.
UM-BBD compound ID umbbd.compound The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds.
EAWAG Biocatalysis/Biodegradation Database umbbd.enzyme The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds.
EAWAG Biocatalysis/Biodegradation Database umbbd.pathway The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds.
EAWAG Biocatalysis/Biodegradation Database umbbd.reaction The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds.
EAWAG Biocatalysis/Biodegradation Database umbbd.rule The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds.
Unified Medical Language System Concept Unique Identifier umls The Unified Medical Language System is a repository of biomedical vocabularies.
Unified Medical Language System Atomic Unique Identifier umls.aui An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source.
UniChem compound ID unichem identifier of a compound in the UniChem database.
UniGene unigene A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
Unique Ingredient Identifier unii The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices.
Unimod protein modification database for mass spectrometry unimod Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications.
UniProt Archive uniparc The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources.
UniPathway Compound unipathway.compound UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions.
UniPathway Reaction unipathway.reaction UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions.
UniProt Protein uniprot The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases.
Association-Rule-Based Annotator uniprot.arba Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins.
UniProt Chain uniprot.chain This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein.
UniProt Diseases uniprot.disease The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary.
UniProt Isoform uniprot.isoform The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases.
UniProt journal uniprot.journal identifier for a scientific journal, in the UniProt database.
UniProt Keywords uniprot.keyword UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries.
UniProt Subcellular Locations uniprot.location The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms.
UniProt Proteomes uniprot.proteome UniProt provides proteome sets of proteins whose genomes have been completely sequenced.
UniProt Post-Translational Modification uniprot.ptm The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL).
UniProt Resource uniprot.resource The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources.
Tissue List uniprot.tissue The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues.
UniProt Variants uniprot.var The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species.
UniRef uniref The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.
UniRule unirule Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates.
Database of Sequence Tagged Sites unists UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments.
Molecular database for the identification of fungi unite UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database.
Universal Natural Products Database unpd
Units of measurement ontology uo Ontology of standardized units.
Unipathway upa A manually curated resource for the representation and annotation of metabolic pathways.
Unified Phenotype Ontology upheno The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
United States Patent and Trademark Office uspto The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S.
Vaccine Adjuvant Compendium vac The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community.
ValidatorDB validatordb Database of validation results for ligands and non-standard residues in the Protein Data Bank.
Veterans Administration National Drug File vandf The National Drug File (NDF) is produced by the U.S.
A vocabulary for annotating vocabulary descriptions vann This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes.
Variation Ontology vario The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations.
Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse vbase2 The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.
Vertebrate Breed Ontology vbo Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.
Viral Bioinformatics Resource Center vbrc The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families.
VCell Published Models vcell Models developed with the Virtual Cell (VCell) software prorgam.
Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens vectorbase VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens.
Vertebrate Genome Annotation Database vega A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.
VegBank vegbank VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification.
Virtual Fly Brain vfb An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.
VFDB Gene vfdb.gene VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.
VFDB Genus vfdb.genus VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.
Vertebrate Gene Nomenclature Committee vgnc The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes.
Vertebrate Homologous Organ Group Ontology vhog vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project.
Virtual International Authority File viaf The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service.
The Virus Infectious Disease Ontology vido The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO).
ViolinNet violinnet Defunct vaccine information source from the He Lab.
Virus Pathogen Resource vipr The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses.
ViralZone viralzone ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences.
Vir-Mir db virmirdb A database containing predicted viral miRNA candidate hairpins.
VIRsiRNA virsirna The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions.
Virus-HostDB virushostdb Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts.
Variation Modelling Collaboration vmc
VMH Gene vmhgene The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.
VMH metabolite vmhmetabolite The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.
VMH reaction vmhreaction The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.
Vaccine Ontology vo The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination.
Vocabulary of Interlinked Datasets void The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets.
Vertebrate Skeletal Anatomy Ontology vsao Vertebrate skeletal anatomy ontology.
Veterinary Substances DataBase vsdb Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality.
Ontology for vector surveillance and management vsmo an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems.
Vital Sign Ontology vso The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS).
Vertebrate trait ontology vt An ontology of traits covering vertebrates.
Vertebrate Taxonomy Ontology vto Comprehensive hierarchy of extinct and extant vertebrate taxa.
Veterans Health Administration (VHA) unique identifier vuid The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year.
ViralZone vz ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures.
WormBase RNAi wb.rnai WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes.
C. elegans Gross Anatomy Ontology wbbt Ontology about the gross anatomy of the C.
C. elegans development ontology wbls Ontology about the development and life stages of the C.
C. elegans phenotype wbphenotype Ontology about C.
Web Elements webelements Browser for the periodic table of the elements.
WGS84 Geo Positioning wgs84 A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum.
WiCell Research Institute Cell Collection wicell Cell line collections.
Wikidata wikidata Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation.
Wikidata Property wikidata.property Wikidata is a free and open knowledge base that can be read and edited by both humans and machines. Wikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others.
WikiGenes wikigenes WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool.
WikiPathways wikipathways WikiPathways is a database of biological pathways maintained by and for the scientific community.
Wikipedia wikipedia.en Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model.
C. elegans ORFeome cloning project worfdb WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans.
The World-2DPAGE database world2dpage A public repository, standards compliant, for proteomics image data published in the literature.
Wormbase Gene ID wormbase WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes.
Wormpep wormpep Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.
WoRMS-ID for taxa worms The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms.
World Wildlife Fund Ecoregion wwf.ecoregion WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
Xenopus Anatomy Ontology xao XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.
Experimental condition ontology xco Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.
Xenbase xenbase Xenbase is the model organism database for Xenopus laevis and X.
Ximbio ximbio Cell line collections.
Cross-linker reagents ontology xl A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.
HUPO-PSI cross-linking and derivatization reagents controlled vocabulary xlmod A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.
Xenobiotics Metabolism Database xmetdb Metabolites in the Xenobiotics Metabolism Database.
Extensible Markup Language xml The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document.
Xenopus Phenotype Ontology xpo XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.
XML Schema Definition xsd This document describes the XML Schema namespace.
XUO xuo
Yeast Deletion and the Mitochondrial Proteomics Project ydpm The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project.
Yeast Intron Database v4.3 yeastintron The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae.
Yeast Searching for Transcriptional Regulators and Consensus Tracking yeastract YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.
YeTFasCo yetfasco The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.
Yeast Genome Order Browser ygob YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.
Yeast Intron Database v3 yid The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae.
Yeast Metabolome Database ymdb The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast).
Yeast Phenotype Ontology ypo
YRC PDR yrcpdr The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast).
Maize gross anatomy zea Maize gross anatomy.
Zebrafish Experimental Conditions Ontology zeco Ontology of Zebrafish Experimental Conditions.
Zenodo zenodo.record Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts.
Zebrafish anatomy and development ontology zfa ZFA description.
Zebrafish Information Network Gene zfin ZFIN serves as the zebrafish model organism database.
Zebrafish developmental stages ontology zfs Developmental stages of the Zebrafish.
ZINC is not Commercial zinc ZINC is a free public resource for ligand discovery.
Zebrafish Phenotype Ontology zp The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.