The registry contains metadata about ontologies, controlled vocabularies, and resources including their preferred prefix, name, description, homepage, mappings to other registries, and more. An alternate view over the registry by keywords can be found here.
Anyone can suggest improvements, request a new prefix, 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. |
| Abcam | abcam |
Vendor for assays, cells, and antibodies. |
| 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 (Providers). |
| 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). |
| Arctic Data Center Academic Disciplines Ontology | adcad |
An ontology to support disciplinary annotation of Arctic Data Center datasets. |
| AddexBio cell line products | addexbio |
Cell line collections (Providers). |
| Addgene Plasmid Repository | addgene |
Addgene is a non-profit plasmid repository. |
| Asset Description Metadata Schema Vocabulary | adms |
A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. |
| 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. |
| African Population Ontology | afpo |
AfPO is an ontology that can be used in the study of diverse populations across Africa. |
| Assembling the Fungal Tree of Life - Category | aftol.category |
Categories in the AFTOL database. |
| 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. |
| Ambystoma Genetic Stock Center | agsc |
The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. |
| Animal Genome Size Database | agsd |
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. |
| The Artificial Intelligence Ontology | aio |
This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases. |
| 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. |
| Australian New Zealand Clinical Trials Registry | anzctr |
The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. |
| 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 |
An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. |
| 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 |
Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. |
| 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 | 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. |
| Asteraceae Genome Database | asteraceaegd.genome |
The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. |
| Asteraceae Genome Database | asteraceaegd.plant |
The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. |
| 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. |
| Authenticus ID | authenticus |
ID of a researcher in Authenticus website. |
| Authorea author ID | authorea.author |
identifier for an author on the Authorea writing service. |
| Babelon | babelon |
Babelon is a simple standard for managing ontology translations and language profiles. |
| BacDive | 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 Biology Consortium | bcbc |
One of the many goals of the BCBC was to develop and maintain databases of useful research resources. |
| 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 (Providers). |
| Banco de Celulas do Rio de Janeiro | bcrj |
Cell line collections (Providers). |
| 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 (Providers). |
| 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 (bulk RNA-Seq, scRNA-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. |
| Biocompute Object | biocompute |
BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. |
| 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. |
| BioDeep Database | biodeep |
The BioDeep database is a comprehensive database of metabolite information in living organisms: by aggregating metabolite information from multiple public databases and large-scale natural language text mining work, we have built a large scale knowledge network for biological knowledge interpretation. |
| Biofactoid | biofactoid |
Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications. |
| 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. |
| BioKC | biokc |
BioKC (Biological Knowledge Curation), is a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML). |
| 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. |
| BioSchemas | bioschemas |
Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. |
| 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. |
| BioTop | biotop |
Upper-Level ontology for Biology and Medicine. |
| 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 | 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 Enzyme | 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). |
| BridgeDb Vocabulary | bridgedb |
A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc. |
| 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 Ontology | 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. |
| CABI Digital Library | cabi |
Research and learning in agriculture, the environment and the applied life sciences. |
| 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. |
| Chemical Analysis Ontology | cao |
An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. |
| CAPS-DB | caps |
CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. |
| Carnegie Stage | carnegie.stage |
One of the 23 stages of embryo development. |
| Common Anatomy Reference Ontology | caro |
The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. |
| 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. |
| Creative Commons Rights Expression Language | cc |
The Creative Commons Rights Expression Language (ccREL) lets you describe copyright licenses in RDF. |
| 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. |
| Human Reference Atlas Common Coordinate Framework Ontology | ccf |
The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). |
| 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 |
a formalization of concepts and relations relevant to 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 |
The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. |
| 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.
Note that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D. |
| Cell Biolabs cell line products | cell_biolabs |
Cell line collections (Providers). |
| 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. |
| Chemical Book | chemicalbook |
A hybrid chemical enyclopedia and supplier advertizing system for chemicals. |
| 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 |
The chemical information ontology (cheminf) describes information entities about chemical entities. |
| 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. |
| Chinese Clinical Trial Registry | chictr |
Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. |
| 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. |
| Chromosome Ontology | chr |
The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts. |
| 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. |
| CIÊNCIAVITAE ID | cienciavitae |
identifier of scientific author in www.cienciavitae.pt. |
| 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 Molecular Profile | civic.mpid |
CIViC Molecular Profiles are combinations of one or more CIViC variants. |
| 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 Group | civic.vgid |
Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. |
| CIViC variant | 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. |
| ChecklistBank | clb |
ChecklistBank is an index and repository for taxonomic and nomenclatural datasets. |
| Cell Line Database | cldb |
The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. |
| Clinical Genome Resource Panel | clingen.affiliation |
identifier for a panel. |
| ClinGen Allele Registry | clingene |
The allele registry provides and maintains identifiers for genetic variants. |
| ClinicalTrials.gov | 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 is a community-based ontology of cell lines. |
| Cell Lines Service | cls |
Cell line collections (Providers). |
| 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. |
| French National Center for Scientific Research - Research Group Identifier | cnrs |
identifier for an academic research group issued by the CNRS. |
| 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 | co_367 |
Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. |
| 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. |
| COEXISTENCE | coexistence |
COEXISTENCE - Thesaurus of intersectionality and decolonial issues: black studies, gender, sexuality and feminist studies. |
| 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. |
| COI Catalogue | coi |
COI Catalogue is a herbarium with c. |
| Catalogue of Life | col |
Identifier of a taxon or synonym in the Catalogue of Life. |
| 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 | 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. |
| Conference Ontology | conference |
The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. |
| 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. |
| The Comprehensive R Archive Network | cran |
Repository of packages for the R programming language. |
| Crates.io | crates |
A repository of software packages written in Rust. |
| Creative Biolabs | creativebiolabs.antibody |
Creative Biolabs Antigen provides identifiers for antibody-based entities such as recombinant, functional, engineered, and format-specific antibodies as well as antibody processing tools, which are essential for applications in diagnostics, therapeutics, and immunology. |
| Creative Biolabs | creativebiolabs.protein |
Creative Biolabs Protein provides identifiers for protein-related entities, including therapeutic proteins, proteolytic enzymes, antibody-like scaffold proteins, soluble T cell receptors, and tetramers. |
| 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 |
CRISP is a terminology used for indexing biomedical information. |
| 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 Science and Technology Resources | cstr |
CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. |
| 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 Information System | ctis |
This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). |
| 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. |
| India Clinical Trials Registry | ctri |
The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. |
| 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. |
| Data Commons | datacommons |
A large RDF store built from American governmental data. |
| 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 |
|
| 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. |
| DBLP author ID | dblp.author |
identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/). |
| 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. |
| DBPedia | dbpedia |
A semi-automatically generated knowledgebase. |
| 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 Elements (1.1) | dc |
Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.
Deprecation Notice: While the |
| 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 Initiative Terms | 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 anatomies of the slime-mold Dictyostelium discoideum. |
| Dewey Decimal Classification | ddc |
The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. |
| 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. |
| DevTox | devtox |
The DevTox Project harmonizes the nomenclature used to describe developmental anomalies in laboratory animals, assists in the visual recognition of developmental anomalies with the aid of photographs, and provides a historical control database of developmental effects in laboratory animals. |
| 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. |
| Kyoto Stock Center | dggr |
Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. |
| Drosophila Genomics Resource Center | dgrc |
Cell line collections (Providers). |
| Developing Human Brain Atlas | dhba |
A controlled vocabulary to support the study of transcription in the developing human brain. |
| Dialnet article ID | dialnet.article |
identifier of an article in Dialnet. |
| Dialnet author ID | dialnet.author |
identifier of an author in Dialnet. |
| Dialnet book ID | dialnet.book |
identifier of a book in Dialnet. |
| Dialnet journal ID | dialnet.journal |
identifier of a journal in Dialnet. |
| 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 (Providers). |
| 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. |
| Docker Hub repository | dockerhub.repo |
Docker repository hosted on Docker Hub. |
| DockerHub User | dockerhub.user |
A user in DockerHub. |
| 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. |
| Descriptive Ontology for Linguistic and Cognitive Engineering | dolce |
DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). |
| 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 of commonly encountered and/or high level Drosophila phenotypes. |
| Description of Plant Viruses | dpv |
Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. |
| Data Privacy Vocabulary | dpvocab |
The Data Privacy Vocabulary provides an ontology (classes and properties) and taxonomies of concepts to represent information regarding how personal data is processed in the form of an ontology or a knowledge graph. |
| 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 | drduke |
identifier for chemicals linked to information on occurrence in plants. |
| German Clinical Trials Register | drks |
The German Clinical Trials Register (DRKS) is the German WHO primary registry. |
| The Drug Ontology | dron |
An ontology to support comparative effectiveness researchers studying claims data. |
| AnVIL DRS | drsanv0 |
This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program 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 Target v4 | drugbank.bioentity |
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 Condition | drugbank.condition |
Indications and other conditions in drugbank. |
| DrugBank Metabolite | drugbank.metabolite |
Metabolites in drugbank. |
| DrugBank Reaction | drugbank.reaction |
Reactions in drugbank. |
| DrugBank Salts | drugbank.salt |
DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. |
| 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. |
| Darwin Core Terms | dwc |
Darwin Core is a vocabulary standard for transmitting information about biodiversity. |
| 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 (Providers). |
| 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. |
| Echinobase | echinobase |
Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species. |
| 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 and Conclusion 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. |
| The Ecosystem Ontology | ecso |
DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases. |
| 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. |
| EDAM Ontology | 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. |
| Mouse Developmental Anatomy Ontology with Theiler Stage | emaps |
EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. |
| 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. |
| European Medicines Evaluation Agency | emea |
Product number for the European Medicines Agency. |
| Elementary Multiperspective Material Ontology | emmo |
EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. |
| Crystallographic Information Framework | emmo.cif |
A crystallography domain ontology based on EMMO and the CIF core dictionary. |
| 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. |
| Environmental Molecular Sciences Laboratory Project | emsl.project |
As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. |
| 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 (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are 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. |
| EPA Hazardous Wastes | epawaste |
This resource provides identifiers for listed hazardous wastes which are substances explicitly identified due to their potential harm to human health and the environment. |
| 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. |
| FAIRsharing Organization | fairsharing.organization |
An organization in FAIRsharing, including universities, labs, etc. |
| FAIRsharing User | fairsharing.user |
A user of FAIRsharing. |
| 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. |
| Aquatic Sciences and Fisheries Information System | fao.asfis |
The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. |
| 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 representing the gross anatomy of Drosophila melanogaster. |
| FlyBase Controlled Vocabulary | fbcv |
A structured controlled vocabulary used for various aspects of annotation by FlyBase. |
| Drosophila development | fbdv |
A structured controlled vocabulary of the development of Drosophila melanogaster. |
| 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).
. |
| Fetal Calf Serum-Free Database | fcsfree |
Cell line databases/resources. |
| FDA Application | fda.application |
This prefix is for FDA application identifiers. |
| Flavor and Extract Manufacturers Association | fema |
FEMA provides identifiers for flavor ingredients deemed safe for food use. |
| FerroLigandDB | ferroliganddb |
FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors. |
| 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 |
Food-Drug interactions automatically extracted from scientific literature. |
| 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 | foodb.compound |
FooDB is resource on food and its constituent compounds. |
| FooDB Food | foodb.food |
Foods in FooDB. |
| Food Classification and Description System (from FSA Food Type identifiers) | foodex2 |
Food Type identifiers, supporting codes and vocabularies based on the EFSA FoodEx2 (https://www.efsa.europa.eu/en/data/data-standardisation) that are being tested in the development of the FSA's code and data standards repository. |
| 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 |
These are the terms that are improted for FOVT to describe vertebrate traits. |
| 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. |
| Functional Requirements for Bibliographic Records Entity-Relationship Model | frbrer |
This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. |
| 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. |
| FunderRegistry | 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. |
| Gainesville Core Ontology | gainesville.core |
Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations. |
| GALEN | galen |
A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic. |
| Plant Gall Ontology | gallont |
Ontology of plant gall phenotypes. |
| 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. |
| Gene Expression Analysis Resource | gear |
The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains. |
| 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). |
| GenBase | genbase |
GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC. |
| 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. |
| GeneAnnot: Microarray Gene Annotation | genecards.geneannot |
GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. |
| Gene Location | genecards.geneloc |
GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. |
| Gene Normal Tissue Expression | genecards.genenote |
GeneNote is a database of human genes and their expression profiles in healthy tissues. |
| 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 username | 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. |
| Glottolog | glottolog |
Comprehensive reference information for the world's languages, especially the lesser known languages. |
| 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. |
| 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. |
| GND ID | gnd |
The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. |
| Glycan Naming and Subsumption Ontology | gno |
An ontology for glycans based on GlyTouCan, but organized by subsumption. |
| Genome Aggregation Database | gnomad |
The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community (from https://gnomad.broadinstitute.org). |
| GnpIS | gnpis |
GnpIS is an integrative information system focused on plants and fungal pests. |
| Global Natural Products Social Molecular Networking Task | gnps.task |
GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS). |
| Gene Ontology | go |
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. |
| Gene Product Information Schema | go.gpi |
This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files. |
| 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 Rules | go.rule |
GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. |
| 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 |
The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. |
| GOLD metadata | gold.meta |
|
| 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. |
| GPCR Natural Variants database | gpcrnava |
The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (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. |
| Genome Taxonomy Database | gtdb |
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny. |
| 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). |
| Hymenoptera Anatomy Reference | hao.ref |
Literature references in the Hymenoptera Anatomy Ontology Portal. |
| 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. |
| Health Canada Clinical Trials Database | hc.trial |
Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. |
| Human Cell Atlas Ontology | hcao |
Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas. |
| Human Chromosome Ontology | hco |
The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes. |
| 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 Project | 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. |
| Handle | hdl |
Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). |
| Homeodomain Research | hdr |
The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. |
| HemOnc Terminology | hemonc |
HemOnc.org is the largest freely available medical wiki of interventions, regimens, and general information relevant to the fields of hematology and oncology. |
| Health Procedure Ontology | hepro |
HEPRO is an ontology of informational entities and processes related to health procedures and health activities. |
| UK Higher Education Statistics Agency | hesa |
An identifier for institutions in the United Kingdom, used in GRID and ROR. |
| 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. |
| Human Genome Variation Society Nomenclature | hgvs |
The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. |
| 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 (Providers). |
| 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 Library of Integrated Network-based Cellular Signatures Antibodies | hms.lincs.antibody |
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. |
| HMS LINCS Cell | hms.lincs.cell |
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. |
| 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. |
| HMS Library of Integrated Network-based Cellular Signatures Datasets | hms.lincs.dataset |
|
| Hölzel Diagnostika | hoelzel |
Hölzel is a life science reagent vendor based in Cologne, Germany. |
| 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. |
| Homosaurus | homosaurus |
An international LGBTQ+ linked data vocabulary. |
| Horizon Discovery cell line collection | horizon_discovery |
Cell line collections (Providers). |
| Healthcare Organizations and Services Ontology | hoso |
HOSO is an ontology of informational entities and processes related to healthcare organizations and services. |
| 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. |
| Human Protein Complex Map | humap |
The hu.MAP integrates several large scale protein interaction datasets to obtain a comprehensive view of protein complexes. |
| 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. |
| Integrated Chemical Environment - Chemical data | icechem |
The Integrated Chemical Environment (ICE) provides high-quality curated data and appropriate tools to support development and evaluation of new, revised, and alternative methods. |
| 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 (Providers). |
| Insect Cell Line Database | icldb |
We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. |
| 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. |
| Integrated Resource for Domestic Dog | idog |
Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. |
| 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 Assays | iedb.assay |
Identifiers for specific experimental assays that serve as evidence for immune-related studies. |
| Immune Epitope Database Epitopes | iedb.epitope |
Identifiers for epitopes, which are the specific parts of antigens recognized by the immune system. |
| Immune Epitope Database MHC Restrictions | iedb.mhc |
Identifiers for Major Histocompatibility Complex (MHC) restrictions of immune cells, detailing genetic factors that influence immune recognition. |
| Immune Epitope Database Receptors | iedb.receptor |
Identifiers for immune receptors, representing receptor complexes or groups studied for their interactions with antigens or epitopes. |
| Immune Epitope Database References | iedb.reference |
Identifiers for references, typically linking to sources of evidence such as publications that support data within IEDB. |
| IEEE Xplore author ID | ieee.author |
identifier for an author in IEEE Xplore. |
| IEEE Xplore document ID | ieee.document |
identifier for a document in IEEE Xplore. |
| 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 (Providers). |
| 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. |
| IMGT/PRIMER-DB | imgt.primerdb |
The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR). |
| 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. |
| NHMRC Australian PhenomeBank | imsr.apb |
The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. |
| European Mouse Mutant Archive | imsr_em |
Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. |
| Taconic Biosciences | imsr_tac |
Supplier of mice for research purposes. |
| 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. |
| InformAll Allergenic Food Database | informall |
The InformAll database was developed to provide a credible source of information on allergenic food materials of both plant and animal origin. |
| 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 has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. |
| 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 accessions | insdc.gca |
The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. |
| Genome assembly database - RefSeq accessions | insdc.gcf |
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. |
| Integbio | integbio |
Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. |
| 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. |
| Interlinking Ontology for Biological Concepts | iobc |
Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. |
| International Protein Index | ipi |
IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. |
| Iranian Registry of Clinical Trials | irct |
Iranian Registry of Clinical Trials. |
| 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 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. |
| Influenza Sequence and Epitope Database | ised |
ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea. |
| 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. |
| ISO 15926-14 | iso15926 |
The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. |
| International Traditional Medicine Clinical Trial Registry | isrctn |
The ISRCTN registry is a primary clinical trial registry recognised by WHO and ICMJE that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. |
| 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. |
| ISTransbase | istransbase |
ISTransbase is a highly reliable and accessible database that focuses on inhibitors and substrates of drug transporters, offering a wealth of vital information encompassing experimental methods, transport parameters, and references. |
| Integrated Taxonomic Information System | itis |
Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world. |
| International Traditional Medicine Clinical Trial Registry | itmctr |
The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. |
| 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. |
| Influenza Virus Database | ivdb |
IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. |
| 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 (Providers). |
| 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). |
| Joint FAO/WHO Expert Committee on Food Additives | jecfa |
JECFA provides identifiers for flavors, food additives, contaminants, toxicants, and veterinary drugs. |
| Joint Genome Institute Proposals | jgi.proposal |
Identifiers for proposals/projects at the Joint Genome Institute. |
| Japan Registry of Clinical Trials | jrct |
This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. |
| 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. |
| e-Rad researcher number | kaken |
identifier for researchers in Japan used in goverment-based research funding (from 1980s). |
| Korean Cell Line Bank | kclb |
Cell line collections (Providers). |
| Korean Clinical Research Information Service | kcris |
The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. |
| 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 (Providers). |
| KESTREL Ontology | kestrelo |
An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains. |
| 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 (Providers). |
| 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". |
| Lattes Platform number | lattes |
number for the Lattes Platform entry on the person or group. |
| Lebanon Clinical Trials Registry | lbctr |
The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. |
| Livestock Breed Ontology | lbo |
A vocabulary for cattle, chicken, horse, pig, and sheep breeds. |
| Library of Congress Control Number | lccn |
LCCN Permalinks are persistent URLs for bibliographic records in the LC Catalog and authority records in LC Authorities. |
| Library of Congress Subject Headings | lcsh |
Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. |
| Leafsnap | 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. |
| Genderal Ontology for Linguistic Description | linguist.gold |
|
| LinkedIn personal profile ID | linkedin |
identifier for a person, on the LinkedIn website. |
| 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 | 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. |
| Loop ID | loop |
identifier for a person, in the Loop database of researcher impact. |
| 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. |
| LifeWatch Metadata Catalogue | lw |
The LifeWatch Metadata Catalogues plays a crucial role in managing metadata for digital objects, including Datasets, Services, Workflows and Virtual Research Environments. |
| Metadata4Ing | m4i |
The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. |
| 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. |
| Maggot | maggot |
Sharing descriptive Metadata is the first essential step towards Open Scientific Data. |
| 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 | 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. |
| Mastodon | mastodon |
address on the Mastodon decentralized social network (the form is 'user@server.domain' without a leading '@'). |
| 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. |
| Multiplexed Assays of Variant Effect Database | mavedb |
Some IDs may represent experiment sets, e.g. |
| 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. |
| Model Card Report Ontology | mcro |
An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). |
| Molecular Design Limited Hash | mdl |
The MDL number contains a unique identification number for each reaction and variation. |
| 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. |
| MediaDive Ingredient | mediadive.ingredient |
The mission of MediaDive is to transform poorly structured media recipes into a standardized database. |
| MediaDive Medium | mediadive.medium |
The mission of MediaDive is to transform poorly structured media recipes into a standardized database. |
| MediaDive Solution | mediadive.solution |
The mission of MediaDive is to transform poorly structured media recipes into a standardized database. |
| 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. |
| Merriam Webster Dictionary | merriamwebster |
Online Dictionary. |
| 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. |
| Medical Subject Headings Vocabulary | mesh.vocab |
Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump. |
| 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. |
| Metabolic Encyclopedia for Pathway/Genome Databases | metacyc.pathway |
MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. |
| 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 (Providers). |
| 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 | 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. |
| 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. |
| Metadata Management and distribution system for Multiple GNSS Networks | moid |
M3G stands for “Metadata Management and distribution system for Multiple GNSS Networks”. |
| 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. |
| Mondo 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. |
| Manufacturers of Vaccines | mvx |
The CDC's National Center for Immunization and Respiratory Diseases (NCIRD) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). |
| 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. |
| Nanbyo Disease Ontology | nando |
Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan. |
| 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. |
| NCBI Data Repository Service | ncbidrs |
This is the namespace for the archive of sequence and other files provided by NCBI e.g. |
| NCBI 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 Orthologs | ncbiortholog |
Database of one-to-one ortholog information provided by the NCBI as a subset of their Gene resource. |
| 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 Drug Dictionary ID | nci.drug |
identifier of an entry in the NCI Drug Dictionary. |
| 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. |
| Neuroscience Multi-Omic BRAIN Initiative Data | nemo |
This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects. |
| Neural ElectroMagnetic Ontology | nemo2 |
Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). |
| 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. |
| Ontology for computer aided process engineering | nfdi4chem.ontocape |
OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). |
| Ontology for simulation, modelling, and optimization | nfdi4chem.osmo |
OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. |
| Next Generation Biobanking Ontology | ngbo |
Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. |
| 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 (Providers). |
| 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. |
| NIAID ChemDB ID | niaid.chemdb |
ID in NIAID ChemDB. |
| 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 Human Embryonic Stem Cell Registry | nihhesc |
The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. |
| 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. |
| NIST/CODATA ID | nist.codata |
identifier for a physical constant. |
| Networked Knowledge Organization Systems/Services/Structures | nkos |
NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet.
Knowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. |
| NLFFF Database | nlfff |
Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database. |
| National Library of Medicine Catalog | nlm |
The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. |
| NLM Publisher Codes | nlm.publisher |
Publisher short codes appearin in the NLM Catalog. |
| 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 | 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. |
| CAMEO Chemicals ID | noaa.cameo |
CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazards—such as explosions or toxic fumes. |
| 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. . |
| The Natural Products Atlas | npatlas |
Identifiers for microbially derived natural products that contains compound structures, producing organism taxonomy, biosynthetic and chemical properties. |
| Node Package Manager | npm |
A repository of software packages written in Javascript, TypeScript, and related. |
| 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. |
| National Repository of Fish Cell Lines | nrfc |
The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. |
| 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 Swine Resource and Research Center | nsrrc |
Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. |
| 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 | nucleardb |
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. |
| National Xenopus Resource | nxr |
National stock center for X. |
| New Zealand Threat Classification System | nztcs |
identifier for species classified under the New Zealand Threat Classification System. |
| 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. |
| Open Biomedical Annotations | oban |
It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. |
| Ontology for Biomarkers of Clinical Interest | obci |
The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects. |
| 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. |
| The Extensible Observation Ontology | oboe |
The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. |
| OBO in OWL | oboinowl |
This meta-ontology is self-describing. |
| Austrian Library Network | obv |
The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections. |
| 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. |
| Occupation Ontology | occo |
An ontology representing occupations. |
| Open Citation Identifier | oci |
Each OCI (Open Citation Identifier) has a simple structure: oci: |
| 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. |
| ODAM Data explorer | odamexplorer |
ODAM (Open Data for Access and Mining) is an Experimental data table management software (EDTMS) 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. |
| Open Digital Rights Language Ontology | odrl |
The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model. |
| OECD Harmonised Templates | oecd.template |
The Organisation for Economic Co-operation and Development (OECD) Harmonised Templates (OHTs) are standard data formats for reporting information used for the risk assessment of chemicals, mainly studies done on chemicals to determine their properties or effects on human health and the environment, but also for storing data on use and exposure. |
| 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: 1. |
| 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 (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). |
| OMIA variants | omia.variant |
Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). |
| Ontologized MIABIS | omiabis |
An ontological version of MIABIS (Minimum Information About BIobank data Sharing). |
| OpenCitations Meta Identifier | omid |
Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). |
| 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. |
| Overview of Medical Research in the Netherlands | omon |
The new national clinical trials registry of the Netherlands. |
| 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 for Modeling and Representation of Social Entities | omrse |
The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. |
| OncoMX Dataset | omx.dataset |
OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. |
| 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 |
An ontology for description of concepts in the nutritional studies domain. |
| Ontology for Immune Epitopes | ontie |
The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes. |
| 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. |
| OntoRXN | ontorxn |
OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies. |
| Ontology of Organizational Structures of Trauma centers and Trauma systems | oostt |
The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). |
| 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. |
| openWEMI Vocabulary | openwemi |
openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item. |
| 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. |
| IUPAC Compendium of Analytical Nomenclature (Orange Book) | orangebook |
The first number is the chapter then the remainder are subsections. |
| 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. |
| Open Science Framework ID | osf |
ID in osf.io. |
| 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. |
| Office of Scientific and Technical Information (OSTI) | osti.article |
The U.S. |
| 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. |
| Ontological Interpretations for Web Property Graphs | owlstar |
This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. |
| 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. |
| Packagist | packagist |
A repository of software packages written in PHP. |
| Pan African Clinical Trials Registry | pactr |
The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. |
| 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. |
| PANTHER Family | 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 | 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 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. |
| PEPhub | pephub |
PEPhub is a database, web interface, and API for sharing, retrieving, and validating sample metadata. |
| 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 (Providers). |
| 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. |
| PesticideInfo chemical ID | pesticideinfo |
chemical in the database supplied by Pesticide Action Network North America. |
| 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. |
| PharmGKB Gene | 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 Curation | phosphosite.curation |
PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. |
| 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. |
| Philippine Health Research Registry | phrr |
The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. |
| 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 |
|
| PLOS Thesaurus | plos |
An ontologization of Public Library of Science (PLOS) journal keywords and topics. |
| 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. |
| PubMed Central | 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. |
| Protege Ontology | protege |
An ontology of metadata from protege. |
| 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) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. |
| 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 | 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 | 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 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. |
| RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting | rdfa |
RDFa Core is a specification for attributes to express structured data in any markup language. |
| 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). |
| Brazilian Registry of Clinical Trials | rebec |
Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). |
| 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. |
| Peruvian Clinical Trial Registry | repec |
The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. |
| 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. |
| ResearchGate profile ID | researchgate.profile |
identifier for a person, used by ResearchGate profiles. |
| 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 | 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 |
RNAJunction is a database of RNA junctions and kissing loop structures. |
| 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. |
| RNA Virus Database | rnavdb |
The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. |
| 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. |
| Cuban Registry of Clinical Trials | rpcec |
The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. |
| 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 Resource and Research Center | rrrc |
Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. |
| 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. |
| RubyGems | rubygems |
A repository of software packages written in Ruby. |
| 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. |
| Salmon Ontology | salmon |
An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. |
| Subcellular Anatomy Ontology | sao |
SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. |
| The State of Alaska's Salmon and People Ontology | sasap |
An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. |
| 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. |
| SCancerRNA | scancerrna |
SCancerRNA provides identifiers for non-coding RNA biomarkers, including long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA, with data on their differential expression at the cellular level in cancer. |
| 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. |
| Sciflection | sciflection |
Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions. |
| SciProfiles ID | sciprofiles |
numerical identifier for an author in SciProfiles by MDPI. |
| Selventa Complexes | scomp |
Selventa legacy complex namespace used with the Biological Expression Language. |
| Structural Classification of Proteins - Unique Identifier | scop |
SCOP(e) unique identifier. |
| SCOP(e) concise classification string | scop.sccs |
This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. |
| Structural Classification of Protein - Stable Domain Identifier | scop.sid |
A 7-character sid consists of "d" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('' if not). |
| Scopus Researcher | scopus |
Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. |
| Scopus affiliation ID | scopus.affiliation |
identifier for an organisation in author affiliations per Scopus. |
| Scopus Publication | scopus.publication |
identifier for a source/publication venue (journal, conference, etc) in Scopus. |
| Scopus Work | scopus.work |
unique academic work identifier assigned in Scopus bibliographic database. |
| 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). |
| SEED Subsystem | 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. |
| Semantic Mapping Vocabulary | semapv |
The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata. |
| Semion author ID | semion |
identifier of an author or reviewer, in Semion. |
| Sensitive Data Ontology | senso |
The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing. |
| Scientific Event Ontology | seo |
SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops. |
| 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 | sh |
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. |
| Scientific Information Retrieval and Exchange Network | siren |
A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods. |
| 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. |
| Stress Knowledge Map | skm |
Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. |
| 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. |
| Sri Lanka Clinical Trials Registry | slctr |
The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. |
| SUM Breast Cancer Cell Line Knowledge Base | slkbase |
Cell line databases/resources. |
| SwissLipid | slm |
SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. |
| Space Life Sciences Ontology | slso |
The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data. |
| 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. |
| Swiss National Clinical Trials Portal | snctp |
The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. |
| 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. |
| Sensor, Observation, Sample, and Actuator Ontology | sosa |
This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group. |
| SoyBase | 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. |
| 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. |
| Semantic Sensor Network Ontology | ssn |
This ontology describes sensors, actuators and observations, and related concepts. |
| System capabilities, operating ranges, and survival ranges ontology | ssn.system |
This ontology describes system capabilities, operating ranges, and survival ranges. |
| Social Science Research Network Article | ssrn.article |
identifier for an article/paper at the SSRN. |
| Social Science Research Network Author | ssrn.author |
identifier for an author at the Social Science Research Network. |
| Simple Standard for Sharing Ontological Mappings | sssom |
SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). |
| 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. |
| FDA Submission Tracking Number | stn |
The pre-IND tracking number for submissions to the FDA. |
| 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. |
| StreptomeDB | streptomedb |
Identifers for natural products isolated or mutasynthesized by bacteria of the genus Streptomyces. |
| 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. |
| 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. |
| Synapse Data Repository | synapse |
Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. |
| Synthetic Binding Proteins Binding Target | synbip.bts |
Identifiers for the binding targets of synthetic binding proteins (SBP), describing the specific molecules or complexes that SBPs interact with for their intended applications. |
| Synthetic Binding Protein Epitope | synbip.epitope |
Identifiers for synthetic binding protein-target complexes, detailing their components, 3D structures and docking statistics. |
| Synthetic Binding Protein Protein Scaffold | synbip.pss |
Identifiers for the protein scaffolds of synthetic binding proteins (SBP), detailing their structural frameworks and roles in facilitating SBP function. |
| Synthetic Binding Protein | synbip.sbp |
Identifiers for synthetic binding proteins, providing detailed information on their sequences, structures, targets, and functional properties for research, diagnostic, and therapeutic applications. |
| 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. |
| terms4FAIRskills | t4fs |
A terminology for the skills necessary to make data FAIR and to keep it FAIR. |
| 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. |
| Thai Clinical Trials Registry | tctr |
The TCTR was estabished in 2009 and has been operated by Clinical Research Collaboration Network (CRCN), an organization under the Medical Research Foundation, which is a non-profit organization, and financially supported by Thailand Center of Excellence for Life Sciences (TCELS). |
| TDWG Taxon Rank LSID Ontology | tdwg.taxonrank |
Ontology describing a controlled vocabulary for taxon ranks. |
| 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 |
TGN is a structured vocabulary currently containing around 1,106,000 names and other information about places. |
| 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 (Providers). |
| Plant Trait Ontology | to |
A controlled vocabulary to describe phenotypic traits in plants. |
| TogoID Ontology | togoid |
TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. |
| TogoVar | togovar |
TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them. |
| 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. |
| tricdb | tricdb |
Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. |
| 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. |
| Tetrahymena Stock Center | tsc |
Centralized repository and distribution site for variety of Tetrahymena strains and species. |
| 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 |
|
| UK Universities and Colleges Admissions Service | ucas |
An identifier for institutions in the United Kingdom, used in GRID and ROR. |
| 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. |
| UK Provider Reference Number | ukprn |
identifier for an educational organization issued by the UK Register of Learning Providers. |
| UM-BBD compound | 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. |
| University hospital Medical Information Network Clinical Trial Registry | uminctr |
An additional Japanese clinical trial registry. |
| 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 | 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 Core Ontology | uniprot.core |
Properties and classes used for protein annotation. |
| 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 | uniprot.mnemonic |
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 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. |
| UR-DBMS Syndrome Finder | urdbms.syndromefinder |
|
| United States Patent and Trademark Office | uspto |
The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. |
| UTRdb | utrdb |
A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. |
| 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. |
| Virtual Contact File | vcard |
vCard is a specification developed by the Internet Engineering Task Force (IETF) for the description of people and organisations. |
| VCell Published Models | vcell |
Models developed with the Virtual Cell (VCell) software prorgam. |
| Vienna Drosophila Resource Center | vdrc |
Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. |
| Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens | vectorbase |
VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. |
| 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. |
| Veterinary Nomenclature | venom |
The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems. |
| 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. |
| VIAF ID | viaf |
The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. |
| Vibrational Spectroscopy Ontology | vibso |
The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR. |
| 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. |
| VIPERdb | viperdb |
VIPERdb is a database for icosahedral virus capsid structures . |
| 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. |
| VirGen | virgen |
VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. |
| Vir-Mir db | virmirdb |
A database containing predicted viral miRNA candidate hairpins. |
| VirOligo | viroligo |
The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. |
| 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. |
| Virus' miRNA target | vita |
ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. |
| Vitro Application Ontology | vitro |
Vitro is a full stack framework for building semantic web applications. |
| VIVO Ontology | vivo |
An ontology about scholarship. |
| 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 community-based biomedical ontology in the domain of vaccine and vaccination. |
| A vocabulary for the catalysis disciplines | voc4cat |
Voc4Cat is a SKOS vocabulary for the catalysis disciplines. |
| 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 |
The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. |
| 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. |
| 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 (Providers). |
| 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. |
| WikiPathways Ontology | wikipathways.vocab |
An ontology supporting data modeling in WikiPathways. |
| Wikipedia | wikipedia.en |
Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. |
| Wiktionary | wiktionary |
A free dictionary. |
| 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. |
| Computational Chemistry Ontology | worldavatar.compchem |
Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. |
| Ontology for Chemical Kinetic Reaction Mechanisms | worldavatar.kin |
Represents chemical kinetic reaction mechanisms. |
| WormBase | 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. |
| Web of Science ID (work) | wos |
unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix). |
| ResearcherID | wos.researcher |
identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829. |
| 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 (Providers). |
| 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). |
| Zazuko Prefix Server | zazuko |
This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. |
| 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. |