A type for entries in the Bioregistry's registry.
A type for entries in the Bioregistry's metaregistry.
A type for entries in the Bioregistry's collections
Resources used in the semantic web, drawing from lists in [BioContext](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) and [LinkML](https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/linked_data.curated.yaml) as well as W3C recommendations.
The data sources used in xrefs in the ChEBI ontology. More information in the "Data Sources" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx).
International Classifications of Diseases
This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions.
This collection contains various brain atlases from the Allen Institute.
The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF.
Prefixes useful in annotating documentation provenance.
Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project.
Prefixes mentioned on the _external_ list on the FHIR [Code Systems](https://hl7.org/fhir/terminologies-systems.html) page. This list is mostly complete. Notably, some entries that have not been curated: - HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460)) - [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries - [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_ - [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_ - [MDC](https://www.iso.org/standard/37890.html) (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation
Global Biodata Coalition - Global Core Biodata Resources
The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are: - [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.) - [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC) - [GENCODE](https://www.gencodegenes.org/) (uses GenBank) - [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc) - [STRING](https://string-db.org/) (uses UniProt)
A collection of ontologies relevant for chemistry. The NFDI program deploys a [custom instance](https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1) of the Ontology Lookup Service (OLS) that provides the ontologies in this list. A further analysis of the metadata landscape of the ontologies in this list can be found [here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat). OntoCompChem and OntoKin appear on the NFDI4Cat list but have not yet been registered in the Bioregistry because the resources are missing/incomplete such that they do not meet minimum Bioregistry metadata standards. These might be added in the future if additional metadata can be found.
A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)
These resources represent software repositories
A collection of ontologies relevant within the [NFDI4Chem project](https://www.nfdi4chem.de/) that is mostly based on the overview paper [Ontologies4Chem: the landscape of ontologies in chemistry](https://doi.org/10.1515/pac-2021-2007). NFDI4Chem deploys a [custom instance](https://terminology.nfdi4chem.de/ts/) of the Ontology Lookup Service (OLS), called NFDI4Chem Terminology Services (TS), that provides the ontologies in this list. This list contains ontologies that cover various domains of chemistry (e.g. ChEBI, CHMO, and RXNO), those that are dependencies of these chemistry specific ontologies (e.g. BFO, RO, IAO, and OBI) as well as those ontologies, which where indexed in the NFDI4Chem TS for interoperability research purposes (e.g. PROV-O, SOSA, and OBOE).
A collection of resources added during Biocuration 2025 in Kansas City, MO, USA.
A curated list by Sage Bionetworks of external resources that are automatically linked on Synapse.org and affiliated data portals
Prefixes relevant for the [Data Literacy Alliance (DALIA)](https://dalia.education/en) project
Resources for modeling Open Educational Resources
The prefixes appearing in this collection correspond resources whose entities could appear as values for target groups, media types, educational levels, and other fields in OER data models. It can also include parts that are used to construct schemas for OERs It was originally curated as part of the publication [_Teaching RDM in a smart advanced inorganic lab course and its provision in the DALIA platform_ (arxiv:2509.18902)](https://arxiv.org/pdf/2509.18902).
Prefixes relevant for the digital humanities
[KonsortSWD (Strengthen, Widen, Deepen)](https://www.nfdi.de/consortia-konsortswd) is the German National Data Infrastructure (NFDI) consortium for social, educational, behavioral, and economic sciences. This collection reflects the prefixes collected by NFDI Section Metadata for ontologies and controlled vocabularies used by members of the consortium.
Prefixes for ontologies relevant for the NFDI4Energy
Prefixes for ontologies relevant for the NFDI4Ing
Prefixes for ontologies relevant for the DataPLANT (i.e. the NFDI consortium for plants)
Prefixes for ontologies relevant for [FAIRmat](https://www.nfdi.de/consortia-fairmat).
Prefixes for ontologies relevant for NFDI4Culture.
Prefixes for ontologies relevant for DAPHNE4NFDI.
A collection of ontologies, controlled vocabularies, database, and schemas relevant for MaRDI
A collection of ontologies, controlled vocabularies, database, and schemas relevant for BERD@NFDI
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4DataScience
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Earth
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI-MatWerk
A collection of ontologies, controlled vocabularies, database, and schemas relevant for PUNCH4NFDI
A collection of ontologies, controlled vocabularies, database, and schemas relevant for FAIRagro
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4BIOIMAGE
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDIxCS
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Objects
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Memory
A collection of ontologies, controlled vocabularies, database, and schemas relevant for Text+
A collection of ontologies, controlled vocabularies, database, and schemas relevant for GHGA
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Biodiversity
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Health
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Microbiota
A collection of ontologies, controlled vocabularies, database, and schemas relevant for NFDI4Immuno
A web-developer centric archive of prefixes and URI prefixes
An identifier for a resource or metaresource.
The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved.
The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved.
The pattern for identifiers in the given resource
For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource.
A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc.
A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix. See examples [here](https://bioregistry.io/highlights/relations#canonical).
The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix
Terms from the source appear in the target resource
The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved.
An expanded example URL for a resource or metaresource.
The pattern for expanded URIs in the given resource
Resources mentioned in "Sharing biological data: why, when, and how"
These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible.
3DMET is a database collecting three-dimensional structures of natural metabolites.
The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.
4D Nucleome Data Portal Experiment Replicate
Database portal containing replicate experiments of different assays and samples
Identifiers represent antibody-antigen complexes in the Antigen-Antibody Complex Database (AACDB), which provides comprehensive structural and functional annotations including paratope and epitope information, antibody developability data, and antigen-drug target relationships to support immunoinformatics research and therapeutic antibody development.
Identifier of an entry from the AAindex database.
A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.
Vendor for assays, cells, and antibodies
The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies
Applied Biological Materials cell line products
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.
The AntiBody Sequence Database is a public dataset for antibody sequence data. It provides unique identifiers for antibody sequences, including both immunoglobulin and single-chain variable fragment sequences. These are are critical for immunological studies, and allows users to search and retrieve antibody sequences based on sequence similarity and specificity, and other biological properties.
Audubon Core Subtype Controlled Vocabulary
Audubon Core uses the terms ac:subtype and ac:subtypeLiteral to refine the type of a media item to a level more specific than the Dublin Core Type Vocabulary, http://purl.org/dc/dcmitype/. This controlled vocabulary provides values for ac:subtype and ac:subtypeLiteral.
Audubon Core Variant Controlled Vocabulary
Audubon Core uses the terms ac:variant and ac:variantLiteral to provide information about the size, extent, and availability of the Service Access Point of a media item. This controlled vocabulary provides values for those terms.
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). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.
The Basic Access Control ontology describes how access rights (access control) are defined on the web.
Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.
The Addiction Ontology (AddictO) is an ontology being developed all aspects of addiction research.
Asset Description Metadata Schema Vocabulary
A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies).
Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.
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. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page).
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
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. Multiple probe sets may be available for each gene under consideration.
AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms.
Assembling the Fungal Tree of Life - Category
Assembling the Fungal Tree of Life - 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. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.
This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.
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. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.
AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages.
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. [from homepage]
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.
This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases.
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 is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.
Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease.
The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data.
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. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
identifier for a species, in the AmphibiaWeb database
The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.
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.
International repository of Adverse Outcome Pathways.
The AOPO provides classes and relationships for the semantic representation of the Adverse Outcome Pathway framework.
An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege.
The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.
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). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.
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). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.
A structured controlled vocabulary for the phenotypes of Ascomycete fungi.
ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.
Website with general information about Arabidopsis and functionalities such as a genomic viewer
ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.
The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.
Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver.
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 is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome.
A Systematic Annotation Package for Community Analysis of Genomes
ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources.
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. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).
Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue.
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 facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information.
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 facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information.
Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes.
Identifier of an object from the ASTD database.
The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collection refers to the genomic data of Asteraceae species.
The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collections refers to the broader phenotypic and genetic resources of Asteraceae plants.
Anatomical Therapeutic Chemical Vetinary
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. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.
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. This collections refers to transcription factor families, and the species in which they are found.
Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource
ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment. ATOL aims to: provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; represent traits as generic as possible for livestock vertebrates; make the ATOL ontology as operational as possible and closely related to measurement techniques; and structure the ontology in relation to animal production.
AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.
ID of a researcher in Authenticus website
identifier for an author on the Authorea writing service
Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation.
BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.
BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.
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 (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.
Basic Register of Thesauri, Ontologies & Classifications
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. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).
Blue Brain Project's published data as knowledge graphs and Web Studios.
Blue Brain Project Topological sampling Knowledge Graph
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 ).
One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]
An application ontology built for beta cell genomics studies.
The Behaviour Change Intervention Ontology
The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.
Berkeley Drosophila Genome Project EST database
The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).
BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.
The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.
BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.
The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.
The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents.
Biological and Environmental Research Variable Ontology
A representation of variables appearing in models in the environmental research space.
Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.
Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.
Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.
BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments.
BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolites.
BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.
BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.
This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource.
Accession number of an entry from the BIND database.
BindingDB is the first public database of protein-small molecule affinity data.
BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps.
The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all.
BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format.
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. By using the BioDeep database, it is possible to query such large scale metabolic knowledge network.
Identifiers for lipid-protein interactions, including details about protein functions, protein families, lipid classifications, lipid-protein binding affinities, membrane association type, and atomic structures.
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 is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.
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 is a life sciences supply vendor.
A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations.
A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids.
Database of the dielectric properties of biological tissues.
BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.
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. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment.
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.
Vocabulary used in the RDF representation of SBML models.
BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data.
biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology
bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate.
Manually curated collections of resources stored in the bioregistry
Schema for the export of the Bioregistry as RDF
Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]
BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools.
BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).
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 is a registry of databases and software with tools, services, and workflows for biological and biomedical research.
Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network
Redistributor of bilogics and biomedical supplies
Biomedical Informatics Research Network Lexicon
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.
Bitbucket is a Git-based source code repository hosting service owned by Atlassian.
BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.
BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.
SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.
An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects.
The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively.
Ontology representation of the Climate and Forecast (CF) standard names parameter vocabulary, which is intended for use with climate and forecast data in the atmosphere, surface and ocean domains. Every CF parameter is captured as a SKOS concept.This vocabulary is a simplified version of the CF vocabulary P07 from the NERC Vocabulary Server (NVS), National Oceanography Centre - British Oceanographic Data Centre (BODC), https://vocab.nerc.ac.uk.
Terms used to classify groups of sensors, instruments, sources of algorithmically computed data (numerical models) or samplers (collectors of water, SPM, sediment, rock, air or biota samples).
British Oceanographic Data Centre data storage units
terms approved for use by BODC to describe the measurement units for data held in its repositories.
The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.
Database of biopesticides maintained by the University of Hertfordshire
A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc.
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. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.
SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library.
BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.
BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols.
The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.
Research and learning in agriculture, the environment and the applied life sciences
Common Access to Biological Resources and Information Project
CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it.
Cancer Data Standards Registry and Repository
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.
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. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins.
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. These predictions are regularly compared against reference structures from PDB.
CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.
One of the 23 stages of embryo development
CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.
The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains.
The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features.
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.
A precursor that was later replaced with the Creative Commons Rights Expression Language (ccREL)
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. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC.
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. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.
Human Reference Atlas Common Coordinate Framework Ontology
The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.
Datasets around different cancer cell lines generated by the Broad Institute and Novartis
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
a formalization of concepts and relations relevant to evolutionary comparative analysis
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. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).
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.
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.
Cellosaurus identifeirs for publications, like Pubmed
The set of prefixes used in the Cellosaurus resource
The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines
Assigns identifiers to datasets indexed by CELLxGENE, such those resulting from scRNA-seq experiments
The COVID-19 epidemiology and monitoring ontology
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.
An anatomical and developmental ontology for cephalopods
Ontology for Certificates and crypto stuff.
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. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.
Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)
The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.
CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.
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).
A dataset in the ChemBioSys data platform
An institution in the ChemBioSys data platform
An investigation in the ChemBioSys data platform
An organism in the ChemBioSys data platform
A project in the ChemBioSys data platform
A publication in the ChemBioSys data platform
A strain in the ChemBioSys data platform
ChEMBL database of bioactive drug-like small molecules - Cell lines section
ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.
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.
The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible ontology describing the functions and actions of biologically important chemicals including primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals. The identifiers in this semantic space correspond to individual chemicals.
The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible ontology describing the functions and actions of biologically important chemicals including primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals. The identifiers in this semantic space correspond to entries in the ChemFOnt ontology that are used to organize individual chemicals. Terms can be looked up using the following URL (https://www.chemfont.ca/ontology_browse/term_info/18), but not directly by ID
A hybrid chemical enyclopedia and supplier advertizing system for chemicals.
ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for compounds that compete with probes for binding to target proteins.
ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for chemoproteomic probes used to label human proteins in living cells.
ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for human proteins that interact with chemoproteomic probes.
The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts.
The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.
identifier of scientific author in www.cienciavitae.pt
An ontology to capture confidence information about annotations.
One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes.
CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC.
Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance
Concepts for encoding bibliometric information
ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.
ChecklistBank is an index and repository for taxonomic and nomenclatural datasets
The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.
ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for a panel of experts performing variant pathogenecity evaluation.
ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides and maintains identifiers for alleles.
ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for curations representing evidence aggregation and expert panel assertions based on standardized evaluation procedures
ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.
ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).
This ontology integrates cell type markers for cells in the Cell Ontology from various sources along with details of marker context (anatomical context, assay), confidence (where available) and provenance. [from repository]
Costal and Marine Ecological Classification Standard
Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.
This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain
The China National Center for Bioinformation's (CNCB) Genome Warehouse (GWH) is a public repository holding genetic information for a wide range of species including humans, plants, animals, and microorganisms. Identifiers in this resource correspond to genomes of various species. The goal of the resource is to make genomic data accessible to researchers in areas like precision medicine and biotechnology.
French National Center for Scientific Research - Research Group Identifier
identifier for an academic research group issued by the CNRS
This vocabulary is intended to provide a flexible framework within different usage scenarios to semantically represent any type of content, be it on the Web or in local storage media. For example, it can be used by web quality assurance tools such as web accessibility evaluation tools to record a representation of the assessed web content, including text, images, or other types of formats. In many cases, it can be used together with HTTP Vocabulary in RDF 1.0, which allows quality assurance tools to record the HTTP headers that have been exchanged between a client and a server. This is particularly useful for quality assurance testing, conformance claims, and reporting languages like the W3C Evaluation And Report Language (EARL). [from homepage]
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The IBP Rice Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Based on SES, Rice Descriptor and IRIS DB.
This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Its focus is on traits and variable used in field trials for breeding.
The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
Coconut Ontology v1.0 - Coconut trait dictionary started by CIRAD, based on the "Guidelines for collecting coconut germplasm characterisation data during prospecting missions", COGENT (to be published); the "Descriptors for Coconut, (Cocos nucifera L.)", IPGRI (1995); and the "Manual on standardized research techniques in coconut breeding", IPGRI (1996).
The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies.
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Sweet Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution and breeding company within the project. Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Beet Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
Crop-specific trait ontologies enhance the interoperability and effectiveness of data exchange between the data sources which adopt it, by providing standard concepts that are use to describe phenotypes stored in those sources. As one of them, the Cassava Ontology is actively used and shared in different databases such as the BMS (Breeding Management system) of the IBP or the CassavaBase. Cassava, a major staple crop, is the main source of calories for 500 million people across the globe. A perennial woody shrub native to Latin America, cassava is primarily grown as an annual crop in the humid tropics. A cash crop as well as a subsistence crop, cassava's large edible starchy roots are a source of low-cost carbohydrates for millions. Cassava end products range from fresh roots cooked, boiled, baked or fried at the household level, to highly processed starch as a food additive.
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Common Bean Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
The Groundnut Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
Development of crop-specific trait ontologies including the Chickpea Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
The Lentil Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
The Cowpea Trait Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Pigeon Pea Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Yam Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Brachiaria Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
The Mungbean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.
The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.
Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Brassica Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Oat Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. The Oat Trait Dictionary was commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/).
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Vitis Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
The Woody Plant Ontology lists reference variables used for experimentations and observations on woody plants (forest trees and shrubs, and possibly fruit trees). It is an international initiative based on various communities (French, Portuguese and European). Terms are collected from various sources and organized following the Crop Ontology standard which provides harmonized variables composed by a triplet: (i) a trait, the studied character, (ii) a method, the measurement protocol and (iii) a scale, the unit of measurement or scoring scale.
This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.
Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Sugar Kelp Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology.
This ontology is a part of the the Crop Ontology project , as an essential source of traits and variables to support the standardization of the breeding databases.
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. Quinoa Phenotyping Consortium Creation Date 23.05.2021
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. This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 894215.
COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a "flat" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties.
GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
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. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).
COEXISTENCE - Thesaurus of intersectionality and decolonial issues: black studies, gender, sexuality and feminist studies
Higher-level classifications of COG Pathways
COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.
Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.
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
Contains identifiers of cohesin binding sites in human cells from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.
Contains identifiers for genes that are part of cohesin regulated CRMs (cis-regulatory modules) from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each identifier represents a single cohesin-related CRM. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.
CohesinDB - cohesin-related chromatin loop
Contains identifiers of cohesin-related chromatin loops from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each identifier represents a single cohesin-related chromatin loop. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information.
COI Catalogue is a herbarium with c. 800.000 specimens, organised in separate collections due to the research priorities over the years.
Identifier of a taxon or synonym in the Catalogue of Life
Identifier (name code) for a taxon in the catalogue of life in taiwan
This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.
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. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.
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. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.
Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.
The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)
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 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
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.
Contextual Ontology-based Repository Analysis Library - Context and Measurement Ontology
The Context and Measurement Ontology (COMO) contains ontological terms to describe the context for various types of experimental data and measurements. It is useful in its current state for several different environmental microbiology projects. This ontology is used in multiple CORAL (Contextual Ontology-based Repository Analysis Library) deployments.
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).
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. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.
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. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.
Comprehensive Resource of Mammalian protein complexes
The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.
Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease.
The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
Ontology to describe companies and their supply network, employees, products, production materials, industries, events and relations.
Crisis and hazard related taxonomy developed by CRED for disaster preparedness and humanitarian actions at national and international level.
An ontology for modeling global trade alerts, mainly inspired by the Global Trade Alerts repository.
An ontology for modeling trade agreements
An ontology for modeling international trade flows.
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). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.
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 Protein provides identifiers for protein-related entities, including therapeutic proteins, proteolytic enzymes, antibody-like scaffold proteins, soluble T cell receptors, and tetramers.
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. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data.
A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.
A data model describing machine learning experiments
CropMRespository is a database of soil and crop biophysical process models.
The CryoEM Ontology for describing objects and workflows in Single Particle Analysis by Cryo Electron Microscopy.
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. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.
The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode.
Computer Retrieval of Information on Science Projects Thesaurus
CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains. Note that while still available and included in Unified Medical Language System (UMLS), it has not been updated since 2006.
Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.
Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.
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.
This document describes the RDFS vocabulary description used in the Metadata Vocabulary for Tabular Data along with the default JSON-LD Context.
Common Terminology Criteria for Adverse Events
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. The CTCAE system is a product of the US National Cancer Institute (NCI).
The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.
The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.
Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.
Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.
An ontology to describe entities related to cardiovascular diseases
DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.
DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.
A UUID for a community indexed in the Data Liteacy Alliance (DALIA) web application
A UUID for an open educational resource indexed in the Data Liteacy Alliance (DALIA) web application
A representation of the periodic table of the elements in OWL, with both elements and a hierarchical classification. This is from the DARPA Agent Markup Language (DAML) project, which has been inactive since the mid 2000's.
Distributed Archives for Neurophysiology Data Integration
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. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.
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. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.
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 integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA 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. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.
A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces.
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 currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.
Database of Arabidopsis Transcription Factors
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.
Identifiers represent antimicrobial peptides in the Database of Antimicrobial Peptides (dbAMP) which is an open-access, manually curated database of antimicrobial peptides (AMPs).
The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins.
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.
identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/)
Database of human Major Histocompatibility Complex
This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.
NCBI Probe database Public registry of nucleic acid reagents
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.
Database of Genomic Structural Variation - Study
Database of Genomic Structural Variation - Variant
Dublin Core Metadata Initiative Abstract Model
A metadata model for Dublin Core metadata
A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum.
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. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system.
Data Documentation Initiative Vocabulary
A set of controlled vocabularies in the Data Documentation Initiative, each of which has its own code.
Curated Drug-Drug Interactions Database - Drug
Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.
Curated Drug-Drug Interactions Database - Interaction
Dictyostelium discoideum phenotype ontology
A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.
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.
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. Each protease sequence is curated and, when necessary, cloned and sequenced.
Dynamic Ecological Information Management System - Site and Dataset Registry - Activity
Dynamic Ecological Information Management System - Site and Dataset Registry - Dataset
Dynamic Ecological Information Management System - Site and Dataset Registry - Locations
Dynamic Ecological Information Management System - Site and Dataset Registry - Network
Dynamic Ecological Information Management System - Site and Dataset Registry - Sensor
Dynamic Ecological Information Management System - Site and dataset registry
DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry) is an information management system powered by eLTER. It allows you to discover long-term ecosystem research sites around the globe, along with the data gathered at those sites and the people and networks associated with them. DEIMS-SDR describes a wide range of sites, providing a wealth of information, including each site’s location, ecosystems, facilities, parameters measured and research themes. It is also possible to access a growing number of datasets and data products associated with the sites.
Dynamic Ecological Information Management System - Site and Dataset Registry - Taxonomy
The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.
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
A vocabulary of university course subjects
Assists in resolving data across cloud resources.
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.
Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID]
DiabetesOmic is a multi-omics database designed to collect and analyze transcriptional regulatory information across five high-throughput sequencing modalities, including ChIP-seq, RNA-seq, ATAC-seq, scATAC-seq, and scRNA-seq. This database's identifiers each represent a single sample. It contains clinical complication annotations including diabetic nephropathy, retinopathy, and atherosclerosis to enhance translational relevance. It enables the identification of disease-associated regulatory elements, epigenetic modifications, and cell type-specific molecular signatures, providing valuable insights into the molecular mechanisms of diabetes and its complications.
The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information.
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
The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology
An ontology demonstrating rich ontology for rubber extrusion.
A formal represention for drug-drug interactions knowledge.
The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions
Drivers of human diseases including environmental, maternal and social exposures.
Legacy disease classes that later became MONDO
The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities.
DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences.
Circular double stranded DNA sequences composed
DOULIX lab-tested standard biological parts, in this case, full length constructs.
Assigns persistent identifiers to multidisciplinary research outputs with focus on research originating in Africa, such as in cultural heritage and indigenous knowledge.
The DOME registry is a curated set of papers related to machine learning methods in biology, each with its own unique DOME identifier.
DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.
DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes.
Database of Quantitative Cellular Signaling: Model
The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models.
Database of Quantitative Cellular Signaling: Pathway
The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways.
Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.
The Data Quality Vocabulary (DQV) is seen as an extension to DCAT to cover the quality of the data, how frequently is it updated, whether it accepts user corrections, persistence commitments etc. When used by publishers, this vocabulary will foster trust in the data amongst developers.
DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.
DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.
DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.
DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.
Data Repository of Antimicrobial Peptides
Identifiers repesent antimicrobial peptides in the Data Repository of Antimicrobial Peptides (DRAMP) database which is an open-access, manually curated database of antimicrobial peptides (AMPs).
A project supporting the DRAO application ontology, a hierarchy of specific research domains and descriptors which imports subsets of terms from over 40 publicly-available terminologies. (from repository)
Dutch Research Council file numbers are used for approved grants.
Dr. Duke's Phytochemical and Ethnobotanical Databases chemical
identifier for chemicals linked to information on occurrence in plants
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. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research.
The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.
The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.
Close to 5K Categorizations for drugs, similar to ATCC.
Indications and other conditions in drugbank
DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.
Diagnostic and Statistical Manual of Mental Disorders (4th Edition)
A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]
Deutsche Sammlung von Mikroorganismen und Zellkulturen
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). The following designations are used as part of local unique identifiers: - `PC`: positive control - `NC`: negative control - `AS`: antiserum - `PV`: plant viruses - `RT`: recommended test - `ACC`: human or animal cell line - `DSM`: microorganism cell line
Version 0.4 to 1.0 fixed reversed dsw:locates and dsw:locatedAt. Added labels. Changed comments and descriptions to conform to DC and DwC precedent. Added subClassOf relations to RO hasEvidence and isEvidenceFor. Specified preferred direction for inverse object property pairs., Changes from version 0.2.1 to version 0.3: removal of all functional and inverse function properties of object property terms, use of dwctype classes, deprecation of terms replaced by dwciri: terms, removal of references to TDWG Ontology., Changes from version 0.3 to 0.4 change DwC class namespace from dwctype: to dwc: to follow class proposal, removed references to TDWG TaxonConcept ontology; deprecated terms that now have equivalent terms in Darwin Core., Change from version 1.0 to 1.0.1 Add CC0 license.
DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.
Darwin Core is a vocabulary standard for transmitting information about biodiversity. This document lists all terms in namespaces currently used in the vocabulary.
Degree of Establishment Controlled Vocabulary
The Darwin Core term degreeOfEstablishment provides information about degree to which an Organism survives, reproduces, and expands its range at the given place and time. The Degree of Establishment Controlled Vocabulary provides term that should be used as values for dwc:degreeOfEstablishment and dwciri:degreeOfEstablishment
Establishment Means Controlled Vocabulary
The Darwin Core term establishmentMeans provides information about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans. The Establishment Means Controlled Vocabulary provides terms that should be used as values for dwc:establishmentMeans and dwciri:establishmentMeans.
Darwin Core pathway controlled vocabulary
The Darwin Core term pathway provides information about the process by which an Organism came to be in a given place at a given time. The Pathway Controlled Vocabulary provides terms that should be used as values for dwc:pathway and dwciri:pathway.
Discovery tool for biomedical research resources available at institutions throughout the U.S.
EARL is a vocabulary, the terms of which are defined across a set of specifications and technical notes, and that is used to describe test results. The primary motivation for developing this vocabulary is to facilitate the exchange of test results between Web accessibility evaluation tools in a vendor-neutral and platform-independent format. It also provides reusable terms for generic quality assurance and validation purposes. [from homepage]
The Audience Types Controlled Vocabulary was created for NSF's EarthCube program's Resource Registry. The vocabulary defines the types of audience each resource in the program is targeted to. At this point the vocabulary is very bare - no term definitions even; however, the intention is to extend the vocabulary over time. If you would like to assist with this or in extending any of the other controlled vocabularies/ontologies developed as part of the Resource Registry project, please see https://github.com/earthcubearchitecture-ecresourcereg.
Data Model Language Controlled Vocabulary
The Data Model Language Controlled Vocabulary was created for NSF's EarthCube Program's Resource Registry. At this point it merely lists a few of the languages used by data model resources in the registry.
This ontology defines a taxonomy of software functions based on the work of the NSF-funded EarthCube Resource Registry working group. The functions are generally organized by their role in the research process.
The Semantic Resource Types Vocabulary was created for NSF's EarthCube Program's Resource Repository. Includes entries for things like 'thesaurus', 'ontology', 'controlled vocabulary', 'taxonomy'.
This mini-ontology contains classes and instances for each version of the licenses that are commonly used in software projects, particularly open source software projects. The URI's for each are the canonical URI's for that license (where they exist).
European Bank for induced pluripotent Stem Cells
The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.
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 is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.
Dating from 1978 when catalogues of the Central Library of the Commission of the European Communities (now the European Union) were computerised, ECLAS is a thesaurus created by the Central Library of the Commission of the European Communities for indexing the publications and documents acquired by the Central Library of the Commission. ECLAS was based on the Macrothesaurus of OECD and complemented by the ILO thesaurus. After creation of EUROVOC in 1984, convergence started in order to bring ECLAS in line with EUROVOC, but it was never complete. ECLAS contains nineteen areas of interest in a hierarchical tree structure consisting of four levels. ECLAS is fully available in English and in French. The OP COMM ECLAS is maintained by the Publications Office of the European Union on the EU Vocabularies website.
identifier for a chemical compound per EINECS or ELINCS
Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.
Database of Escherichia coli Sequence and Function
The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.
EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology.
EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes.
DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases
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. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.
E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments.
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. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.
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. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.
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.
A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.
A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.
A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.
EDCC Taxonomy contains the terms that are used to classify citizens' requests to the Europe Direct Contact Centre (EDCC). EDCC Taxonomy is maintained by the Directorate-General for Communication of the European Commission and published by the Publications Office of the European Union on the EU Vocabularies website.
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. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.
FIBO defines the sets of things that are of interest in financial business applications and the ways that those things can relate to one another. In this way, FIBO can give meaning to any data (e.g., spreadsheets, relational databases, XML documents) that describe the business of finance
An Educational and Career-Oriented Recommendation Ontology
An educational ontology for personalised recommendation learning systems that is based on learning path and user profile. It represents the key components for a personalised learning system based on our requirement analysis.
The European Genome-phenome Archive (EGA) is a global network for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Jointly managed by the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre for Genomic Regulation (CRG) in Barcelona.
eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).
Human developmental anatomy, timed version
A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.
Human developmental anatomy, abstract version
A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.
European Joint Programme for Rare Disease Ontology
This ontology is designed to support data search, retrieval and information identification in the EJP-RD catalogs which covers the registries and biobanks for rare diseases. (from repository)
An ontology to describe legislation, based on the FRBR model, that encodes the ELI metadata fields.
Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.
European Language Social Science Thesaurus
The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,000 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information and communication technology and, increasingly, environmental science. [from homepage]
Mouse gross anatomy and development, timed
A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).
Product number for the European Medicines Agency
Catalog of purchasable reagents and building blocks
Experimental Measurements Purposes and Treatments ontologY
The Experimental Measurements, Purposes, and Treatments ontologY (EMPTY) is a structured vocabulary designed to capture and standardize the scientific reasoning behind experimental measurements. It addresses a critical gap in existing metadata standards, which primarily focus on technical specifications rather than scientific intent. The ontology provides a common language to express why a measurement was taken and the conceptual conditions under which it should be interpreted. By focusing on experimental purposes and treatments, EMPTY is designed to significantly improve the findability, interoperability, and reusability of scientific data. This enables researchers to discover relevant datasets for meta-analyses and cross-disciplinary research based on shared scientific goals. (from https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2753)
Environmental Molecular Sciences Laboratory Project
As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including: - Research team and institution - The EMSL project DOI - Link to project data available in EMSLs Data Portal - Project type
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.
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. This collection is concerned with bacterial genomes.
Ensembl Fungi, the Ensembl database for accessing genome-scale data from 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. This collection is concerned with fungal genomes.
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. This collection is concerned with protist genomes.
The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used.
enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.
Thesaurus for long-term ecological research, monitoring, experiments
The Environmental Thesaurus is a controlled vocabulary built to aid integration of the data resulting from long term ecological research and monitoring in Europe (eLTER). It provides described and semantically well defined terms for later analysis and it serves as harmonized specification of parameters in the observation and measurement of ecosystem processes.
Enzo Life Sciences is an antibody vendor.
The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.
Predicates in the Encyclopedia of Life data schema for describing animals, plants, and other organisms
A collaborative project intended to create an encyclopedia documenting all living species known to science
This resource provides identifiers for listed hazardous wastes which are substances explicitly identified due to their potential harm to human health and the environment. These are categorized into four groups (F, K, P, and U) based on specific criteria, such as their source or inherent properties.
Collection of European paediatric cardiac coding files
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. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.
An ontology designed to support the semantic annotation of epidemiology resources
The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research.
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.
An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.
Endogenous Regulatory OligoPeptide knowledgebase-Moscow
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.).
Educational Resource Discovery Index Schema
A metadata stadnard to model data science training materials. Later, was replaced by Bioschemas' [training materials specification](http://bioschemas.org/specifications/TrainingMaterial/specification/).
Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.
ESCO - International Standard Classification of Occupations
The European Skills, Competences, Qualifications and Occupations (ESCO) International Standard Classification of Occupations (ISCO).
The ontology of the taxonomy "European Skills, Competences, qualifications and Occupations". The ontology considers three ESCO pillars (or taxonomy) and 2 registers. The three pillars are: 1) Occupation, 2) Skill (and competences), and 3) Qualification
The ESCO occupations pillar is built on ISCO-08 which serves as its hierarchical structure. ISCO-08 provides the top four levels for the occupations pillar and ESCO occupations are located at level 5 and lower. In ESCO, each occupation is mapped to exactly one ISCO-08 code. [from homepage]
A vocabulary of knowledge, skills and competences relevant to the European labour market. In ESCO v1.2.0, the skills pillar is structured in a hierarchy which contains the following four sub-classifications: 1) Knowledge, 2) Language skills and knowledge, 3) Skills, and 4) Transversal skills. [adapted from homepage]
eukaryotic Subcellular Localization database
eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.
European Searchable Tumour Line Database
European Union Publications Office dataset
Datasets published by the Publications Office of the European Union
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.
Enabling and Unlocking Biology in the Open
EUbOPEN is a project focusing on organizing chemogenic library collections, advancing chemical probe discovery, profiling bioactive compounds, and making project data more accessible.
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.
The Digital Competence Framework for Citizens standard list identifies the key components of digital competence in 5 broader, and a total of 21 narrower areas, with eight proficiency levels for each concept and a few contextualising examples of use. It is maintained by DG EMPL and published by the Publications Office of the European Union on the EU Vocabularies website.
European Commission Participant Identification Code (PIC)
European Science Vocabulary (EuroSciVoc) is the taxonomy of fields of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with fields of science categories extracted from CORDIS content through a semi-automatic process developed with Natural Language Processing (NLP) techniques. (from homepage)
Publications Office of the European Union
The Euvoc ontology, published by the Publications Office of the European Union, supports the development of authority tables (Name Authority Lists or NALs), Eurovoc and EU corporate datasets. It contains a set of classes and properties enabling all the information to be expressed in multilingual format. It helps define relationships between terms and concepts across multiple domains, supporting interoperability and standardization across European Union documentation and databases. It also defines a set a commonly use properties (i.e: start date, end dates, status), and supports the reusability on common data (currencies, languages, countries). The Euvoc ontology is maintained by the Publications Office of the European Union and disseminated on the EU Vocabularies website.
EuroVoc is the EU's multilingual and multidisciplinary thesaurus. It contains keywords, organized in 21 domains and 127 sub-domains, which are used to describe the content of documents in EUR-Lex. [from homepage]
eVOC (Expressed Sequence Annotation for Humans)
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.
The EVORAO Ontology provides a structured and harmonized vocabulary for describing shareable pathogens as characterized biological materials, along with their derived products and associated services, organized into collections. Developed within the EVORA project, it supports consistent metadata annotation across research infrastructures, promoting findability, accessibility, interoperability, and reusability (FAIR). By aligning with relevant standards and ontologies, EVORAO facilitates cross-domain collaboration, integration, and sharing of pathogenic resources and services to enhance pandemic preparedness and response. While initially focused on virology, EVORAO is designed to be extensible and also supports metadata harmonization for other pathogens. [from repository]
An open, community-driven registry of conference and event venues. EVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research organizations. This benefits researchers assembling information about in-person conferences and events by enabling them to refer in an unambiguous way to the venue where it takes place. This repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w), meaning that the data and code are all in one repository that anyone can contribute to.
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. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.
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. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.
Vocabulary to describe an Exif format picture data. All Exif 2.2 tags are defined as RDF properties, as well as several terms to help this schema.
A core reference ontology built upon BFO about exercise medicine. This ontology contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise.
FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.
An organization in FAIRsharing, including universities, labs, etc.
Functional Genome Annotations with Transcriptional Activities
Functional annotations of genomes for studying gene regulation, with a primary focus on cis-regulatory elements (CREs) such as promoters and enhancers.
A structured controlled vocabulary for the anatomy of fungi.
Aquatic Sciences and Fisheries Information System
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. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage)
An ontology representing the gross anatomy of Drosophila melanogaster.
A structured controlled vocabulary of the development of Drosophila melanogaster.
International Fungal Working Group Fungal Barcoding.
DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.
http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T
The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
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).
This prefix is for FDA application identifiers. There are multiple types of FDA applications (https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications), including New Drug Application (NDA). FDA.report provides access to all FDA databases, including applications, in a single portal, and can resolve FDA application identifiers.
Flavor and Extract Manufacturers Association
FEMA provides identifiers for flavor ingredients deemed safe for food use. These entities include chemical compounds and natural substances used as flavoring agents, each reviewed by the FEMA Expert Panel for GRAS (Generally Recognized As Safe) status. The identifiers link to safety data and regulatory assessments, including evaluations by the U.S. FDA and, where applicable, the Joint FAO/WHO Expert Committee on Food Additives (JECFA).
FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors.
FHIR United States Implementation Guides
A set of guides on implementing various processes within hospitals or healthcare systems.
Food Interactions with Drugs Evidence Ontology
Food-Drug interactions automatically extracted from scientific literature
Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.
Five Stars of Online Research Articles Ontology
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.
FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field.
Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)
A database of fly neurons and pathways with an associated 3D viewer.
FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.
FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.
Food Classification and Description System (from FSA Food Type identifiers)
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. These codes may be used within FSA data.
Identifier for a journal article in the fossilworks website
Identifier for an animal, plant, or microorganism from the fossilworks website
FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.
An ontology that enables the description of reviews of scientific articles and other scholarly resources.
Functional Requirements for Bibliographic Records
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. It is imported by FaBiO and BiRO.
Functional Requirements for Bibliographic Records Entity-Relationship Model
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. (from https://www.iflastandards.info/fr/frbr/frbrer.html)
The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.
Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.
Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.
Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.
Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.
Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.
Identifiers represent experimental growth profiles documenting fungal species' ability to utilize specific carbon sources (plant biomass components, polysaccharides, and monosaccharides) in the FUNG-GROWTH database, which provides phenotypic data to support functional genome annotation and comparative analysis of carbohydrate metabolism across fungal species.
FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.
identifier for a fungus taxon in Index Fungorum
Fission Yeast Experimental Conditions Ontology
PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase.
A hierarchical classification of congenital heart disease
A formal ontology of phenotypes observed in fission yeast.
Network of Different Plant Genomic Research Projects
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. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.
Generative Artificial Intelligence Delegation Taxonomy
The Generative Artificial Intelligence Delegation Taxonomy (GAIDeT) assigns identifiers to contributor roles as an extension to the Contributor Roles Taxonomy (CRediT) to support promoting transparency and accountability in academic publishing when AI contribtors are involved in research. It is operationalized in the [GAIDeT Declaration Generator](https://panbibliotekar.github.io/gaidet-declaration/), an interactive tool for researchers to disclose the delegation of tasks to generative AI (GAI) tools in accordance with the GAIDeT taxonomy.
A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.
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. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.
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.
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.
The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains.
An ontology to represent genomics cohort attributes.
General Multilingual Environmental Thesaurus Concept
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. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.
General Multilingual Environmental Thesaurus Group
General Multilingual Environmental Thesaurus Relation
General Multilingual Environmental Thesaurus Theme
GenAtlas is a database containing information on human genes, markers and phenotypes.
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
Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases.
GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match.
GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources
GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E.
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 is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.
Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl.
The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI.
GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013
The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.
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.
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. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace".
The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.
All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes.
An ontology used to enable annotating geospatial semantic information to entities in GeoNames
Predicates that are used to construct the GESIS Knowledge Graph, a bibliometrics KG.
The Ecological Trait-data Standard defines terms for the use in datasets containing quantitative and qualitative functional traits.
The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas.
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 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. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
GitHub is an online host of Git source code repositories.
An issue in any public repository on GitHub.
A pull request in any public repository on GitHub.
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. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability.
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. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors.
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. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.
Comprehensive reference information for the world's languages, especially the lesser known languages. [from homepage]
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. This collection references Glycoepitopes.
A database of GlycoMaps containing 2585 conformational maps.
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 is a website for carbohydrate research. It consists of the "GlycoNAVI Database" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI tools" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools.
GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.
A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates.
Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.
Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.
Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.
Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.
Golm Metabolome Database Reference Substance
Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.
Gmelin's Handbook of Inorganic Chemistry
The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.
The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners.
GND stands for "Gemeinsame Normdatei" (Integrated Authority File) and offers a broad range of elements to describe authorities. The GND originates from the German library community and aims to solve the name ambiguity problem in the library world.
An ontology for glycans based on GlyTouCan, but organized by subsumption.
GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.
Global Natural Products Social Molecular Networking 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)
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.
An issue on the Gene Ontology GitHub issue tracker
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. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.
The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made.
A database-specific registry supporting curation in the Gene Ontology
GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio.
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). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.
Represent chemical entities having particular CHEBI roles
A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.
- DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.
- DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.
IUPAC Gold Book Compendium of Chemical Terminology
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. It is one of the series of IUPAC "Colour Books" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books. Terminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry. The API can be accessed [here](https://goldbook.iupac.org/pages/api)
Search the world's most comprehensive index of full-text books.
Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.
Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.
The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.
The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans.
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.
The WikiPatwhays Graphical Pathway Markup Language (GPML) vocabulary.
A database for Triticeae and Avena references.
A database for Triticeae and Avena gene symbols.
Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.
Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.
GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.
Gleaning Resource Descriptions from Dialects of Languages
GRDDL is a mechanism for Gleaning Resource Descriptions from Dialects of Languages. It is a technique for obtaining RDF data from XML documents and in particular XHTML pages. Authors may explicitly associate documents with transformation algorithms, typically represented in XSLT, using a link element in the head of the document. Alternatively, the information needed to obtain the transformation may be held in an associated metadata profile document or namespace document. Clients reading the document can follow links across the Web using techniques described in the GRDDL specification to discover the appropriate transformations. This document uses a number of examples from the GRDDL Use Cases document to illustrate, in detail, the techniques GRDDL provides for associating documents with appropriate instructions for extracting any embedded data. (from homepage)
A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.
International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.
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 (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.
The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.
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). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.
The initial focus of the GS1 Web Vocabulary is consumer-facing properties for clothing, shoes, food beverage/tobacco and properties common to all products. [from homepage]
General Standard for Food Additives Online Database
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. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database.
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.
Identifiers in the GTN correspond to training materials in various formats (markdown, slides, video). The users can apply learned concepts directly within the framework via galaxy workflows.
The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease
The Genetic Testing Registry provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease.
Genitourinary Development Molecular Anatomy Project
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.
An _gentle_ implementation of the Unified Foundational Ontology (UFO), which is an upper level ontology like BFO that is concerned with e.g. expressing temporal relationships between events.
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. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central 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. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central 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. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.
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. This collection references experiments.
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. This collection references genes.
GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.
GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals
High-quality Automated and Manual Annotation of microbial Proteomes
HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.
Human ancestry ontology for the NHGRI GWAS Catalog
A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)
Literature references in the Hymenoptera Anatomy Ontology Portal
Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world.
A Database of Human Hemoglobin Variants and Thalassemias
This is a relational database of information about hemoglobin variants and mutations that cause thalassemia.
Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.
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 is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers.
the European Hepatitis C Virus Database (euHCVdb, euhcvdb.lyon.inserm.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.
Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)
The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.
HemOnc.org is the largest freely available medical wiki of interventions, regimens, and general information relevant to the fields of hematology and oncology.
HEPRO is an ontology of informational entities and processes related to health procedures and health activities.
An identifier for institutions in the United Kingdom, used in GRID and ROR.
The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.
The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.
Human Genome Variation Society Nomenclature
The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/).
H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.
H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.
H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.
Human Induced Pluripotent Stem Cells Initiative
HMS Library of Integrated Network-based Cellular Signatures Antibodies
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
Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog.
Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.
Database of Complete Genome Homologous Genes Families
HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.
An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.
The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the animal semantic space correspond to animals that samples in the database are obtained from.
The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the samples semantic space represent samples derived from animals in HoloFood trials.
This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.
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. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.
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. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.
HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
An international LGBTQ+ linked data vocabulary
Healthcare Organizations and Services Ontology
HOSO is an ontology of informational entities and processes related to healthcare organizations and services.
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 Protein Atlas tissue profile information
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. Primary access to this collection is through Ensembl Gene identifiers.
An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. The original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]
The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.
The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.
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.
hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).
The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas.
Database of homology-derived secondary structure of proteins
HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.
An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines
Human BioMolecular Atlas Program Collection
The collections section of HuBMAP groups related datasets, samples, and metadata into organized categories. Each collection has a unique identifier that links it to its constituent datasets.
Human BioMolecular Atlas Program Dataset
The HuBMAP dataset collection provides high resolution molecular data from human tissues, with unique identifiers that enable tracking, citation, and integration of datasets across diverse assay types and donor samples for biomedical research.
The HuBMAP donors dataset contains demographic and clinical metadata for individuals who donated tissue samples. Each donor has a unique identifier used to link them to their associated tissue samples and derived experimental data.
The samples subsection of HuBMAP provides metadata about individual tissue samples collected from donors, and are the downstream experimental datasets for scRNA sequencing. Each sample has a unique identifier that links it to donor information, anatomical source, and related datasets.
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.
The hu.MAP integrates several large scale protein interaction datasets to obtain a comprehensive view of protein complexes.
A lightweight vocabulary for hypermedia-driven Web APIs
Information Artifact Ontology Issue Tracker
An issue on the Information Artifact Ontology GitHub issue tracker
A vocabulary for calendar events and related objects
ICEberg cis-integrative and mobilizable element
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. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.
ICEberg integrative and conjugative element
ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.
ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.
ICEberg integrative and mobilizable element
Integrated Chemical Environment - Chemical data
The Integrated Chemical Environment (ICE) provides high-quality curated data and appropriate tools to support development and evaluation of new, revised, and alternative methods. ICE provides free online access to curated in vivo and in vitro test data, in silico toxicity predictions and chemical property data, reference chemical lists, and computational tools for chemical characterization and predicting toxicity. ICE supports the following: (i) Data integration: brings together available data, including data on formulations; (ii) Results exploration: enables dynamic, graphical exploration with publication-quality graphics; (iii) Data analysis: allows characterization of data using online workflows, and (iv) FAIR data access: data are findable, accessible, interoperable, and reusable.
Integrative and Conjugative Element Ontology
A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.
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.
We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage)
This resource is about projects in the Indian Crop Phenome Database (ICPD). The ICPD is a domain of the Indian Biological Data Center (IBDC), Regional Centre for Biotechnology, Faridabad, developed for the digitization of crop phenome data. Being the global agricultural powerhouse, the bulk of biological data generated in India is associated with agricultural trials. Ironically most of the trial data has been inaccessible to other researchers, and remains unpublished, and is lost as time passes. Therefore, ICPD would act as single-stop user-friendly platform for freely archiving, organizing, analyzing, and sharing the multi-crop phenome data following FAIR (Findable, Accessible, Interoperable and Re-usable) data principles. [from homepage]
This resource is about studies in the Indian Crop Phenome Database (ICPD). The ICPD is a domain of the Indian Biological Data Center (IBDC), Regional Centre for Biotechnology, Faridabad, developed for the digitization of crop phenome data. Being the global agricultural powerhouse, the bulk of biological data generated in India is associated with agricultural trials. Ironically most of the trial data has been inaccessible to other researchers, and remains unpublished, and is lost as time passes. Therefore, ICPD would act as single-stop user-friendly platform for freely archiving, organizing, analyzing, and sharing the multi-crop phenome data following FAIR (Findable, Accessible, Interoperable and Re-usable) data principles. [from homepage]
International Committee on Taxonomy of Viruses Ontology
Ontology representation of the [International Committee on Taxonomy of Viruses (ICTV)](https://ictv.global/) for the [EVORA project](https://evora-project.eu/)
Intrinsically Disordered proteins with Extensive Annotations and Literature
IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.
The COVID-19 Infectious Disease Ontology
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). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.
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. In addition, iDog provides online tools for performing genomic data visualization and analyses.
Intrinsically Disordered Proteins Ontology
IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR.
Identifiers for specific experimental assays that serve as evidence for immune-related studies.
Identifiers for epitopes, which are the specific parts of antigens recognized by the immune system.
Immune Epitope Database MHC Restrictions
Identifiers for Major Histocompatibility Complex (MHC) restrictions of immune cells, detailing genetic factors that influence immune recognition.
Identifiers for immune receptors, representing receptor complexes or groups studied for their interactions with antigens or epitopes.
Identifiers for references, typically linking to sources of evidence such as publications that support data within IEDB.
identifier for a document in IEEE Xplore
The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.
Integrated Genomic Resources of human Cell Lines for Identification
IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents.
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. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.
International Histocompatibility Workshop cell lines
The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics.
Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.
International Medical Device Regulators Forum
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.
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.
The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.
The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.
ImMunoGeneTics database covering immunoglobulins and T-cell receptors
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/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.
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
The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members.
Molecule role (INOH Protein name/family name ontology)
MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.
The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]
Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID]
Supplier of mice for research purposes. [from RRID]
The identifier for an observation in iNaturalist
The information resource registry is a listing of data sources present in the NCATS Data Translator system. Each information resource has an identifier, a short description, and a URL to more information about that resource.
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
The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.
A Knowledge Resource for Innate Immunity Interactions and Pathways
InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation.
he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.
The coding sequence or protein identifiers as maintained in INSDC.
Genome assembly database - INSDC accessions
The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.
Genome assembly database - RefSeq accessions
The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage.
The INSPIRE theme register contains all spatial data themes, as defined in the Annexes of the INSPIRE Directive ( Directive 2007/2/EC of the European Parliament and of the Council of 14 March 2007 establishing an Infrastructure for Spatial Information in the European Community (INSPIRE)). The descriptions of the themes are based on version 3.0 of the "Definition of Annex Themes and Scope (D 2.3)" by the data specifications drafting team and subsequent updates by the INSPIRE Thematic Working Groups (TWGs). (from homepage)
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.
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. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)
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. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants.
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. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings.
Interlinking Ontology for Biological Concepts
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. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: "Interlinking Ontology for Biological Concepts © National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International".
Individual Organism Information Ontology
An ontology of information entities about an individual
IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers.
Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).
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. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.
Database of experimentally verified IRES structures
The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.
The International Standard Book Number (ISBN) is for identifying printed books.
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.
ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.
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. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC. The mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described.
Since the introduction of ISO 639-3 in 2007, access to language information has increased tremendously. The code set initially adopted as ISO639-3:2007 was based on a harmonization of ISO 639-2 with the code set of SIL’s Ethnologue 15th edition and languages from Linguist List to form a comprehensive set of code elements for world languages. SIL International, the Language Coding Agency for 639-3, relies on the contributions of linguists, language coding experts, and language users around the world to maintain and improve the code set through the change request process defined in the ISO 639 standard. [from homepage]
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 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.
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.
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. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.
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. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.
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. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.
IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.
Japan Consortium for Glycobiology and Glycotechnology Database
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. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.
The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.
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 provides identifiers for flavors, food additives, contaminants, toxicants, and veterinary drugs. Each entry includes chemical details, acceptable or tolerable intake limits, and links to related reports and monographs.
Identifiers for proposals/projects at the Joint Genome Institute
JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.
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 is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.
identifier for researchers in Japan used in government-based research funding (from 1980s)
Kinetic Data of RNA-Protein Interactions Database
Identifiers represent RNA-protein interaction entries with quantitative kinetic data in the Kinetic Data of Biomolecular Interactions for RNA-Protein database (KDBI-RP), which is an open-access database cataloging association rates, dissociation rates, and equilibrium dissociation constants for RNA-protein interactions.
KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.
An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains
A vocabulary describing licenses for data and code
Langual stands for "langua alimentaria" or "language of food". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases
number for the Lattes Platform entry on the person or group. Relationship between entry and subject must be supported by a source.
The Livestock Breed Ontology (LBO) is a controlled vocabulary for the unambiguous description of breeds. Its utility include proper identification of inherited variation sources in genetics/genomic studies.
LCCN Permalinks are persistent URLs for bibliographic records in the LC Catalog and authority records in LC Authorities. These links are constructed using the record's LCCN (or Library of Congress Control Number), an identifier assigned by the Library of Congress to bibliographic and authority records. LCCN Permalinks are also available for citation records in the Handbook for Latin American Studies (HLAS). [from homepage]
A set of best practices and simple approach for a read-write Linked Data architecture, based on HTTP access to web resources that describe their state using the RDF data model.
identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide
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). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.
LG Chemical Entity Detection Dataset (LGCEDe)
LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).
The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.
Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.
In this ontology, we defined nine distinct categories that encompass various aspects of lifestyle factors (LSFs), creating a unified Lifestyle Factors Ontology (LSFO) across these categories. Within the context of lifestyle, we have identified nine categories that can collectively describe all LSFs, namely: 1-Nutrition, a category that covers different branches such as dietary habits, food groups, food processing and preparation, macronutrients, and micronutrients, among others. 2-Socioeconomic factors, which includes social and economic conditions such as income, wealth, education and socioeconomic status. 3-Environmental exposures, includes exposure to various environmental factors, such as air pollution, water quality, and workplace hazards, that can impact an individual’s health. 4-Substance use, covers concepts such as smoking, as well as illicit drug use. 5-Physical activities, includes regular exercise and physically demanding activities like leisure time, occupational, and household physical activities. 6-Non-physical leisure time activities, describes any activity an individual might engage in during their free time that is not a physical activity. 7-Personal care products and cosmetic procedures, covers activities related to hygiene, use of cosmetic and cleaning products as well as invasive procedures that people undergo to improve their appearance, such as cosmetic surgery. 8-Sleep, covers sleep quality, stages, and habits. 9-Mental health practices, includes the behaviors and habits related to maintaining good mental health and emotional well-being such as meditation, and psychotherapy.
Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.
LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.
Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.
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. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.
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. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).
The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.
Registry of programming languages for the Linguist program for detecting and highlighting programming languages.
Genderal Ontology for Linguistic Description
identifier for a person, on the LinkedIn website
Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks.
LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
An ontology representation of the LIPIDMAPS nomenclature classification.
LncBook accommodates a high-quality collection of human lncRNA genes and transcripts, and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional signatures of lncRNAs in human diseases and different biological contexts.
A comprehensive compendium of human long non-coding RNAs
Relator terms and their associated codes designate the relationship between an agent and a bibliographic resource.
Library of Congress Resource Types Scheme
A controlled vocabulary of media resources, such as audio, cartographic, manuscript, multimedia, etc.
The ISA Programme Location Core Vocabulary provides a minimum set of classes and properties for describing any place in terms of its name, address or geometry. The vocabulary is specifically designed to aid the publication of data that is interoperable with EU INSPIRE Directive.
Une ontologie "historique" utilisée par l'outil en ligne de commande cwm, au temps des balbutiements du web sémantique (~ 2000 - 2003 ?)
Contains information about cells and data sheets related to transfection.
identifier for a person, in the Loop database of researcher impact
The localization and quantitation atlas of the yeast proteome
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, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.
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.
Laboratory of Systems Pharmacology Compound
Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)
Long Term Ecological Research Controlled Vocabulary
The LifeWatch Metadata Catalogues plays a crucial role in managing metadata for digital objects, including Datasets, Services, Workflows and Virtual Research Environments. This catalogue serves as the central repository, ensuring that resources are accessible and reusable by stakeholders.
A structured controlled vocabulary of the adult anatomy of the mouse (Mus)
Mechanism, Annotation and Classification in Enzymes
MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.
Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond.
MaizeGDB is the maize research community's central repository for genetics and genomics information.
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.
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).
An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.
MarkerDB is a freely available electronic database that attempts to consolidate information on all known clinical and pre-clinical biomarkers into a single resource. It provides identifiers for known clinical and pre-clinical biomarkers. Each entry provides detailed annotations, including biomarker descriptions, associated conditions, specificity, sensitivity, molecular structures, chromosomal locations, and clinical approval status.
MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).
address on the Mastodon decentralized social network (the form is 'user@server.domain' without a leading '@')
MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides
MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.
Multiplexed Assays of Variant Effect Database
Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a
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. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.
The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number. [wikipedia]
The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.
Medical Dictionary for Regulatory Activities Terminology
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. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).
Medical Dictionary for Regulatory Activities
MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.
This vocabulary is used internally inside MedGen to assign temporary identifiers to terms that will later get put in UMLS. Mappings between MedGen, MedGen CIDs, and UMLS can be found [here](https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz).
The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]
MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.
Chemical reactions in the Merck Index. This website doesn't exist anymore
The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors.
The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.
MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012.
MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.
Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump
Metabolic Encyclopedia for Pathway/Genome Databases
MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data. MetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)]. The majority of pathways occurring in it are from microorganisms and plants. MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number
MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.
MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.
MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.
MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.
Metabolite and Tandem Mass Spectrometry Database
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. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.
The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another.
Microbial Ecophysiological Trait and Phenotype Ontology
METPO (Microbial Ecophysiological Trait and Phenotype Ontology) provides standardized terms for describing microbial phenotypes, growth characteristics, and culture conditions. It includes classes for growth media, temperature tolerances, pH tolerances, and relationships like "grows in" and "does not grow in".
A public place to process, interpret and share GC/MS metabolomics datasets.
The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.
A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.
An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.
The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).
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.
Analyses of microbiome data within MGnify
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. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.
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. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.
The free-to-use MGnify platform provides assembly, analysis and archiving of microbiome-derived nucleic acid sequence data from a wide range of biomes, with analysis results providing taxonomic and functional profiles. The platform also includes MGnify Proteins, a database of protein sequences derived from the analysis of metagenomic assemblies, and MGnify Genomes, a resource of biome-specific catalogues of microbial genomes, including extensive functional annotations.
Molecular Interactions Controlled Vocabulary
The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.
Minimal Information About Anatomy ontology
Minimum Anformation About a Phylogenetic Analysis Ontology
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. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.
Minimum Information about a Biosynthetic Gene Cluster data repository
MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a data repository and associated data standard designed to describe biosynthetic gene clusters involved in the production of specialized metabolites. It also stores data on measured biological activities and links to other resources such as NCBI, NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and training dataset for machine learning.
MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.
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. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
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. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.
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 is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.
The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.
The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.
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. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.
mircoRNA Gene Database is a collection of animal microRNA genes. This database allows researchers to analyze mircoRNA properties like secondary structure and features in a phylogenetic context.
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 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. The Registry provides unique and perennial URIs for each entity of those data collections.
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.
An application ontology for use with miRNA databases.
miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.
Application ontology for entities related to insecticide resistance in mosquitos
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. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.
This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs
Minimum Information about a Tailoring Enzyme data repository
MITE (Minimum Information about a Tailoring Enzyme) is a data repository and associated data standard designed to capture the reaction- and substrate-specificities of tailoring enzymes. Community-driven and fully expert-reviewed, it represents enzymatic reactions using reaction SMARTS and links to established resources such as UniProt, NCBI GenPept, Rhea, and MIBiG. MITE serves as a knowledgebase for enzyme and pathway annotation, in silico biosynthesis, and machine learning applications.
Minimum Information about any (x) Sequence
The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample.
MLCommons Association artifacts, including benchmark results, datasets, and saved models.
The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.
A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.
MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.
MarDB includes all sequenced marine microbial genomes regardless of level of completeness.
MarFun is manually curated database for marine fungi which is a part of the MAR databases.
MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.
Mutant Mouse Resource and Research Centers
The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.
MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats.
The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included.
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 is a database of protein disorder and mobility annotations.
The Mobilome Ontology describes bacterial mobile genetic elements, their mechanisms, and associated epidemiology.
ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.
Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models.
Metadata Management and distribution system for Multiple GNSS Networks
M3G stands for “Metadata Management and distribution system for Multiple GNSS Networks”. M3G allows to upload, validate, and distribute GNSS station metadata such as IGS-style site logs, information about local networks, DOIs, nominal data provision, data licenses attached to the daily RINEX data, etc...
Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.
MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for cell lines used in assays measuring molecular bioactivity, linking them to associated compounds and proteins.
MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for chemical compounds with experimentally validated bioactivity in cellular contexts.
MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for proteins that serve as molecular targets in cell-based bioactivity measurements.
Identifiers correspond to molecular glue compounds in the MolGlueDB which is a free and open-access online database dedicated to the collection and integration of molecular glue compound information.
MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations.
The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits.
An issue on the MONDO GitHub issue tracker
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.
An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io).
The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.
An ontology of minimum information regarding potential drug-drug interaction information.
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.
The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can
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.
The Unified Medical Language System® (UMLS®) Metathesaurus (MTH) was developed and is maintained by the U.S. National Library of Medicine (NLM). MTH contains concept names, attributes, relationships, and other data that were created by NLM to facilitate construction of the UMLS Metathesaurus.
The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated.
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).
NFDI-MatWerk aims to establish a digital infrastructure for Materials Science and Engineering (MSE), fostering improved data sharing and collaboration. This repository provides comprehensive documentation for NFDI MatWerk Ontology (MWO) v3.0.0, a foundational framework designed to structure research data and enhance interoperability within the MSE community. To ensure compliance with top-level ontology standards, MWO v3.0.0 is aligned with the Basic Formal Ontology (BFO) and incorporates the modular approach of the NFDIcore mid-level ontology, enriching metadata through standardized classes and properties. The mwo addresses key aspects of MSE research data, including the NFDI-MatWerk community structure, covering task areas, infrastructure use cases, projects, researchers, and organizations. It also describes essential NFDI resources, such as software, workflows, ontologies, publications, datasets, metadata schemas, instruments, facilities, and educational materials. Additionally, mwo represents NFDI-MatWerk services, academic events, courses, and international collaborations. As the foundation for the MSE Knowledge Graph, mwo facilitates efficient data integration and retrieval, promoting collaboration and knowledge representation across MSE domains. This digital transformation enhances data discoverability, reusability, and accelerates scientific exchange, innovation, and discoveries by optimizing research data management and accessibility. (from repository)
MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.
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.
An ARK resolver as well as resolver built with common prefixes as in Identifiers.org
The ontology and metadata schema for the NFDI4Earth Knowledge Hub. See serializations of this schema as an OWL ontology here: - [RDF/XML](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.xml) - [RDF/Turtle](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.ttl) - [RDF/JSON-LD](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.jsonld) - [RDF/N-Triples](https://nfdi4earth.pages.rwth-aachen.de/knowledgehub/nfdi4earth-kh-schema/ontology.owl.nt)
The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO).
Natural Product-Drug Interaction Research Data Repository
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).
NAPP (Nucleic Acids Phylogenetic Profiling) is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.
National Academic Research and Collaborations Information System
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.
NASA Open Science Data Repository Biospecimen
Identifiers for biospecimens used in experiments that investigate biological and health responses of terrestrial life to spaceflight
NASA Open Science Data Repository Experiment
Identifiers for space-related data from experiments that investigate biological and health responses of terrestrial life to spaceflight
NASA Open Science Data Repository Hardware
Identifiers for hardware used in experiments that investigate biological and health responses of terrestrial life to spaceflight
NASA Open Science Data Repository Mission
Identifiers for missions associated with experiments that investigate biological and health responses of terrestrial life to spaceflight
NASA Open Science Data Repository Payload
Identifiers for payloads associated with experiments that investigate biological and health responses of terrestrial life to spaceflight
Identifiers for space-related data from studies that investigate biological and health responses of terrestrial life to spaceflight
NASA Open Science Data Repository Subject
Identifiers for subjects of experiments that investigate biological and health responses of terrestrial life to spaceflight
The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
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. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.
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. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.
National Center for Advancing Translation Sciences 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. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays.
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. NCATS Inxight Drugs contains information on ingredients in medicinal products, including: - US Approved Drugs - Marketed Drugs - Investigational Drugs - Other Substances
Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.
This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.
A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources
The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover.
This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace.
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. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number.
Database of one-to-one ortholog information provided by the NCBI as a subset of their Gene resource. Used for users to access ortholog information for over 1000 species of vertebrates and arthropods.
identifier of an entry in the NCI Drug Dictionary
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. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.
An ontology for non-coding RNA, both of biological origin, and engineered.
FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements.
The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge.
NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4 includes robust protein predictions (NemPep4), and protein families for 63 nematode species, over 600,000 ESTs and over 250,000 proteins.
Neuroscience Multi-Omic BRAIN Initiative Data
This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects.
A small ontology expressing skills and competencies.
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). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource.
NEPOMUK Annotation Ontology Specification
The annotation ontology provides vocabulary that enables users to attach custom descriptions, identifiers, tags and ratings to resources on their desktop. Via other properties, the user is also able to make generic relationships between related resources explicit. Some relationships between resources are too general to be included at the domain ontology level. Instead, these properties are also defined in the annotation ontology. Given the high-level status of this ontology, these propreties can be used to link any related resources on the user's desktop, as well as provide custom human-readable textual annotations. (from homepage)
NEPOMUK Contact Ontology describes contact information, common in many places on the desktop. It evolved from the VCARD specification (RFC 2426) and has been inspired by the Vcard Ontology by Renato Ianella. The scope of NCO is much broader though. This document gives an overview of the classes, properties and intended use cases of the NCO ontology. (from homepage)
The PIMO Ontology can be used to express Personal Information Models of individuals. It is based on RDF and NRL, the NEPOMUK Representational Language and other Semantic Web ontologies. This document describes the principle elements of the language and how to use them. (from homepage)
NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons.
BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it.
NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.
Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images.
Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images.
NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones.
NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. (Developed by the SIB Swiss Institute of Bioinformatics)
A mid-level ontology for representing metadata related to NFDI resources, including individuals, organizations, projects, data portals, and more
Assigns identifiers to knowledge graphs (KGs) that are used and/or maintained within any NFDI consortium.
The NFDI4Culture portal offers all content as Linked Open Data over this RESTful API. The API implements the Hydra-Specification of the W3C Hydra Community Group. The semantic description of this API can be retrieved by clients via the Hydra documentation file (JSON). Each metadata record offered via this API can also be retrieved in one of following machine-readable LOD serializations. The API is the basis for the Culture Research Information Graph, which together with the Culture Research Data Graph forms the [Culture Knowledge Graph](https://nfdi4culture.de/services/details/culture-knowledge-graph.html) (for more details see [this presentation](https://doi.org/10.5281/zenodo.7748740)) (from homepage).
Identifiers represent experimental tools and resources for neurofibromatosis (NF) research in the NF Data Portal Tools catalog.
Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.
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.
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.
NIFEXT covers IRIs that were "external" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed.
NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing.
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. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)
The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species.
Networked Knowledge Organization Systems/Services/Structures
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. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004).
United States Geological Survey - National Land Cover Database
A vocabulary for describing the usage of land cover (e.g., pasture, wetlands, barren, forest, water) extended from the original 16 land cover classes proposed by the [Anderson Level II classification system](https://doi.org/10.3133/pp964) in 1976
Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database
Publisher short codes appearin in the NLM Catalog.
NLXANAT covers anatomy terms. Almost all terms are also in Uberon.
NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).
NLXCELL conatins cell types with a focus on neuron types.
NLXCHEM covers chemicals. Most classes are also in ChEBI.
NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc.
NIF Standard Ontology: Cognitive Function
NLXFUNC covers terms for cognitive function.
NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.
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
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).
NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).
NIF Standard Ontology: Digital Resources
NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites
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
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 database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties.
compounds appearing in nmrXiv that have associated spectra.
spectra (samples) in the nmrXiv database
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.
Identifier for a species on the noaa fisheries website
A nomenclatural ontology for biological names
NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.
NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.
NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.
NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.
Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.
A vendor of antibodies and other biologics
Natural Product Activity and Species Source Database
Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.
Identifiers for microbially derived natural products that contains compound structures, producing organism taxonomy, biosynthetic and chemical properties.
An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.
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. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)
Identifier used by the Cancer Chemotherapy National Service Center.
Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research.
National Swine Resource and Research Center
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. [from RRID]
National Uniform Claim Committee Characteristic
The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan.
NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.
The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
SKOS concept collections held in the NERC Vocabulary Server. A concept collection is useful where a group of concepts shares something in common, and it is convenient to group them under a common label. In the NVS, concept collections are synonymous with controlled vocabularies or code lists. Each collection is associated with its governance body. An external website link is displayed when applicable.
National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]
New Zealand Threat Classification System
identifier for species classified under the New Zealand Threat Classification System
Ontology of Arthropod Circulatory Systems
OArCS is an ontology describing the Arthropod ciruclatory system.
It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]
Ontology for Biomarkers of Clinical Interest
The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects.
Ontology of Biological and Clinical Statistics
OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)
The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.
Open Biological and Biomedical Ontologies
The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.
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.
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.
This Occupaton Ontology (OccO) is an ontology in the domain of human occupaitons. Current OccO version is developed based on the US Bureau of Labor Statistics Standard Occupation Classification (SOC) and the related O*Net System. The OccO development follows the principles of the Open Biological and Biomedical (OBO) Foundry.
The Crystallographic Defect Core Ontology (CDCO) defines the common terminology shared across all types of crystallographic defects, providing a unified framework for data integration in materials science.
Each OCI (Open Citation Identifier) has a simple structure: oci:<identifier>-<identifier>, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first <identifier> is the identifier for the citing bibliographic resource, while the second <identifier> is the identifier for the cited bibliographic resource.
'ocid' stands for "Ontology Concept Identifiers" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.
The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.
Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.
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. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines. ODAM allows datasets to be explored and then extracted in whole or in part as needed. For more information/explanation, see ODAM User's Guide : https://inrae.github.io/ODAM/
Open Data Commons for Spinal Cord Injury
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
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.
OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors
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.
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.
Austrian Fields of Science and Technology Classification
The Austrian Fields of Science and Technology Classification (ÖFOS 2012) is the Austrian version of the revised international Fields of Science and Technology Classification of the OECD (FOS) published in the Frascati Manual 2015 as Fields of Research and Development (FORD). These fields are adjusted to national needs, whose application for international comparisons is binding, particularly within the European Statistical System. The six major Fields of Science: Natural Sciences; Technical Sciences; Human Medicine, Health Sciences; Agricultural Sciences, Veterinary Medicine; Social Sciences and Humanities remained unchanged in comparison to ÖFOS 2002. In order to ensure international comparability, the previous 2-digit levels from 2002, which are no longer applicable, were replaced by new 3-digit levels (groups) according to the international FOS respectively FORD. These 3-digit levels were provided with further sub-groups (4-digits) taking into account the comments of the international classification. It is therefore feasible that the new Austrian Fields of Science adapt to national peculiarities of the Austrian research activities. The research area with the corresponding 6-digits in alphabetical order serves as a description of the fields of activities and research projects and/or for the coverage of the main scientific activities of a statistical unit in the research and development surveys. (Current revision status: August 2017)
A vocabulary for embedding provenance metadata into webpages via RDFa
Open Geospatial Consortium Simple Features Vocabulary
An RDF/OWL vocabulary for defining SimpleFeature geometry types
OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.
An ontology that formalizes the genomic element by defining an upper class genetic interval
Ontology of Genetic Susceptibility Factor
An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.
Ontology of Host-Microbiome Interactions
OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.
OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).
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.
The OpenID Connect vocabulary used by the Solid-OIDC authentication specification
OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.
Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference.
OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.
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). The 'omia' prefix is used for phenes, either across species (omia:001000) or in a specific species (omia:001000-9615)
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). The 'omia.variant' prefix is used for genetic variants associated with phenes listed in OMIA
Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure entity_type_abbreviation/supplier_prefixsequential_number. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted.
A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.
Overview of Medical Research in the Netherlands
The new national clinical trials registry of the Netherlands
OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX.
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.
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.
OntoDM-core defines the most essential data mining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. (from abstract)
The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.
Ontology of Organizational Structures of Trauma centers and Trauma systems
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).
The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.
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 is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item.
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
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.
Orientation of Proteins in Realistic Lipid Membranes
Orientations of Proteins in Realistic Lipid Membranes (OPRLM) is a database for visualizing proteins in realistic lipid membranes. It includes the classification of proteins into types, superfamilies, and families, and also provides information on intracellular localizations of the proteins. Identifiers represent proteins.
IUPAC Compendium of Analytical Nomenclature (Orange Book)
The first number is the chapter then the remainder are subsections.
The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).
Vocabulary for describing organizational structures, specializable to a broad variety of types of organization.
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. This collection references Saccharomyces cerevisiae.
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. This collection references Schizosaccharomyces pombe.
An application ontology designed to annotate next-generation sequencing experiments performed on RNA.
The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.
OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups
Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.
Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.
The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.
Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.
Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.
Office of Scientific and Technical Information (OSTI)
The U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) is the main metadata archive for permanent storage of registered [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service) (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord) is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services)) and can be alternatively used as the main product identifier endpoint when [searching OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below). OSTI.GOV is the primary registry and search tool for all Department of Energy (DOE) funded science, technology, and engineering research and development (R&D) results and the organizational hub for information about the DOE Office of Scientific and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761 - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761 - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761 **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/ - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/
Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.
Identifier for an entity in open tree of life
Ontological Interpretations for Web Property Graphs
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. [from GitHub]
Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.
Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.
Identifiers correspond to curated multigene families in the human genome from the Phylogenomic Analysis of Human Genome (PAHG) database, focusing on evolutionary relationships and gene duplication events across vertebrates.
The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.
Protein and Associated NucleotideDomains with Inferred Trees
PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.
Protein Alignment organised as Structural Superfamily
The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.
PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana.
Pathguide contains information about 325 biological related resources and molecular interaction related resources.
PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant® also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.
PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.
PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.
The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.
Physiologically-Based Pharmacokinetic Ontology
An ontology for modeling and understanding of pharmacokinetics in biological systems.
PDBsum; at-a-glance overview of macromolecular structures
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.
An ontology to describe entities related to prescription of drugs
Life cycle stages for Platynereis dumerilii
Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a "peer"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs.
PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored.
PEPhub is a database, web interface, and API for sharing, retrieving, and validating sample metadata. PEPhub uses Portable Encapsulated Projects (PEP) biological metadata standard to store, edit, and access PEPs in one place.
The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.
A product catalog for PerkinElmer, a laboratory supplies vendor
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.
chemical in the database supplied by Pesticide Action Network North America
Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets.
The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation.
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. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt "neoplasm" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs.
PhageDive is a database for bacteriophages and archaeal viruses. It provides information regarding taxonomy, host strain, phage morphology, life cycle, origin and genomic data.
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. Query by cell line.
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. Query by 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. Query by tissue.
SNPs and other variants that can be mapped to dbSNP.
The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium.
Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.
A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants.
PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.
PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.
PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications.
PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.
PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.
Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur.
PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.
Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.
Database of structurally defined protein interfaces
PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected.
NCI Pathway Interaction Database: 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. This datatype provides access to pathway information.
A combination of an ISBN and local unique identifier for articles and other published works. Please see the [Wikipedia page](https://en.wikipedia.org/wiki/Publisher_Item_Identifier) for a detailed explanation. Some PIIs are used as the local identifiers in DOIs, such as https://doi.org/10.1136/S0003-4967(24)38620-0.
Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.
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. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
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 an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration.
PLANT REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with the Reactome editorial staff and cross-referenced to many bioinformatics databases. These include project databases like Gramene, Ensembl, UniProt, ChEBI small molecule databases, PubMed, and Gene Ontology.
The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.
A database of chemicals relevant for plastics and polymer sciences.
An ontologization of Public Library of Science (PLOS) journal keywords and topics. It's not clear how the IDs correspond to the actual pages. Appears in ADCAD.
Identifiers correspond to curated and proteomics-inferred associations between protein post-translational modifications (PTM) and drug sensitivity.
The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).
The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.
The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.
The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers.
Resource for the community to store, retrieve, search, reference, and reuse CellML models.
Workspace (Git repository) for modeling projects managed by the Physiome Model Repository
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. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries.
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.
Reproductive and behavioural traits of both adult and larval stages, as well as information on environmental preferences and a few morphological traits.
PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties.
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.
PRINTS compendium of protein fingerprints
PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.
The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation.
ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities.
ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.
ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information.
A comprehensive proteomics data and process provenance ontology.
PRO Research: An ontology for describing RDM-Policies in a structured way
PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.
This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures).
ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.
ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.
ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.
ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.
The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.
This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.
The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.
Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.
Documentation of the Phenoscape Curation Workflow
Protein Structure and Stability Knowledge Base
PSSKB allows researchers to model post translational modifications and amino acid substitutions in proteins, providing 3D structural representations. Identifiers represent protein motifs on which PSSKB provides data.
Identifiers for product types (product, price, and company data) based on Wikipedia
This specification contains a framework for representing pointers - entities that permit identifying a portion or segment of a piece of content - making use of the Resource Description Framework (RDF). It also describes a number of specific types of pointers that permit portions of a document to be referred to in different ways. When referring to a specific part of, say, a piece of web content, it is useful to be able to have a consistent manner by which to refer to a particular segment of a web document, to have a variety of ways by which to refer to that same segment, and to make the reference robust in the face of changes to that document. This specification is part of the Evaluation And Report Language (EARL) but can be reused in other contexts too. [from homepage]
NCBI PubChem database of bioassay records
PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results.
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. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records.
PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number.
PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records.
identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)
Database of researchers to track publications, citation metrics, peer reviews, and journal editing work.
The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.
An ontology of qualifications, distinctions, and certifications that uses the Phenotype And Trait Ontology term quality (PATO:0000001) as a root term.
The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]
RAiD is an identifier and global system, governed by ISO 23527:2022, to uniquely identifiy research projects, collaboratively, collect and publicly share information about them.
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. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB.
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. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB.
The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters
(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.
Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center.
Registry and database of bioparts for synthetic biology
This database provides identifiers for catalytic bioparts which are fundamental to the design, construction, and optimization of biological systems for specific metabolic pathways. It provides basic information, function information (including catalytic functions, qualitative and quantitative parameters, and biopart expression), and sequence information (nucleotide sequence and amino acid sequence)
RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting
RDFa Core is a specification for attributes to express structured data in any markup language. The embedded data already available in the markup language (e.g., HTML) can often be reused by the RDFa markup, so that publishers don't need to repeat significant data in the document content. (from https://www.w3.org/TR/rdfa-core/)
Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms.
Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.
Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier.
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). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.
The Recommendation Ontology specification provides basic concepts and properties for describing recommendations on/for the Semantic Web.
Human Plasma Membrane Receptome Families
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
REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).
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. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.
RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database.
RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database.
identifier for a person, used by ResearchGate profiles
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. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.
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. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.
Ribocentre is designed to contain comprehensive information of all natural ribozymes.
Identifiers represent computationally predicted and experimentally verified translatable circular RNAs (circRNAs) across six model species (human, mouse, rat, worm, fly, and zebrafish), including ribosome-associated circRNAs and their encoded peptides with systematic annotation of sequence, structure, and function.
RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project
The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.
RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.
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 STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database.
Database of RNA Junctions and Kissing loop Structures
RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale.
Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank.
A comprehensive listing of post-transcriptionally modified nucleosides from RNA -
The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.
Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.
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. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species.
The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.
Rodent Unidentified Gene-Encoded Large Proteins
The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
Registry of Toxic Effects of Chemical Substances
RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments.
runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive.
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 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. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information.
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. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.
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. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.
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. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information.
Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
Scientific research institute for neuroscience, genetics, immunology, plant biology and more.
An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms.
SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.
This ontology extends the SAREF ontology for the Agricultural domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Agricultural domain.
This ontology extends the SAREF ontology for the Smart City domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Smart City domain.
SAREF4MARI: an extension of SAREF for the maritime domain
SAREF4MARI is an extension of SAREF for the maritime domain.
The State of Alaska's Salmon and People Ontology
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
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. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.
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.
Selventa legacy chemical namespace used with the Biological Expression Language
Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions
numerical identifier for an author in SciProfiles by MDPI
Selventa legacy complex namespace used with the Biological Expression Language
This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family.
Structural Classification of Protein - Stable Domain Identifier
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). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1.
Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. Delivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts and humanities, Scopus features smart tools to track, analyze and visualize research.
identifier for an organisation in author affiliations per Scopus
identifier for a source/publication venue (journal, conference, etc) in Scopus
unique academic work identifier assigned in Scopus bibliographic database
The Supply Chain Operation Reference (SCOR) is a cross-industry approach to lay the groundwork for more efficient and effective information exchange in supply networks.
Saccharomyces cerevisiae promoter database
Database containing promotor sequences found in Saccharomyces cerevisiae.
The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources.
ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.
Un vocabulaire pour décrire des services SPARQL publiés via le protocole SPARQL 1.1 pour RDF. Ces descriptions fournissent un mécanisme par lequel un client ou un utilisateur final peuvent obtenir des informations sur le service SPARQL, telles que les extensions de fonctions supportées ou les détails à propos des jeux de données disponibles.
Structural Database of Allergenic Proteins
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.
The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.
The Science Data Discovery Ontology (sddo) is being developed to provide a semantic foundation for the discovery of information managed by NASA's Science Mission Directorate. This information spans many scientific disciplines, fields and subfields, including heliophysics, earth science, planetary science, astrophysics, biology, astrobiology, and physical science. [from repository]
Sustainable Development Goals Interface Ontology
The Sustainable Development Goals Interface Ontology (SDGIO) aims to provide a semantic bridge between 1) the Sustainable Development Goals, their targets, and indicators and 2) the large array of entities they refer to. SDGIO will reuse existing ontologies where appropriate.
Selventa legacy disease namespace used with the Biological Expression Language
This vocabulary extends the data cube vocabulary to support publication of statistical data in RDF, using an information model based on SDMX
Immunology Database and Analysis Portal (ImmPort)
ImmPort is a scientific data resource funded by the National Institutes of Health (NIH) to preserve and share immunology research and clinical trials data generated by NIH researchers and external organizations. ImmPort uses FAIR principles to maximize reuse of deposited data for advancement of biomedical sciences.
Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).
Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).
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. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.
ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.
With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [Fellowship for Interpretation of Genomes (FIG)](http://thefig.info/) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. This prefix provides identifiers for molecular roles that describe the function of one or more proteins in microbes and plants.
Southwestern Environmental Information Network
A vocabulary about species to support the environmental research community in Arizona and New Mexico
The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata.
identifier of an author or reviewer, in Semion
The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing.
The Scientific Event Ontology (SEO) is a reference ontology for modeling data about scientific events such as conferences, symposioums, and workshops.
Sample processing and separation techniques
A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.
SEP developers via the PSI and MSI mailing lists
Selventa legacy protein family namespace used with the Biological Expression Language
Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).
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.
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 is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone.
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.
A vocabulary used in tandem with SHACL for representing node shapes
This shapes graph can be used to validate SHACL shapes graphs against a subset of the syntax rules.
SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.
SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.
Sigma Aldrich is a life sciences supply vendor.
The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.
Identifiers for relationships between proteins and complexes, along with their type and provenance
SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes. It assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed.
Semantically-Interlinked Online Communities Access Ontology
Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining basic information on permissions and access rights.
Semantically-Interlinked Online Communities Actions Ontology
An ontology of predicates for actions in SIOC
Semantically-Interlinked Online Communities Argumentation Ontology
A vocabulary of argumentation predicates for SIOC
Semantically-Interlinked Online Communities Core Ontology
Semantically-Interlinked Online Communities, or SIOC, is an attempt to link online community sites, to use Semantic Web technologies to describe the information that communities have about their structure and contents, and to find related information and new connections between content items and other community objects. SIOC is based around the use of machine-readable information provided by these sites.
Semantically-Interlinked Online Communities Services Ontology - Quote Ontology
Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining basic information on community-related web services.
Semantically-Interlinked Online Communities Services Ontology - SWAN Mapping
Mappings from SIOC to SWAN, with a small number of aux terms
Semantically-Interlinked Online Communities Types Ontology
Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining subclasses and subproperties of SIOC terms.
Scientific Information Retrieval and Exchange Network
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
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. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.
SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.
Stemcell Knowledge and Information Portal
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, 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.
SKOS-Thes: An extension to SKOS based on the ISO 25964 data model. The ISO 25964 standard, published in 2011, covers all aspects of developing thesauri and setting up mappings across vocabularies to encourage high quality information retrieval across networked resources. [from https://www.dublincore.org/specifications/skos-thes/]
SUM Breast Cancer Cell Line Knowledge Base
SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.
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
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.
Secondary Metabolism Collaboratory - biosynthetic gene cluster
The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for individual biosynthetic gene clusters (BGCs) linked to their corresponding bacterial or archaeal source.
Secondary Metabolism Collaboratory - taxon
The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for bacteria and archaea sources linked to their associated set of biosynthetic gene clusters (BGCs).
Simplified molecular-input line-entry system
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.
The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.
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.
Contains identifiers for human small nucleolar RNAs (snoRNAs) from snoDB, an interactive database of human small nucleolar RNAs (snoRNAs) that includes up-to-date information on snoRNA features, genomic location, conservation, host gene, snoRNA–RNA targets and snoRNA abundance and provides links to other resources.
A comprehensive database of human H/ACA and C/D box snoRNAs.
SNP to Transcription Factor Binding Sites
SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome.
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.
SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.
SoyBase is a repository for curated genetics, genomics and related data resources for soybean.
Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality.
The SPARC Data Repository Service (DRS) is an implementation of the Global Alliance for Genomics and Health (GA4GH) DRS specification that provides a standardized API that enables researchers and other data consumers to access and retrieve data objects from various data repositories in a consistent and cloud-agnostic way. This implementation provides information for data objects in the SPARC repository (sparc.science).
Used for operations in SPARQL, such as ceil() and bound().
SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases.
An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).
Swiss Personalized Health Network Schema
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. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/).
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. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.
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. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.
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.
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. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways.
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. It utilizes multiple external vocabularies.
identifier for an article/paper at the SSRN
identifier for an author at the Social Science Research Network
Simple Standard for Sharing Ontological Mappings
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). Most metadata elements, such as "sssom:mapping_justification" are defined in the sssom namespace.
Sequence-Structural Templates of Single-member Superfamilies
SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies.
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 refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB).
The pre-IND tracking number for submissions to the FDA
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. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.
Datasets inside StoreDB at University of Cambridge
File inside StoreDB at University of Cambridge
Study inside StoreDB at University of Cambridge
Identifers for natural products isolated or mutasynthesized by bacteria of the genus Streptomyces.
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 serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.
SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.
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. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands.
The Simplified Upper Level Ontology (SULO) is ontology with a minimal set of classes and relations to guide the development of a personal health knowledge graph. [from homepage]
SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt.
The SustainGraph ontology is developed to track the United Nations Sustainable Development Goals(SDGs) at national and regional level, their evolution accross time and inter-connectedness with existing and emerging policies and directives at European Union (EU) and global level. It is described using W3C RDF Schema and the Web Ontology Language.
Semantic Web Applications in Neuromedicine
SWAN ontology consists in a collection of ontologies used to create, manage and share scientific knowledge bases.
Software Heritage is the universal archive of software source code.
The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences.
A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form.
Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.
Synthetic Binding Proteins Binding Target
Identifiers for the binding targets of synthetic binding proteins (SBP), describing the specific molecules or complexes that SBPs interact with for their intended applications
Identifiers for synthetic binding protein-target complexes, detailing their components, 3D structures and docking statistics
Synthetic Binding Protein Protein Scaffold
Identifiers for the protein scaffolds of synthetic binding proteins (SBP), detailing their structural frameworks and roles in facilitating SBP function.
Identifiers for synthetic binding proteins, providing detailed information on their sequences, structures, targets, and functional properties for research, diagnostic, and therapeutic applications.
Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.
The anatomy of the Tick, Families: Ixodidae, Argassidae
Terminology of Anatomy of Human Embryology
Terminology of Anatomy of Human Histology
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus.
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept
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.
A vocabulary of taxonomic ranks (species, family, phylum, etc)
Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle
Access to Biological Collection Data Schema
Controlled vocabulary for the Dublin Core term format
Ontology describing a controlled vocabulary for taxon ranks.
The TDWG Vocabulary Maintenance Standard consists of a single document: the Vocabulary Maintenance Specification.
The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]
Classification of Transcription Factors in Mammalia
TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here..
transcription factor binding site prediction
The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.
A structured controlled vocabulary of the anatomy of mosquitoes.
The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]
Theiler stages (TS) define mouse development by a set of morphological criteria ([Theiler, 1989](https://doi.org/10.1007/978-3-642-88418-4)). This staging scheme is used because embryos at the same gestational age can have developed at different rates and therefore exhibit different morphological characteristics. Theiler stages may in some cases correspond to a single gestation age, but more often cover a range of ages. (from [https://www.informatics.jax.org/glossary/theiler](https://www.informatics.jax.org/glossary/theiler))
ThermoFisher is a life sciences supply vendor.
This ontology describes concepts related to greenhouses. It mainly describes Dutch greenhouses, but can also be applied to greenhouses outside of The Netherlands. The ontology describes multiple aspects of the domain of greenhouses.
Modular Ontology Modeling for Food Supply Chains
This concept scheme contains skos concepts for analysis methods used to produce observation results with information about the physical properties, chemical or isotopic composition, crystallography, or molecular structure of material samples. Based on spreadsheet compilation of method vocabularies from Geo.X, GEOROC, PetDB and OSIRIS-REx. Definitions added and updated based on web research, and SKOS serialization by S.M. Richard. Note that although there are high-level method categories for 'Physical property measurements' and the 'Bioanalytical method', these are placeholders and only include a few examples that are relevant to analytical methods in geo- or cosmochemistry.
An instance of the EBI Lookup Service deployed by TIB
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.
Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells.
TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)
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.
The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.
Topology Data Bank of Transmembrane Proteins
The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.
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 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. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.
The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes.
Transcriptional Regulatory Element Database
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 is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.
TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.
TreeHub is a taxonomical database for trees. TreeHub contains extracted phylogenetic data and integrates relevant species information for each identifier.
Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine.
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. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
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. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
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.
Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]
Identifiers correspond to curated associations between diseases and tRNA-derived small RNAs (tsRNAs) in the tsRNADisease database.
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. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each 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. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.
An ontology covering the taxonomy of teleosts (bony fish)
Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms. In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp
An issue on the UBERON GitHub Issue tracker
NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.
UK Universities and Colleges Admissions Service
identifier for an educational organization issued by the UK Register of Learning Providers
EAWAG Biocatalysis/Biodegradation Database enzyme
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.
EAWAG Biocatalysis/Biodegradation Database pathway
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.
EAWAG Biocatalysis/Biodegradation Database reaction
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.
EAWAG Biocatalysis/Biodegradation Database rule
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.
Unified Medical Language System Atomic Unique Identifier
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. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus.
UniCarb-DB stores structural and mass spectrometry (MS) glycomic data, and has now grown to be one of the largest experimental glycomic MS databases. Identifiers correspond to individual glycan structures and corresponding MS spectra.
identifier of a compound in the UniChem database
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.
Unimod protein modification database for mass spectrometry
Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).
UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.
UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.
Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system.
This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein.
Properties and classes used for protein annotation
The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary.
identifier for a scientific journal, in the UniProt database
UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries.
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.
The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. This entry represents UniProt mnemonics which combine an alphanumeric representation the protein name and a species identification code representing the biological source of the protein.
The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format
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.
The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified.
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.
Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites.
UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.
Molecular database for the identification of fungi
UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa.
The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
United States Department of Agriculture Veterinary Biological Product Code Number
A Product Code Number (PCN) assigned by the Animal and Plant Health Inspection Service (APHIS)'s Center for Veterinary Biologics (CVB) to veterinary biological products such as vaccines, bacterins, antibodies, diagnostic products, antitoxins, bacterin-toxoids, and toxioids approved for veterinary use by the United States Department of Agriculture Veterinary (USDA). A quarterly release, as PDF, can be found [here](https://www.aphis.usda.gov/sites/default/files/currentprodcodebook.pdf). The PDF document states (verbatim): The alphanumeric system used for product codes provides for a six-digit number of number-letter combination to be assigned to each product, i.e., the first digit denotes product types; second and third, group by agents; fourth, the viability of vaccine, (live, killed, modified live, etc.); fifth, substrates; and sixth, miscellaneous variables
United States Patent and Trademark Office
The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.
A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets.
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. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs.
Database of validation results for ligands and non-standard residues in the Protein Data Bank.
Veterans Administration National Drug File
The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.
The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.
Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse
The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.
An issue on the Vertebrate Breed Ontology GitHub issue tracker
The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.
vCard is a specification developed by the Internet Engineering Task Force (IETF) for the description of people and organisations
Models developed with the Virtual Cell (VCell) software prorgam.
Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]
Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host.
A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.
VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited.
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.
An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.
VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.
VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.
The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee.
Vertebrate Homologous Organ Group Ontology
vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 "historical homology". Each mapping has been manually reviewed, and we provide confidence codes and references when available.
The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.
The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.
Defunct vaccine information source from the He Lab
VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.
The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.
ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.
VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences.
A database containing predicted viral miRNA candidate hairpins.
The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place.
The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.
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-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys.
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. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons.
Vitro is a full stack framework for building semantic web applications. It is not domain specific.
The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.
This vocabulary was created in the FOAF project, based on experience with FOAF, Dublin Core and other early RDF vocabularies. Deployment experience shows that changing namespace URIs is expensive and unrewarding, so this vocabulary provides terms to support in-place evolution of structured data vocabularies. By indicating status at the level of terms rather than vocabularies, dictionary-style, fine grained improvements become easier. Different organizations and parties can agree or disagree on the status of a vocabulary term; however the status published alongside the term may deserve special attention. Future work could include patterns for citing announcements and decisions, or using SKOS to decentralise the extension of the basic status levels. (from artifact)
Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source.
Ontology for vector surveillance and management
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.
The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.
Comprehensive hierarchy of extinct and extant vertebrate taxa.
Veterans Health Administration (VHA) unique identifier
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 is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.
Ontology about the gross anatomy of the C. elegans
Ontology about the development and life stages of the C. elegans
Ontology about C. elegans and other nematode phenotypes
Protocol for Web Description Resources (POWDER) Schema
A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum
World Health Organization Verbal Autopsy Code
Identifiers assigned by the World Health Organization for coding causes of death from verbal autopsy (VA) reports. These codes are produced as outputs in standard VA analysis software.
WiCell Research Institute Cell Collection
An ontology supporting data modeling in WikiPathways
Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.
This semantic artifact describes the semantic relationships between entities which model the setup of a biodiversity monitoring project based on capturing audiovisual digital recordings. It encodes the semantics of the Wildlife Monitoring Ontology and at the same time provides the datamodel behind the wildlive.senckenberg.de platform.
WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends).
A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots.
Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.
The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.
identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829
unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)
he WOT, or Web Of Trust, schema is designed to facilitate the use of Public Key Cryptography tools such as PGP or GPG to sign RDF documents and document these signatures.
Web of Things Hypermedia Controls Ontology
an ontology for links and forms, the main hypermedia controls in use on the Web. This ontology offers, among others, a means to reify RDF statements interpreted as links between Web resources. It also provides a versatile exchange format for links and forms in RESTful Web applications. [from homepage]
an RDF vocabulary for the security metadata definitions
The Thing Model (TM) ontology is an RDF axiomatization of the TM concepts, one of the building blocks of the Web of Things (WoT). Besides providing an alternative to the standard JSON representation format for TM documents, the TM ontology can also be used to process contextual information on Things and for alignments with other WoT-related ontologies. [from homepage]
WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
This is a vocabulary collection utilized by XHTML Family modules and document types using XHTML Modularization, including XHTML Role and XHTML + RDFa as defined in rdfa-syntax. The XHTML specifications are developed by the W3C XHTML 2 Working Group as part of the W3C HTML Activity. [from homepage]
An SKOS extension for representing statistical classifications
An extension of SKOS for representaion of nomenclatures
Metabolites in the Xenobiotics Metabolism Database.
The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML.
Yeast Deletion and the Mitochondrial Proteomics Project
The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.
The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].
Yeast Searching for Transcriptional Regulators and Consensus Tracking
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.
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.
YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.
The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].
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). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.
This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from <https://prefix.zazuko.com/about>)
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. The standard provides a general way to represent activities.
Arctic Data Center Academic Disciplines Ontology
An ontology to support disciplinary annotation of Arctic Data Center datasets.
AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology
The process component of the Allotrope ontology suite
The quality component of the Allotrope ontology suite
The result component of the Allotrope ontology suite
The role component of the Allotrope ontology suite
The Amphioxus Development and Anatomy Ontology
An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).
AntiFam is a database of spurious protein families that have been removed from Pfam due to incorrect hidden Markov model prediction.
An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.
Antibiotic resistance genes and mutations
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.
Anatomical Therapeutic Chemical Classification System
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. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.
WHO Collaborating Centre for Drug Statistics Methodology
An EMMO-based domain ontology for atomistic and electronic modelling.
A battery interface domain ontology based on EMMO.
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). This collection references genes in Bgee.
Bibliographic Framework Initiative Vocabulary
The Bibframe vocabulary consists of RDF classes and properties used for the description of items cataloged principally by libraries, but may also be used to describe items cataloged by museums and archives. Classes include the three core classes - Work, Instance, and Item - in addition to many more classes to support description. Properties describe characteristics of the resource being described as well as relationships among resources. For example: one Work might be a "translation of" another Work; an Instance may be an "instance of" a particular Bibframe Work. Other properties describe attributes of Works and Instances. For example: the Bibframe property "subject" expresses an important attribute of a Work (what the Work is about), and the property "extent" (e.g. number of pages) expresses an attribute of an Instance.
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.
BioCyc collection of metabolic pathway databases
BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.
A disease/condition-specific instantiation of a canonical biomarker
Biomarker Knowledgebase - Canonical Biomarker
A canonical biomarker, which describes the composition of a measurement on a change to an entity. For example, the increase in IL6 level
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. BioPortal functionality includes the ability to browse, search and visualize ontologies.
BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories.
The bioRxiv is a preprint server for biology
The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.
An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.
BlastRules (identifiers starting with the “NBR” prefix) are a type of evidence for functional classification of proteins based on BLAST (Basic Local Alignment Search Tool). A BlastRule consists of one or more 'model' proteins with known biological function, and BLAST identity and coverage cutoffs. Any protein aligning to a model protein above the cutoffs is considered a BlastRule hit. [from homepage]
German Federal Ministry of Education and Research Glossary
A german-language glossary provides you with definitions of the terms used in the portal in the fields of education, science, research and innovation and is updated regularly.
The Building ontology has been developed to perform as the core module of the BIMERR Ontology Network, containing information related to building topology, and components. The model is constructed as an extention of the BOT ontology that provides the vocabulary to describe the topology of a building as well as the relationships between their main components such as zones, spaces, and building elements. The taxonomy of building components is based on the proposed by the IFC 4.1 standard.
Citation Counting and Context Characterisation Ontology
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.
An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)
The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification.
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. This collection references cattle QTLs.
The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.
Creative Commons Rights Expression Language
The Creative Commons Rights Expression Language (ccREL) lets you describe copyright licenses in RDF. For more information on describing licenses in RDF and attaching those descriptions to digital works, see [ccREL](https://wiki.creativecommons.org/CC_REL) in the [Creative Commons wiki](https://wiki.creativecommons.org/).
CCSO is an educational ontology acting as a data model for concepts and entities within an academic setting, enabling also the annotation of potentially available resources. The ontology aims to conceptualize educational entities within Curriculum and Syllabus with appropriate coverage and quality, in order to support rich services on top for improving curriculum management and automatically enabling syllabus semantic processes. (from homepage)
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.
Common Entity Data Standards - Domain Entity Schema
The Common Entity Data Standards (CEDS) Domain Entity Schema (DES) provides a hierarchy of domains, entities, categories, and elements. It is intended for use primarily by people as an index to search, map, and organize elements in a logical way. [from homepage]
A vocabulary for learning resource types
The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.
Assigns identifiers to collections of datasets indexed by CELLxGENE. CELLxGENE is an interactive data visualization and exploration tool developed by the Chan Zuckerberg Initiative that enables researchers to analyze and share single-cell genomics datasets. It provides a user-friendly interface for biologists and computational scientists to interrogate gene expression patterns across different cell types.
Consortium of European Social Science Data Archives Vocabulary
A vocabulary service for the social sciences, covering the Data Documentation Initiative (DDI) is an international standard for describing data produced by surveys and other observational methods in the social, behavioural, economic, and health sciences.
Names of organisations providing metadata for CESSDA Data Catalogue.
This vocabulary holds the definitions and descriptions of the collections included in the CESSDA Data Catalogue.
Lists the types of persistent identifiers that CESSDA accepts as study level PIDs in its data catalogue.
ISO 3166-1 alpha-2 country codes and names.
A typology of main themes or subjects of data.
This controlled vocabulary contains terms to describe the mechanism of action for a chemical-target interaction. The terms can be retrieved from ACTION_TYPE table in ChEMBL's SQL dump and are used to annotate the DRUG_MECHANISM table. Because these aren't really identifiers, they are transformed by lowercasing and replacing spaces with dashes to form 'identifiers'. The pattern in the Bioregistry record contains an enumeration of the 33 allowed values as of ChEMBL v35.
Tissues used to annotate cells and cell lines, cross-referenced to EFO, BTO, UBERON, and CALOHA
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. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.
Chemical Entity Materials and Reactions Ontological Framework
A data model for managing information about chemical entities, ranging from atoms through molecules to complex mixtures.
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. These entries are supplemented with additional properties, related information and links back to original data sources.
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. This collection references chicken QTLs.
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. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website)
A vocabuarly for describing the background and methodology for the design of the DataCite profile of DCAT-AP (CiteDCAT-AP), as well as the defined mappings.
An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.
CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).
ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.
Morphological and physiological measurement records generated from clinical and model organism research and health programs.
CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.
Core Ontology for Biology and Biomedicine
COB brings together key terms from a wide range of OBO projects to improve interoperability.
CODATA Research Data Management Terminology
The goal of the CODATA Research Data Management Terminology is to gather the key terms needed for a common understanding of the research data management domain. The RDMT was revised by the CODATA RDM Terminology Working Group, shared for public review, and then confirmed and finalised in 2023. The RDMT grew out of the CASRAI Research Data Management Glossary, which was intended as a practical reference for individuals and groups concerned with the improvement of research data management (RDM). In 2020, CASRAI requested that CODATA assume responsibility for the curation of this valued resource. To that end, the RDM Terminology Working Group uses a lightweight and pragmatic biennial process to review the resource now restructured as the CODATA RDM Terminology and suggest any edits, additions and removals that are required in order to develop and improve this important reference resource.
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.
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). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.
The COnCEPT upper-level Design Ontology (COnDO).
Core Ontology for Robotics and Automation
This is the OWL implementation of CORA in IEEE 1872-2015. It only includes the taxonomy of concepts and relations, with some few axioms reggarding disjointness, property characteristics and property ranges/domains. The OWL implementation is an underspecified version of the SUO-KIF implementation in IEEE 1872-2015. That is, the set of allowed models of the SUO-KIF implementation is a proper subset of the allowed models by the OWL implementation. Concept definitions in natural language and othe clarifications can be found in the IEEE 1872-2015 standard.
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
Repository of packages for the R programming language
A repository of software packages written in Rust.
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. The roles describe each contributor’s specific contribution to the scholarly output.
This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage)
German Archaeological Institute Thesaurus
A thesaurus of terms useful for digital archaeology
The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.
A semi-automatically generated knowledgebase
Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. **Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).
DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web
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.
Identifies the type of aggregation used to combine related categories, usually within a common branch of a hierarchy, to provide information at a broader level than the level at which detailed observations are taken. (From: The OECD Glossary of Statistical Terms)
Describes the entity being analyzed in the study or variable. This vocabulary can also be used to describe the unit of observation, which is the unit being observed, or from which data are collected. The unit of observation can be the same as, or different from the unit of analysis.
Standard set of characters upon which many character encodings are based (Wikipedia).
Describes the degree of similarity between two items or schemes (collections of items).
Identifies the type of data, which has a bearing on the acceptable data values, the operations that can be performed with the data, and the ways in which the data are stored.
Describes the physical format(s) of the data documented in the logical product(s) of a study unit.
Describes the level of proficiency of an individual in a natural language.
Specifies the event happening over the data life cycle that is considered significant enough to document.
The procedure, technique, or mode of inquiry used to attain the data.
Indicates the entity that provided the information carried by the variable.
Indicates the statistical software package used in the production/processing/dissemination of the data. Data collection software is not covered in this list.
Specifies the type of summary statistic. Summary statistics are a single number representation of the characteristics of a set of values.
Describes the time dimension of the data collection.
Time zone specification as an offset from UTC (Coordinated Universal Time) in terms of hours and minutes.
Identifies the type of address entered as contact information for an individual or an organization.
Specifies the rationale for creating a concept group.
Indicates the frequency of data collection events.
Includes a typology of data collection instruments.
Identifies the type of telephone entered as contact information for an individual or an organization.
A typology of methods used to translate data collection instruments, including questionnaires, individual questions, measurements, data capture flows, etc.
CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms
An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO.
Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells.
DFG Classification of Subject Areas Ontology - 2020-2024
DFG Fachsystematik Ontology / DFG Classification of Subject Areas Ontology (DFGFO) encodes the DFG Classification of Subject Areas into an ontology, where each subject number are is enconded into a Class with subclass statements following the DFG Classification of Subject Areas hierarchy. Labels are provide German and English.
A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics
The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information.
An ontology to represent the enhancement of building data throughout the construction lifecycle stages
Digital Construction Occupancy ontology represents those aspects of construction and renovation projects that concern the comfort, safety and health of occupants, including visual and thermal comfort, indoor air quality and building acoustics, as well as related sensor observations.
DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature.
DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects.
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).
Descriptive Ontology for Linguistic and Cognitive Engineering
DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use.
With the DataPLANT biology ontology (DPBO), DataPLANT provides an intermediate ontology that acts as a broker and bridge between the individual researcher/domain experts and main ontology providers. DPBO enables easy and agile collection of missing vocabulary as well as relationships between terms for (meta)data annotation using DataPLANT’s Swate tool.
An ontology of commonly encountered and/or high level Drosophila phenotypes.
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.
An ontology to support comparative effectiveness researchers studying claims data.
DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.
Diagnostic and Statistical Manual of Mental Disorders (5th Edition)
The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science.
European Collection of Authenticated Cell Culture
The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs).
The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes.
EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.
The Europeana Data Model (EDM) is aimed at being an integration medium for collecting, connecting and enriching the descriptions provided by Europeana data providers. The RDF vocabulary for http://www.europeana.eu/schemas/edm/ defines the elements introduced by EDM (as opposed to the ones EDM re-uses from other namespaces).
An ontology for mouse anatomy covering embryonic development and postnatal stages.
Mouse Developmental Anatomy Ontology with Theiler Stage
EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823
The Electron Microscopy (EM) Glossary is a widespread community effort to harmonize terminology in the electron and ion microscopies. It is created in a not-for profit collaboration between academic and non-university research institutions including domain and metadata experts. It provides harmonized terminology for application level semantic artifacts to source from and align with. [from homepage]
The EMI ontology is used to structure spectrum annotation provenance by reusing the PROV-O ontology (a W3C recommendation) and sample and observation data by applying the SOSA ontology. EMI reuses the SOSA ontology as a data schema for struturing the Sample and Observation data. SOSA (Sensor, Observation, Sample, and Actuator) is a subset of SSN (Semantic Sensor Network Ontology) that is a W3C recommendation. [from homepage]
A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)
Collections of images, based on topics, such as the human skull collection
A reusable element of a vector graphic for an anatomical entity useful for biological and biomedical informatics applications.
A vector graphic for an anatomical entity useful for biological and biomedical informatics applications.
A collection of graphics that relate to a theme
A unit of a vector graphic for an anatomical entity useful for biological and biomedical informatics applications.
The 'Energy Market Roles' ontology module represents the energy market roles of energy agents. Additionally, it includes the consumer role, as it is reused in most of Smart Grid scenarios. This ontology module reuses the knowledge of the 'Actor' ontology module.
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. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO.
Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate 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. This collection is concerned with metazoa genomes.
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. This collection is concerned with plant genomes.
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. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.
A application driven Epilepsy Ontology with official terms from the ILAE.
European Food Information Resource Network
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.
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. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.
The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.
Feature Annotation Location Description Ontology
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
A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
This subject heading system has beeen developed for use in FID BAUdigital and its future web services. It covers scientific fields of Civil Engineering, Architecture and Urban Studies with a special section on digitization. This subject classification has been mapped to several other classification systems. The latest version of the subject classification including these mappings is available at https://gitlab.com/fid-bau/terminologie/fid-baudigital-faecherklassifikation/-/raw/main/Subject_Headings_all_mappings.owl.
The FIESTA-IoT ontology takes inspiration from the well-known Noy et al. methodology for reusing and interconnecting existing ontologies. To build the ontology, we leverage a number of core concepts from various mainstream ontologies and taxonomies, such as Semantic Sensor Network (SSN), M3-lite (a lite version of M3 ontology), WGS84, IoT-lite, Time, and DUL ontology.
FINDEX Bau as a SKOS Thesaurus - Facetted Indexing System for Civil Engineering
SKOS Model of FINDEX Bau by Fraunhofer-Informationszentrum Raum und Bau IRB
SKOS-Modellierung des Thesaurus FINDEX Raum des Fraunhofer-Informationszentrums Raum und Bau IRB
An ontology of physico-chemical methods and properties.
The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.
Funding, Research Administration and Projects Ontology
An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.
The FTOnto enables reseachers to sematically describe a physical fischertechnik factory simulation environment. This is archieved by aligning concepts from MASON and SOSA with own concepts. Furthermore the FTOnto can capture knowledge about semantic web services which are used to interact between the service-layer and the cyber-physical layer in a cyber-physical production system. This includes precondition which have to be met before a webservice can be performed, postconditions which check if the webservice execution was performed successfully and effects which describe the changed state of the domain after performing a service. [from homepage]
The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.
Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations
Genetic and Rare Diseases Information Center
Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.
A gazetteer constructed on ontological principles. The countries are actively maintained.
The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.
The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. It uses the language of visual communication, illustration, and technical drawing. The GDO is rooted in the Basic Formal Ontology (BFO) and uses several classes from the Information Entity Ontology of the Common Core Ontologies as a mid-level ontology. [from https://gdo.endlessforms.info/about]
The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.
The OGC GeoSPARQL standard supports representing and querying geospatial data on the Semantic Web. GeoSPARQL defines a vocabulary for representing geospatial data in RDF, and it defines an extension to the SPARQL query language for processing geospatial data. In addition, GeoSPARQL is designed to accommodate systems based on qualitative spatial reasoning and systems based on quantitative spatial computations.
The GESAH Graphic Arts Ontology is designed for the inventory, classification and structured description of works on paper.
The Category Scheme Election Studies provides the ability to categorize election studies at the question and/or variable level.
This CV, developed within the framework of the DP-R|EX joint project, involving the partner institutions DeZIM, Qualiservice and GESIS, maps the central concepts and theoretical approaches in research on racism and right-wing extremism. The compilation is based on a systematic evaluation of the relevant national and international empirical research literature. The CV equally takes into account the different thematic (racism, right-wing extremism, discrimination) as well as methodological (qualitative research, standardised surveys, data from social media and messaging services) research strands.
This CV, developed as part of the DP-R|EX joint project, involving the partner institutions DeZIM, Qualiservice and GESIS, maps the data types relevant to the research field. The CV includes data types that can result from a variety of different collection methods. These include, for example, standardised or unstandardised surveys, individual or repeated observations, as well as process-produced or user-generated types of data generation. The data types can be subject-, event-, space- or time-related and refer to the individual or aggregate level.
Diversification criteria of R|EX research
This CV, developed within the framework of the DP-R|EX joint project, involving the partner institutions DeZIM, Qualiservice and GESIS, maps the dimensions of discrimination and racialised characteristics relevant to the research area. The compilation is based on a systematic evaluation of the relevant national and international empirical research literature. These include self-attributed characteristics as well as anticipated attributions by others. The characteristics do not necessarily correspond to the studied units in the data set, but can also be the subject of studied concepts or theories in the surveys, such as on specific prejudices and attitudes.
Variables relations for Social Sciences research data
As the variable is one of the most relevant entities to enhance data reuse in the Social Sciences, we provide a framework design to better semantics the variables' relations descriptions. These explicit relations between variables enable comparability and facilitate harmonization across waves. We provide a brief textual identification of the relation type, supported by a controlled vocabulary (CV) and an extended description of the relationship. These relations within variables include but are not limited to different versions, derived formats in new waves, new labels and name wording, and alternative response schema through questionnaires and surveys. For instance, a given variable label is changed from one wave to another, even though its concept remains the same. Their values also are subject to change, such as new cardinalities settings, their categorization, or response scheme and scale measurement. They change based on different conditions, e.g., values are updated by any constraints or modified to comply with the study evolution requirements or a new sociological approach. In the Social Sciences, Economics, and Behaviour Sciences, which investigate, for instance, the social structure of the population, political attitudes of voters and candidates, opinions on family, work, religion, politics and society or competencies of adults, those topics are highly subject to change to fit the empirical reality in a constantly changing world. Thus, we propose widening relations descriptions for Social Sciences variables within datasets beginning from the BasedOnObjectType DDI as a first approach.
The AAT includes generic terms, and associated dates, relationships, and other rich information about concepts related to or required to catalog, discover, and retrieve information about art, architecture, and other visual cultural heritage, including related disciplines such as archaeology and conservation. Visual works include not only visual cultural works classified as "art" according to Western aesthetics, but also utilitarian and ceremonial works. Terminology may be used for work types, roles, materials, styles, cultures, techniques, subject, etc., so long as terms are within the defined scope of AAT. [from https://www.getty.edu/research/tools/vocabularies/aat/aat_faq.html]
CONA compiles titles, attributions, depicted subjects, and other metadata about works of art, architecture, and cultural heritage, both extant and historical, physical and conceptual. Metadata is gathered and linked from museum collections, special collections, archives, libraries, scholarly research, and other sources. CONA is linked to the AAT, TGN, ULAN, and the IA (Iconography Authority). Through rich metadata and links, CONA may provide a powerful conduit for research and discovery for digital art history. [from homepage]
The GVP Ontology defines classes, properties and values (skos:Concepts) used in GVP LOD. As of version 3.0, it is complete regarding AAT, TGN and ULAN, and will be extended in time with more elements needed for other GVP vocabularies (CONA).
The Getty Iconography Authority ™ (IA), Cultural Objects Name Authority ® (CONA), the Union List of Artist Names ® (ULAN), the Art & Architecture Thesaurus ® (AAT), the Getty Thesaurus of Geographic Names ® (TGN) are structured resources that can be used to improve access to information about art, architecture, and other material culture. The Vocabularies are not simply 'value vocabularies,' but knowledge bases. Through rich metadata and links, the Getty Vocabularies provide powerful conduits for knowledge creation, complex research, and discovery for digital art history and related disciplines. [from https://www.getty.edu/research/tools/vocabularies/cona/about.html#purpose_ia]
The Thesaurus of Geographic Names (TGN) is a terminology that focuses on places relevant to art, architecture, and related disciplines, recording names, relationships, place types, dates, notes, and coordinates for current and historical cities, nations, empires, archaeological sites, lost settlements, and physical features. The TGN is one of 5 Getty Vocabularies intended to provide terminology and other information about the objects, artists, concepts, and places important to various disciplines that specialize in art, architecture, and other material culture.
The Getty Thesaurus of Geographic Names (TGN) is a structured vocabulary, including names, descriptions, and other metadata for extant and historical cities, empires, archaeological sites, and physical features important to research of art and architecture. TGN may be linked to GIS (Geographical Information System), maps, and other geographic resources. [from https://collectionstrust.org.uk/resource/thesaurus-of-geographic-names-tgn-getty/]
gist is a minimalist upper ontology created by Semantic Arts.
GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.
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).
Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.
Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.
Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.
Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny.
Health Canada Drug Identification Number
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. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada.
The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada.
A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.
International Classification of Diseases, 10th Revision, Clinical Modification
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
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). For more information about ICD-9-CM, see the ICD-9-CM source synopsis. ICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.
International Classification of Diseases, 11th Revision (Foundation Component)
The ICD-11 Foundation is the comprehensive base layer of the International Classification of Diseases, encompassing all diagnostic concepts, definitions, and semantic relationships, designed for flexibility and adaptability across various use cases, including research, ontology development, and detailed health data analysis.
An ICD-11 code is a standardized alphanumeric identifier used to classify and document diseases, conditions, and health-related issues for global healthcare and statistical purposes.
International Classification of Diseases, 9th Revision, Clinical Modification
ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.
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. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.
International Classification of Diseases for Oncology
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
The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.
An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.
Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.
International Data Spaces Information Model
This ontology defines classes and properties for describing participants, infrastructure, data and services of the International Data Spaces (formerly known as Industrial Data Space).
Internet Engineering Task Force Language Tag
Shorthand representations of languages and their subtypes
International Standard for Intelligent Information Request and Delivery Core Ontology
An ontology encoding the core metadata based on the Intelligent Information Request and Delivery (iiRDS) standard
International Standard for Intelligent Information Request and Delivery Machinery Ontology
An ontology encoding machinery based on the Intelligent Information Request and Delivery (iiRDS) standard
International Standard for Intelligent Information Request and Delivery Software Ontology
An ontology encoding software based on the Intelligent Information Request and Delivery (iiRDS) standard
The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.
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. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.
InfoSecSoS - Ontology for Information Security Management in Systems-of-Systems
International Nucleotide Sequence Database Collaboration (INSDC) Run
An experimental run, served thrugh the ENA
IntAct provides a freely available, open source database system and analysis tools for protein interaction data.
Industrial Ontology Foundry (IOF) Core Ontology
The IOF Core Ontology contains notions found to be common across multiple manufacturing domains. This file is an RDF implementation of these notions. The ontology utilizes the Basic Formal Ontology or BFO as a top-level ontology but also borrows terms from various domain-independent or mid-level ontologies. The purpose of the ontology is to serve as a foundation for ensuring consistency and interoperability across various domain-specific reference ontologies the IOF publishes.
Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage) Note that the website uses a different identifier then the one reported in this semantic space.
International Standard Classification of Education, 2013 Edition
ISCED is designed to serve as a framework to classify educational activities as defined in programmes and the resulting qualifications into internationally agreed categories. The basic concepts and definitions of ISCED are therefore intended to be internationally valid and comprehensive of the full range of education systems.
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. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)
Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world.
International Traditional Medicine Clinical Trial Registry
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. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website)
A catalogue of mouse strains supplied by The Jackson Laboratory. Each identifier corresponds to a mouse strain.
This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website)
Korean Clinical Research Information Service
The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page) Note that the web page that resolves this trial does not correspond to the semantic space
Interdisziplinäre Forschungsfeldklassifikation
Klassifikation für interdisziplinäre Forschungsfelder im Rahmen des Kerndatensatz Forschung
KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups. Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc. Structure - grouped as similar chemical structures having the same skeleton, etc. Target - grouped by drug targets Class - drug classes often representing similar mechanisms of action Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters Chemical groups are often used for identifying essentially the same active ingredients of drugs in different countries.
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. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.
KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links.
KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.
KEGG Genome is a collection of organisms whose genomes have been completely sequenced.
The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.
KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.
KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.
KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
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.
Allgemeines Metadatenprofil für Bildungsressourcen
A cross-sectoral metadata profile for describing teaching and learning resources, primarily based on [schema.org](https://schema.org) and the Learning Resource Metadata Initiative LRMI, and additionally utilizing elements of the Simple Knowledge Organization System SKOS. A JSON-LD11-compliant data structure is defined in the form of this HTML specification, including a JSON schema against which data can be automatically checked for conformity with the profile.
Identifiers describing conditions of access to an object (login) as defined by the [OER metadata group](https://oerworldmap.org/resource/urn:uuid:fd06253e-fe67-4910-b923-51db9d27e59f).
A controlled vocabulary for education levels, such as primary eduation, secondary education, and post-secondary education
This is a vocabulary for educational sectors as used in the OER World Map (https://oerworldmap.org)
A controlled vocbualry of higher education resource types
German University Subject Classification System
A classification of subjects in Hochschule (universities of applied sciences)
This ontology is a formal representation that captures the fundamental concepts and their relationships to one another in the field of curriculum design and implementation of the German school system.
This SKOS vocabulary describes types of primary and secondary schools in Germany, such as Grundschule, Gymnasium, and Realschule. This does not include post-secondary education such as universities or hochschulen.
A vocabulary describing subjects taught in German primary and secondary school (not university/hochschulen), such as German, math, and art.
Vocabulary of Materials Tribology Lab at KIT
Objects of this class contain a self-bound collection of mass bearing particles.
KNApSAcK provides information on metabolites and the taxonomic class with which they are associated.
The Key Performance Indicator module aims to model the metrics defined at the beginning of building renovation activities to monitor the conformance with typical requirements related to energy efficient buildings.
The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage)
Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)
Library of Congress Subject Headings - Genre Forms
A subset of Library of Congress (LOC) subject headings
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. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).
The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.
This is an ontology draft for the description of metadata of traffic observations, in particular video recordings of road traffic. The traffic observations are e.g. used to design test scenarios for the effectiveness assessment of automated driving systems. The ontology draft resulted from an exchange of the Chair of Automobile Engineering at TU Dresden (https://tu-dresden.de/bu/verkehr/iad/kft?set_language=en) with representatives of NFDI4Ing (Community Cluster 4.4, Archetype Golo, Base Services S3) and FID move in NFDI4Ing's Special Interest Group "Metadata and Ontologies". An essential part of that meeting was the presentation of the reseaerch data management approach at the Chair of Automobile Engineering, in particular its tooling, its metadata approach and its workflow. Traffic observations are managed with ListDB, a solution combined of a SharePoint instance and a virtual machine for data servicing . An accompanying Codebook defines relevant metadata that should be provided for each road traffic observation. ListDB is currently used internally within TU Dresden, but is intentended to be hosted publicly until spring 2023. The ontology draft is, in fact, based on the Codebook (v. 1.0.0.) and an attempt to make a machine-readable document out of it, applying standards from the Semantic Web Stack (RDF(S) and OWL). The draft is constantly being developed further in this context.
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. All LRGs are generated and maintained by the NCBI and EMBL-EBI.
Learning Resource Metadata Innovation Terms
The Learning Resource Metadata Innovation (LRMI) specification is a collection of classes and properties for markup and description of educational resources. The specification builds on the extensive vocabulary provided by Schema.org and other standards. LRMI terms not included in schema.org may nevertheless be used to augment and enrich Schema.org markup. (from homepage)
A concept scheme that defines the types of relationships between a learning resource and a node in an educational framework.
LRMI Educational Audience Role Vocabulary
A concept scheme that defines the primary or intended roles of the audience (beneficiary) of the resource being described.
A concept scheme that enumerates the educational uses of a learning resource.
A concept scheme that defines the predominate interact mode of the learning resource being described.
LRMI Learning Resource Type Concept Scheme
A top-level concept scheme that enumerates different types of Learning Resource, designed to supplement existing more generic resource type schemes and which can support local extensions.
Machine-readable Cataloging (MARC) List for Languages
MARC List for Languages provides three-character lowercase alphabetic strings that serve as the identifiers of languages and language groups. The codes are usually based on the first three letters of the English form or, in some cases, vernacular form of the corresponding language name. The codes are varied where necessary to resolve conflicts and are not intended to be abbreviations of a language name. When the name of a language is changed in the list, the original code is generally retained. The codes in this list are equivalent to those of ISO 639-2 (Bibliographic) codes and some codes from ISO 639-5, although the language name labels may differ. They are linked to the equivalent codes in ISO 639-2 and ISO 639-5 and the corresponding two-character codes in ISO 639-1. The list contains over 480 discrete codes. It is also searchable at: MARC Code List for Languages.
This is the MathModDB Ontology for documenting mathematical models.
The midlevel energy ontology (MENO) is a BFO-based midlevel ontology. It comprises the concepts for energy qualities, energy-based dispositions and energy-driven transformation and transfer processes and their interrelations. It has the goal to provide an upper level structure for these concepts for energy-related domain ontologies.
MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.
A subspace of Metabolic Atlas for compartment-specific records for metabolites.
A subspace of Metabolic Atlas for reactions.
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.
Ontology of Prokaryotic Phenotypic and Metabolic Characters
An ontology of prokaryotic phenotypic and metabolic characters
Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.
Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace.
The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.
The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).
An ontology with predicates to formalization of the concept of mentions. The mentions may be either explicit (e.g. as when well stated into an article "Dr. Johnson's groundbreaking research on climate change") or implicit (e.g. such as discussing "seminal studies in the field"). MiTO contains the object property mito:mentions and its inverse mito:isMentionedBy.
A representation of the variety of methods used to make clinical and phenotype measurements.
MobiVoc is an open vocabulary for future-oriented mobility solutions.
Modern Science Ontology (ModSci), for modeling relationships between modern science branches and related entities, such as scientific discoveries, phenomena, renowned scientists, instruments, etc. ModSci is an upper ontology that provides a unifying framework for the various domain ontologies that make up the Science Knowledge Graph Ontology Suite. The Systematic Approach for Building Ontologies (SABiO) has been followed in the development of ModSci. ModSci is a poly-hierarchical ontology that can be utilized in semantic web applications. ModSci powers two projects for semantically representing scholarly information: Open Research Knowledge Graph (for the categorization of research papers) and OpenResearch.org (for the categorization of the information about scientific events, research projects, scientific papers, publishers, and journals).
An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students.
A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes
Metabolomics Standards Initiative Ontology
an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.
MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.
MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).
MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.
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. This collection references Mycobacteria leprae information.
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. This collection references Mycobacteria marinum information.
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. This collection references Mycobacteria smegmatis information.
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. This collection references Mycobacteria tuberculosis information.
Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan.
The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex).
neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases.
NeXusOntology: Machine-readable ontology of the NeXus definitions
Ontology for computer aided process engineering
OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources.
Ontology for simulation, modelling, and optimization
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. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)
The NFDI4Culture Ontology (CTO) is a domain-specific ontology module developed within the Task Area 5 of the NFDI4Culture initiative. (from homepage)
The NFDI4DS ontology (nfdi4dso) is an ontology describing various resources all resources (datasets, data providers, persons, projects and other entities) within the domain of NFDI4DataScience. nfdi4dso is a module that builds upon the NFDIcore Ontology (https://ise-fizkarlsruhe.github.io/nfdicore/2.0.0/) and maintains alignment with the Basic Formal Ontology (BFO). [from homepage]
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.
The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library's holdings in LocatorPlus, NLM's online public access catalog, are also provided. [from homepage]
NIF Standard Ontology: Subcellular Entities
NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO).
NMR-instrument specific component of metabolomics investigations
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.
National Organization for Rare Disorders
A website containing information about rare diseases, powered by Wordpress.
A repository of software packages written in Javascript, TypeScript, and related.
National Uniform Claim Committee 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. This includes the transactions mandated under HIPAA. The taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct "Levels" including Provider Grouping, Classification, and Area of Specialization. - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc. - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology. - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards.
The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture.
A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.
The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.
A list of values for class levels. Created in the context of the OpenEduHub
A RDF vocabulary for OER content on the web.
The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.
An ontology for describing software components, including their metadata (attribution, licensing, usage instructions, how to get support) and their inputs, outputs and variables. The ontology extends schema.org and codemeta vocabularies and is based on OntoSoft, which proposed a vocabulary for describing software by asking scientists questions.
An ontological version of MIABIS (Minimum Information About BIobank data Sharing)
The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).
Observational Medical Outcomes Partnership
The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format.
Ontology for Modeling and Representation of Social Entities
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.
OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies.
This ontology describes the openADR protocol based on the documentation provided by the openADR Profile B
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. ORCID records hold non-sensitive information such as name, email, organization name, and research activities.
OASIS Open Services for Lifecycle Collaboration Core Vocabulary
Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains.
OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).
A repository of software packages written in PHP.
The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage)
The ExPaNDS Photon and Neutron Experimental Techniques (PaNET) ontology provides a taxonomy and thesaurus of photon and neutron (PaN) experimental techniques. Based mainly on accelerator-based light sources and neutron facilities, the primary use of the ontology is to enhance the FAIRness of PaN data catalogues services. The ontology defines specific techniques in terms of more general technique classes and provides synonyms and references.
Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible.
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 tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.
Provenance, Authoring, and Versioning Vocabulary
PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.
The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public.
The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.
The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients.
Pathogen Host Interaction Phenotype Ontology
Ontology of species-neutral phenotypes observed in pathogen-host interactions.
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. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]
PhySH (Physics Subject Headings) is a physics classification scheme developed by the American Physical Society to organize journals, meetings, and other content by topic. The development of PhySH is motivated by the lack of a fully open, high quality classification scheme for physics. It is intended initially to meet the specific goals of the APS for our journal, meeting, and other content. A longer term goal is to make it available for use by the broader community. (...) Right now, the main use of PhySH is to classify manuscripts within the APS peer-review process and, ultimately, published journal articles. The assigned concepts will be used for ensuring articles are routed to the most appropriate handling editor who is knowledgeable in that area. They also help editors in finding similar articles previously submitted and in finding suitable referees. As one might expect with something so new, the refinement of PhySH is still very much underway. The facets and disciplines have been identified and almost 3,000 concepts have been added to PhySH through an iterative process that is still ongoing. Many APS journal editors are involved in this process, primarily by lending their expertise in the various subfields in physics. The assignment of concepts to the various facets can be rather subjective. Thus, we expect to make many adjustments to PhySH as we receive feedback from the community (especially authors using PhySH to classify their submissions) and as we incorporate PhySH into the APS journal websites. As we iteratively refine PhySH over the coming months, the rate of new concept additions, concept reassignments within facets, and new relationships among concepts should abate significantly.
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. This collection references pig QTLs.
The PMD Core Ontology (PMDco) is a comprehensive framework for representing knowledge that encompasses fundamental concepts from the domains of materials science and engineering (MSE). The PMDco has been designed as a mid-level ontology to establish a connection between specific MSE application ontologies and the domain neutral concepts found in established top-level ontologies. The primary goal of the PMDco is to promote interoperability between diverse domains. PMDco's class structure is both understandable and extensible, making it an efficient tool for organizing MSE knowledge. It serves as a semantic intermediate layer that unifies MSE knowledge representations, enabling data and metadata to be systematically integrated on key terms within the MSE domain. With PMDco, it is possible to seamlessly trace data generation. By building on this foundation, PMDco facilitates the integration of data from various sources and the creation of complex workflows. In summary, PMDco is a valuable tool for researchers and practitioners in the MSE domains. It provides a common language for representing and sharing knowledge, allowing for efficient collaboration and promoting interoperability between diverse domains. Its design allows for the systematic integration of data and metadata, enabling seamless traceability of data generation. Overall, PMDco is a crucial step towards a unified and comprehensive understanding of the MSE domain. PMDco at GitHub: https://github.com/materialdigital/core-ontology Documentation: https://materialdigital.github.io/core-ontology/docs/
mechanical engineering, energy technology
PolyMat is a domain ontology designed for polymer membrane research and tailored for immediate integration within Electronic Laboratory Notebooks (ELNs), facilitating efficient documentation of laboratory experiments and advancing the domain's FAIRification process.
The Plant Phenotyping Experiment Ontology (PPEO) is an implementation of the Minimal Information About Plant Phenotyping Experiment. It lists and organises all the informations necessary to describe and reuse a phenotyping dataset following FAIR principles (Findable Interoperable Accessible Reusable). It has been initiated with experts from Elixir, Emphasis, Bioversity International - CGIAR and RDA.
An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.
Ontology for PREMIS 3, the international standard for metadata to support the preservation of digital objects and ensure their long-term usability.
Proteomics Identification Database Ontology
The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays.
The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects.
PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.
An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians.
An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity.
The Python Package Index (PyPI) is a repository for Python packages.
This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI).
Quantities, Units, Dimensions, and Types Ontology
Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.
This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts
The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)
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. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility.
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.
The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.
Internet Standard -- IETF Request for Comments
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.
ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations. ROR is jointly operated by California Digital Library, Crossref, and Datacite.
The ROSETTA ontology of industrial robotics devices and robotic skills.
The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)
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. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.
Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID]
A repository of software packages written in Ruby.
The SAGE Social Science Thesaurus is a multidisciplinary vocabulary of the most important concepts in the social sciences. SAGE uses this vocabulary as its principal keyword vocabulary for automated tagging of content on SAGE Knowledge and SAGE Research Methods. You are welcome to browse, download, use and transform the vocabulary for any non-commercial purpose. The majority of concepts in the thesaurus have been mined from headwords in SAGE encyclopedias and other reference works. Relationships between concepts have been inferred from implicit structures in those works, for example subject indexes and readers' guides. As such, the thesaurus is a structured representation of what the editors of those reference works consider to be the most important concepts in the social sciences. Additional scraping work has extracted and structured concept-specific metadata, such as dates (for events and people) and definitions. In addition to broader-narrower relationships, concepts are grouped by type: concepts, people, organizations, events, methods, theories or laws.
The Smart Applications REFerence ontology (SAREF) is intended to enable interoperability between solutions from different providers and among various activity sectors in the Internet of Things (IoT), thus contributing to the development of the global digital market.
SAREF4AUTO: an extension of SAREF for the automotive domain
This ontology extends the SAREF ontology for the automotive domain. This work has been developed in the context of the STF 566, which was established with the goal to create four SAREF extensions, one of them for the automotive domain.
This ontology extends the SAREF ontology for the building domain by defining building devices and how they are located in a building. This extension is based on the ISO 16739:2013 Industry Foundation Classes (IFC) standard for data sharing in the construction and facility management industries. The descriptions of the classes and properties extracted from IFC have been taken from the IFC documentation.
SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain
The objective of SAREF4EHAW is to extend SAREF ontology for the eHealth/Ageing-well (EHAW) vertical. Clause 4.1 of the present document shortly introduces a high level view of the envisioned SAREF4EHAW semantic model and modular ontology, with the retained concepts (i.e. classes) and their relations. SAREF4EHAW extension has been specified and formalised by investigating EHAW domain related resources, as reported in ETSI TR 103 509, such as: potential stakeholders, standardization initiatives, alliances/associations, European projects, EC directives, existing ontologies, and data repositories. Therefore, SAREF4EHAW modular ontology shall both: - Allow the implementation of a limited set of typical EHAW related use cases already identified in ETSI TR 103 509, i.e. - Use case 1 ?elderly at home monitoring and support?, - Use case 2 ?monitoring and support of healthy lifestyles for citizens?, - Use case 3 ?Early Warning System (EWS) and Cardiovascular Accidents detection?. - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509, mainly the ontological ones that were mostly taken as input for the ontology specification. SAREF4EHAW mainly reuses the following existing ontologies: SAREF, ETSI SmartBAN reference model, SAREF 4 Environment extension and W3C SSN System module. The following figure presents the high level view of SAREF4EHAW ontology. ![SAREF4SYST overview](diagrams/SAREF4EHAW_Model.jpg) For semantic interoperability handling purposes, an ontology based solution, combined with sensing-as-a-service and WoT strategies, is retained for SAREF4EHAW. Therefore, an upper level ontology, at service level, shall also behas been fully modelled (Service class and sub-classes depicted in the previous figure). For embedded semantic analytics purposes, SAREF4EHAW shall behas been designed using the modularity principle (see ETSI TR 103 509) and can thus be mainly described by the following self-contained knowledge sub-ontologies (or modules): HealthActor, Ban, HealthDevice, Function (measured data related concepts included) and Service., i.e. - Use case 1 “elderly at home monitoring and support”, - Use case 2 “monitoring and support of healthy lifestyles for citizens”, - Use case 3 “Early Warning System (EWS) and Cardiovascular Accidents detection”. - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509
This ontology extends the SAREF ontology for the environment domain, specifically for the light pollution domain, including concepts like photometers, light, etc.
SAREF4GRID: an extension of SAREF for the Smart Grid domain
This ontology extends the SAREF ontology for the smart grid domain.
SAREF4INMA: an extension of SAREF for the industry and manufacturing domain
SAREF4INMA is an extension of SAREF for the industry and manufacturing domain. SAREF4INMA focuses on extending SAREF for the industry and manufacturing domain to solve the lack of interoperability between various types of production equipment that produce items in a factory and, once outside the factory, between different organizations in the value chain to uniquely track back the produced items to the corresponding production equipment, batches, material and precise time in which they were manufactured. SAREF4INMA is specified and published by ETSI in the TS 103 410-5 associated to this ontology file. SAREF4INMA was created to be aligned with related initiatives in the smart industry and manufacturing domain in terms of modelling and standardization, such as the Reference Architecture Model for Industry 4.0 (RAMI), which combines several standards used by the various national initiatives in Europe that support digitalization in manufacturing. The full list of use cases, standards and requirements that guided the creation of SAREF4INMA are described in the associated ETSI TR 103 507.
SAREF4LIFT: an extension of SAREF for the Smart Lifts domain
This ontology extends the SAREF ontology for the Smart Lifts domain.
SAREF4SYST: an extension of SAREF for typology of systems and their inter-connections
The present document is the technical specification of SAREF4SYST, a generic extension of [ETSI TS 103 264 SAREF](https://www.etsi.org/deliver/etsi_ts/103200_103299/103264/02.01.01_60/ts_103264v020101p.pdf) that defines an ontology pattern which can be instantiated for different domains. SAREF4SYST defines Systems, Connections between systems, and Connection Points at which systems may be connected. These core concepts can be used generically to define the topology of features of interest, and can be specialized for multiple domains. The topology of features of interest is highly important in many use cases. If a room holds a lighting device, and if it is adjacent with an open window to a room whose luminosity is low, then by turning on the lighting device in the former room one may expect that the luminosity in the latter room will rise. The SAREF4SYST ontology pattern can be instantiated for different domains. For example to describe zones inside a building (systems), that share a frontier (connections). Properties of systems are typically state variables (e.g. agent population, temperature), whereas properties of connections are typically flows (e.g. heat flow). SAREF4SYST has two main aims: on the one hand, to extend SAREF with the capability or representing general topology of systems and how they are connected or interact and, on the other hand, to exemplify how ontology patterns may help to ensure an homogeneous structure of the overall SAREF ontology and speed up the development of extensions. SAREF4SYST consists both of a core ontology, and guidelines to create ontologies following the SAREF4SYST ontology pattern. The core ontology is a lightweight OWL-DL ontology that defines 3 classes and 9 object properties. Use cases for ontology patterns are described extensively in [ETSI TR 103 549 Clauses 4.2 and 4.3](https://www.etsi.org/deliver/etsi_tr/103500_103599/103549/01.01.01_60/tr_103549v010101p.pdf). For the Smart Energy domain: - Electric power systems can exchange electricity with other electric power systems. The electric energy can flow both ways in some cases (from the Public Grid to a Prosumer), or in only one way (from the Public Grid to a Load). Electric power systems can be made up of different sub-systems. Generic sub-types of electric power systems include producers, consumers, storage systems, transmission systems. - Electric power systems may be connected one to another through electrical connection points. An Electric power system may have multiple connection points (Multiple Winding Transformer generally have one single primary winding with two or more secondary windings). Generic sub-types of electrical connection points include plugs, sockets, direct-current, single-phase, three-phase, connection points. - An Electrical connection may exist between two Electric power systems at two of their respective connection points. Generic sub-types of electrical connections include Single-phase Buses, Three-phase Buses. A single-phase electric power system can be connected using different configurations at a three-phase bus (RN, SN, TN types). For the Smart Building domain: - Buildings, Storeys, Spaces, are different sub-types of Zones. Zones can contain sub-zones. Zones can be adjacent or intersect with other zones. - Two zones may share one or more connections. For example some fresh air may be created inside a storey if it has two controllable openings to the exterior at different cardinal points. A graphical overview of the SAREF4SYST ontology is provided in Figure 1. In such figure: - Rectangles are used to denote Classes. The label of the rectangle is the identifier of the Class. - Plain arrows are used to represent Object Properties between Classes. The label of the arrow is the identifier of the Object Property. The origin of the arrow is the domain Class of the property, and the target of the arrow is the range Class of the property. - Dashed arrows with identifiers between stereotype signs (i.e. "`<< >>`") refer to OWL axioms that are applied to some property. Four pairs of properties are inverse one of the other; the property `s4syst:connectedTo` is symmetric, and properties `s4syst:hasSubSystem` and `s4syst:hasSubSystem` are transitive. - A symbol =1 near the target of an arrow denotes that the associated property is functional. A symbol ? denotes a local existential restriction. ![SAREF4SYST overview](diagrams/overview.png)
This ontology extends the SAREF ontology for the water domain. This work has been developed in the context of the STF 566, which was established with the goal to create three SAREF extensions, one of them for the water domain.
SAREF4WEAR: an extension of SAREF for Wearables
SAREF4WEAR is an extension of SAREF for Wearables
SARGON (SmArt eneRGy dOmain oNtology) is an open-source effort to define semantic descriptions of the smart assets in building automation and smart grid and the relationships between them. SARGON consists of an extensible dictionary of terms and concepts in and around building and smart grid, a set of relationships for linking and composing concepts together, and a flexible data model permitting seamless integration of SARGON with existing tools and databases. Through the use of powerful Semantic Web technology, SARGON can describe the broad set of Devices and custom features, assets and subsystems found across the building stock in a consistent matter.
Structural Classification of Proteins - Unique Identifier
SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.).
Scholarly Contributions and Roles Ontology
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. the role of article guarantor or illustrator).
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. This collection references sheep QTLs.
The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces.
SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.
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
The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary.
The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)
C. elegans Small Molecule Identifier Database
SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications.
The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]
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. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.
Software Package Data Exchange RDF Vocabulary
A dictionary of named properties and classes for Software Package Data Exchange (SPDX) - an open standard for communicating software bill of material information, including components, licenses, copyrights, and security references. SPDX reduces redundant work by providing a common format for companies and communities to share important data, thereby streamlining and improving compliance. [from homepage]
Search Tool for Interactions of Chemicals
STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.
Search Tool for Retrieval of Interacting Genes/Proteins
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. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.
Identifiers for chemicals used as additives
Identifiers for chemicals used as buffers
Interactions are SupraBank's way to collect information about experiments that describe the binding interaction between molecules. The form for creating an interaction enables you to list all experimental conditions. An interaction is similar to an entry in a table in your scientific publication, but providing machine readable comprehensive information. (from homepage)
Identifiers for chemicals used as solvents in SupraBank
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Agriculture
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Commerce
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Decision
SWEET Ontology Human Environmental Assessment
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Environmental Assessment
SWEET Ontology Human Environmental Control
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Environmental Control
SWEET Ontology Human Environmental Conservation
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Environmental Conservation
SWEET Ontology Human Environmental Standards
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Environmental Standards
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Jurisdiction
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Knowledge Domain
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Research
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Transportation
SWEET Ontology Human Technology Readiness
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Human Technology Readiness
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Materials
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Aerosol
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Biomass
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Compound
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Element
SWEET Ontology Material Elemental Molecule
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Elemental Molecule
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Energy
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Equipment
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Facility
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Industrial
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Instrument
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Ion
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Isotope
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Microbiota
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Mineral
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Animal
SWEET Ontology Material Natural Resource
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Natural Resource
SWEET Ontology Material Organic Compound
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Organic Compound
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Particle
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Plant
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Rock
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Rock Igneous
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Sediment
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Material Water
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere
SWEET Ontology Phenomena Atmosphere Cloud
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Cloud
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Fog
SWEET Ontology Phenomena Atmosphere Front
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Front
SWEET Ontology Phenomena Atmosphere Lightning
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Lightning
SWEET Ontology Phenomena Atmosphere Precipitation
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Precipitation
SWEET Ontology Phenomena Atmosphere Pressure
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Pressure
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Sky
SWEET Ontology Phenomena Atmosphere Transport
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Transport
SWEET Ontology Phenomena Atmosphere Wind
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Wind
SWEET Ontology Phenomena Atmosphere Wind Mesoscale
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Atmosphere Wind Mesoscale
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Biology
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Cycle Material
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Cryosphere
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Cycle
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ecology
SWEET Ontology Phenomena Environmental Impact
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Environmental Impact
SWEET Ontology Phenomena ElectroMagnetic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena ElectroMagnetic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Energy
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Fluid Dynamics
SWEET Ontology Phenomena Fluid Instability
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Fluid Instability
SWEET Ontology Phenomena Fluid Transport
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Fluid Transport
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Fault
SWEET Ontology Phenomena Geologic Geomorphology
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Geomorphology
SWEET Ontology Phenomena Geologic Seismicity
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Seismicity
SWEET Ontology Phenomena Geologic Tectonic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Tectonic
SWEET Ontology Phenomena Geologic Volcano
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Geologic Volcano
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Heliosphere
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Hydrosphere
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Mixing
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ocean
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ocean Coastal
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Ocean Dynamics
SWEET Ontology Phenomena Planetary Climate
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Planetary Climate
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Reaction
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Solid
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Star
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena System
SWEET Ontology Phenomena System Complexity
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena System Complexity
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Wave
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Phenomena Wave Noise
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process Chemical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process Physical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process State Change
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Process Wave
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Binary
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Capacity
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Categorical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Charge
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Chemical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Conductivity
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Count
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Difference
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Diffusivity
SWEET Ontology Property Dimensionless Ratio
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Dimensionless Ratio
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Energy
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Energy Flux
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Fraction
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Function
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Index
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Mass
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Mass Flux
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Ordinal
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Pressure
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Quantity
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Rotation
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Direction
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Distance
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Height
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Location
SWEET Ontology Property Space Multidimensional
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Multidimensional
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Speed
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Space Thickness
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Temperature
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Time Frequency
SWEET Ontology Property Temperature Gradient
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Temperature Gradient
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Property Time
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Atmospheric
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Astrophysical Body
SWEET Ontology Realm Atmospheric Boundary Layer
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Atmospheric Boundary Layer
SWEET Ontology Realm Astrophysical Heliosphere
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Astrophysical Heliosphere
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Astrophysical
SWEET Ontology Realm Atmospheric Weather
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Atmospheric Weather
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Biologic Biome
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Cryosphere
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Climate Zone
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Earth Reference
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Basin
SWEET Ontology Realm Geologic Constituent
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Constituent
SWEET Ontology Realm Geologic Continental
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Continental
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Oceanic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Geologic Orogen
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Hydrosphere
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Hydrosphere Body
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Landform
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Aeolian
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Coastal
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Fluvial
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Glacial
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Orographic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Protected
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Tectonic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Land Volcanic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Ocean
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Ocean Feature
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Ocean Floor
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Region
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Realm Soil
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Chemical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Climate
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Human
SWEET Ontology Relationships Mathematical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Mathematical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Physical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Provenance
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Scientific
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Space
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Relationships Time
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation
SWEET Ontology Representation Data Format
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Format
SWEET Ontology Representation Data Model
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Model
SWEET Ontology Representation Data Product
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Product
SWEET Ontology Representation Data Service
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service
SWEET Ontology Representation Data Servcie Analysis
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Servcie Analysis
SWEET Ontology Representation Data Service Geospatial
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service Geospatial
SWEET Ontology Representation Data Service Reduction
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service Reduction
SWEET Ontology Representation Data Service Validation
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Data Service Validation
SWEET Ontology Representation Mathematics
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics
SWEET Ontology Representation Mathematics Function
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Function
SWEET Ontology Representation Mathematics Function Orthogonal
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Function Orthogonal
representation mathematics function orthogonal
SWEET Ontology Representation Mathematics Graph
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Graph
SWEET Ontology Representation Mathematics Operation
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Operation
SWEET Ontology Representation Mathematics Solution
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Solution
SWEET Ontology Representation Mathematics Statistics
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Mathematics Statistics
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space
SWEET Ontology Representation Scientific Component
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Component
SWEET Ontology Representation Space Coordinate
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Coordinate
SWEET Ontology Representation Space Direction
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Direction
SWEET Ontology Representation Scientific Function
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Function
SWEET Ontology Representation Space Geometry
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Geometry
SWEET Ontology Representation Space Geometry 3D
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Geometry 3D
SWEET Ontology Representation Scientific Law
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Law
SWEET Ontology Representation Representation Scientific Methodology
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Representation Scientific Methodology
representation representation scientific methodology
SWEET Ontology Representation Scientific Model
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Model
SWEET Ontology Representation Science Provenance
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Science Provenance
SWEET Ontology Representation Space Reference System
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Space Reference System
SWEET Ontology Representation Scientific Units
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Scientific Units
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Time
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Time Day
SWEET Ontology Representation Time Season
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for Representation Time Season
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Biological
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Chemical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Data Processing
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Energy Flux
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Fluid
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Ordinal
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Physical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Biological
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Chemical
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Realm
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Geographic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Impact
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role
SWEET Ontology State Role Representative
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Representative
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Role Trust
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Spectral Band
SWEET Ontology State Space Configuration
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Space Configuration
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Spectral Line
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Solid
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Space
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Space Scale
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Storm
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State System
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Time Cycle
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Time Frequency
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Time Geologic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Thermodynamic
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Time
The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for State Visibility
A Semantic Web Rule Language Combining OWL and RuleML
SWRL enables Horn-like rules to be combined with an OWL knowledge base.
Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa
The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.
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). CRCN has been retitled the Medical Research Network (MedResNet) since June 15, 2012. (from homepage)
Domain ontology for thin-film solar cells and related tandem solar cells. Contains relevant terms and concepts from BFO, IAO, UO, PATO, OBI, CHMO.
The (Dutch) Basic Classification (nl Nederlandse basisclassificatie), BK or NBC is a hierarchical classification system developed by Dutch libraries specifically for scientific works. The classification system was introduced at the end of the 1980s under the direction of the Royal Library of the Netherlands and has been in use since 1990. Since then it has been continually revised. The BK is mainly used in the Netherlands and in the Common Library Network (GBV).
This file contains the Base Ontology of oneM2M as specified in TS-0012
The Damage Topology Ontology (DOT) allows the definition of damage representations and their relations with other damages and affected construction components. The ontology supports a generic damage modeling approach and therefore could be applied for any type of degradation as well as for any construction type (e.g. buildings or bridges). Damage representations can be modeled either as damaged areas (dot:DamageArea) or elementary damage elements (dot:DamageElement). Thereby, instances of dot:DamageElement should be aggregated in a dot:DamageArea, however significant damages e.g. large cracks could be modelled as dot:DamageElement without dot:DamageArea. For grouping multiple coherent damages, a damage pattern could be defined by using dot:DamagePattern as third type for damage representation. Besides the topological damage classes, damage can also be categorized acording to a certain damage type using subclasses of dot:ClassifiedDamage as defined in extensions of DOT. A division between structural and non-structural damage is made by using the dot:StructuralDamage or dot:Defect classes. In addition to the topology, damage documentation that is commonly created during inspections and damage assessment can be linked to the damages as well as to the damaged components.
Holistic Ontology for semiconductor manufacturing and development, products and systems containing semiconductors and connected supply chains.
The Heat Pump Ontology (HPOnt) aims to formalize and represent all the relevant information of Heat Pumps. The HPOnt has been developed as part of the REACT project which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 824395.
OWL ontology for the IFC conceptual data schema and exchange file format for Building Information Model (BIM) data
An ontology for the description of information objects.
The Internet of Construction Ontology (IoC) construction process ontology is intended to represent a comprehensive solution of how processes in the construction industry can be modelled. Due to the iterative nature of creating an ontology, the construction process ontology presented here can at best be considered a working state at the time of publication. Our approach emphasizes the simplest and most comprehensive mapping possible, which is only extended based on insights from practical use when otherwise compelling limitations in usability and applicability arise. Thus, the extension and refinement of the developed construction process ontology strongly depends on the integration of further areas of the construction value chain and the connection of further domain ontologies.
The Industrial Data Ontology is an upper ontology for industrial data, inspired by the ISO 15926-2 data model and Basic Formal Ontology.
The material properties ontology provides the vocabulary to describe the composition of building elements.
The Materials Design Ontology is designed to enable semantic query and integrated query over multiple databases. By generating mappings between MDO and the schemas of materials databases, we can create MDO-enabled query interfaces. The querying can occur, for instance, via MDO-based query expansion, MDO-based mediation or through MDO-enabled data warehouses.
Simple Knowledge Organization System (SKOS) version of Materials Data Vocabulary
A version of the Materials Data Vocabulary structured as Simple Knowledge Organization System (SKOS). The XML was originally created by the TemaTres software. This vocabulary describes the applicability to material science of records in the NIST Materials Resource Registry (NMRR - https://materials.registry.nist.gov/). The NMRR allows for the registration of materials resources, bridging the gap between existing resources and the end users. The NMRR functions as a node in a federated system, making the registered information available for research to the materials community. This is being developed at the National Institute of Standards and Technology and is made available to solicit comments from the Material Science community. (An Excel version of the file is also included in the distributions for ease of use.) Please cite this resource as: Medina-Smith, Andrea; Becker, Chandler (2017), Simple Knowledge Organization System (SKOS) version of Materials Data Vocabulary , National Institute of Standards and Technology, https://doi.org/10.18434/T4/1435037
Controlled vocabulary for the classification of the theme for a mobility dataset.
The Audio Commons Ontology has been created in the context of the European project [Audio Commons](https://www.audiocommons.org/), which were aimed at favouring sharing and reuse of audio content (both of musical and non-musical nature), specially using [Creative Commons](https://creativecommons.org/) licenses. It is designed specifically to integrate access to multiple heterogeneously structured audio content providers. In particular the following ones have been considered in the project: - [Freesound](https://freesound.org/), a collaborative database of Creative Commons Licensed sounds; - [Jamendo](https://www.jamendo.com/), a music website for independent artists; - [Europeana Sounds](https://www.eusounds.eu/), a European project collecting and sharing data from several archives of sounds and sound-related media; - [Internet Archive](https://archive.org/), a non-profit library of millions of freely accessible media contents. ### The base model ![A diagram showing the entities Work, Expression, Manifestation, Item](./img/FRBR-Group-1-entities-and-basic-relations.svg.png) The Audio Commons ontology is based on [Functional Requirements for Bibliographic Records (FRBR)](https://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records), a bibliographic model designed for user tasks of retrieval and access in online library catalogues and bibliographic databases. FRBR distinguish the products of intellectual or artistic endeavor in four main classes: work, expression, manifestation, item. It is available as RDF vocabulary at https://vocab.org/frbr/core. For further information on FRBR, check the [standard](https://repository.ifla.org/handle/123456789/811). Another important model related to audio is the [Music Ontology](http://musicontology.com/), which is also based on the FRBR model. Our ontology is more generic than the Music Ontology but is interoperable with it to support the specificities of music-related audio content. The Audio Commons ontology works also in conjunction with - [Dublin Core](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/) for basic metadata, - [EBU Core](https://www.ebu.ch/metadata/ontologies/ebucore/) for technical properties of audio files, - [SKOS](https://www.w3.org/TR/skos-primer/) to support taxonomic classifications, - [Creative Commons Licensing schema](https://creativecommons.org/ns) to represent media licensing, - [Event ontology](http://motools.sf.net/event/event.html) for the formalisation of events, - [Audio Features Ontology](https://w3id.org/afo/onto/) for the characterisation of audio features. ### Ontology overview ![A diagram showing the main classes of the Audio Commons ontology](./img/AC-Ontology-Skeleton.png) The figure above shows the most general classes and properties of the Audio Commons ontology and their relationship with classes of the FRBR and the Music Ontology: - **`ac:AudioExpression`**, the specific intellectual or artistic form that a work takes each time it is _realised_, in the audio domain, e.g., the recording or synthesis of music or sounds; - **`ac:AudioManifestation`**, the physical embodiment of an audio expression, e.g., a musical track, a sound, an album; - **`ac:AudioItem`**, a single exemplar of an audio manifestation, e.g., a copy of a CD or a specific media file. The FRBR class Work, representing a distinct intellectual or artistic creation on a more conceptual level, has not been specialised in Audio Commons. The Audio Commons ontology provides a generic schema for audio classification through the property **`ac:audioCategory`** that associates any audio expression, manifestation, or item to some generic **`ac:AudioCategory`**. These two terms can be specialised to provide spefic categorisations. ### Manifestations: audio clips and collections ![A diagram showing the main classes of the Audio Commons ontology](./img/AC-Ontology-Manifestation.png) The figure above shows classes and properties related to audio manifestations. An instance of **`ac:AudioClip`**, a subclass of `ac:AudioManifestation`, is any audio segment that has been published in some form or uploaded for consumption, for example, a track in a music label's repository or a sound in an audio repository, library or archive. The class **`ac:AudioCollection`**, another subclass of `ac:AudioManifestation`, is used to represent collections of audio clips. The class **`ac:AudioCollectionNode`** is used to represent single nodes of a collection, offering local information like the index in the collection and pointers to previous and next nodes. The separation between the collection node and its actual content (e.g., an `ac:AudioClip`) permits the same content to be shared in multiple collections. The content of each node of a collection is not limited to an `ac:AudioClip`, but may contain any `ac:AudioManifestation`. Collections can thus contain other collections to support specific cases, e.g. a mapping to the Music Ontology model where an `mo:Release` can contain multiple `mo:Record`(s) that can in turn contain multiple `mo:Track`(s). ### Items: audio files ![A diagram showing ac:Item class and related class and properties](./img/AC-Ontology-Item.png) An `ac:AudioItem` is a concrete exemplar of an audio manifestation. In our domain, the main exemplars are the actual audio files. The corresponding class **`ac:AudioFile`** is a subclass of `ac:AudioItem`. It is subclass of `ebu:MediaResource` too and the corresponging properties of EBU Core can be used to describe the file (e.g., `ebu:hasEncodingFormat`, `ebu:fileSize`). ### Expressions: audio signals ![A diagram showing ac:Expression class and related class and properties](./img/AC-Ontology-Expression.png) While `ac:AudioFile` represents a concrete file encoded in a certain format, **`ac:DigitalSignal`** is the representation of the corresponding digital signal. `ac:DigitalSignal` is a subclass of `ac:MusicalExpression`. The data properties `ac:sampleRate`, `ac:bitsPerSample`, and `ac:channels`, associate a signal with its basic features specific to digital representations. The property `ac:publicationOf` can be used to associate an `ac:AudioClip` with the corresponding digital signal. The property `ac:encodes` instead, associates an `ac:AudioFile` with the encoded digital signal. ### Events: recording/syntesis ![A diagram showing ac:SignalProduction class and related class and properties!](./img/AC-Ontology-SignalProduction.png) The description of temporal events is crucial to formalise and document transitions in the workflow of audio production and publication. The class `event:Event` of the Event Ontology is thus specialised for specific actions that are interesting for the audio domain. Using the `event:Event` class, details of an event such as its location in time and space, its factor and its products may be explicitly described. Moreover, events can be composed using the property `event:sub_event`, to build complex events. The class `ac:SignalProduction` represents the act of producing a `ac:Signal`, which could be either an `ac:AnalogSignal` or a `ac:DigitalSignal`. This is complemented by **`ac:Recording`**, representing the process of recording a sound (`ac:Sound`) or the product of **`ac:Synthesis`**, in case of artificially generated sounds. ### Events (continued): publication ![A diagram showing ac:Publication class and related class and properties!](./img/AC-Ontology-Publication.png) The event **`ac:AudioPublication`** represents the public release of a piece of work, e.g., the release of a new album by a band. ### Usage Example ![A diagram showing an example of ontology usage!](./img/AC_Example-AudioClip.png) The figure above shows an example of use of the Audio Commons ontology to represent a sound from the Freesound database. For simplicity only the classes `ac:AudioClip`, `ac:AudioFile`, and `ac:AudioCategory` are used in this case.
Ontology for manufacturing and logistics
An ontology of the Retail Energy Market of Great Britain created by Lidcast Data Limited.
An ontology to describe standards related to Industry 4.0 and Smart Manufacturing
The scope of the TUBES ontology is to explicitly define the topology of interconnected building service system and their relationship to the spatial structure. It has a strong alignment to other ontologies within the W3C community and aims to provide the means to link information at data level within the AEC industry.
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. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars.
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. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.
Tribology Ontology for Artificial Intelligence
The tribAIn1 ontology aims to formalize knowledge gained from tribological experiments for reuse, comparison and documentation. Therefore, the tribAin ontology provides concepts for the specification of methodological background knowledge of experimental design, the documentation of the experimental setup and the representation of different kinds of results (e.g. measurements series, analysis, interpretation in natural-language). Using the EXPO2 (ontology of scientific experiments) as basis, gives tribAIn a generic background about scientific experimental design, methodology and results representation.
The Unified Astronomy Thesaurus (UAT) is an open, interoperable and community-supported thesaurus being developed to unify the existing divergent and isolated Astronomy & Astrophysics thesauri into a single high-quality, freely-available open-source thesaurus which will be of immediate value to both research and research support, and provide a mechanism for reviewing, discussing and evaluating the continuous evolution of terminology in these fields.
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) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business.
An ontology transcription of definitions in the Functional Mock-up Interface (FMI) standard document from https://fmi-standard.org/ that enables representing Functional Mock-up Units (FMUs) in RDF
Ontology for representing systems, models and simulations in RDF.
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.
University hospital Medical Information Network Clinical Trial Registry
An additional Japanese clinical trial registry
The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases.
The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information.
UniProt provides proteome sets of proteins whose genomes have been completely sequenced.
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.
A manually curated resource for the representation and annotation of metabolic pathways
A vocabulary for annotating vocabulary descriptions
This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes.
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 Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary.
Vehicle Signal Specification Core Ontology
This ontology describes the car's attributes, branches and signals defined in the Vehicle Signal Specification.
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.
Protocol for Web Description Resources (POWDER): POWDER-S Vocabulary
The Protocol for Web Description Resources (POWDER) allows metadata to be associated with groups of resources such as those found on a Web site. Its main 'unit of information' is the Description Resource (DR), one or more of which are contained in a POWDER document. Processing such a document yields RDF triples describing the resources that are within the scope of the DRs. POWDER documents are written in XML and have relatively loose semantics, however, a GRDDL transform, associated with the root namespace, renders the data in RDF/OWL with more formal semantics. [from homepage]
Browser for the periodic table of the elements
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 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. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.
WikiPathways is a database of biological pathways maintained by and for the scientific community.
An ontology that represents object-oriented programming languages
OntoSpecies - Chemical Species Ontology for Data Integration and Knowledge Discovery
OntoSpecies is an ontology developed for representing chemical species.
This ontology aims to model the Web of Things domain according to the W3C Interest Group (http://w3c.github.io/wot/)
XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.
Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.
HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.
This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language.
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).
Der Thesaurus enthält Vokabular zu allen ökonomischen Themenstellungen: über 6.000 Schlagwörter und über 28.000 zusätzliche Synonyme als Zugangshilfe, um individuelle Formulierungen bei der Suche aufzufangen. Auch Fachbegriffe aus benachbarten Bereichen wie z.B. Recht, Soziologie oder Politik sowie Geobegriffe sind dort zu finden. Wenn Sie Schlagwörter aus diesem Vokabular auswählen, können Sie sicher sein Treffer zu erhalten, die zu dem gewünschten Sachgebiet passen. [from homepage]
Zebrafish Experimental Conditions Ontology
Ontology of Zebrafish Experimental Conditions
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
ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.
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). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.
Alliance of Genome Resources Knowledge Base
The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) 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: - [ZFIN](https://zfin.org) - Zebrafish Information Network - [WormBase](https://wormbase.org) - [MGI](https://www.mgi.org) - Mouse Genome Informatics - [RGD](https://rgd.mcw.edu) - Rat Genome Database - [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database - [FlyBase](https://flybase.org) - [Xenbase](https://www.xenbase.org)
This vocabulary defines education levels for pre-kindergarten through grade 12 for the United States. It also defines general categories for post-secondary education (vocational, professional and life-long learning).
Australian New Zealand Clinical Trials Registry
The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. In 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)
arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.
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.
BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.
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.
An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.
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. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.
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. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.
Big Open Network of Sustainability Assessment Information Ontology
The BONSAI ontologies provides elements of description for product footprint concepts defined in the bonsai.uno data base
The Building Topology Ontology (BOT) is a minimal ontology for describing the core topological concepts of a building.
BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.
Information for ligands in the BRENDA database.
Information for ligand groups (chemical classes).
Brick is an open-source effort to standardize semantic descriptions of the physical, logical and virtual assets in buildings and the relationships between them. Brick consists of an extensible dictionary of terms and concepts in and around buildings, a set of relationships for linking and composing concepts together, and a flexible data model permitting seamless integration of Brick with existing tools and databases. Through the use of powerful Semantic Web technology, Brick can describe the broad set of idiosyncratic and custom features, assets and subsystems found across the building stock in a consistent matter. Adopting Brick as the canonical description of a building enables the following: 1) Brick lowers the cost of deploying analytics, energy efficiency measures and intelligent controls across buildings, 2) Brick presents an integrated, cross-vendor representation of the multitude of subsystems in modern buildings: HVAC, lighting, fire, security and so on, 3) Brick simplifies the development of smart analytics and control applications, and 4) Brick reduces the reliance upon the non-standard, unstructured labels endemic to building management systems.
CATH Protein Structural Domain Superfamily
CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence.
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.
The CIDOC Conceptual Reference Model (CRM) is a theoretical and practical tool for information integration in the field of cultural heritage. It can help researchers, administrators and the public explore complex questions with regards to our past across diverse and dispersed datasets. The CIDOC CRM achieves this by providing definitions and a formal structure for describing the implicit and explicit concepts and relationships used in cultural heritage documentation and of general interest for the querying and exploration of such data. Such models are also known as formal ontologies. These formal descriptions allow the integration of data from multiple sources in a software and schema agnostic fashion. [from homepage]
A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.
Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.
Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).
A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis
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. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.
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. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.
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. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.
ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.
A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.
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. This collection references genes.
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. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]
An anatomical and developmental ontology for ctenophores (Comb Jellies)
The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage) Note that the identifier in this semantic space is not the one used in the webpages
The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records.
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.
A controlled vocabulary to support the study of transcription in the developing human brain
DICOM — Digital Imaging and Communications in Medicine — is the international standard for medical images and related information (ISO 12052). It defines the formats for medical images that can be exchanged with the data and quality necessary for clinical use. DICOM is implemented in almost every radiology, cardiology imaging, and radiotherapy device (X-ray, CT, MRI, ultrasound, etc.), and increasingly in devices in other medical domains such as ophthalmology and dentistry. With tens of thousands of imaging devices in use, DICOM is one of the most widely deployed healthcare messaging standards in the world. There are literally billions of DICOM images currently in use for clinical care. Since its first publication in 1993, DICOM has revolutionized the practice of radiology, allowing the replacement of X-ray film with a fully digital workflow. Much as the Internet has become the platform for new consumer information applications, DICOM has enabled advanced medical imaging applications that have “changed the face of clinical medicine”. From the emergency department, to cardiac stress testing, to breast cancer detection, DICOM is the standard that makes medical imaging work — for doctors and for patients.
An ontology for energy systems and energy efficiency in the construction and renovation domain
DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature.
A controlled vocabulary to support the study of transcription in the developing mouse brain
Ontology Modeling for Intelligent Domotic Environments
The DogOnt ontology supports device/network independent description of houses, including both controllable and architectural elements.
The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website)
The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.
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. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.
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. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.
The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.
Electron Microscopy Public Image Archive
EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure
The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers.
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.
ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.
This is the formal vocabulary (ontology) describing the FAIR principles.
A structured controlled vocabulary used for various aspects of annotation by FlyBase.
Traits and phenotypes of flowering plants occurring in digitized Floras
FlyBase is the database of the Drosophila Genome Projects and of associated literature.
FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world.
FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data
Global Biodiversity Information Facility
Database of living organisms, taxonomic. The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.
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).
The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.
The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.
A controlled vocabulary to support the study of transcription in the human brain
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. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website]
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.
The official list of MIME types, now renamed to media types
International Classification of Functioning, Disability and Health
The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels.
A classification system for the subject matter of works of art, originating from work from Henri van de Waal in the 1940.
Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.
Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools.
IMGT/HLA human major histocompatibility complex sequence database
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/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.
The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.
The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.
InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
International Standard Classification of Education, 1997 Edition
International Standard Classification of Education, 2011 Edition
An identifier for a country in numeric format per ISO 3166-1
International Clinical Trials Registry Platform
The International Clinical Trials Registry Platform, originally called International Standard Randomised Controlled Trial Number (ISRCTN) registry, is a primary clinical study registry recognised by the World Health Organisation (WHO) and the International Committee of Medical Journal Editors (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. All study records in the database are freely accessible and searchable. (from homepage)
The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.
KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.
Library of Congress Format Description Document
The digital content format descriptions accessible here provide specific information about individual formats and their characteristics. Each description provides moderately detailed information and citations. Planned for inclusion are a wide variety of formats: file formats, file-format classes, bitstream structures and encodings, and the mechanisms used to compress files or bitstreams. Inclusion of a description for a format does not imply that the format is preferred or acceptable for Library of Congress collections. [from homepage]
Logical Observation Identifiers Names and Codes
The international standard for identifying health measurements, observations, and documents.
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.
A controlled vocabulary to support the study of transcription in the mouse brain
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.).
Metabolic Encyclopedia of metabolic and other pathways
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.
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.
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.
The aim of DALIA project is to build a platform for learning material for Research Data Management (RDM) and Data Science. The platform is based on a knowledge graph. We introduce MoDalia, the base ontology of DALIA knowledge graph. Modalia inherits some modules from EduCOR. It includes also modelling of micro -credentials and certificates
MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.
A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.
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. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily.
National Drug File - Reference Terminology
NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction].
This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties
OEO is a domain reference ontology for energy system modeling.
The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.
Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.
An ontology of phenotypes covering microbes
Ontology of Precision Medicine and Investigation
OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.
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).
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. This collection references groups of genes that have been organised as families.
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. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.
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. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.
A controlled vocabulary to support the study of transcription in the primate brain
The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.
The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands.
Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas.
The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.
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. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.
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. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.
PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets.
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.
RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary.
The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.
Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant.
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.
An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.
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. This collection references genes.
Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants. Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB.
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. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.
SAREF4EE: the EEbus/Energy@home extension of SAREF
This is the extension of SAREF for the EEBus and Energy@Home project. The documentation of SAREF4EE is available at http://ontology.tno.nl/SAREF4EE_Documentation_v0.1.pdf. SAREF4EE represents 1) The configuration information exchanged in the use case 'Remote Network Management' according to the EEBus Technical Report, Protocol Specification- Remote Network Management, version 1.0.0.2, 2015-09-19; 2) The scheduling information about power sequences exchanged in the use cases Appliance scheduling through CEM and remote start' and 'Automatic cycle rescheduling', according to the message structures described in General Message Structures, version 0.1.1, 2015-10-07; 3) The monitor and control information exchanged in the use case 'Communicate appliance status and info on manually planned cycles', according to the monitoring and control part of the Energy@Home Data Model, version 1.0; and 4) the event-based data exchanged in the use case 'Demand Response', according to General Message Structures, version 0.1.1, 2015-10-07.
Scientific Evidence and Provenance Information Ontology
An ontology for representing the provenance of scientific claims and the evidence that supports them.
The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.
A language for validating RDF graphs against a set of conditions
Sensor, Observation, Sample, and Actuator Ontology
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.
System Science of Biological Dynamics dataset
Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations.
System Science of Biological Dynamics project
This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.
System capabilities, operating ranges, and survival ranges ontology
This ontology describes system capabilities, operating ranges, and survival ranges. Please report any errors to the W3C Spatial Data on the Web Working Group via the SDW WG Public List public-sdw-wg@w3.org
The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases.
A controlled vocabulary to describe phenotypic traits in plants.
Unified Medical Language System Concept Unique Identifier
The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.
The UNESCO Thesaurus is a controlled and structured list of terms used in subject analysis and retrieval of documents and publications in the fields of education, culture, natural sciences, social and human sciences, communication and information. Continuously enriched and updated, its multidisciplinary terminology reflects the evolution of UNESCO's programmes and activities. [from homepage]
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. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.
Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.
Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)
Ontology for Chemical Kinetic Reaction Mechanisms
Represents chemical kinetic reaction mechanisms.
WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.
Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.
ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.
The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.
ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries
Clytia hemisphaerica Development and Anatomy Ontology
Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.
The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.
The Digital Object Identifier System is for identifying content objects in the digital environment.
The Echinoderm Anatomy and Development Ontology
A structured controlled vocabulary of stage-specific anatomical structures of the developing human.
Elementary Multiperspective Material Ontology
EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)
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). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.
FaBiO, the FRBR-aligned Bibliographic Ontology
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.
The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.
International Classification of Diseases, 10th Revision
The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. Note that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.
International Classification of Diseases, 9th Revision
The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.
KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.
KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.
KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.
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. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. "Inheritance" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method × object of research.
The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.
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.
The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.
The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measures, and dimensions.
An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).
An ontology to standardize research output of nutritional epidemiologic studies.
Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.
Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages.
Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology
PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.
An ontology describing the anatomical structures and characteristics of Porifera (sponges)
The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.
A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research. RadLex provides the foundation for vital data resources used in radiology: - The LOINC/RSNA Radiology Playbook - RadElement Common Data Elements -RadReport Radiology Reporting Templates The development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.
RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization.
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. SBO is a project of the BioModels.net effort.
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.
The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.
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.
The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.
A terminology for the skills necessary to make data FAIR and to keep it FAIR.
The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clinical vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.
A vocabulary for the catalysis disciplines
Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science.
The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories. The Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html). There are few notable resources providing access to the Enzyme Nomenclature: Website Homepage Notes ExplorEnz https://www.enzyme-database.org This is the resource officially recommended by IUBMB IUBMB (via by Queen Mary) https://iubmb.qmul.ac.uk/enzyme This is a web-based version of the 1992 publication. IntEnz https://www.ebi.ac.uk/intenz Shutdown in 2024 ExPaSy https://enzyme.expasy.org EnzymePortal https://www.ebi.ac.uk/enzymeportal
The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.
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.
A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.
Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.
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.
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. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01). Landis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf
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. This collection is species-independent.
STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.
Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.
Compositional Dietary Nutrition Ontology
The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class ‘dietary nutritional component’ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe ‘analytical methods’ for quantification, ‘physical properties’ or ‘dietary function’. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the ‘nutritional component concentration’ class may be used to represent quantification of components described in the ‘dietary nutritional component’ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) ‘Food product by organism’, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum.
CHMO, the chemical methods ontology, describes methods used to
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. This collections also references outgroup organisms.
The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.
Gender, Sex, and Sexual Orientation Ontology
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. A large focus of the ontology is its consideration of LGBTQIA+ terminology.
The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.
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. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.
The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.
An ontology of human and animal behaviours and behavioural phenotypes
Ontology for Avida digital evolution platform
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. This unique ontology has the potential to change this picture overnight. OntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA). More information can be found at https://obofoundry.org/ontology/ontoavida.html
PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.
PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.
The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.
An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.
The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.
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.
DUO is an ontology which represent data use conditions.
LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.
MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.
The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world.
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
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.
post-translational modification site prediction
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.
The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.
EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).
The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.
The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.
The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.
PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.
RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.
The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.
Ontology for the Anatomy of the Insect SkeletoMuscular system
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.
CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.
Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.
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.
XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.
These are the terms that are improted for FOVT to describe vertebrate traits.
An ontology for description of concepts in the nutritional studies domain.
Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.
An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.
The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.
Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.
Environmental conditions, treatments and exposures ontology
ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).
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. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.
An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.
Microbial Conditions Ontology is an ontology...
The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.
AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities
Contains entries for various database identifiers
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.
The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).
The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database.
The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations.
The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.
The LifeWatch ERIC repository of semantic resources for the ecological domain.
PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.
The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools
Chemical Entities of Biological Interest
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.
The upper level ontology upon which OBO Foundry ontologies are built.
An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease.
The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms
The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.
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. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
HL7 External Code Systems are stored within the greater OID system
National Center for Biotechnology Information Registry
Pathguide contains information about 702 biological pathway related resources and molecular interaction related resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated. (from homepage)
The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe 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. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).
A vocabulary and ontology repository for agronomy and related domains.
A vocabulary in LOV gathers definitions of a set of classes and properties (together simply called terms of the vocabulary), useful to describe specific types of things, or things in a given domain or industry, or things at large but for a specific usage. Terms of vocabularies also provide the links in linked data, in the above case between a Person and a City. The definitions of terms provided by the vocabularies bring clear semantics to descriptions and links, thanks to the formal language they use (some dialect of RDF such as RDFS or OWL). In short, vocabularies provide the semantic glue enabling Data to become meaningful Data. [from https://lov.linkeddata.es/dataset/lov/about]
A modeling paradigm-specific registry of prefixes and their URL expansions
EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use.
An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries.
The TIB Terminology Service is an instance of the EBI OLS.
Semantic Web for Earth and Environment Technology Ontology
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. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research).
Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis.
The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate.
The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions.
The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry
AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets.
A registry of commonly used prefixes in the life sciences and linked data. The source data for this registry is a spreadsheet on Google called the Life Science Registry. This registry was previously known as Prefix Commons and was available at https://prefixcommons.org.
A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.
The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession).
BioContext contains modular JSON-LD contexts for bioinformatics data.