identifier name homepage description pattern example email uri_format download.owl download.obo synonyms deprecated aberowl agroportal bartoc biocontext bioportal cellosaurus cheminf cropoct ecoportal edam hl7 integbio lov miriam n2t obofoundry ols ontobee pathguide prefixcc prefixcommons re3data rrid togoid uniprot wikidata zazuko part_of provides has_canonical 3dmet 3D Metabolites http://www.3dmet.dna.affrc.go.jp/ 3DMET is a database collecting three-dimensional structures of natural metabolites. ^B\d{5}$ B00162 http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1 True 3DMET 2635 nbdc00351 3dmet 3dmet 3dmet P2796 4dn.biosource 4D Nucleome Data Portal Biosource https://data.4dnucleome.org/biosources The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. ^4DN[A-Z]{2}[A-Z0-9]{7}$ 4DNSR73BT2A2 Job.Dekker@umassmed.edu https://data.4dnucleome.org/biosources/$1 4DN False 4DN 4dn 4dn 4dn.replicate 4D Nucleome Data Portal Experiment Replicate https://data.4dnucleome.org/experiment-set-replicates/ Database portal containing replicate experiments of different assays and samples 4DNESWX1J3QU https://data.4dnucleome.org/experiment-set-replicates/$1 False aaindex AAindex http://www.genome.ad.jp/aaindex/ Identifier of an entry from the AAindex database. BUNA790102 shuichi@hgc.jp http://www.genome.jp/dbget-bin/www_bget?aaindex:$1 False 1128 nbdc00004 aaindex aao Amphibian gross anatomy http://github.com/seger/aao A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. ^\d{7}$ 0000138 david.c.blackburn@gmail.com http://purl.obolibrary.org/obo/AAO_$1 True AAO AAO aao aao abcam Abcam https://www.abcam.com Vendor for assays, cells, and antibodies ab275461 https://www.abcam.com/$1.html False Abcam abcd AntiBodies Chemically Defined database https://web.expasy.org/abcd/ The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies AD834 Pierre.Cosson@unige.ch https://web.expasy.org/abcd/ABCD_$1 False ABCD DB-0236 abm Applied Biological Materials cell line products https://www.abmgood.com/Cell-Biology.html Cell line collections (Providers) T0599 https://www.abmgood.com/search?query=$1 False ABM abs Annotated Regulatory Binding Sites http://genome.crg.es/datasets/abs2005/ The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. ^A\d+$ A0014 enrique.blanco@crg.eu http://genome.crg.es/datasets/abs2005/entries/$1.html False ABS 2741 abs abs 217 abs ac Activity Streams http://www.w3.org/ns/activitystreams 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. Add http://www.w3.org/ns/activitystreams#$1 False aceview.worm Aceview Worm https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. ^[a-z0-9-]+$ aap-1 mieg@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1 False ACEVIEW.WORM aceview.worm aceview.worm aceview.worm adcad Arctic Data Center Academic Disciplines Ontology https://arcticdata.io/ An ontology to support disciplinary annotation of Arctic Data Center datasets. ^\d{5}$ 00000 brycemecum@gmail.com https://purl.dataone.org/odo/ADCAD_$1 False ADCAD ADCAD addexbio AddexBio cell line products https://www.addexbio.com/productshow?id=4 Cell line collections (Providers) C0020004/4992 https://www.addexbio.com/productdetail?pid=$1 False AddexBio addgene Addgene Plasmid Repository http://addgene.org/ Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$ 50943 joanne.kamens@addgene.org http://addgene.org/$1 False nbdc00356 addgene addgene addgene r3d100010741 Addgene adms Asset Description Metadata Schema Vocabulary http://www.w3.org/ns/adms 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). Asset bert.van.nuffelen@tenforce.com http://www.w3.org/ns/adms#$1 False adms ado Alzheimer's Disease Ontology https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining. ^\d{7}$ 0000001 alpha.tom.kodamullil@scai.fraunhofer.de http://purl.obolibrary.org/obo/ADO_$1 False ADO ADO ado ado ADO adw Animal natural history and life history http://www.animaldiversity.org Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. ^[A-Z_a-z]+$ Lycalopex_vetulus adw_geeks@umich.edu https://animaldiversity.org/accounts/$1 True ADW ADW ADW ADW adw adw adw aeo Anatomical Entity Ontology https://github.com/obophenotype/human-developmental-anatomy-ontology/ AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology ^\d{7}$ 0001017 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/AEO_$1 http://purl.obolibrary.org/obo/aeo.obo AEO_RETIRED True AEO 181 AEO AEO aeo aeo AEO aeon Academic Event Ontology https://tibonto.github.io/aeon/ The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page). ^\d{7}$ 0000001 Philip.Stroemert@tib.eu http://purl.obolibrary.org/obo/AEON_$1 https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl False aero Adverse Event Reporting Ontology http://purl.obolibrary.org/obo/aero The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events ^\d{7}$ 0000125 mcourtot@gmail.com http://purl.obolibrary.org/obo/AERO_$1 True AERO AERO AERO aero aero affy.probeset Affymetrix Probeset http://www.affymetrix.com/ An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration. ^\d{4,}((_[asx])?_at)$ 243002_at https://www.affymetrix.com/LinkServlet?probeset=$1 False AFFY.PROBESET affy.probeset affy.probeset AffyProbeset afo Allotrope Merged Ontology Suite https://www.allotrope.org/ Allotrope Merged Ontology Suite more.info@allotrope.org False AFO AFO afo AFO afpo African Population Ontology https://github.com/h3abionet/afpo 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. 0000440 mcmelek@msn.com http://purl.obolibrary.org/obo/AfPO_$1 False AFPO AFPO afpo AfPO aftol.category Assembling the Fungal Tree of Life - Category https://aftol.umn.edu Categories in the AFTOL database 229 davem@umn.edu https://aftol.umn.edu/glossary?category=$1 False aftol.taxonomy Assembling the Fungal Tree of Life - Taxonomy https://aftol.umn.edu The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. ^\d+$ 959 davem@umn.edu http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1 False AFTOL.TAXONOMY aftol.taxonomy aftol.taxonomy agilent.probe Agilent Probe https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699. ^A_\d+_.+$ A_24_P98555 False agricola Agricultural Online Access http://agricola.nal.usda.gov/ 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. ^\d+$ 50018 judith.blake@jax.org https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1 AGR|AGRICOLA_ID False AGRICOLA agricola agricola DB-0266 agrkb Alliance of Genome Resources Knowledge Base https://www.alliancegenome.org "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations. The Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location: - [ZFIN](https://zfin.org) - Zebrafish Information Network - [WormBase](https://wormbase.org) - [MGI](https://www.mgi.org) - Mouse Genome Informatics - [RGD](https://rgd.mcw.edu) - Rat Genome Database - [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database - [FlyBase](https://flybase.org) - [Xenbase](https://www.xenbase.org)" ^[1-9][0-9]{14}$ 100000000000001 cjmungall@lbl.gov https://www.alliancegenome.org/accession/$1 False agro Agronomy Ontology https://github.com/AgriculturalSemantics/agro AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities ^\d{8}$ 00020007 m.a.laporte@cgiar.org http://purl.obolibrary.org/obo/AGRO_$1 https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo False AGRO AGRO AGRO AGRO agro agro AGRO agrovoc Agronomy Vocabulary https://data.apps.fao.org/catalog/organization/agrovoc AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages. ^[a-z0-9]+$ 2842 agrovoc@fao.org http://aims.fao.org/aos/agrovoc/c_$1 False AGROVOC 305 AGROVOC P8061 agsc Ambystoma Genetic Stock Center https://ambystoma.uky.edu/genetic-stock-center/ 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] 100E srvoss@uky.edu https://scicrunch.org/resolver/RRID:AGSC_$1 False AGSC agsd Animal Genome Size Database http://www.genomesize.com 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. 4779 http://www.genomesize.com/result_species.php?id=$1 False agsd r3d100012517 aio The Artificial Intelligence Ontology https://github.com/berkeleybop/artificial-intelligence-ontology This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases. Causal_Graphical_Model MJoachimiak@lbl.gov https://w3id.org/aio/$1 https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.owl https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.obo False AIO AIO aism Ontology for the Anatomy of the Insect SkeletoMuscular system https://github.com/insect-morphology/aism The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research. ^\d{7}$ 0000027 entiminae@gmail.com http://purl.obolibrary.org/obo/AISM_$1 False AISM AISM aism aism AISM alfred The ALlele FREquency Database http://alfred.med.yale.edu 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. LO362836C https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1 True alfred allergome Allergome http://www.allergome.org/ Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. ^\d+$ 1948 adriano.mari@allergome.org http://www.allergome.org/script/dettaglio.php?id_molecule=$1 False ALLERGOME nbdc01708 allergome allergome allergome DB-0160 alzforum.mutation Alzforum Mutations https://www.alzforum.org/mutations Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease. app-d678n-tottori https://www.alzforum.org/mutations/$1 Alzforum_mut False alzgene Alzheimer Gene Database http://www.alzgene.org 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. 88 bertram@helix.mgh.harvard.edu http://www.alzgene.org/geneoverview.asp?geneid=$1 False alzgene amoebadb AmoebaDB http://amoebadb.org/amoeba/ AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^EDI_\d+$ EDI_244000 oharb@upenn.edu https://amoebadb.org/amoeba/app/record/gene/$1 False AMOEBADB nbdc01207 amoebadb amoebadb amoebadb r3d100012457 amphx The Amphioxus Development and Anatomy Ontology https://github.com/EBISPOT/amphx_ontology An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). ^\d+$ 1000160 hescriva@obs-banyuls.fr http://purl.obolibrary.org/obo/AMPHX_$1 False AMPHX AMPHX amphx amphx AMPHX antibodyregistry Antibody Registry http://antibodyregistry.org/ The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. ^\d{6}$ 493771 http://antibodyregistry.org/AB_$1 False ANTIBODYREGISTRY nbdc01696 antibodyregistry antibodyregistry AB antweb AntWeb http://www.antweb.org/ AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. ^casent\d+(\-D\d+)?$ casent0106247 http://www.antweb.org/specimen.do?name=$1 False ANTWEB nbdc01710 antweb antweb antweb P5299 anzctr Australian New Zealand Clinical Trials Registry https://anzctr.org.au " The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. In 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)" ^ACTRN\d+$ ACTRN12623000498695 https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1 ACTRN False aop AOPWiki https://aopwiki.org/ International repository of Adverse Outcome Pathways. ^\d+$ 98 https://aopwiki.org/aops/$1 False AOP aop aop aop.events AOPWiki (Key Event) https://aopwiki.org/ International repository of Adverse Outcome Pathways. ^\d+$ 3 https://aopwiki.org/events/$1 False AOP.EVENTS aop.events aop.events aop.relationships AOPWiki (Key Event Relationship) https://aopwiki.org/ International repository of Adverse Outcome Pathways. ^\d+$ 5 https://aopwiki.org/relationships/$1 False AOP.RELATIONSHIPS aop.relationships aop.relationships aop.stressor AOPWiki (Stressor) https://aopwiki.org/ International repository of Adverse Outcome Pathways. ^\d+$ 9 https://aopwiki.org/stressors/$1 False AOP.STRESSOR aop.stressor aop.stressor apaonto Psychology Ontology https://bioportal.bioontology.org/ontologies/APAONTO 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. Abdomen awalker@apa.org http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 False APAONTO APAONTO apd Antimicrobial Peptide Database http://aps.unmc.edu/AP/ The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. ^\d{5}$ 01001 gwang@unmc.edu http://aps.unmc.edu/AP/database/query_output.php?ID=$1 False APD apd apd apd r3d100012901 aphidbase.transcript AphidBase Transcript http://www.aphidbase.com/aphidbase AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. ^ACYPI\d{6}(-RA)?$ ACYPI000159 fabrice.legeai@rennes.inra.fr http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 False APHIDBASE.TRANSCRIPT aphidbase.transcript aphidbase.transcript aphidbase apid.interactions APID Interactomes http://cicblade.dep.usal.es:8080/APID/ APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ P01116 http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1 False APID.INTERACTIONS apid.interactions apid.interactions uniprot apo Ascomycete phenotype ontology http://www.yeastgenome.org/ A structured controlled vocabulary for the phenotypes of Ascomycete fungi. ^\d{7}$ 0000184 stacia@stanford.edu http://purl.obolibrary.org/obo/APO_$1 False APO APO APO apo apo APO apollosv Apollo Structured Vocabulary https://github.com/ApolloDev/apollo-sv An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. ^\d{8}$ 00000443 hoganwr@gmail.com http://purl.obolibrary.org/obo/APOLLO_SV_$1 False APOLLO_SV APOLLO-SV apollo_sv apollo_sv APOLLO_SV arachnoserver ArachnoServer http://www.arachnoserver.org/ ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. ^AS\d{6}$ AS000060 glenn.king@imb.uq.edu.au http://www.arachnoserver.org/toxincard.html?id=$1 False ARACHNOSERVER 2578 nbdc01221 arachnoserver arachnoserver arachnoserver r3d100012902 DB-0145 araport Arabidopsis Information Portal https://www.araport.org/ Website with general information about Arabidopsis and functionalities such as a genomic viewer ^AT.G[0-9]{5}$ AT5G05330 hello@vivekkrish.com https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1 False nbdc02433 tair.name 768 DB-0221 archdb ArchDB http://sbi.imim.es/archdb 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. 39421 narcis.fernandez@gmail.com http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1 False nbdc01795 archdb ardb Antibiotic Resistance Genes Database http://ardb.cbcb.umd.edu/ The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. ^[A-Z_]{3}[0-9]{4,}$ CAE46076 http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1 False ARDB ardb ardb ark Archival Resource Key https://arks.org Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver. ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ /53355/cl010066723 jakkbl@gmail.com http://n2t.net/ark:$1 False ARK ark ark aro Antibiotic Resistance Ontology https://github.com/arpcard/aro Antibiotic resistance genes and mutations ^\d{7}$ 1000001 mcarthua@mcmaster.ca http://purl.obolibrary.org/obo/ARO_$1 http://purl.obolibrary.org/obo/aro.obo False ARO ARO ARO aro aro ARO arrayexpress ArrayExpress https://www.ebi.ac.uk/arrayexpress/ ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. ^[AEP]-\w{4}-\d+$ E-MEXP-1712 brazma@ebi.ac.uk https://www.ebi.ac.uk/arrayexpress/experiments/$1 False ARRAYEXPRESS ArrayExpress nbdc00009 arrayexpress arrayexpress arrayexpress r3d100010222 arrayexpress.platform ArrayExpress Platform https://www.ebi.ac.uk/arrayexpress/ ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results. ^[AEP]-\w{4}-\d+$ A-GEOD-50 https://www.ebi.ac.uk/arrayexpress/arrays/$1 False ARRAYEXPRESS.PLATFORM arrayexpress.platform arrayexpress.platform arraymap ArrayMap https://www.arraymap.org arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. ^[\w\-:,]{3,64}$ icdom:8500_3 mbaudis@me.com https://www.arraymap.org/pgx:$1 False ARRAYMAP arraymap arraymap r3d100012630 arxiv arXiv https://arxiv.org/ arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ 0807.4956v1 https://arxiv.org/abs/$1 False 20434 ARXIV arxiv arxiv arxiv P818 asap A Systematic Annotation Package for Community Analysis of Genomes http://asap.ahabs.wisc.edu/asap/home.php ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. ^[A-Za-z0-9-]+$ ABE-0009634 glasner@svm.vetmed.wisc.edu http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1 False ASAP asap asap asap r3d100010666 ascl Astrophysics Source Code Library http://ascl.net/ The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). ^[0-9\.]+$ 1801.012 aallen@ascl.net http://ascl.net/$1 False ASCL ascl ascl r3d100011865 asin Amazon Standard Identification Number https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182 Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue. ^[0-9]{10}$ 0471491039 https://amzn.com/$1 False ASIN asin asin aspgd.locus Aspergillus Genome Database http://www.aspgd.org/ The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information. ^[A-Za-z_0-9]+$ ASPL0000349247 http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1 False ASPGD.LOCUS aspgd.locus aspgd.locus aspgd.protein AspGD Protein http://www.aspgd.org/ The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information. ^[A-Za-z_0-9]+$ ASPL0000349247 http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1 False ASPGD.PROTEIN aspgd.protein aspgd.protein asrp Arabidopsis Small RNA Project https://asrp.danforthcenter.org/ Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes. ASRP1423 kasschau@cgrb.oregonstate.edu http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1 False asrp astd ASTD http://www.ebi.ac.uk/astd/ Identifier of an object from the ASTD database. ENSG00000136147 http://www.ebi.ac.uk/astd/geneview.html?acc=$1 True 2367 astd ensembl atc Anatomical Therapeutic Chemical Classification System http://www.whocc.no/atc_ddd_index/ The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ A10BA02 whocc@fhi.no http://www.whocc.no/atc_ddd_index/?code=$1 ATC_code|ATTC False ATC 449 ATC ATC 3103 2.16.840.1.113883.6.73 atc atc atc Atc P267 atcc American Type Culture Collection https://www.lgcstandards-atcc.org The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. ^([a-zA-Z]+-)?\d+(\.\d)?$ 11303 https://www.atcc.org/products/$1 ATCC|ATCC number|ATCC(dna)|ATCC(in host) False ATCC ATCC 2.16.840.1.113883.6.77 atcc atcc atcvet Anatomical Therapeutic Chemical Vetinary http://www.whocc.no/atcvet/atcvet_index/ The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. ^Q[A-Z0-9]+$ QJ51RV02 http://www.whocc.no/atcvet/atcvet_index/?code=$1 False ATCVET atcvet atcvet atfdb.family Animal TFDB Family http://www.bioguo.org/AnimalTFDB/family_index.php The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. ^\w+$ CUT http://www.bioguo.org/AnimalTFDB/family.php?fam=$1 False ATFDB.FAMILY atfdb.family atfdb.family ato Amphibian taxonomy http://www.amphibanat.org Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource ^\d{7}$ 0000000 david.c.blackburn@gmail.com http://purl.obolibrary.org/obo/ATO_$1 True ATO ATO ATO ato atol Animal Trait Ontology for Livestock http://www.atol-ontology.com ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production. ^\d{7}$ 0002233 pylebail@rennes.inra.fr http://opendata.inra.fr/ATOL/ATOL_$1 http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl False ATOL ATOL ATOL atol autdb AutDB http://autism.mindspec.org/autdb/ AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. ^[A-Z]+[A-Z-0-9]{2,}$ ADA http://autism.mindspec.org/GeneDetail/$1 False AUTDB autdb autdb authenticus Authenticus ID https://www.authenticus.pt ID of a researcher in Authenticus website ^[A-Z]-[0-9A-Z]{3}-[0-9A-Z]{3}$ P-008-GD6 https://www.authenticus.pt/$1 False P7834 authorea.author Authorea author ID https://www.authorea.com identifier for an author on the Authorea writing service ^[1-9]\d*$ 229233 https://www.authorea.com/users/$1 False P5039 babelon Babelon https://monarch-initiative.github.io/babelon/ Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation. ^[a-z][a-z0-9_]+[a-z0-9]$ translation_language nicolas.matentzoglu@gmail.com https://w3id.org/babelon/$1 False bacdive BacDive https://bacdive.dsmz.de/ BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. ^[0-9]+$ 131392 contact@bacdive.de https://bacdive.dsmz.de/strain/$1 False bacdive bacdive r3d100013060 P2946 bacmap.biog BacMap Biography http://bacmap.wishartlab.com/ BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. ^\d+$ 1050 http://bacmap.wishartlab.com/organisms/$1 False BACMAP.BIOG bacmap.biog bacmap.biog bacmap.map BacMap Map http://bacmap.wishartlab.com/ BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. ^\w+(\_)?\d+(\.\d+)?$ AP011135 http://bacmap.wishartlab.com/maps/$1/index.html False BACMAP.MAP bacmap.map bacmap.map bactibase Bactibase http://bactibase.hammamilab.org Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria. BAC045 ismail.fliss@fsaa.ulaval.ca http://bactibase.hammamilab.org/$1 False bactibase r3d100012755 bams Brain Architecture Knowledge Management System Neuroanatomical Ontology https://bams1.org BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions. True bao BioAssay Ontology http://bioassayontology.org The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. ^\d{7}$ 0002989 sschurer@med.miami.edu http://www.bioassayontology.org/bao#BAO_$1 http://www.bioassayontology.org/bao/bao_complete.owl BAO False BAO BAO BAO bao bao bao BAO bartoc Basic Register of Thesauri, Ontologies & Classifications https://bartoc.org "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries. The main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO)." ^[1-9][0-9]*$ 241 voss@gbv.de https://bartoc.org/en/node/$1 False 2054 P2689 bbkg Blue Brain Project Knowledge Graph https://portal.bluebrain.epfl.ch Blue Brain Project's published data as knowledge graphs and Web Studios. ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$ topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a https://bbp.epfl.ch/nexus/web/studios/public/$1 False bbkg bbtp Blue Brain Project Topological sampling Knowledge Graph https://portal.bluebrain.epfl.ch "Input data and analysis results for the paper ""Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 )." ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$ f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1 False bbtp bcbc Beta Cell Biology Consortium http://www.betacell.org/ One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage] ^\d+$ 4623 https://scicrunch.org/resolver/RRID:BCBC_$1 False nbdc00375 BCBC bcgo Beta Cell Genomics Ontology https://github.com/obi-bcgo/bcgo An application ontology built for beta cell genomics studies. ^\d{7}$ 0000015 jiezheng@pennmedicine.upenn.edu http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1 https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl True BCGO BCGO BCGO BCGO bcgo bcgo BCGO bcio The Behaviour Change Intervention Ontology https://www.humanbehaviourchange.org/ The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation. ^\d{6}$ 040000 srodriguez142857@gmail.com https://w3id.org/BCI-ontology#$1 http://humanbehaviourchange.org/ontology/bcio.owl False BCI-O BCI-O bcio bco Biological Collections Ontology https://github.com/BiodiversityOntologies/bco An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. ^\d{7}$ 0000081 rlwalls2008@gmail.com http://purl.obolibrary.org/obo/BCO_$1 False BCO BCO BCO BCO BCO bco bco BCO bcrc BCRC Strain Collection Catalog https://catalog.bcrc.firdi.org.tw Cell line collections (Providers) ^\d+$ 60316 https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 False BCRC bcrj Banco de Celulas do Rio de Janeiro https://bcrj.org.br/pesquisa/ Cell line collections (Providers) ^\d{4}$ 0278 http://bcrj.org.br/celula/$1 False BCRJ bdgp.est Berkeley Drosophila Genome Project EST database https://www.ncbi.nlm.nih.gov/dbEST/index.html The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). ^\w+(\.)?(\d+)?$ EY223054.1 https://www.ncbi.nlm.nih.gov/nucest/$1 False BDGP.EST bdgp.est bdgp.est flybase.est dbest bdgp.insertion BDGP insertion DB http://flypush.imgen.bcm.tmc.edu/pscreen/ BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. ^\w+$ KG09531 spradling@ciwemb.edu http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1 False BDGP.INSERTION bdgp.insertion bdgp.insertion bdgp bdsc Bloomington Drosophila Stock Center https://bdsc.indiana.edu/about/mission.html The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. ^\d+$ 33607 https://bdsc.indiana.edu/stocks/$1 False bdsc bdsc BDSC beetlebase Tribolium Genome Database -- Insertion http://beetlebase.org/ BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. ^TC\d+$ TC010103 sjbrown@ksu.edu http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 False BEETLEBASE nbdc01820 beetlebase beetlebase beetlebase r3d100010921 begdb Benchmark Energy & Geometry Database http://www.begdb.com The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. ^[0-9]+$ 4214 pavel.hobza@uochb.cas.cz http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 False BEGDB begdb begdb r3d100011166 beiresources BEI Resources https://www.beiresources.org Cell line collections (Providers) MRA-253 https://www.beiresources.org/Catalog/cellBanks/$1.aspx BEI_Resources False BEI_Resources bel Biological Expression Language https://biological-expression-language.github.io/ The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents. 9-1-1 Complex support@bel.bio False bfo Basic Formal Ontology http://ifomis.org/bfo/ The upper level ontology upon which OBO Foundry ontologies are built. ^\d{7}$ 0000001 phismith@buffalo.edu http://purl.obolibrary.org/obo/BFO_$1 False BFO BFO BFO BFO bfo bfo BFO bgee.family Bgee family http://bgee.unil.ch/bgee/bgee Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. ^(ENSFM|ENSGTV:)\d+$ ENSFM00500000270089 http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1 True BGEE.FAMILY bgee.family bgee.family bgee.gene Bgee gene https://www.bgee.org Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. ^[A-Za-z0-9]+$ FBgn0000015 sebastien.moretti@sib.swiss https://www.bgee.org/gene/$1 False BGEE.GENE bgee.gene bgee.gene bgee bgee.organ Bgee organ http://bgee.unil.ch/bgee/bgee Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures. ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$ EHDAA:2185 http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1 True BGEE.ORGAN bgee.organ bgee.organ bgee.stage Bgee stage http://bgee.unil.ch/bgee/bgee Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages. ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$ HsapDO:0000004 http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1 True BGEE.STAGE bgee.stage bgee.stage bibo The Bibliographic Ontology https://bibliontology.com/ 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. authorList fred@fgiasson.com http://purl.org/ontology/bibo/$1 False bibo bibo bido Bibliometric Data Ontology http://www.sparontologies.net/ontologies/bido An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF. CategorialBibliometricData silvio.peroni@unibo.it http://purl.org/spar/bido/$1 False bigg.compartment BiGG Compartment http://bigg.ucsd.edu/compartments/ BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. ^[a-z_A-Z]+$ c http://bigg.ucsd.edu/compartments/$1 False BIGG.COMPARTMENT bigg.compartment bigg.compartment bigg.metabolite BiGG Metabolite http://bigg.ucsd.edu/universal/metabolites BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolites. ^[a-z_A-Z0-9]+$ 12dgr161 http://bigg.ucsd.edu/models/universal/metabolites/$1 False BIGG.METABOLITE bigg.metabolite bigg.metabolite bigg.model BiGG Model http://bigg.ucsd.edu/models BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models. ^[a-z_A-Z0-9]+$ iECABU_c1320 http://bigg.ucsd.edu/models/$1 False BIGG.MODEL bigg.model bigg.model bigg.reaction BiGG Reaction http://bigg.ucsd.edu/universal/reactions BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions. ^[a-z_A-Z0-9]+$ 13GS http://bigg.ucsd.edu/models/universal/reactions/$1 False BIGG.REACTION bigg.reaction bigg.reaction bila Bilateria anatomy http://4dx.embl.de/4DXpress This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource. ^\d{7}$ 0000000 henrich@embl.de http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1 True BILA bila bila 4dxpress bind BIND accession number http://bind.ca Accession number of an entry from the BIND database. 98346 http://www.bind.ca/Action?identifier=bindid&idsearch=$1 True BIND 1129 1 bind bindingdb BindingDB https://www.bindingdb.org BindingDB is the first public database of protein-small molecule affinity data. ^\w\d+$ e999 mgilson@health.ucsd.edu http://www.bindingdb.org/compact/$1 False BINDINGDB bindingdb bindingdb 50 bindingdb r3d100012074 DB-0127 biocarta.pathway BioCarta Pathway https://www.biocarta.com/ BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. ^([hm]\_)?\w+Pathway$ h_aktPathway https://cgap.nci.nih.gov/Pathways/BioCarta/$1 False BIOCARTA.PATHWAY biocarta.pathway biocarta.pathway biocatalogue.service BioCatalogue Service https://www.biocatalogue.org/ The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. ^\d+$ 614 carole.goble@manchester.ac.uk https://www.biocatalogue.org/services/$1 False BIOCATALOGUE.SERVICE biocatalogue.service biocatalogue.service biocatalogue biocompute Biocompute Object https://biocomputeobject.org BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format. ^\d+$ 000001 mazumder@gwu.edu https://biocomputeobject.org/BCO_$1 False biocyc BioCyc collection of metabolic pathway databases http://biocyc.org BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ ECOLI:CYT-D-UBIOX-CPLX pkarp@ai.sri.com http://biocyc.org/getid?id=$1 False BIOCYC 2104 nbdc00252 biocyc biocyc 8 biocyc DB-0005 biofactoid Biofactoid https://biofactoid.org/ Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications. ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ fdb8a927-45c3-48b7-9743-cbb5e16837fa jeffvin.wong@utoronto.ca https://biofactoid.org/document/$1 False biofactoid biogrid BioGRID http://thebiogrid.org/ BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. ^\d+$ 31623 md.tyers@umontreal.ca http://thebiogrid.org/$1 False BIOGRID biogrid biogrid 7 biogrid r3d100010350 DB-0184 biogrid.interaction BioGRID Interactions https://thebiogrid.org/ BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. ^\d+$ 2649230 md.tyers@umontreal.ca https://thebiogrid.org/interaction/$1 False 2628 biogrid biokc BioKC https://wwwen.uni.lu/lcsb BioKC (Biological Knowledge Curation), is a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML). ^bkc[0-9]*$ bkc640 https://biokb.lcsb.uni.lu/fact/$1 False biokc biolegend BioLegend https://www.biolegend.com BioLegend is a life sciences supply vendor. ^\d+$ 3403 https://www.biolegend.com/Default.aspx?ID=6664&productid=$1 False biolink Biolink Model https://biolink.github.io/biolink-model/ A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. ^\S+$ Gene cjmungall@lbl.gov https://w3id.org/biolink/vocab/$1 False BIOLINK BIOLINK biolink biomagresbank BioMagResBank http://www.bmrb.wisc.edu/ A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids. 10046 http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1 False biomagresbank biominder Bio-MINDER Tissue Database https://datalab.rwth-aachen.de/MINDER Database of the dielectric properties of biological tissues. ^[a-z0-9\-]+$ aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 https://datalab.rwth-aachen.de/MINDER/resource/$1 False BIOMINDER biominder biominder biomodels.db BioModels Database https://www.ebi.ac.uk/biomodels/ BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BIOMD0000000048 mhucka@caltech.edu https://www.ebi.ac.uk/biomodels/$1 BIOMD False BIOMODELS.DB biomodels.db biomodels.db biomodels biomodels.kisao Kinetic Simulation Algorithm Ontology https://github.com/SED-ML/KiSAO The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. ^\d+$ 0000057 jonrkarr@gmail.com http://purl.obolibrary.org/obo/KISAO_$1 biomodels.kisao|kisao False KISAO KISAO KISAO biomodels.kisao biomodels.kisao kisao kisao KISAO kisao biomodels.teddy Terminology for Description of Dynamics http://teddyontology.sourceforge.net/ The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. ^\d+$ 0000066 biomodels-net-support@lists.sf.net https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1 http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl teddy False TEDDY BIOMODELS.TEDDY TEDDY biomodels.teddy biomodels.teddy teddy teddy biomodels.vocabulary SBML RDF Vocabulary http://biomodels.net/rdf/vocabulary.rdf Vocabulary used in the RDF representation of SBML models. ^[A-Za-z]+$ rateRule http://biomodels.net/rdf/vocabulary.rdf#$1 False BIOMODELS.VOCABULARY biomodels.vocabulary biomodels.vocabulary bionumbers BioNumbers https://bionumbers.hms.harvard.edu BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. ^\d+$ 104674 https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1 False BIONUMBERS 2660 bionumbers bionumbers bionumbers biopixie biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology http://pixie.princeton.edu/pixie/ 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. 12 http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1 True biopixie bioportal BioPortal http://bioportal.bioontology.org/ BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. ^(\d+)|(\w+)$ 1046 support@bioontology.org http://bioportal.bioontology.org/ontologies/$1 False BIOPORTAL nbdc02144 bioportal bioportal bioportal r3d100012344 bioproject BioProject https://www.ncbi.nlm.nih.gov/bioproject BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. ^PRJ[DEN][A-Z]\d+$ PRJDB3 mizrachi@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/bioproject/?term=$1 False BIOPROJECT bioproject bioproject r3d100013330 Bioproject bioregistry Bioregistry https://bioregistry.io The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database. bioregistry cthoyt@gmail.com https://bioregistry.io/registry/$1 False 18951 bioregistry.collection Bioregistry Collections https://bioregistry.io/collection Manually curated collections of resources stored in the bioregistry ^\d{7}$ 0000001 cthoyt@gmail.com https://bioregistry.io/collection/$1 False bioregistry.registry Bioregistry Metaregistry https://bioregistry.io/metaregistry/ The Bioregistry's meta-registry miriam cthoyt@gmail.com https://bioregistry.io/metaregistry/$1 False bioregistry.schema Bioregistry Schema https://bioregistry.io/schema Schema for the export of the Bioregistry as RDF ^\d{7}$ 0000001 cthoyt@gmail.com https://bioregistry.io/schema/#$1 False biorxiv bioRxiv https://biorxiv.org The bioRxiv is a preprint server for biology ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$ 2022.07.08.499378 https://www.biorxiv.org/content/10.1101/$1 False P3951 biosample BioSample https://www.ebi.ac.uk/biosamples/ The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. ^SAM[NED](\w)?\d+$ SAMEA2397676 mizrachi@ncbi.nlm.nih.gov https://www.ebi.ac.uk/biosamples/sample/$1 biosamples False BIOSAMPLE BioSamples biosample biosample r3d100012828 SAMN Biosample bioschemas BioSchemas https://bioschemas.org 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] Dataset https://bioschemas.org/profiles/$1 bioschema False biosimulations biosimulations https://icahn.mssm.edu/ BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools. ^[a-zA-Z0-9_-]{3,}$ Yeast-cell-cycle-Irons-J-Theor-Biol-2009 https://biosimulations.org/projects/$1 False biosimulations r3d100013361 biosimulators BioSimulators https://biosimulators.org/ BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML). ^[a-zA-Z0-9-_]+$ vcell karr@mssm.edu https://biosimulators.org/simulators/$1 False biosimulators r3d100013432 biostudies BioStudies database https://www.ebi.ac.uk/biostudies/ The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. ^S-[A-Z]{4}[\-\_A-Z\d]+$ S-EPMC6266652 ugis@ebi.ac.uk https://www.ebi.ac.uk/biostudies/studies/$1 False nbdc02279 biostudies biostudies r3d100012627 biosystems BioSystems https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. ^\d+$ 001 lewis.geer@nih.gov https://www.ncbi.nlm.nih.gov/biosystems/$1 False BIOSYSTEMS nbdc00379 biosystems biosystems biosystems r3d100011033 biotools BioTools https://bio.tools/ BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research. ^[-A-Za-z0-9\_]*$ bioregistry haiiu@dtu.dk https://bio.tools/$1 False BIOTOOLS biotools biotools r3d100013668 biozil BIOZIL https://www.biozol.de/en Redistributor of bilogics and biomedical supplies ls-c35719-120 https://www.biozol.de/en/product/$1 False birnlex Biomedical Informatics Research Network Lexicon https://bioportal.bioontology.org/ontologies/BIRNLEX The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. ^\d+$ 2023 wbug@ncmir.ucsd.edu http://uri.neuinfo.org/nif/nifstd/birnlex_$1 False BIRNLEX BIRNLEX biro Bibliographic Reference Ontology http://www.sparontologies.net/ontologies/biro An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively. BibliographicRecord silvio.peroni@unibo.it http://purl.org/spar/biro/$1 False biro bitbucket Bitbucket https://www.atlassian.com/ Bitbucket is a Git-based source code repository hosting service owned by Atlassian. ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$ andreadega/systems-biology-compiler https://bitbucket.org/$1 False bitbucket r3d100013478 bitterdb.cpd BitterDB Compound http://bitterdb.agri.huji.ac.il/dbbitter.php BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. ^\d+$ 46 http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1 False BITTERDB.CPD bitterdb.cpd bitterdb.cpd bitterdb.rec BitterDB Receptor http://bitterdb.agri.huji.ac.il/dbbitter.php BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. ^\d+$ 1 http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1 False BITTERDB.REC bitterdb.rec bitterdb.rec bko SBGN Bricks data and ontology http://www.sbgnbricks.org/ SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way. ^\d+$ 0000204 adrienrougny@gmail.com http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1 False BKO BKO bmrb Biological Magnetic Resonance Data Bank http://www.bmrb.wisc.edu/ BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. ^(bmr|bmse|bmst)?[0-9]{1,6}$ 15000 markley@nmrfam.wisc.edu http://rest.bmrb.wisc.edu/bmrb/$1/html False nbdc00380 bmrb r3d100010191 DB-0256 bmrb.restraint NMR Restraints Grid https://restraintsgrid.bmrb.io/NRG/MRGridServlet The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively. ^\d+$ 28789 https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1 False bold.taxonomy BOLD Systems taxon http://www.boldsystems.org/ The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. ^\d+$ 27267 phebert@uoguelph.ca http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 False BOLD.TAXONOMY bold.taxonomy bold.taxonomy bold P3606 bootstrep Gene Regulation Ontology http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html vlee@ebi.ac.uk http://purl.obolibrary.org/obo/BOOTSTREP_$1 True BOOTSTREP bootstrep bpdb Bio-Pesticides DataBase https://sitem.herts.ac.uk/aeru/bpdb/index.htm Database of biopesticides maintained by the University of Hertfordshire ^\d+$ 2404 https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm False brenda BRENDA Enzyme https://www.brenda-enzymes.org/ BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ 1.1.1.1 D.Schomburg@tu-braunschweig.de https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 False BRENDA brenda brenda 51 brenda r3d100010616 eccode brenda.ligand BRENDA Ligand https://www.brenda-enzymes.de/ligand.php Information for ligands in the BRENDA database. ^\d+$ 278 https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1 False brenda.ligandgroup BRENDA Ligand Group https://www.brenda-enzymes.de/ligand.php Information for ligand groups (chemical classes). ^\d+$ 18030 https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1 False bridgedb BridgeDb Vocabulary https://bridgedb.org A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc. hasPrimaryUriPattern http://vocabularies.bridgedb.org/ops#$1 False broad Broad Fungal Genome Initiative https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. ^S\d+$ S7000002168151102 https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1 False BROAD broad broad bs Biosapiens Protein Feature Ontology https://github.com/The-Sequence-Ontology/SO-Ontologies SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library. ^\d+$ 00042 https://biopragmatics.github.io/providers/bs/$1 https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo False bspo Biological Spatial Ontology https://github.com/obophenotype/biological-spatial-ontology An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. ^\d{7}$ 0000029 cjmungall@lbl.gov http://purl.obolibrary.org/obo/BSPO_$1 https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo False BSPO BSPO BSPO bspo bspo BSPO bto BRENDA Tissue Ontology http://www.brenda-enzymes.org The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. ^\d{7}$ 0000590 c.dudek@tu-braunschweig.de http://purl.obolibrary.org/obo/BTO_$1 BTO False BTO BTO BTO BTO bto bto bto bto BTO bto P5501 bugbase.expt BugBase Expt http://bugs.sgul.ac.uk/E-BUGS BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. ^\d+$ 288 http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1 False BUGBASE.EXPT bugbase.expt bugbase.expt bugbase.protocol BugBase Protocol http://bugs.sgul.ac.uk/E-BUGS BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. ^\d+$ 67 http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=$1 False BUGBASE.PROTOCOL bugbase.protocol bugbase.protocol bykdb Bacterial Tyrosine Kinase Database https://bykdb.ibcp.fr/BYKdb/ The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. ^[A-Z0-9]+$ A0A009E7X8 cozzone@ibcp.fr https://bykdb.ibcp.fr/data/html/annotated/$1.html False BYKDB bykdb bykdb bykdb uniprot c4o Citation Counting and Context Characterisation Ontology http://www.sparontologies.net/ontologies/c4o An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date. InTextReferencePointer silvio.peroni@unibo.it http://purl.org/spar/c4o/$1 False c4o cabri Common Access to Biological Resources and Information Project http://www.cabri.org/ CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ dsmz_mutz-id:ACC 291 paolo.romano@hsanmartino.it http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1] False CABRI 2380 cabri cabri cadsr Cancer Data Standards Registry and Repository https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR. ^[0-9]*$ 3771992 https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1] False cadsr cadsr caloha CALIPHO Group Ontology of Human Anatomy https://github.com/calipho-sib/controlled-vocabulary This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins. ^TS-\d+$ TS-0001 Paula.Duek@sib.swiss https://www.nextprot.org/term/$1 https://raw.githubusercontent.com/calipho-sib/controlled-vocabulary/master/caloha.obo False cameo Continuous Automated Model Evaluation https://cameo3d.org The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. ^[0-9\-_]+$ 2019-08-03_00000089_1 torsten.schwede@unibas.ch https://www.cameo3d.org/sp/targets/target/$1 False CAMEO cameo cameo cao Chemical Analysis Ontology https://champ.stuchalk.domains.unf.edu An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology) ^\d+$ 000064 williams.antony@epa.gov http://champ-project.org/images/ontology/cao.owl#CAO_$1 False CAO CAO cao caps CAPS-DB http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. ^\d+$ 434 http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1 False CAPS caps caps caro Common Anatomy Reference Ontology https://github.com/obophenotype/caro/ The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. ^\d{7}$ 0000000 haendel@ohsu.edu http://purl.obolibrary.org/obo/CARO_$1 http://purl.obolibrary.org/obo/caro.obo False CARO CARO CARO caro caro CARO cas CAS Registry Number https://commonchemistry.cas.org/ CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. ^\d{1,7}\-\d{2}\-\d$ 50-00-0 ajacobs@cas.org https://commonchemistry.cas.org/detail?cas_rn=$1 CASID|CAS_RN|SECONDARY_CAS_RN|cas_id False CAS 000446 1002 2.16.840.1.113883.6.61 cas cas cas P231 casspc Eschmeyer's Catalog of Fishes https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp ^\d+$ 5359 https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1 True cath CATH Protein Structural Domain Superfamily http://www.cathdb.info CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$ 1.10.8.10 c.orengo@ucl.ac.uk http://www.cathdb.info/cathnode/$1 False CATH 2700 nbdc01888 cath cath cath r3d100012629 cath.domain CATH domain http://www.cathdb.info/ The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. ^\w+$ 1cukA01 http://www.cathdb.info/domain/$1 False CATH.DOMAIN 1040 cath.domain cath.domain cath.superfamily CATH superfamily http://www.cathdb.info/ The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ 1.10.10.200 http://www.cathdb.info/cathnode/$1 False CATH.SUPERFAMILY cath.superfamily cath.superfamily cath cattleqtldb Animal Genome Cattle QTL https://www.animalgenome.org/QTLdb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs. ^\d+$ 4685 https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 False CATTLEQTLDB cattleqtldb cattleqtldb cattleqtldb qtldb cazy Carbohydrate Active EnZYmes http://www.cazy.org/ The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ GT10 nicolas.terrapon@univ-amu.fr http://www.cazy.org/$1.html False CAZY cazy cazy cazy r3d100012321 DB-0136 cba Chinese Biological Abstracts http://www.cba.ac.cn CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE. ^\d+$ 375364 https://europepmc.org/article/CBA/$1 False cbioportal The cBioPortal for Cancer Genomics http://www.cbioportal.org The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. ^[a-z0-9\_]+$ laml_tcga_pub gaoj@mskcc.org https://www.cbioportal.org/study/summary?id=$1 False cbioportal cbioportal cc Creative Commons Rights Expression Language https://creativecommons.org/ns The Creative Commons Rights Expression Language (ccREL) lets you describe copyright licenses in RDF. For more information on describing licenses in RDF and attaching those descriptions to digital works, see [ccREL](https://wiki.creativecommons.org/CC_REL) in the [Creative Commons wiki](https://wiki.creativecommons.org/). ^\w+$ Work https://creativecommons.org/ns#$1 False CC cc cc ccdc CCDC Number https://www.ccdc.cam.ac.uk/ The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC. ^\d{6,7}$ 1829126 https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG False ccdc ccds Consensus CDS http://www.ncbi.nlm.nih.gov/CCDS/ The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. ^CCDS\d+\.\d+$ CCDS13573.1 murphyte@ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 False CCDS nbdc00023 ccds ccds ccds Ccds DB-0187 ccf Human Reference Atlas Common Coordinate Framework Ontology https://bioportal.bioontology.org/ontologies/CCF The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA. ^\S+$ extraction_set katy@indiana.edu https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1 False CCF CCF ccf r3d100012657 ccle Cancer Cell Line Encyclopedia Cells https://www.cbioportal.org/study/summary?id=ccle_broad_2019 Datasets around different cancer cell lines generated by the Broad Institute and Novartis BT20_BREAST https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1 ccle.cell False CCLE cco Cell Cycle Ontology http://www.semantic-systems-biology.org/apo The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. ^\w+$ 0000003 kuiper@bio.ntnu.no https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1 https://www.bio.ntnu.no/ontology/CCO/cco.owl https://www.bio.ntnu.no/ontology/CCO/cco.obo False CCO 20461 CCO CCO cco cco cco cco ccrid National Experimental Cell Resource Sharing Platform http://www.cellresource.cn Cell line databases/resources 4201PAT-CCTCC00348 http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1 False CCRID cdao Comparative Data Analysis Ontology https://github.com/evoinfo/cdao a formalization of concepts and relations relevant to evolutionary comparative analysis ^\d{7}$ 0000072 balhoff@renci.org http://purl.obolibrary.org/obo/CDAO_$1 False CDAO CDAO CDAO CDAO cdao cdao CDAO cdd Conserved Domain Database at NCBI https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. ^(cd)?\d{5}$ cd00400 https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 False CDD 2666 nbdc00401 cdd cdd cdd r3d100012041 DB-0214 cdno Compositional Dietary Nutrition Ontology https://cdno.info/ 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. ^\d{7}$ 0000013 landreshdz@gmail.com http://purl.obolibrary.org/obo/CDNO_$1 False CDNO CDNO CDNO cdno cdno CDNO cdpd Canadian Drug Product Database http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). ^\d+$ 63250 http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1 False CDPD cdpd cdpd cdt Current Dental Terminology https://www.ada.org/publications/CDT "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment. Note that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D." ^\d{7}$ 1000001 https://raw.githubusercontent.com/oral-health-and-disease-ontologies/ohd-ontology/f19378ff192b6f9ea16133e85671e8359fc371cd/src/ontology/archive/CDTCodes%20as%20Classes_pruned.owl False 20299 2.16.840.1.113883.6.116 cell_biolabs Cell Biolabs cell line products https://www.cellbiolabs.com Cell line collections (Providers) AKR-270 https://www.cellbiolabs.com/search?keywords=$1 False Cell_Biolabs cell_model_passport Sanger Cell Model Passports https://cellmodelpassports.sanger.ac.uk/ Cell line databases/resources SIDM01262 https://cellmodelpassports.sanger.ac.uk/passports/$1 False Cell_Model_Passport cellbank.australia CellBank Australia https://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/ 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. ab-1-ha https://www.cellbankaustralia.com/$1.html False CBA cellimage Cell Image Library http://cellimagelibrary.org/ The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. ^\d+$ 24801 dorloff@ncmir.ucsd.edu http://cellimagelibrary.org/images/$1 False CELLIMAGE cellimage cellimage cellimage r3d100000023 cellopub Cellosaurus Publication https://web.expasy.org/cellosaurus/ Cellosaurus identifeirs for publications, like Pubmed ^CLPUB\d+$ CLPUB00496 https://web.expasy.org/cellosaurus/cellopub/$1 False CelloPub cellosaurus Cellosaurus https://cellosaurus.org The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines. ^[A-Z0-9]{4}$ 0440 Amos.Bairoch@sib.swiss https://www.cellosaurus.org/CVCL_$1 https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo CVCL False CELLOSAURUS Cellosaurus nbdc02180 cellosaurus cellosaurus r3d100013293 CVCL Cellosaurus P3289 cellosaurus.resource Cellosaurus Registry https://web.expasy.org/cellosaurus/ The set of prefixes used in the Cellosaurus resource 4DN https://bioregistry.io/metaregistry/cellosaurus/$1 False cellrepo Cell Version Control Repository https://www.cellrepo.com/ The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines ^[0-9]+$ 82 https://www.cellrepo.com/repositories/$1 False cellrepo cemo The COVID-19 epidemiology and monitoring ontology https://github.com/NuriaQueralt/covid19-epidemiology-ontology The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response. ^[0-9a-z_-]+$ secondary_attack_rate n.queralt_rosinach@lumc.nl https://biopragmatics.github.io/providers/cemo/$1 https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl False ceph Cephalopod Ontology https://github.com/obophenotype/cephalopod-ontology An anatomical and developmental ontology for cephalopods ^\d{7}$ 0000109 cjmungall@lbl.gov http://purl.obolibrary.org/obo/CEPH_$1 https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo True CEPH CEPH CEPH ceph ceph CEPH cgd Candida Genome Database http://www.candidagenome.org/ The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. ^CAL\d{7}$ CAL0003079 gsherloc@stanford.edu http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 False CGD nbdc00391 cgd cgd cgd r3d100010617 DB-0126 cghdb CGH Data Base http://www.cghtmd.jp/CGHDatabase/index_e.jsp Cell line databases/resources 300165/p13898_2106T http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en False CGH-DB cgnc Chicken Gene Nomenclature Consortium http://birdgenenames.org/cgnc/ Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans) ^\d+$ 10087 fionamcc@arizona.edu http://birdgenenames.org/cgnc/GeneReport?id=$1 BirdBase|CGNC False cgnc r3d100012429 cgsc Coli Genetic Stock Center http://cgsc.biology.yale.edu/index.php The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. ^\d+$ 74 kelly.hughes@utah.edu http://cgsc.biology.yale.edu/Site.php?ID=$1 False CGSC cgsc cgsc cgsc r3d100010585 charprot CharProt http://www.jcvi.org/charprotdb CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. ^CH_\d+$ CH_001923 http://www.jcvi.org/charprotdb/index.cgi/view/$1 False CHARPROT charprot charprot chebi Chemical Entities of Biological Interest http://www.ebi.ac.uk/chebi Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. ^\d+$ 138488 amalik@ebi.ac.uk http://purl.obolibrary.org/obo/CHEBI_$1 CHEBI|CHEBIID|ChEBI False CHEBI 558 CHEBI CHEBI ChEBI 000407 1174 nbdc00027 chebi chebi chebi chebi CHEBI chebi r3d100012626 Chebi P683 chembank ChemBank http://chembank.broad.harvard.edu 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). 1000000 http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1 True CHEMBANK chembank chembl ChEMBL https://www.ebi.ac.uk/chembl ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. ^CHEMBL\d+$ CHEMBL4303805 dmendez@ebi.ac.uk https://www.ebi.ac.uk/chembl/entity/$1 ChEMBL|ChEMBL_ID|chembl False 000412 nbdc02555 chembl chembl r3d100010539 DB-0174 chembl.cell ChEMBL database of bioactive drug-like small molecules - Cell lines section https://www.ebi.ac.uk/chembldb Chemistry resources ^CHEMBL\d+$ CHEMBL3307800 dmendez@ebi.ac.uk https://www.ebi.ac.uk/chembl/cell_line_report_card/$1 ChEMBL-Cells False ChEMBL-Cells chembl chembl.compound ChEMBL https://www.ebi.ac.uk/chembldb/ ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. ^CHEMBL\d+$ CHEMBL465070 dmendez@ebi.ac.uk https://www.ebi.ac.uk/chembl/compound/inspect/$1 False CHEMBL.COMPOUND 2646 chembl.compound chembl.compound ChemblCompound P592 chembl chembl.target ChEMBL target https://www.ebi.ac.uk/chembldb/ ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. ^CHEMBL\d+$ CHEMBL3467 dmendez@ebi.ac.uk https://www.ebi.ac.uk/chembl/target/inspect/$1 ChEMBL-Targets False CHEMBL.TARGET ChEMBL-Targets chembl.target chembl.target ChemblTarget chembl chemdb ChemDB http://cdb.ics.uci.edu/ ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. ^\d+$ 3966782 pfbaldi@uci.edu http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 False CHEMDB chemdb chemdb chemdb chemidplus ChemIDplus https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. ^\d+\-\d+\-\d+$ 57-27-2 https://chem.nlm.nih.gov/chemidplus/rn/$1 ChemIDplus False CHEMIDPLUS 2658 nbdc01837 chemidplus chemidplus chemidplus cheminf Chemical Information Ontology https://github.com/semanticchemistry/semanticchemistry The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals. ^\d{6}$ 000410 egon.willighagen@gmail.com http://purl.obolibrary.org/obo/CHEMINF_$1 https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl False CHEMINF CHEMINF CHEMINF cheminf cheminf cheminf CHEMINF chemrof Chemical Entity Materials and Reactions Ontological Framework https://chemkg.github.io/chemrof/ CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof FullySpecifiedAtom cjmungall@lbl.gov https://chemkg.github.io/chemrof/$1 False CHEMROF CHEMROF chemspider ChemSpider http://www.chemspider.com/ ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. ^\d+$ 56586 pencehe@oneonta.edu http://www.chemspider.com/Chemical-Structure.$1.html ChemSpiderID|Chemspider False CHEMSPIDER 000405 1173 nbdc01863 chemspider chemspider chemspider r3d100010205 P661 chickenqtldb Animal Genome Chicken QTL https://www.animalgenome.org/QTLdb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. ^\d+$ 14362 https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 False CHICKENQTLDB chickenqtldb chickenqtldb chickenqtldb qtldb chictr Chinese Clinical Trial Registry https://www.chictr.org.cn Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website) ^ChiCTR(-[A-Z]+-)?\d+$ ChiCTR2300070727 False chiro ChEBI Integrated Role Ontology https://github.com/obophenotype/chiro 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. vasilevs@ohsu.edu http://purl.obolibrary.org/obo/CHIRO_$1 False CHIRO CHIRO chiro chiro CHIRO chmo Chemical Methods Ontology https://github.com/rsc-ontologies/rsc-cmo CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). ^\d{7}$ 0002902 batchelorc@rsc.org http://purl.obolibrary.org/obo/CHMO_$1 http://purl.obolibrary.org/obo/chmo.obo False CHMO 20509 CHMO CHMO chmo chmo CHMO cido Coronavirus Infectious Disease Ontology https://github.com/cido-ontology/cido The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment. ^\d{7}$ 0000005 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/CIDO_$1 https://github.com/CIDO-ontology/cido/raw/master/cido.owl False CIDO CIDO cido cido CIDO cienciavitae CIÊNCIAVITAE ID https://www.ciencia-id.pt identifier of scientific author in www.cienciavitae.pt ^([0-9A-F]{4}-){2}[0-9A-F]{4}$ 0C1F-DA6C-4B02 https://www.cienciavitae.pt/$1 False P7893 cio Confidence Information Ontology https://github.com/BgeeDB/confidence-information-ontology An ontology to capture confidence information about annotations. ^\d{7}$ 0000040 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/CIO_$1 False CIO CIO CIO cio cio CIO citexplore CiteXplore https://www.ebi.ac.uk/citexplore/ One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes. C6155 maria.taboada@usc.es https://europepmc.org/article/CTX/$1 CTX False citexplore cito Citation Typing Ontology http://www.sparontologies.net/ontologies/cito An ontology that enables characterization of the nature or type of citations, both factually and rhetorically. sharesAuthorInstitutionWith silvio.peroni@unibo.it http://purl.org/spar/cito/$1 False cito civic.aid CIViC Assertion https://civicdb.org/ A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC. ^[0-9]+$ 3 mgriffit@wustl.edu https://civicdb.org/links/assertions/$1 civic.assertion False civic.aid civic civic.did CIViC Disease https://civicdb.org/ Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement. ^[0-9]+$ 46 mgriffit@wustl.edu https://civicdb.org/links/diseases/$1 civic.disease False civic.did civic civic.eid CIViC Evidence https://civicdb.org/ Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract). ^[0-9]+$ 1199 mgriffit@wustl.edu https://civicdb.org/links/evidence/$1 civic.evidence False civic.eid civic civic.gid CIViC gene https://civicdb.org/ A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis ^[0-9]+$ 272 mgriffit@wustl.edu https://civicdb.org/links/gene/$1 civic.gene False civic.gid P11277 civic civic.mpid CIViC Molecular Profile https://civicdb.org/ CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC. ^[0-9]+$ 559 mgriffit@wustl.edu https://civicdb.org/links/molecular_profile/$1 civic.molecularprofile False civic.mpid civic.sid CIViC Source https://civicdb.org/ In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source. ^[0-9]+$ 62 mgriffit@wustl.edu https://civicdb.org/links/sources/$1 civic.source False civic.sid civic civic.tid CIViC Therapy https://civicdb.org/ Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant. ^[0-9]+$ 14 mgriffit@wustl.edu https://civicdb.org/links/drugs/$1 civic.therapy False civic.tid civic civic.vgid CIViC Variant Group https://civicdb.org/ Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance ^[0-9]+$ 16 mgriffit@wustl.edu https://civicdb.org/links/variant_group/$1 civic.variantgroup False civic.vgid civic.vid CIViC variant https://civicdb.org/ CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making. ^[0-9]+$ 12 mgriffit@wustl.edu https://civicdb.org/links/variant/$1 civic.variant False civic.vid P3329 civic cl Cell Ontology https://obophenotype.github.io/cell-ontology/ The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. ^\d{7}$ 0000062 addiehl@buffalo.edu http://purl.obolibrary.org/obo/CL_$1 https://github.com/obophenotype/cell-ontology/raw/master/cl.obo False CL CL CL CL CL cl cl cl cl CL cl P7963 clao Collembola Anatomy Ontology https://github.com/luis-gonzalez-m/Collembola CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda). ^\d{7}$ 0000088 lagonzalezmo@unal.edu.co http://purl.obolibrary.org/obo/CLAO_$1 False CLAO CLAO clao clao CLAO classyfire ClassyFire http://classyfire.wishartlab.com/ ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API. ^\d{7}$ 0004828 http://classyfire.wishartlab.com/tax_nodes/C$1 http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip CHEMONTID False classyfire clb ChecklistBank https://www.checklistbank.org ChecklistBank is an index and repository for taxonomic and nomenclatural datasets ^[0-9]+(LR)?$ 1010 https://www.checklistbank.org/dataset/$1 False clb cldb Cell Line Database http://bioinformatics.hsanmartino.it/hypercldb/indexes.html The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. ^(cl|tum)\d+$ cl3603 http://bioinformatics.hsanmartino.it/hypercldb/$1.html hypercldb False CLDB CLDB cldb cldb clingene ClinGen Allele Registry https://reg.clinicalgenome.org The allele registry provides and maintains identifiers for genetic variants ^CA\d+$ CA981206459 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1 CAID False clinicaltrials ClinicalTrials.gov https://clinicaltrials.gov/ ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries ^NCT\d{8}$ NCT00222573 https://www.clinicaltrials.gov/study/$1 NCT|clinicaltrial|ctgov False CLINICALTRIALS clinicaltrials clinicaltrials clinicaltrials P3098 clinvar ClinVar Variation http://www.ncbi.nlm.nih.gov/clinvar/ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. ^\d+$ 12345 maglott@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 clinvar.variant|clinvar.variation False ClinVarVariant ClinVar 2.16.840.1.113883.6.319 nbdc01514 clinvar clinvar r3d100013331 Clinvar P1929 clinvar.record ClinVar Record http://www.ncbi.nlm.nih.gov/clinvar/ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. ^RCV\d+(\.\d+)?$ RCV000033555.3 http://www.ncbi.nlm.nih.gov/clinvar/$1 False CLINVAR.RECORD clinvar.record clinvar.record clinvar clinvar.submission ClinVar Submission http://www.ncbi.nlm.nih.gov/clinvar/ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. ^SCV\d+(\.\d+)?$ SCV000151292 http://www.ncbi.nlm.nih.gov/clinvar?term=$1 False CLINVAR.SUBMISSION clinvar.submission clinvar.submission clinvar.submitter ClinVar Submitter https://www.ncbi.nlm.nih.gov/clinvar/ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs). ^\d+$ 26957 https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1 False clinvar.submitter clo Cell Line Ontology https://github.com/CLO-Ontology/CLO The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. ^\d{7}$ 0000091 zhengj2007@gmail.com http://purl.obolibrary.org/obo/CLO_$1 CLO False CLO CLO CLO CLO clo clo clo CLO clo P2158 cls Cell Lines Service https://www.cytion.com/ Cell line collections (Providers) 300108/p3934_A-172 https://www.cytion.com/$1 False CLS clyh Clytia hemisphaerica Development and Anatomy Ontology https://github.com/EBISPOT/clyh_ontology Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica. ^\d+$ 1000100 lucas.leclere@obs-vlfr.fr http://purl.obolibrary.org/obo/CLYH_$1 False CLYH CLYH clyh clyh CLYH cmecs Costal and Marine Ecological Classification Standard https://cmecscatalog.org/cmecs Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard. ^\d+$ 595 kate.rose@noaa.gov https://cmecscatalog.org/cmecs/classification/unit/$1.html False CMECS CMECS cmf CranioMaxilloFacial ontology https://code.google.com/p/craniomaxillofacial-ontology/ This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain engelsta@ohsu.edu http://purl.obolibrary.org/obo/CMF_$1 True CMF CMF cmf CMF cmo Clinical measurement ontology http://rgd.mcw.edu/rgdweb/ontology/search.html Morphological and physiological measurement records generated from clinical and model organism research and health programs. ^\d{7}$ 0001350 jrsmith@mcw.edu http://purl.obolibrary.org/obo/CMO_$1 False CMO CMO CMO cmo cmo CMO cmpo Cellular Microscopy Phenotype Ontology http://www.ebi.ac.uk/cmpo CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. ^\d{7}$ 0000435 jupp@ebi.ac.uk http://www.ebi.ac.uk/cmpo/CMPO_$1 False CMPO CMPO cmpo cnrs French National Center for Scientific Research - Research Group Identifier https://annuaire.cnrs.fr identifier for an academic research group issued by the CNRS ^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\d+$ UMR7315 https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u False P4550 co_320 Rice ontology https://cropontology.org/ontology/CO_320/Rice Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables ^\d{7}$ 0000618 j.detras@cgiar.org https://cropontology.org/rdf/CO_320:$1 False CO_320 CO_320 co_320 co_321 Wheat ontology https://cropontology.org/ontology/CO_321/Wheat July 2018 ^\d{7}$ 0000449 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_321:$1 False CO_321 CO_321 co_321 co_322 Maize ontology https://cropontology.org/ontology/CO_322/Maize Maize Trait Dictionary in template 5 - CIMMYT- September 2016 ^\d{7}$ 0000773 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_322:$1 False CO_322 CO_322 co_322 co_323 Barley ontology https://cropontology.org/ontology/CO_323/Barley ICARDA - TDv5 - Sept 2018 ^\d{7}$ 0000252 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_323:$1 False CO_323 CO_323 co_323 co_324 Sorghum ontology https://cropontology.org/ontology/CO_324/Sorghum Sorghum TDv5 - Oct 2019 ^\d{7}$ 0000111 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_324:$1 False CO_324 CO_324 co_324 co_325 Banana ontology https://cropontology.org/ontology/CO_325/Banana Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019 ^\d{7}$ 0000519 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_325:$1 False CO_325 CO_325 co_325 co_326 Coconut ontology https://cropontology.org/ontology/CO_326/Coconut Draft version ^\d{7}$ 0000254 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_326:$1 False CO_326 CO_326 co_326 co_327 Pearl millet ontology http://www.cropontology.org/ontology/CO_327/Pearl%20millet Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 ^\d{7}$ 0000095 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_327:$1 False CO_327 CO_327 co_327 co_330 Potato ontology https://cropontology.org/ontology/CO_330/Potato CIP - potato ontology - december 2018 ^\d{7}$ 0000106 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_330:$1 False CO_330 CO_330 co_330 co_331 Sweet Potato ontology http://www.cropontology.org/ontology/CO_331/Sweet%20Potato Sweet Potato Trait Dictionary in template v5 - CIP - November 2019 ^\d{7}$ 0000088 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_331:$1 False CO_331 CO_331 co_331 co_333 Beet Ontology ontology http://www.cropontology.org/ontology/CO_333/Beet%20Ontology This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017. ^\d+$ 3000045 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_333:$1 False CO_333 CO_333 co_333 co_334 Cassava ontology https://cropontology.org/ontology/CO_334/Cassava Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016 ^\d{7}$ 0000070 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_334:$1 False CO_334 CO_334 co_334 co_335 Common Bean ontology http://www.cropontology.org/ontology/CO_335/Common%20Bean CIAT Common bean trait dictionary - version August 2014 ^\d{7}$ 0000189 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_335:$1 False CO_335 CO_335 co_335 co_336 Soybean ontology https://cropontology.org/ontology/CO_336/Soybean Soybean Trait Dictionary in template v5 - IITA - July 2015 ^\d{7}$ 0000339 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_336:$1 False CO_336 CO_336 co_336 co_337 Groundnut ontology https://cropontology.org/ontology/CO_337/Groundnut Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 ^\d{7}$ 0000054 tm.shah@cgiar.org https://cropontology.org/rdf/CO_337:$1 False CO_337 CO_337 co_337 co_338 Chickpea ontology https://cropontology.org/ontology/CO_338/Chickpea Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015 ^\d{7}$ 0000138 tm.shah@cgiar.org https://cropontology.org/rdf/CO_338:$1 False CO_338 CO_338 co_338 co_339 Lentil ontology https://cropontology.org/ontology/CO_339/Lentil Lentil Trait Dictionary in template v5 - ICARDA - July 2015 ^\d{7}$ 0000032 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_339:$1 False CO_339 CO_339 co_339 co_340 Cowpea ontology https://cropontology.org/ontology/CO_340/Cowpea Cowpea Trait Dictionary in template v5 - IITA - August 2015 ^\d{7}$ 0000639 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_340:$1 False CO_340 CO_340 co_340 co_341 Pigeonpea ontology https://cropontology.org/ontology/CO_341/Pigeonpea Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 ^\d{7}$ 0000140 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_341:$1 False CO_341 CO_341 co_341 co_343 Yam ontology https://cropontology.org/ontology/CO_343/Yam version 2019 - pvs ^\d{7}$ 0100010 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_343:$1 False CO_343 CO_343 co_343 co_345 Brachiaria ontology https://cropontology.org/ontology/CO_345/Brachiaria Brachiaria (forages) ontology TD v5 - Version Oct 2016 ^\d{7}$ 0000127 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_345:$1 False CO_345 CO_345 co_345 co_346 Mungbean ontology https://cropontology.org/ontology/CO_346/Mungbean oct 2016 ^\d{7}$ 0000199 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_346:$1 False CO_346 CO_346 co_346 co_347 Castor bean ontology http://www.cropontology.org/ontology/CO_347/Castor%20bean March 2017 version ^\d{7}$ 0000108 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_347:$1 False CO_347 CO_347 co_347 co_348 Brassica ontology https://cropontology.org/ontology/CO_348/Brassica Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France). ^\d+$ 1100107 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_348:$1 False CO_348 CO_348 co_348 co_350 Oat ontology https://cropontology.org/ontology/CO_350/Oat Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo ^\d{7}$ 0000215 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_350:$1 False CO_350 CO_350 co_350 co_356 Vitis ontology https://cropontology.org/ontology/CO_356/Vitis Grape Ontology including OIV and bioversity descriptors. INRA July 2017 ^\d+$ 4000027 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_356:$1 False CO_356 CO_356 co_356 co_357 Woody Plant Ontology ontology http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE. ^\d+$ 1000290 celia.michotey@inrae.fr https://cropontology.org/rdf/CO_357:$1 False CO_357 CO_357 co_357 co_358 Cotton ontology https://cropontology.org/ontology/CO_358/Cotton Cotton ontology from CottonGen database - June 2019 ^\d{7}$ 0000139 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_358:$1 False CO_358 CO_358 co_358 co_359 Sunflower ontology https://cropontology.org/ontology/CO_359/Sunflower December 2019 ^\d{7}$ 0000947 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_359:$1 False CO_359 CO_359 co_359 co_360 Sugar Kelp trait ontology http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait Sugar Kelp trait ontology ^\d{7}$ 0000071 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_360:$1 False CO_360 CO_360 co_360 co_365 Fababean ontology https://cropontology.org/ontology/CO_365/Fababean developed by ICARDA - Dec 2018 ^\d{7}$ 0000205 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_365:$1 False CO_365 CO_365 co_365 co_366 Bambara groundnut ontology http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut version Dec 2019 ^\d{7}$ 0000072 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_366:$1 False CO_366 CO_366 co_366 co_367 Quinoa Ontology http://cropontology.org/term/CO_367:ROOT Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021 ^\d{7}$ 0000004 helpdesk@cropontology-curationtool.org https://cropontology.org/rdf/CO_367:$1 False CO_367 CO_367 co_370 Apple Ontology http://cropontology.org/term/CO_370:ROOT Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales. ^\d{7}$ 0000890 ekaterina.chuprikova@eurac.edu https://cropontology.org/rdf/CO_370:$1 False CO_370 CO_370 cob Core Ontology for Biology and Biomedicine https://obofoundry.org/COB/ COB brings together key terms from a wide range of OBO projects to improve interoperability. ^\d{7}$ 0000080 bpeters@lji.org http://purl.obolibrary.org/obo/COB_$1 False COB COB cob cob COB coconut COlleCtion of Open Natural ProdUcTs https://coconut.naturalproducts.net "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a ""flat"" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties." ^CNP\d{7}(\.\d+)?$ CNP0171505 https://coconut.naturalproducts.net/compound/coconut_id/$1 False codelink GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release). ^GE\d+$ GE86325 False cog Cluster of orthologous genes https://www.ncbi.nlm.nih.gov/research/cog/ 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. ^COG\d+$ COG0001 cogs@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/research/cog/cog/$1 COG_Cluster False cog cog Cog cog.category COG Categories https://www.ncbi.nlm.nih.gov/research/cog/ Higher-level classifications of COG Pathways K cogs@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1 False cog cog.pathway COG Pathways https://www.ncbi.nlm.nih.gov/research/cog/pathways 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. NAD%20biosynthesis cogs@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1 False cog cohd MIMIC III Database https://github.com/MIT-LCP/mimic-omop 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 False coi COI Catalogue https://coicatalogue.uc.pt/index.php COI Catalogue is a herbarium with c. 800.000 specimens, organised in separate collections due to the research priorities over the years. 63812 coi@bot.uc.pt https://coicatalogue.uc.pt/index.php?t=specimen&COINumber=$1 False col Catalogue of Life https://www.checklistbank.org Identifier of a taxon or synonym in the Catalogue of Life ^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$ 4QHKG https://www.checklistbank.org/dataset/3LR/taxon/$1 False 1915 col col.taiwan Catalogue of Life in Taiwan http://taibnet.sinica.edu.tw/home.php Identifier (name code) for a taxon in the catalogue of life in taiwan ^[1-9]\d{5}$ 431472 https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1 False P3088 colao Coleoptera Anatomy Ontology https://github.com/insect-morphology/colao The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. ^\d{7}$ 0000000 entiminae@gmail.com http://purl.obolibrary.org/obo/COLAO_$1 False COLAO COLAO colao colao COLAO collagenmutdb Collagen Mutation Database http://www.le.ac.uk/genetics/collagen/ 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. COL3A1 https://eds.gene.le.ac.uk/home.php?select_db=$1 False cmd hgnc.symbol colonatlas Colorectal Cancer Atlas http://www.coloncanceratlas.org Cell line databases/resources ALA http://www.coloncanceratlas.org/search_cell_line?cell_line=$1 False ColonAtlas combine.specifications COMBINE specifications https://co.mbine.org/standards/ The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. ^\w+(\-|\.|\w)*$ sed-ml.level-1.version-1 https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md False COMBINE.SPECIFICATIONS combine.specifications combine.specifications come The Bioinorganic Motif Database https://www.flymine.org/come COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif. MOL000160 https://www.flymine.org/come/entry?gn=$1 False come commoncoreontology Common Core Ontologies http://www.ontologyrepository.com "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." DirectiveInformationContentEntity mpjensen@buffalo.edu http://www.ontologyrepository.com/CommonCoreOntologies/$1 False complexportal Complex Portal https://www.ebi.ac.uk/complexportal A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. ^CPX-[0-9]+$ CPX-263 bmeldal@ebi.ac.uk https://www.ebi.ac.uk/complexportal/complex/$1 ComplexPortal False COMPLEXPORTAL complexportal complexportal r3d100013295 DB-0228 P7718 comptox DSSTox substance https://comptox.epa.gov/dashboard The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. ^DTXSID\d+$ DTXSID2021028 https://comptox.epa.gov/dashboard/$1 False COMPTOX comptox comptox P3117 compulyeast Compluyeast-2D-DB http://compluyeast2dpage.dacya.ucm.es/ Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ O08709 http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1 False COMPULYEAST compulyeast compulyeast compluyeast2dpage uniprot conference Conference Ontology http://www.scholarlydata.org/ontology/doc/ 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) isDocumentRelatedTo https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1 https://w3id.org/scholarlydata/ontology/conference-ontology.owl False confident.event ConfIDent Event https://www.confident-conference.org/index.php/Category:Event Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating. ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$ 37af84f2-bfd7-4653-b608-eaff44febba6 Philip.Stroemert@tib.eu https://www.confident-conference.org/index.php/Event:$1 False confident.series ConfIDent Event Series https://www.confident-conference.org/index.php/Category:Event_Series Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating. AAC Philip.Stroemert@tib.eu https://www.confident-conference.org/index.php/Event_Series:$1 False conoserver ConoServer http://www.conoserver.org/ ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. ^\d+$ 2639 d.craik@imb.uq.edu.au http://www.conoserver.org/?page=card&table=protein&id=$1 False CONOSERVER conoserver conoserver DB-0156 conso Curation of Neurodegeneration Supporting Ontology https://pharmacome.github.io/conso/ An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases. ^CONSO\d{5}$ CONSO00010 https://pharmacome.github.io/conso/$1 False cordis.article CORDIS Article https://cordis.europa.eu/ The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020). ^\d+$ 436605 https://cordis.europa.eu/article/id/$1 False cordis.project CORDIS Project https://cordis.europa.eu/ The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020). ^\d+$ 817732 https://cordis.europa.eu/project/id/$1 False coriell Coriell Institute for Medical Research http://ccr.coriell.org/ The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. ^[A-Z]{2}\d+$ GM17027 http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 False Coriell Coriell coriell coriell corrdb CorrDB https://www.animalgenome.org A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies. ^[0-9]+$ 37232 zhu@iastate.edu https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1 False corrdb r3d100011496 corum Comprehensive Resource of Mammalian protein complexes https://mips.helmholtz-muenchen.de/genre/proj/corum/ The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. ^\d+$ 100 andreas.ruepp@helmholtz-muenchen.de https://mips.helmholtz-muenchen.de/corum/?id=$1 False CORUM corum corum 322 corum DB-0224 cosmic COSMIC Gene http://cancer.sanger.ac.uk/cosmic/ COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. ^[A-Z0-9]+$ BRAF jt6@sanger.ac.uk http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1 False COSMIC Cosmic 3264 cosmic cosmic cosmic.cell COSMIC Cell Lines https://cancer.sanger.ac.uk/cell_lines/ COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer ^\d+$ 906801 https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1 False Cosmic-CLP covid19 COVID-19 Surveillance Ontology https://covid19.sfb.uit.no Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease. ^\w+_COVID19_[-\w]+$ SFB_COVID19_MW286762 dylan.mcgagh@magd.ox.ac.uk https://covid19.sfb.uit.no/api/records/$1 False COVID19 COVID19 covid19 covoc CoVoc Coronavirus Vocabulary https://github.com/EBISPOT/covoc The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. ^\d{7}$ 0010034 zmp@ebi.ac.uk http://purl.obolibrary.org/obo/COVOC_$1 https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl https://github.com/EBISPOT/covoc/releases/download/current/covoc.obo False covoc cp Cellular Phenotypes True cpc Cooperative Patent Classification https://worldwide.espacenet.com/classification The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ A01M1/026 https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 False CPC cpc cpc cpt Current Procedural Terminology https://www.aapc.com Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)] ^\d+$ 00103 Intellectual.PropertyServices@ama-assn.org https://www.aapc.com/codes/cpt-codes/$1 ama-cpt False CPT CPT cran The Comprehensive R Archive Network https://cran.r-project.org/ Repository of packages for the R programming language ggplot2 https://cran.r-project.org/web/packages/$1 False P5565 crates Crates.io https://crates.io A repository of software packages written in Rust. curies https://crates.io/crates/$1 False credit CASRAI Contributor Roles Taxonomy https://credit.niso.org/ CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output. ^(conceptualization|data-curation|formal-analysis|funding-acquisition|investigation|methodology|project-administration|resources|software|supervision|validation|visualization|writing-original-draft|writing-review-editing)$ software liz.allen@f1000.com https://credit.niso.org/contributor-roles/$1 False crisprdb CRISPRdb http://crispr.i2bc.paris-saclay.fr/ "Repeated CRISPR (""clustered regularly interspaced short palindromic repeats"") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data." ^[0-9]+$ 551115 Christine.Pourcel@u-psud.fr http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1 False CRISPRDB nbdc02213 crisprdb crisprdb cro Contributor Role Ontology https://github.com/data2health/contributor-role-ontology A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. ^\d{7}$ 0000038 whimar@ohsu.edu http://purl.obolibrary.org/obo/CRO_$1 https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo False CRO CRO CRO cro cro CRO crop2ml CropMRepository http://www.crop2ml.org CropMRespository is a database of soil and crop biophysical process models. ^[0-9]{9}$ 000000001 http://www.crop2ml.org/cropmdb/$1 False crop2ml cryoem Cryo Electron Microscopy ontology http://scipion.i2pc.es/ontology/cryoem Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles ^\d{7}$ 0000052 isanchez@cnb.csic.es http://scipion.i2pc.es/ontology/CRYOEM_$1 False CRYOEM CRYOEM cryoem cryptodb CryptoDB https://cryptodb.org/cryptodb/ CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ cgd7_230 jkissing@uga.edu https://cryptodb.org/cryptodb/app/record/gene/$1 False CRYPTODB nbdc01780 cryptodb cryptodb cryptodb r3d100012265 csa Catalytic Site Atlas https://www.ebi.ac.uk/thornton-srv/databases/CSA/ The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. ^[0-9][A-Za-z0-9]{3}$ 1a05 nickf@ebi.ac.uk https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1 False CSA csa csa csa csd Cambridge Structural Database https://www.ccdc.cam.ac.uk/ The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode. ^[A-Z]{6}(\d{2})?$ PELNAW support@ccdc.cam.ac.uk https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG False csd r3d100010197 csp Computer Retrieval of Information on Science Projects Thesaurus https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains. 2004-2820 af8d@nih.gov http://purl.bioontology.org/ontology/CSP/$1 CRISP|CRISP Thesaurus|CRISP Thesaurus, 2006|CSP2005 True CRISP CRISP 2.16.840.1.113883.6.120 192 cst Cell Signaling Technology Pathways http://www.cellsignal.com/pathways/index.html Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. ^[A-Za-z0-9_-]+$ Akt_PKB http://www.cellsignal.com/reference/pathway/$1.html False CST 2.16.840.1.113883.6.62 cst cst 193 cst.ab Cell Signaling Technology Antibody http://www.cellsignal.com/catalog/index.html Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. ^\d+$ 3305 http://www.cellsignal.com/products/$1.html False CST.AB cst.ab cst.ab cst cstr Common Science and Technology Resources https://www.cstr.cn/en/ CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. ^\w{5}\.\d{2}\..*$ 31253.11.sciencedb.j00001.00123 https://cstr.cn/$1 False cstr ctcae Common Terminology Criteria for Adverse Events https://evs.nci.nih.gov/ftp1/CTCAE/About.html The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI). ^E\d+$ E12768 ncictcaehelp@mail.nih.gov CTCAE True CTCAE CTCAE ctd.chemical CTD Chemical http://ctdbase.org/ 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. ^[CD]\d+$ D001151 http://ctdbase.org/detail.go?type=chem&acc=$1 False CTD.CHEMICAL ctd.chemical ctd.chemical ctd mesh ctd.disease CTD Disease http://ctdbase.org/ The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. ^D\d+$ D053716 http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 False CTD.DISEASE ctd.disease ctd.disease ctd mesh ctd.gene CTD Gene http://ctdbase.org/ The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. ^\d+$ 101 apdavis3@ncsu.edu http://ctdbase.org/detail.go?type=gene&acc=$1 False CTD.GENE ctd.gene ctd.gene DB-0140 ctd ncbigene cteno Ctenophore Ontology https://github.com/obophenotype/ctenophore-ontology An anatomical and developmental ontology for ctenophores (Comb Jellies) ^\d{7}$ 0000047 cjmungall@lbl.gov http://purl.obolibrary.org/obo/CTENO_$1 https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo False CTENO CTENO CTENO cteno cteno CTENO ctis Clinical Trials Information System https://euclinicaltrials.eu/ This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage) ^\d{4}-\d+-\d+-\d+$ 2023-503698-40-00 https://euclinicaltrials.eu/app/#/view/$1 False cto Clinical Trials Ontology https://github.com/ClinicalTrialOntology/CTO/ The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. ^\d{7}$ 0000022 alpha.tom.kodamullil@scai.fraunhofer.de http://purl.obolibrary.org/obo/CTO_$1 False CTO CTO cto cto CTO ctri India Clinical Trials Registry https://ctri.nic.in "The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage) Note that the identifier in this semantic space is not the one used in the webpages" ^CTRI/\d{4}/\d{2,3}/\d+$ CTRI/2023/04/052053 https://trialsearch.who.int/Trial2.aspx?TrialID=$1 False cubedb Cube db http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. ^[A-Za-z_0-9]+$ AKR http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/ True CUBEDB nbdc02094 cubedb cubedb cutg Codon Usage Tabulated from GenBank http://www.kazusa.or.jp/codon/ 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. 9606 http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1 False cutg ncbitaxon cvdo Cardiovascular Disease Ontology https://github.com/OpenLHS/CVDO An ontology to describe entities related to cardiovascular diseases ^\d{7}$ 0000546 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/CVDO_$1 False CVDO CVDO CVDO cvdo cvdo CVDO cvx Vaccine administered code set https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records. ^\d+$ 54 https://biopragmatics.github.io/providers/cvx/$1 False 2.16.840.1.113883.6.59 d1id DataONE https://www.dataone.org DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences. ^\S+$ 00030692-0FE1-4A1B-955E-A2E55D659267 https://cn.dataone.org/cn/v2/resolve/{$1} False D1ID d1id d1id dailymed DailyMed https://dailymed.nlm.nih.gov/dailymed/ DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read. ^[A-Za-z0-9-]+$ 973a9333-fec7-46dd-8eb5-25738f06ee54 https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1 False DAILYMED dailymed dailymed dailymed dandi Distributed Archives for Neurophysiology Data Integration https://dandiarchive.org/ "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders." ^\d{6}(\/\d+\.\d+\.\d+)?$ 000017 yoh@dartmouth.edu https://dandiarchive.org/dandiset/$1 False dandi r3d100013638 darc Database of Aligned Ribosomal Complexes http://darcsite.genzentrum.lmu.de/darc/index.php DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. ^\d+$ 1250 daniel.wilson@uni-hamburg.de http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1 False DARC darc darc dashr Database of small human noncoding RNAs http://lisanwanglab.org/DASHR/ DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ hsa-mir-200a dashr@lisanwanglab.org http://lisanwanglab.org/DASHR/entry/$1 False DASHR dashr dashr dashr.expression DASHR expression https://dashr1.lisanwanglab.org/show-expression-table.php?start=0 DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression. ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ hsa-mir-200a https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable False DASHR.EXPRESSION dashr.expression dashr.expression datacite DataCite Ontology http://www.sparontologies.net/ontologies/datacite An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF. AgentIdentifierScheme silvio.peroni@unibo.it http://purl.org/spar/datacite/$1 False DATACITE DATACITE datacommons Data Commons https://datacommons.org A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces. Gene https://datacommons.org/browser/$1 False datanator.gene Datanator Gene https://datanator.info/ Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. ^K[0-9]+$ K00973 https://www.datanator.info/gene/$1 False datanator.gene datanator datanator.metabolite Datanator Metabolite https://datanator.info/ Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. ^[A-Z\-]+$ OUYCCCASQSFEME-MRVPVSSYSA-N https://www.datanator.info/metabolite/$1 False datanator.metabolite datanator datanator.reaction Datanator Reaction https://icahn.mssm.edu/ " Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms." ^.*?--%3E.*?$ XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N https://datanator.info/reaction/$1 False datanator.reaction datf Database of Arabidopsis Transcription Factors http://datf.cbi.pku.edu.cn/ DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. ^AT[1-5]G\d{5}(\.\d+)?$ AT1G01030.1 http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1 True DATF datf datf 518 datf dbd Transcription Factor Database http://www.transcriptionfactor.org/ The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. ^\d+$ 0045310 http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD False DBD 2716 dbd dbd 496 dbd dbest EST database maintained at the NCBI. https://www.ncbi.nlm.nih.gov/nucest "The dbEST contains sequence data and other information on ""single-pass"" cDNA sequences, or ""Expressed Sequence Tags"", from a number of organisms." ^([A-Z]+)?\d+(\.\d+)?$ BP100000 tmjlowe@ucsc.edu https://www.ncbi.nlm.nih.gov/nucest/$1 False DBEST 1105 nbdc00413 dbest dbest dbest r3d100010648 dbg2introns DBG2 Introns http://webapps2.ucalgary.ca/~groupii/ The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ Cu.me.I1 zimmerly@ucalgary.ca http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1 False DBG2INTRONS dbg2introns dbg2introns mgiid dbgap Database of Genotypes and Phenotypes https://www.ncbi.nlm.nih.gov/gap/ The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. ^phs[0-9]{6}(.v\d+.p\d+)?$ phs000768.v2.p1 feolo@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1 False DBGAP dbGAP nbdc00414 dbgap dbgap dblp.author DBLP author ID https://dblp.org/ identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/) 199/2168 https://dblp.org/pid/$1 False P2456 dbmhc Database of human Major Histocompatibility Complex https://www.ncbi.nlm.nih.gov/gv/mhc/ Cell line databases/resources ^\d+$ 48439 True dbMHC nbdc01831 dbo DBPedia Ontology https://dbpedia.org/ontology 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. careerPrizeMoney https://dbpedia.org/ontology/$1 False dbo dbprobe NCBI Probe database Public registry of nucleic acid reagents https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. ^\d+$ 1000000 https://www.ncbi.nlm.nih.gov/probe/?term=$1 False DBPROBE 2719 dbprobe dbprobe dbprobe dbsnp dbSNP Reference SNP number https://www.ncbi.nlm.nih.gov/snp/ The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. ^rs\d+$ rs121909098 pruitt@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/snp/$1 False dbSNP dbSNP 1106 2.16.840.1.113883.6.284 nbdc00206 dbsnp dbsnp dbsnp r3d100010652 Dbsnp DB-0013 P6861 dbvar.study Database of Genomic Structural Variation - Study https://www.ncbi.nlm.nih.gov/dbvar Studies in dbVar. nstd102 https://www.ncbi.nlm.nih.gov/dbvar/studies/$1 dbvar.studies False dbvar.variant Database of Genomic Structural Variation - Variant https://www.ncbi.nlm.nih.gov/dbvar Variants in dbVar. nsv3875336 https://www.ncbi.nlm.nih.gov/dbvar/variants/$1 dbvar.variants False dc Dublin Core Elements (1.1) https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ "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))." contributor kdurante@stanford.edu http://purl.org/dc/elements/1.1/$1 dc.elements|dc11|dce True dcelements dc DC dce dc dc11 dc_cl Dendritic cell http://www.dukeontologygroup.org/Projects.html ^\d{7}$ 0000003 Lindsay.Cowell@utsouthwestern.edu http://purl.obolibrary.org/obo/DC_CL_$1 True DC_CL dc_cl dcat Data Catalog https://www.w3.org/ns/dcat DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web Dataset kdurante@stanford.edu http://www.w3.org/ns/dcat#$1 False DCAT dcat DCAT dcat dcat dcterms Dublin Core Metadata Initiative Terms https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ 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. title futo@stanford.edu http://purl.org/dc/terms/$1 dc.terms|dct False dcterms dcterms DCTERMS dcterms dcterms dcterms dctypes Dublin Core Types https://dublincore.org/specifications/dublin-core/dcmi-terms/ 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. Collection http://purl.org/dc/dcmitype/$1 False dctypes ddanat Dictyostelium discoideum anatomy http://dictybase.org/ A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum. ^\d{7}$ 0000006 pfey@northwestern.edu http://purl.obolibrary.org/obo/DDANAT_$1 False DDANAT DDANAT DDANAT ddanat ddanat DDANAT ddanat ddc Dewey Decimal Classification http://www.oclc.org/dewey/ The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system. ^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\.[0-9]+(-[0-9]{3}\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$ 325.4 False 241 ddinter.drug Curated Drug-Drug Interactions Database - Drug http://ddinter.scbdd.com 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. ^DDInter\d+$ DDInter20 oriental-cds@163.com http://ddinter.scbdd.com/ddinter/drug-detail/$1 False ddinter.interaction Curated Drug-Drug Interactions Database - Interaction http://ddinter.scbdd.com Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety. ^\d+$ 1122888 oriental-cds@163.com http://ddinter.scbdd.com/ddinter/interact/$1 False ddpheno Dictyostelium discoideum phenotype ontology http://dictybase.org/ A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. ^\d{7}$ 0001417 pfey@northwestern.edu http://purl.obolibrary.org/obo/DDPHENO_$1 https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo False DDPHENO DDPHENO DDPHENO ddpheno ddpheno DDPHENO debio Decentralized Biomedical Ontology https://biopragmatics.github.io/debio A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON. ^\d{7}$ 0000001 cthoyt@gmail.com https://biopragmatics.github.io/debio/$1 https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.owl https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.obo DeBiO False decipher DECIPHER CNV Syndromes https://www.deciphergenomics.org/ CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms ^\d+$ 1 ganesh.swaminathan@sanger.ac.uk https://www.deciphergenomics.org/syndrome/$1 False DECIPHER degradome Degradome Database http://degradome.uniovi.es/ The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. ^[AMCST][0-9x][0-9]$ Ax1 http://degradome.uniovi.es/cgi-bin/protease/$1 False DEGRADOME degradome degradome deo Discourse Elements Ontology http://www.sparontologies.net/ontologies/deo 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. Reference silvio.peroni@unibo.it http://purl.org/spar/deo/$1 False deo depmap DepMap Cell Lines https://depmap.org/portal Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells. ^ACH-\d+$ ACH-000001 https://depmap.org/portal/cell_line/$1 False DepMap depod Human Dephosphorylation Database http://www.depod.bioss.uni-freiburg.de The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. ^[A-Z0-9]+$ PTPN1 depod@embl.de http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 False DEPOD depod depod 584 r3d100011936 DB-0190 hgnc.symbol dermo Human Dermatological Disease Ontology https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders ^\d{7}$ 0000000 pns12@hermes.cam.ac.uk http://purl.obolibrary.org/obo/DERMO_$1 False DERMO DERMO dev.ga4ghdos Development Data Object Service http://github.com/ga4gh/data-object-service-schemas Assists in resolving data across cloud resources. ^[a-zA-Z0-9\-:#\.]+$ 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00 https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1 False DEV.GA4GHDOS dev.ga4ghdos dev.ga4ghdos devtox DevTox https://www.devtox.org/ The DevTox Project harmonizes the nomenclature used to describe developmental anomalies in laboratory animals, assists in the visual recognition of developmental anomalies with the aid of photographs, and provides a historical control database of developmental effects in laboratory animals. ^\d+$ 311935300 rupert.kellner@item.fraunhofer.de https://www.devtox.org/nomenclature/ml_manus.php?mno=$1 False dg.4503 BioData Catalyst https://gen3.biodatacatalyst.nhlbi.nih.gov Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ 0000ffeb-36e0-4a29-b21d-84423bda979d https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1 False dg.4503 dg.4dfc NCI Data Commons Framework Services https://nci-crdc.datacommons.io/ DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ 81944ba1-81d0-436e-8552-33d77a27834b https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1 False dg.4dfc dg.6vts JCOIN https://jcoin.datacommons.io Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ 2afacf00-9a1d-4d80-8c32-69d3923d3913 https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1 False dg.6vts dg.anv0 Anvil https://gen3.theanvil.io DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$ 00077f1c-c45a-47ba-8e6c-1bf6b6b43fce https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1 False dg.anv0 dg.f82a1a Kids First https://kidsfirstdrc.org Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ 00026f50-858a-446b-8ed9-b0e3ecd7b20e https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1 False dg.f82a1a dg5b0d BloodPAC https://data.bloodpac.org/. The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources. ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ 00000d53-99bc-4d3e-8ed7-6dc358baccb7 https://data.bloodpac.org/ga4gh/drs/v1/objects/$1 False dg.5b0d dggr Kyoto Stock Center http://kyotofly.kit.jp/cgi-bin/stocks/data_search.cgi Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID] ^\d+$ 918902 https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=$1 False DGGR dgrc Drosophila Genomics Resource Center https://dgrc.bio.indiana.edu/cells/Catalog Cell line collections (Providers) ^\d+$ 215 https://dgrc.bio.indiana.edu/product/View?product=$1 False DGRC nbdc00048 dhba Developing Human Brain Atlas https://www.brainspan.org/ A controlled vocabulary to support the study of transcription in the developing human brain ^\d+$ 10153 https://biopragmatics.github.io/providers/dhba/$1 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dhba.obo False dialnet.article Dialnet article ID https://dialnet.unirioja.es identifier of an article in Dialnet 262393 https://dialnet.unirioja.es/servlet/articulo?codigo=$1 False P1610 dialnet.author Dialnet author ID https://dialnet.unirioja.es identifier of an author in Dialnet ^[1-9]\d*$ 241889 https://dialnet.unirioja.es/servlet/autor?codigo=$1 False P1607 dialnet.book Dialnet book ID https://dialnet.unirioja.es identifier of a book in Dialnet 187021 https://dialnet.unirioja.es/servlet/libro?codigo=$1 False P1608 dialnet.journal Dialnet journal ID http://dialnet.unirioja.es identifier of a journal in Dialnet ^[1-9]\d{0,6}$ 1119 https://dialnet.unirioja.es/servlet/revista?codigo=$1 False P1609 dicom DICOM Controlled Terminology http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html DICOM Controlled Terminology ^\d+$ 109082 dclunie@dclunie.com http://dicom.nema.org/resources/ontology/DCM/$1 False DCM 1.2.840.10008.2.16.4 dicom dictybase dictyBase http://dictybase.org A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics DDB0191090 pfey@northwestern.edu http://dictybase.org/gene/$1 dictyBase False dictyBase nbdc00420 dictybase r3d100010586 DB-0015 dictybase.est dictyBase Expressed Sequence Tag http://dictybase.org/ The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. ^DDB\d+$ DDB0016567 http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1 False DICTYBASE.EST dictybase.est dictybase.est dictybase dictybase.gene Dictybase Gene http://dictybase.org/ The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. ^DDB_G\d+$ DDB_G0267522 http://dictybase.org/gene/$1 False DICTYBASE.GENE dictybase.gene dictybase.gene dictybase did Decentralized Identifier https://w3c-ccg.github.io/did-spec/ DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary. ^[a-z0-9]+:[A-Za-z0-9.\-:]+$ sov:WRfXPg8dantKVubE3HX8pw https://uniresolver.io/#did:$1 False did did dideo Drug-drug Interaction and Drug-drug Interaction Evidence Ontology https://github.com/DIDEO/DIDEO The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology ^\d{8}$ 00000180 mbrochhausen@gmail.com http://purl.obolibrary.org/obo/DIDEO_$1 False DIDEO DIDEO DIDEO dideo dideo DIDEO dinto The Drug-Drug Interactions Ontology http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto A formal represention for drug-drug interactions knowledge. maria.herrero@kcl.ac.uk http://purl.obolibrary.org/obo/DINTO_$1 True DINTO DINTO DINTO dinto DINTO dip Database of Interacting Proteins https://dip.doe-mbi.ucla.edu/ The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions ^DIP(\:)?\-\d{1,}[ENXS]$ DIP-743N david@mbi.ucla.edu https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 False DIP 2616 nbdc00049 dip dip 3 dip r3d100010670 DB-0016 discoverx DiscoverX cell line products https://www.discoverx.com/product-category/cell-lines-primary-cells/ Cell line collections (Providers) 95-0166C6 https://www.discoverx.com/?post_type=product&s=$1 False DiscoverX disdriv Disease Drivers Ontology http://www.disease-ontology.org Drivers of human diseases including environmental, maternal and social exposures. ^\d+$ 0000000 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/DISDRIV_$1 False DISDRIV DISDRIV disdriv disdriv DISDRIV diseaseclass Disease Class Legacy disease classes that later became MONDO ^\d{7}$ 0000598 https://biopragmatics.github.io/providers/diseaseclass/$1 https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo True diseasesdb Diseases Database http://www.diseasesdatabase.com/ The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities. ^\d+$ 1784 https://www.diseasesdatabase.com/ddb$1.htm False P557 disprot DisProt https://disprot.org/ DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. ^DP\d{5}$ DP00003 silvio.tosatto@unipd.it https://disprot.org/$1 False DISPROT 2723 nbdc01798 disprot disprot disprot r3d100010561 DB-0017 disprot.region DisProt region https://www.disprot.org DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature. ^DP\d{5}r\d{3}$ DP00086r013 https://www.disprot.org/$1 False disprot.region disprot dlxb Linear double stranded DNA sequences https://doulix.com DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences. ^[A-Z0-9]{6,7}$ 6VDC956 https://doulix.com/biomodules/$1 False dlxb dlx dlxc Circular double stranded DNA sequences composed https://doulix.com DOULIX lab-tested standard biological parts, in this case, full length constructs. ^[A-Z0-9]{6,7}$ M77F7JM https://doulix.com/constructs/$1 False dlxc dlx dmba Developing Mouse Brain Atlas https://developingmouse.brain-map.org/ A controlled vocabulary to support the study of transcription in the developing mouse brain ^\d+$ 15567 https://biopragmatics.github.io/providers/dmba/$1 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo False doap Description of a Project https://github.com/ewilderj/doap/wiki DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects. Project edd@usefulinc.com http://usefulinc.com/ns/doap#$1 False doap doap dockerhub.repo Docker Hub repository https://hub.docker.com/ Docker repository hosted on Docker Hub gitea/gitea https://hub.docker.com/r/$1 False P8778 dockerhub.user DockerHub User https://hub.docker.com/ A user in DockerHub cthoyt https://hub.docker.com/u/$1 False doco Document Components Ontology http://www.sparontologies.net/ontologies/doco An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix). Paragraph silvio.peroni@unibo.it http://purl.org/spar/doco/$1 False doco doi Digital Object Identifier https://www.doi.org/ The Digital Object Identifier System is for identifying content objects in the digital environment. ^10.\d{2,9}/.*$ 10.1038/s41597-022-01807-3 https://doi.org/$1 False DOI DOI 1188 doi doi doi P356 doid Human Disease Ontology http://www.disease-ontology.org The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. ^\d+$ 0110974 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/DOID_$1 https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo do False DOID 576 DOID DOID nbdc00261 doid doid doid doid DOID do Doid P699 dolce Descriptive Ontology for Linguistic and Cognitive Engineering http://www.loa.istc.cnr.it/dolce/overview.html DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use. True dommino Database of Macromolecular Interactions http://korkinlab.org/dommino DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. ^[0-9][A-Za-z0-9]{3}$ 2GC4 http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1 False DOMMINO dommino dommino 423 door Database for Prokaryotic Operons http://csbl.bmb.uga.edu/DOOR/operon.php DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. ^\d+$ 1398574 http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1 False DOOR door door door r3d100014113 doqcs.model Database of Quantitative Cellular Signaling: Model http://doqcs.ncbs.res.in/ The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. ^\d+$ 57 bhalla@ncbs.res.in http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1 False DOQCS.MODEL doqcs.model doqcs.model doqcs.model doqcs doqcs.pathway Database of Quantitative Cellular Signaling: Pathway http://doqcs.ncbs.res.in/ The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. ^\d+$ 131 bhalla@ncbs.res.in http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1 False DOQCS.PATHWAY doqcs.pathway doqcs.pathway doqcs.pathway doqcs dpo Drosophila Phenotype Ontology http://purl.obolibrary.org/obo/fbcv An ontology for the description of Drosophila melanogaster phenotypes. cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBcv_$1 False DPO DPO dpo dpo DPO fbcv dpv Description of Plant Viruses http://www.dpvweb.net/ Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. ^\d+$ 100 mike.adams@bbsrc.ac.uk http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1 False DPV nbdc02410 dpv dpv dpv dpvweb dragondb.allele DragonDB Allele http://www.antirrhinum.net/ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. ^\w+$ cho http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele True DRAGONDB.ALLELE dragondb.allele dragondb.allele dragondb dragondb.dna DragonDB DNA http://www.antirrhinum.net/ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. ^\d\w+$ 3hB06 http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA True DRAGONDB.DNA dragondb.dna dragondb.dna dragondb dragondb.locus DragonDB Locus http://www.antirrhinum.net/ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. ^\w+$ DEF http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus True DRAGONDB.LOCUS dragondb.locus dragondb.locus dragondb dragondb.protein DragonDB Protein http://www.antirrhinum.net/ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. ^\w+$ AMDEFA http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide True DRAGONDB.PROTEIN dragondb.protein dragondb.protein dragondb drduke Dr. Duke's Phytochemical and Ethnobotanical Databases chemical https://phytochem.nal.usda.gov/phytochem/search/list identifier for chemicals linked to information on occurrence in plants 19 https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1 False P10074 drks German Clinical Trials Register http://drks.de The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website) ^DRKS\d+$ DRKS00031815 https://drks.de/search/en/trial/$1 False dron The Drug Ontology https://github.com/ufbmi/dron An ontology to support comparative effectiveness researchers studying claims data. ^\d{8}$ 00023232 hoganwr@gmail.com http://purl.obolibrary.org/obo/DRON_$1 http://purl.obolibrary.org/obo/dron.obo False DRON DRON DRON dron dron DRON drsanv0 AnVIL DRS https://www.genome.gov/ This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. ^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$ v2_1b0f158a-86e2-3887-b990-89e3cf2d9082 https://data.terra.bio/ga4gh/drs/v1/objects/$1 False drs.anv0 drsc Drosophila RNAi Screening Center http://flyrnai.org/ The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. ^DRSC\d+$ DRSC05221 http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1 False DRSC drsc drsc drugbank DrugBank http://www.drugbank.ca The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. ^DB\d{5}$ DB14938 david.wishart@ualberta.ca http://www.drugbank.ca/drugs/$1 DRUGBANK_ID|DrugBank False 18377 DrugBank DrugBank 000406 2326 nbdc01071 drugbank drugbank 221 drugbank r3d100010544 Drugbank DB-0019 P715 drugbank.bioentity DrugBank Target v4 http://www.drugbank.ca/targets The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database. ^BE\d{7}$ BE0000048 https://go.drugbank.com/bio_entities/$1 drugbank.target|drugbankv4.target False DRUGBANKV4.TARGET drugbankv4.target drugbankv4.target drugbank drugbank.category DrugBank Drug Category https://go.drugbank.com/categories Close to 5K Categorizations for drugs, similar to ATCC. ^DBCAT\d+$ DBCAT000600 https://www.drugbank.ca/categories/$1 False drugbank drugbank.condition DrugBank Condition https://go.drugbank.com Indications and other conditions in drugbank ^DBCOND\d+$ DBCOND0066902 https://go.drugbank.com/indications/$1 False drugbank.metabolite DrugBank Metabolite https://go.drugbank.com Metabolites in drugbank ^DBMET\d+$ DBMET02292 https://go.drugbank.com/metabolites/$1 False drugbank.reaction DrugBank Reaction https://go.drugbank.com Reactions in drugbank ^\d+$ 1537 https://go.drugbank.com/reactions/$1 False drugbank.salt DrugBank Salts http://www.drugbank.ca DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. ^DBSALT\d{6}$ DBSALT001211 https://go.drugbank.com/salts/$1 False drugbank drugcentral Drug Central http://drugcentral.org DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. ^\d+$ 307 toprea@salud.unm.edu http://drugcentral.org/drugcard/$1 Drug_Central False nbdc02192 drugcentral DB-0239 P11198 dsm4 Diagnostic and Statistical Manual of Mental Disorders (4th Edition) https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000) A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia] ^\d+\.\d+$ 315.1 dsm-iv False 2.16.840.1.113883.6.126 P663 dsm5 Diagnostic and Statistical Manual of Mental Disorders (5th Edition) https://en.wikipedia.org/wiki/DSM-5 A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia] ^\d{3}\.\d{2}$ 312.33 dsm-v False 2.16.840.1.113883.6.344 P1930 dsmz Deutsche Sammlung von Mikroorganismen und Zellkulturen https://www.dsmz.de "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" ^(ACC|DSM|NC|PC|RT|AS|PV)-\d+$ ACC-1 https://www.dsmz.de/collection/catalogue/details/culture/$1 DSMZCellDive False DSMZCellDive r3d100010219 dso Data Science Ontology https://www.datascienceontology.org/ 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. classification-model evan@epatters.org https://www.datascienceontology.org/concept/$1 False dto Drug Target Ontology https://github.com/DrugTargetOntology/DTO DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors. ^\d+$ 90000018 sschurer@med.miami.edu http://www.drugtargetontology.org/dto/DTO_$1 False DTO DTO duo Data Use Ontology https://github.com/EBISPOT/DUO DUO is an ontology which represent data use conditions. ^\d{7}$ 0000046 mcourtot@gmail.com http://purl.obolibrary.org/obo/DUO_$1 False DUO DUO DUO duo duo DUO eaglei eagle-i https://hawaii.eagle-i.net Discovery tool for biomedical research resources available at institutions throughout the U.S. 0000012b-5661-2f63-2f73-b43980000000 http://hawaii.eagle-i.net/i/$1 False eagle-i r3d100011564 easychair.cfp EasyChair Call for Paper https://easychair.org/cfp/ Conferences in EasyChair SysBioCancer2022 https://easychair.org/cfp/$1 False easychair.topic EasyChair Topic https://easychair.org/cfp/ Call for paper topics in EasyChair ^\d+$ 27106865 https://easychair.org/cfp/topic.cgi?tid=$1 False ebisc European Bank for induced pluripotent Stem Cells https://www.ebisc.org Cell line collections (Providers) ^E(S|D)i\d+-\w$ ESi007-A https://cells.ebisc.org/$1 False EBiSC ecacc European Collection of Authenticated Cell Culture https://www.phe-culturecollections.org.uk/collections/ecacc.aspx The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs). ^\d+$ 90062901 https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1 False ECACC ecao The Echinoderm Anatomy and Development Ontology https://github.com/echinoderm-ontology/ecao_ontology None ^\d{7}$ 0107180 ettensohn@cmu.edu http://purl.obolibrary.org/obo/ECAO_$1 False ECAO ECAO ecao ecao ECAO eccode Enzyme Commission Code https://www.enzyme-database.org/ The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$ 1.1.1.1 kristian.axelsen@sib.swiss https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 EC|EC number|EC-CODE|ECCODE|EC_CODE|ec-code|intenz False 671 EC-CODE 1011 nbdc00508 ec-code ec-code 106 intenz r3d100010803 Ec DB-0024 P591 ecg Electrocardiogram Ontology https://bioportal.bioontology.org/ontologies/ECG The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. ^\d+$ 000000159 rwinslow@jhu.edu http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1 ECGOntology False ECG ECG echinobase Echinobase https://www.echinobase.org Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species. ^\d+$ 23159291 https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1 False nbdc01512 echobase EchoBASE post-genomic database for Escherichia coli http://www.york.ac.uk/ EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. ^EB\d+$ EB0170 gavin.thomas@york.ac.uk http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 False ECHOBASE echobase echobase echobase r3d100011646 DB-0020 ecmdb E. coli Metabolite Database https://ecmdb.ca The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes. ^ECMDB\d+$ ECMDB00005 http://ecmdb.ca/compounds/$1 ECMDB False 386 ecn EC number https://echa.europa.eu/information-on-chemicals identifier for a chemical compound per EINECS or ELINCS ^\d{3}-\d{3}-\d$ 200-003-9 False 000447 P232 eco Evidence and Conclusion Ontology https://www.evidenceontology.org 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. ^\d{7}$ 0007807 mgiglio@som.umaryland.edu http://purl.obolibrary.org/obo/ECO_$1 False ECO 1028 ECO ECO eco eco eco eco ECO eco P3811 ecocore An ontology of core ecological entities https://github.com/EcologicalSemantics/ecocore Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. ^\d+$ 00000001 p.buttigieg@gmail.com http://purl.obolibrary.org/obo/ECOCORE_$1 False ECOCORE ECOCORE ECOCORE ecocore ecocore ECOCORE ecocyc EcoCyc https://ecocyc.org/ 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. AICARTRANSIMPCYCLO-CPLX pkarp@ai.sri.com https://ecocyc.org/gene?id=$1 False nbdc00262 9 r3d100011277 ecogene Database of Escherichia coli Sequence and Function http://ecogene.org/ The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. ^EG\d+$ EG10173 http://www.ecogene.org/gene/$1 False EcoGene ecogene ecogene ecogene r3d100010546 ecolexicon EcoLexicon http://ecolexicon.ugr.es/en/index.htm EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology. canal False ecoliwiki EcoliWiki from EcoliHub http://ecoliwiki.net/colipedia/ EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. ^[A-Za-z0-9-]+$ aaeA pkarp@ai.sri.com http://ecoliwiki.net/colipedia/index.php/$1:Gene False ECOLIWIKI nbdc02041 ecoliwiki ecoliwiki ecso The Ecosystem Ontology http://bioportal.bioontology.org/ontologies/ECSO DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases ^\d+$ 00000532 brycemecum@gmail.com http://purl.dataone.org/odo/ECSO_$1 https://raw.githubusercontent.com/DataONEorg/sem-prov-ontologies/run4/observation/d1-ECSO.owl False ECSO ECSO ECSO ecto Environmental conditions, treatments and exposures ontology https://github.com/EnvironmentOntology/environmental-exposure-ontology ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). ^\d{7}$ 0000001 annethessen@gmail.com http://purl.obolibrary.org/obo/ECTO_$1 False ECTO ECTO ECTO ecto ecto ECTO ecyano.entity E-cyanobacterium entity http://www.e-cyanobacterium.org/bcs/entity/ E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. ^\d+$ 23 https://www.e-cyanobacterium.org/bcs/entity/$1 False ECYANO.ENTITY ecyano.entity ecyano.entity ecyano ecyano.experiment E-cyanobacterium Experimental Data https://www.e-cyanobacterium.org/experiments-repository/ E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments. ^\d+$ 18 https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1 False ecyano.experiment ecyano ecyano.model E-cyanobacterium model http://e-cyanobacterium.org/models/ E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. ^\d+$ 26 https://e-cyanobacterium.org/models/model/$1 False ECYANO.MODEL ecyano.model ecyano.model ecyano.rule E-cyanobacterium rule http://www.e-cyanobacterium.org/bcs/rule/ E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules. ^\d+$ 56 https://e-cyanobacterium.org/bcs/rule/$1 False ECYANO.RULE ecyano.rule ecyano.rule ecyano edam EDAM Ontology http://edamontology.org EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications). ^(data|topic|operation|format)\_\d{4}$ data_1664 matus.kalas@uib.no https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1 https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo False EDAM EDAM EDAM EDAM edam edam edam EDAM edam edam.data EDAM Data http://edamontology.org Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. ^\d+$ 1664 matus.kalas@uib.no http://edamontology.org/data_$1 https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo False edam edam.format EDAM Format http://edamontology.org A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. ^\d+$ 1915 matus.kalas@uib.no http://edamontology.org/format_$1 https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo False edam edam.operation EDAM Operation http://edamontology.org A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. ^\d+$ 0004 matus.kalas@uib.no http://edamontology.org/operation_$1 https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo False edam edam.topic EDAM Topic http://edamontology.org A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. ^\d+$ 0003 matus.kalas@uib.no http://edamontology.org/topic_$1 https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo False edam edda EDDA Study Designs Taxonomy https://bioportal.bioontology.org/ontologies/EDDA Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. 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. health_care_quality_assessment tanja.bekhuis@tcbinfosci.com http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1 False EDDA EDDA efo Experimental Factor Ontology http://www.ebi.ac.uk/efo The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. ^\d{7}$ 0005147 plwhetzel@gmail.com http://www.ebi.ac.uk/efo/EFO_$1 http://www.ebi.ac.uk/efo/efo.owl http://www.ebi.ac.uk/efo/efo.obo False EFO EFO EFO EFO EFO efo efo efo EFO P11956 ega.dataset European Genome-phenome Archive Dataset https://ega-archive.org/ The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. ^EGAD\d{11}$ EGAD00000000001 tk2@ebi.ac.uk https://www.ebi.ac.uk/ega/datasets/$1 False EGA.DATASET ega.dataset ega.dataset r3d100011242 ega.study European Genome-phenome Archive Study https://www.ebi.ac.uk/ega/studies The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. ^EGAS\d{11}$ EGAS00000000001 https://www.ebi.ac.uk/ega/studies/$1 False EGA.STUDY ega.study ega.study eggnog eggNOG http://eggnog.embl.de/version_3.0/ eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). ^\w+$ veNOG12876 j.huerta@csic.es http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 False EGGNOG eggnog eggnog eggnog DB-0152 ehda Human developmental anatomy, timed version http://genex.hgu.mrc.ac.uk/ A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once. ^\d+$ 1 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/EHDA_$1 True EHDA EHDA EHDA ehda ehda ehdaa Human developmental anatomy, abstract version http://genex.hgu.mrc.ac.uk/ A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release. ^\d+$ 1 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/EHDAA_$1 True EHDAA EHDAA EHDAA ehdaa ehdaa ehdaa2 Human developmental anatomy, abstract https://github.com/obophenotype/human-developmental-anatomy-ontology A structured controlled vocabulary of stage-specific anatomical structures of the developing human. ^\d{7}$ 0000000 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/EHDAA2_$1 EHDAA2_RETIRED|HDAA2|RETIRED_EHDAA2 True EHDAA2 EHDAA2 EHDAA2 ehdaa2 ehdaa2 EHDAA2 elm Eukaryotic Linear Motif Resource http://elm.eu.org/ Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. ^[A-Za-z_0-9]+$ CLV_MEL_PAP_1 toby.gibson@embl.de http://elm.eu.org/elms/elmPages/$1.html False ELM elm elm DB-0223 emap Mouse gross anatomy and development, timed http://emouseatlas.org A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). ^\d+$ 1 Terry.Hayamizu@jax.org http://purl.obolibrary.org/obo/EMAP_$1 True EMAP EMAP emap emap emap.ontology emapa Mouse Developmental Anatomy Ontology http://www.informatics.jax.org/expression.shtml An ontology for mouse anatomy covering embryonic development and postnatal stages. ^\d+$ 26753 Terry.Hayamizu@jax.org http://purl.obolibrary.org/obo/EMAPA_$1 EMAPA_RETIRED False EMAPA 549 EMAPA EMAPA emapa emapa EMAPA emaps Mouse Developmental Anatomy Ontology with Theiler Stage https://www.informatics.jax.org/vocab/gxd/anatomy/ EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823 ^\d+$ 3517823 Terry.Hayamizu@jax.org https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1 False emdb Electron Microscopy Data Bank https://www.ebi.ac.uk/pdbe/emdb/ The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. ^EMD-\d{4,5}$ EMD-1001 help@emdatabank.org https://www.ebi.ac.uk/pdbe/entry/emdb/$1 False EMDB 1146 emdb emdb r3d100010562 DB-0272 emea European Medicines Evaluation Agency https://www.ema.europa.eu/en/medicines Product number for the European Medicines Agency EMEA/H/C/000181 False emmo Elementary Multiperspective Material Ontology https://emmo-repo.github.io 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) 03212fd7_abfd_4828_9c8e_62c293052d4b jesper.friis@sintef.no http://emmo.info/emmo#EMMO_$1 False emmo emmo.cif Crystallographic Information Framework https://www.iucr.org/resources/cif 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/) _space_group_symop.operation_xyz jesper.friis@sintef.no http://emmo.info/emmo/cif-core#$1 False emolecules Reaxys eMolecules https://reaxys.emolecules.com Catalog of purchasable reagents and building blocks ^\d+$ 491187 https://reaxys.emolecules.com/cgi-bin/more?vid=$1 False empiar Electron Microscopy Public Image Archive https://www.ebi.ac.uk/pdbe/emdb EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure ^\d+$ 10595 ardan@ebi.ac.uk https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1 False empiar emsl.project Environmental Molecular Sciences Laboratory Project https://www.emsl.pnnl.gov/projects "As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including: - Research team and institution - The EMSL project DOI - Link to project data available in EMSLs Data Portal - Project type" ^\d+$ 60141 montana.smith@pnnl.gov https://www.emsl.pnnl.gov/project/$1 False ena.embl European Nucleotide Archive https://www.ebi.ac.uk/ena/ The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. ^[A-Z]+[0-9]+(\.\d+)?$ BN000065 datasubs@ebi.ac.uk https://www.ebi.ac.uk/ena/browser/view/$1 ena False ENA.EMBL nbdc00432 ena.embl ena.embl ena r3d100010527 DB-0022 insdc.run encode Encyclopedia of DNA Elements https://www.encodeproject.org The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ ENCSR163RYW gabdank@stanford.edu https://www.encodeproject.org/$1 False ENCODE ENCODE encode encode r3d100013051 enm eNanoMapper ontology http://www.enanomapper.net/ The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. ^\d+$ 8000221 egon.willighagen@maastrichtuniversity.nl http://purl.enanomapper.org/onto/ENM_$1 False ENM ENM enm ensembl Ensembl Gene https://www.ensembl.org/ Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms. ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ ENSG00000139618 flicek@ebi.ac.uk https://www.ensembl.org/id/$1 Ensembl False ENSEMBL 2610 nbdc00054 ensembl ensembl ensembl r3d100010228 DB-0023 P594 ensembl.bacteria Ensembl Bacteria https://bacteria.ensembl.org/ Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ MU9_3181 flicek@ebi.ac.uk https://bacteria.ensembl.org/id/$1 False ENSEMBL.BACTERIA nbdc00433 ensembl.bacteria ensembl.bacteria ensembl.bacteria r3d100011195 DB-0147 ensembl ensembl.fungi Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi. https://fungi.ensembl.org/ Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. ^[A-Z-a-z0-9]+$ CADAFLAT00006211 flicek@ebi.ac.uk https://fungi.ensembl.org/id/$1 False ENSEMBL.FUNGI nbdc00434 ensembl.fungi ensembl.fungi ensembl.fungi r3d100011196 DB-0148 ensembl ensembl.metazoa Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa. https://metazoa.ensembl.org/ Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. ^\w+(\.)?\d+$ FBtr0084214 flicek@ebi.ac.uk https://metazoa.ensembl.org/id/$1 False ENSEMBL.METAZOA nbdc00435 ensembl.metazoa ensembl.metazoa ensembl.metazoa r3d100011198 DB-0149 ensembl.plant Ensembl Plants https://plants.ensembl.org/ Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. ^\w+(\.\d+)?(\.\d+)?$ AT1G73965 https://plants.ensembl.org/id/$1 False ENSEMBL.PLANT ensembl.plant ensembl.plant ensembl.plant ensembl.protist Ensembl Protists https://protists.ensembl.org Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. ^\w+$ PF3D7_1328700 https://protists.ensembl.org/id/$1 False ENSEMBL.PROTIST ensembl.protist ensembl.protist ensembl.protist ensemblglossary Ensembl Glossary http://ensembl.org/glossary The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used. ^\d{7}$ 0000198 http://ensembl.org/glossary/ENSGLOSSARY_$1 False ensemblglossary envipath enviPath https://envipath.org/ enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$ 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea admin@envipath.org https://envipath.org/package/$1 False nbdc02011 envipath r3d100012715 envo Environment Ontology http://environmentontology.org/ The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. ^\d{7,8}$ 09200010 pier.buttigieg@awi.de http://purl.obolibrary.org/obo/ENVO_$1 False ENVO ENVO ENVO ENVO envo envo envo envo ENVO enzo Enzo Life Sciences https://www.enzolifesciences.com Enzo Life Sciences is an antibody vendor. ALX-210-175 https://www.enzolifesciences.com/$1 Enzo Life Sciences False eo Plant Environment Ontology http://planteome.org/ The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. ^\d{7}$ 0007404 jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/EO_$1 True EO EO EO eo eo eo eo eol Environment Ontology for Livestock http://www.atol-ontology.com The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems. ^\d{7}$ 0001927 pylebail@rennes.inra.fr http://purl.org/obo/owlEOL_$1 http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl False EOL EOL EOL eol r3d100011663 eolife Encyclopedia of Life https://eol.org A collaborative project intended to create an encyclopedia documenting all living species known to science ^\d+$ 1044544 secretariat@eol.org https://eol.org/pages/$1 False r3d100010229 P830 epcc European Paediatric Cardiac Codes https://www.aepc.org/european-paediatric-cardiac-coding Collection of European paediatric cardiac coding files False epd Eukaryotic Promoter Database https://epd.expasy.org/epd/ The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. ^[A-Z-_0-9]+$ TA_H3 Philipp.Bucher@sib.swiss https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1 False EPD 2386 nbdc00438 epd epd DB-0205 epio Epilepsy Ontology https://github.com/SCAI-BIO/EpilepsyOntology A application driven Epilepsy Ontology with official terms from the ILAE. ^\d{7}$ 0000011 alpha.tom.kodamullil@scai.fraunhofer.de http://purl.obolibrary.org/obo/EPIO_$1 False EPIO EPIO epio EPIO epo Epidemiology Ontology https://code.google.com/p/epidemiology-ontology/ An ontology designed to support the semantic annotation of epidemiology resources http://purl.obolibrary.org/obo/EPO_$1 https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl True EPO epo EPO epso Epilepsy and Seizure Ontology http://prism.case.edu/prism/index.php/EpilepsyOntology The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ^\d{7}$ 0000400 satyasahoo@ieee.org http://www.case.edu/EpilepsyOntology.owl#$1 False EPSO EPSO EPSO erm European Registry of Materials https://nanocommons.github.io/identifiers/ The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project. ^ERM[0-9]{8}$ ERM00000044 egon.willighagen@gmail.com https://nanocommons.github.io/identifiers/registry#$1 False 000569 erm erm ero eagle-i resource ontology https://open.med.harvard.edu/wiki/display/eaglei/Ontology An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. ^\d{7}$ 0001655 Marc_Ciriello@hms.harvard.edu http://purl.obolibrary.org/obo/ERO_$1 True ERO ERO ERO ero ero ERO eropmoscow Endogenous Regulatory OligoPeptide knowledgebase-Moscow http://erop.inbi.ras.ru 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.). E00002 http://erop.inbi.ras.ru/result2.php?PepName=$1 False nbdc00265 eropmoscow erv Human Endogenous Retrovirus Database https://herv.img.cas.cz/ Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. ^[A-Za-z0-9\-\_]+$ THE1B https://herv.img.cas.cz/s/$1 False ERV erv erv esldb eukaryotic Subcellular Localization database http://gpcr.biocomp.unibo.it/esldb 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. HS000015122 http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1 False esldb estdab European Searchable Tumour Line Database https://www.ebi.ac.uk/ipd/estdab/ Cell line databases/resources ^\d{3}$ 046 https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1 True ESTDAB eu89h JRC Data Catalogue http://data.jrc.ec.europa.eu/ The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. ^[a-z0-9\-_]+$ jrc-eurl-ecvam-chemagora http://data.europa.eu/89h/$1 False EU89H eu89h eu89h euclinicaltrials EU Clinical Trials https://www.clinicaltrialsregister.eu/ "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population." ^\d{4}\-\d{6}\-\d{2}$ 2008-005144-16 https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1 EUCTR False EUCLINICALTRIALS euclinicaltrials euclinicaltrials eugenes Eukaryotic Genes http://eugenes.org/ 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. MGgn0008978 eugenes@iubio.bio.indiana.edu http://eugenes.org:7072/.bin/fbidq.html?$1 False eugenes eupath VEuPathDB ontology https://github.com/VEuPathDB-ontology/VEuPathDB-ontology The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. ^\d{7}$ 0010316 jiezhen@med.umich.edu http://purl.obolibrary.org/obo/EUPATH_$1 True EUPATH EUPATH EUPATH eupath eupath EUPATH eurofir European Food Information Resource Network https://www.eurofir.org EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries. False ev eVOC (Expressed Sequence Annotation for Humans) http://www.evocontology.org/ Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment. ^\d{7}$ 0100011 evoc@sanbi.ac.za http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1 True EV ev evoc evm eVOC mouse development stage True exac.gene ExAC Gene http://exac.broadinstitute.org/ The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. ^ENSG\d{11}$ ENSG00000169174 http://exac.broadinstitute.org/gene/$1 False EXAC.GENE exac.gene exac.gene exac.transcript ExAC Transcript http://exac.broadinstitute.org/ The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. ^ENST\d{11}$ ENST00000407236 http://exac.broadinstitute.org/transcript/$1 False EXAC.TRANSCRIPT exac.transcript exac.transcript exac.variant ExAC Variant http://exac.broadinstitute.org/ The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ 22-46615880-T-C http://exac.broadinstitute.org/variant/$1 False EXAC.VARIANT exac.variant exac.variant exo Exposure ontology https://github.com/CTDbase/exposure-ontology ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. ^\d{7}$ 0000078 annethessen@gmail.com http://purl.obolibrary.org/obo/ExO_$1 ExO False EXO EXO EXO exo exo ExO fabio FaBiO, the FRBR-aligned Bibliographic Ontology https://github.com/sparontologies/fabio The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references. d4e2515 silvio.peroni@unibo.it https://sparontologies.github.io/fabio/current/fabio.html#$1 False FaBiO fabio facebase FaceBase Data Repository https://www.facebase.org FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. ^FB\d{8}$ FB00000917 ychai@usc.edu https://www.facebase.org/data/record/#1/isa:dataset/accession=$1 False FACEBASE nbdc02022 facebase facebase r3d100013263 fairsharing FAIRsharing https://fairsharing.org/ The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. ^(bsg-[dscp]?\d{6})|(FAIRsharing\.\w+)$ bsg-000052 allyson.lister@oerc.ox.ac.uk https://fairsharing.org/$1 False FAIRSHARING fairsharing fairsharing r3d100010142 fairsharing.organization FAIRsharing Organization https://fairsharing.org An organization in FAIRsharing, including universities, labs, etc. ^\d+$ 3851 allyson.lister@oerc.ox.ac.uk https://fairsharing.org/organisations/$1 False fairsharing fairsharing.user FAIRsharing User https://fairsharing.org A user of FAIRsharing ^\d+$ 5112 allyson.lister@oerc.ox.ac.uk https://fairsharing.org/users/$1 False fairsharing faldo Feature Annotation Location Description Ontology http://biohackathon.org/resource/faldo It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources ForwardStrandPosition faldo@googlegroups.com http://biohackathon.org/resource/faldo#$1 False FALDO FALDO faldo FALDO faldo fao Fungal gross anatomy https://github.com/obophenotype/fungal-anatomy-ontology/ A structured controlled vocabulary for the anatomy of fungi. ^\d{7}$ 0000001 vw253@cam.ac.uk http://purl.obolibrary.org/obo/FAO_$1 False FAO FAO FAO fao fao FAO fao fao.asfis Aquatic Sciences and Fisheries Information System https://www.fao.org/fishery/en/collection/asfis/en The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage) ^\d+$ 20560 https://www.fao.org/fishery/en/species/$1 asfis False fbbi Biological Imaging Methods Ontology http://cellimagelibrary.org/ A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. ^\d+$ 00000268 wawong@gmail.com http://purl.obolibrary.org/obo/FBbi_$1 FBbi True FBbi FBbi FBbi fbbi fbbi FBbi fbbi fbbt Drosophila gross anatomy http://purl.obolibrary.org/obo/fbbt An ontology representing the gross anatomy of Drosophila melanogaster. ^\d{8}$ 00007294 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBbt_$1 FBbt|FBbt_root False FBBT FBbt FB-BT fbbt fbbt FBbt fbbt fbcv FlyBase Controlled Vocabulary http://purl.obolibrary.org/obo/fbcv A miscellaneous ontology of terms used for curation in FlyBase, including the DPO. ^\d{7}$ 0000586 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBcv_$1 https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo FBcv False FBCV FBcv FB-CV fbcv fbcv FBcv fbcv flybase fbdv Drosophila development http://purl.obolibrary.org/obo/fbdv An ontology of Drosophila melanogaster developmental stages. ^\d{8}$ 00000000 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBdv_$1 FBdv False FBDV FBdv FB-DV fbdv fbdv FBdv fbdv fbol International Fungal Working Group Fungal Barcoding. http://www.fungalbarcoding.org/ DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. ^\d+$ 2224 http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T True FBOL fbol fbol fbql FlyBase Qualifiers ^\d+$ 00005254 True fbrf FlyBase Reference Report https://flybase.org FlyBase internal citation identifiers ^\d{7}$ 0187632 https://flybase.org/reports/FBrf$1 False flybase fbsp Fly taxonomy http://www.flybase.org/ The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. ^\d{8}$ 00000000 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBSP_$1 True FB-SP FBSP FB-SP fbsp fbsp flybase fbtc Flybase Cell Line https://flybase.org The cell line vocabulary inside FlyBase ^\d{7}$ 0000190 https://flybase.org/reports/FBtc$1 FlyBase_Cell_line False FlyBase_Cell_line flybase fcb the FAIR Cookbook https://w3id.org "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR). " ^FCB\d{3}$ FCB005 https://w3id.org/faircookbook/$1 False fcb fcsfree Fetal Calf Serum-Free Database https://fcs-free.org Cell line databases/resources 240-17-488-3-4-12 https://fcs-free.org/fcs-database?$1 False FCS-free fda.application FDA Application https://fda.report/applications This prefix is for FDA application identifiers. There are multiple types of FDA applications (https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications), including New Drug Application (NDA). FDA.report provides access to all FDA databases, including applications, in a single portal, and can resolve FDA application identifiers. ^\d{6}$ 070886 https://fda.report/applications/$1 False ferroliganddb FerroLigandDB https://ferr.gulab.org.cn/ FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors. 486 guqiong@mail.sysu.edu.cn https://ferr.gulab.org.cn/browse/$1 False fhir.implementation FHIR United States Implementation Guides https://hl7.org/fhir/us/ A set of guides on implementing various processes within hospitals or healthcare systems. immds https://hl7.org/fhir/us/$1 False fideo Food Interactions with Drugs Evidence Ontology https://gitub.u-bordeaux.fr/erias/fideo Food-Drug interactions automatically extracted from scientific literature ^\d{8}$ 00000021 georgeta.bordea@u-bordeaux.fr http://purl.obolibrary.org/obo/FIDEO_$1 False FIDEO FIDEO fideo fideo FIDEO fishbase.species FishBase http://fishbase.org Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years. ^\d+$ 6472 https://www.fishbase.ca/summary/$1 fishbase False nbdc00270 r3d100010912 P938 fivestars Five Stars of Online Research Articles Ontology http://www.sparontologies.net/ontologies/fivestars An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata. hasOpenAccessRating silvio.peroni@unibo.it False fix Physico-chemical methods and properties https://www.ebi.ac.uk/chebi/ An ontology of physico-chemical methods and properties. ^\d{7}$ 0000390 chebi-help@ebi.ac.uk http://purl.obolibrary.org/obo/FIX_$1 True FIX FIX FIX fix fix FIX fix chebi flopo Flora Phenotype Ontology https://github.com/flora-phenotype-ontology/flopoontology Traits and phenotypes of flowering plants occurring in digitized Floras ^\d{7}$ 0005250 robert.hoehndorf@kaust.edu.sa http://purl.obolibrary.org/obo/FLOPO_$1 False FLOPO FLOPO FLOPO FLOPO flopo flopo FLOPO flowrepository FlowRepository https://flowrepository.org/ FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. ^FR\-FCM\-\w{4}$ FR-FCM-ZYGW rbrinkman@bccrc.ca https://flowrepository.org/id/$1 False nbdc01698 flowrepository flowrepository r3d100011280 flu Influenza Ontology http://purl.obolibrary.org/obo/flu/ Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS) ^\d{7}$ 0000404 burkesquires@gmail.com http://purl.obolibrary.org/obo/FLU_$1 True FLU FLU FLU flu flybase FlyBase Gene http://flybase.org/ FlyBase is the database of the Drosophila Genome Projects and of associated literature. ^FB\w{2}\d{7}$ FBgn0011293 vjenkins@morgan.harvard.edu https://flybase.org/reports/$1 FB|FlyBase False FlyBase FlyBase 1089 nbdc00064 fb fb 460 flybase r3d100010591 FlyBase DB-0026 P3852 flybrain.ndb FlyBrain Neuron Database https://flybrain-ndb.virtualflybrain.org A database of fly neurons and pathways with an associated 3D viewer. ^\d+$ 10531 https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html False nbdc01446 flymine.chromosome FlyMine Chromosome Band http://www.flymine.org/ 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. 1047874 https://www.flymine.org/flymine/report/ChromosomeBand/$1 False flymine fma Foundational Model of Anatomy http://si.washington.edu/projects/fma The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. ^\d+$ 63189 mejino@u.washington.edu https://www.ebi.ac.uk/ols4/ontologies/fma/terms?obo_id=FMA:$1 FMAID|FMA_RETIRED True FMA 571 FMA FMA 1182 2.16.840.1.113883.6.119 nbdc00273 fma fma fma fma FMA fma P1402 foaf Friend of a Friend http://xmlns.com/foaf/spec/ 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. familyName rafael.goncalves@stanford.edu http://xmlns.com/foaf/0.1/$1 False foaf foaf FOAF foaf foaf fobi Food-Biomarker Ontology https://github.com/pcastellanoescuder/FoodBiomarkerOntology FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data ^\d{4,6}$ 030719 polcaes@gmail.com http://purl.obolibrary.org/obo/FOBI_$1 False FOBI FOBI FOBI fobi fobi FOBI foodb.compound FooDB compound https://foodb.ca/ FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. ^FDB\d+$ FDB002100 http://foodb.ca/compounds/$1 foodb False FOODB.COMPOUND foodb.compound foodb.compound r3d100012152 P8117 foodb.food FooDB Food https://foodb.ca/foods Foods in FooDB ^FOOD\d+$ FOOD00020 https://foodb.ca/foods/$1 False foodex2 Food Classification and Description System (from FSA Food Type identifiers) https://data.food.gov.uk/codes/_foodtype 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. A0TMC data@food.gov.uk http://data.food.gov.uk/codes/foodtype/id/$1 False FOODEX2 foodon The Food Ontology https://foodon.org/ FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. ^[0-9]{8}$ 03307879 damion_dooley@sfu.ca http://purl.obolibrary.org/obo/FOODON_$1 http://purl.obolibrary.org/obo/foodon.obo False FOODON FOODON FOODON FOODON foodon foodon foodon foodon FOODON fossilworks.journal Fossilworks Journal http://fossilworks.org Identifier for a journal article in the fossilworks website ^\d+$ 61467 http://fossilworks.org/?a=referenceInfo&reference_no=$1 False P7720 fossilworks fossilworks.taxon Fossilworks Taxon http://www.fossilworks.org Identifier for an animal, plant, or microorganism from the fossilworks website ^[1-9]\d{0,5}$ 40565 http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1 False P842 fossilworks fovt FuTRES Ontology of Vertebrate Traits https://github.com/futres/fovt These are the terms that are improted for FOVT to describe vertebrate traits. ^\d{7}$ 0000009 meghan.balk@gmail.com http://purl.obolibrary.org/obo/FOVT_$1 False FOVT FOVT fovt fovt FOVT fplx FamPlex https://sorgerlab.github.io/famplex/ FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. ^[a-zA-Z0-9][A-Za-z0-9_]+$ GPIb_IX_V benjamin_gyori@hms.harvard.edu https://sorgerlab.github.io/famplex/$1 famplex False FPLX FPLX FPLX fplx fplx fr FAIR* Reviews Ontology http://www.sparontologies.net/ontologies/fr An ontology that enables the description of reviews of scientific articles and other scholarly resources. ReviewVersion silvio.peroni@unibo.it False frapo Funding, Research Administration and Projects Ontology http://www.sparontologies.net/ontologies/frapo An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc. Grant silvio.peroni@unibo.it http://purl.org/cerif/frapo/$1 False FRAPO frapo frbr Functional Requirements for Bibliographic Records http://www.sparontologies.net/ontologies/frbr The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO. Expression silvio.peroni@unibo.it http://purl.org/vocab/frbr/core#$1 False frbr frbr frbrer Functional Requirements for Bibliographic Records Entity-Relationship Model https://www.iflastandards.info/fr/frbr/frbrer This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html) 1001 http://iflastandards.info/ns/fr/frbr/frbrer/$1 False frbrer frbr fsnp F-SNP http://compbio.cs.queensu.ca/F-SNP/ The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. ^rs\d+$ rs17852708 http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1 False FSNP fsnp fsnp fsnp ftt Feature Type Thesaurus https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3 Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific. ^\d+$ 273 https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1 False funcbase.fly FuncBase Fly http://func.mshri.on.ca/fly Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. ^\d+$ 10194 http://func.mshri.on.ca/fly/genes/list_functional_scores/$1 False FUNCBASE.FLY funcbase.fly funcbase.fly funcbase.human FuncBase Human http://func.mshri.on.ca/human/ Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data. ^\d+$ 119514 http://func.mshri.on.ca/human/genes/list_functional_scores/$1 False FUNCBASE.HUMAN funcbase.human funcbase.human funcbase.mouse FuncBase Mouse http://func.mshri.on.ca/mouse/ Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. ^\d+$ 1351341 http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 False FUNCBASE.MOUSE funcbase.mouse funcbase.mouse funcbase.yeast FuncBase Yeast http://func.mshri.on.ca/yeast Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. ^\d+$ 2701 http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 False FUNCBASE.YEAST funcbase.yeast funcbase.yeast funderregistry FunderRegistry https://www.crossref.org/ The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world. ^\d{9,9}$ 100000001 http://data.crossref.org/fundingdata/funder/10.13039/$1 FundRef|crossref.funder False funderregistry fungidb FungiDB https://fungidb.org/fungidb FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. ^[A-Za-z_0-9]+$ CNBG_0001 jason.stajich@ucr.edu https://fungidb.org/fungidb/app/record/gene/$1 False FUNGIDB fungidb fungidb r3d100011906 fungorum Index Fungorum http://www.indexfungorum.org identifier for a fungus taxon in Index Fungorum ^[1-9]\d{0,5}$ 154022 http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1 False P1391 fyeco Fission Yeast Experimental Conditions Ontology https://github.com/pombase/fypo PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase. ^\d{7}$ 0000003 vw253@cam.ac.uk False fyler Fyler https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906 A hierarchical classification of congenital heart disease ^\d+$ 4447 False fypo Fission Yeast Phenotype Ontology https://github.com/pombase/fypo A formal ontology of phenotypes observed in fission yeast. ^\d{7}$ 0001707 vw253@cam.ac.uk http://purl.obolibrary.org/obo/FYPO_$1 http://purl.obolibrary.org/obo/fypo.obo False FYPO FYPO FYPO fypo fypo FYPO ga4ghdos Data Object Service http://github.com/ga4gh/data-object-service-schemas Assists in resolving data across cloud resources. ^[a-zA-Z0-9\-:#/\.]+$ dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d https://dataguids.org/ga4gh/dos/v1/dataobjects/$1 False GA4GHDOS ga4ghdos ga4ghdos gabi Network of Different Plant Genomic Research Projects http://www.gabipd.org/ GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. ^\w+$ 2679240 birgit.kersten@thuenen.de http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject False GABI gabi gabi gabi gainesville.core Gainesville Core Ontology http://ontologies.makolab.com/gc06/gc.html Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations Aromatic http://purl.org/gc/$1 http://ontologies.makolab.com/gc06/gc.owl False galen GALEN https://www.opengalen.org A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic. MagnitudeValueType j@deltaflow.com http://www.co-ode.org/ontologies/galen#$1 True GALEN GALEN gallont Plant Gall Ontology https://adeans.github.io/gallont/ Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls. ^\d{7}$ 0000001 adeans@psu.edu http://purl.obolibrary.org/obo/GALLONT_$1 False GALLONT GALLONT GALLONT gallont GALLONT gard Genetic and Rare Diseases Information Center https://rarediseases.info.nih.gov/diseases Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease. ^\d+$ 6038 eric.sid@nih.gov https://rarediseases.info.nih.gov/diseases/$1/index GARD|Genetic and Rare Diseases Information Center False P4317 gateway Health Data Research Innovation Gateway https://www.hdruk.ac.uk The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access. ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$ fd8d0743-344a-4758-bb97-f8ad84a37357 https://web.www.healthdatagateway.org/dataset/$1 False gateway gaz Gazetteer http://environmentontology.github.io/gaz/ A gazetteer constructed on ontological principles. The countries are actively maintained. ^\d{8}$ 00620027 lschriml@som.umaryland.edu http://purl.obolibrary.org/obo/GAZ_$1 http://purl.obolibrary.org/obo/gaz.obo True GAZ GAZ GAZ gaz gaz GAZ P6778 gbif Global Biodiversity Information Facility https://www.gbif.org/species "Database of living organisms, taxonomic. The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth." ^\d+$ 4238 timrobertson100@gmail.com https://www.gbif.org/species/$1 False nbdc00069 r3d100000039 P846 gc Genetic Code https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries. ^\d+$ 11 https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1 gc_id False gcst GWAS Catalog https://www.ebi.ac.uk The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. ^GCST\d{6}\d*$ GCST000035 https://www.ebi.ac.uk/gwas/studies/$1 False gcst gcst gdc Genomic Data Commons Data Portal https://gdc.cancer.gov The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ ae8c77fe-e6c8-44d5-8265-4a38c637bbef https://portal.gdc.cancer.gov/cases/$1 False GDC gdc gdc gdsc Genomics of Drug Sensitivity in Cancer https://www.cancerrxgene.org The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies. ^[0-9]+$ 1242 https://www.cancerrxgene.org/translation/Drug/$1 False GDSC gdsc gdsc gear Gene Expression Analysis Resource https://umgear.org The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains. ^[dp]\.[a-z0-9]{8}$ d.a59037e8 jorvis@gmail.com https://umgear.org/p?id=$1 False gecko Genomics Cohorts Knowledge Ontology https://github.com/IHCC-cohorts/GECKO An ontology to represent genomics cohort attributes. ^\d{7}$ 0000044 rbca.jackson@gmail.com http://purl.obolibrary.org/obo/GECKO_$1 False GECKO GECKO gecko gecko GECKO gemet General Multilingual Environmental Thesaurus https://www.eionet.europa.eu/gemet/en/themes/ The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts. ^\d+$ 627 helpdesk@eionet.europa.eu https://www.eionet.europa.eu/gemet/en/concept/$1 False GEMET 16 genatlas Genatlas http://genatlas.medecine.univ-paris5.fr/ GenAtlas is a database containing information on human genes, markers and phenotypes. ^\w+$ HBB http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 False GENATLAS nbdc00275 genatlas genatlas genatlas DB-0027 genbank GenBank https://www.ncbi.nlm.nih.gov/genbank/ GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). U49845 nawrocke@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/nucleotide/$1 False GenBank 000304 2292 nbdc00276 genbank r3d100010528 DB-0028 genbase GenBase https://ngdc.cncb.ac.cn/genbase/?lang=en 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. C_AA001108.1 zhaoxuetong@big.ac.cn https://ngdc.cncb.ac.cn/genbase/search/gb/$1 False r3d100014353 gendis Genomic Distribution of structural Superfamilies http://caps.ncbs.res.in/gendis/home.html Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases. 46946 http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1 True gendis genecards GeneCards http://www.genecards.org/ The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. ^[A-Za-z-0-9_]+(\@)?$ ABL1 marilyn.safran@weizmann.ac.il https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 False GENECARDS nbdc00242 genecards genecards genecards r3d100012015 DB-0030 genecards.geneannot GeneAnnot: Microarray Gene Annotation http://genecards.weizmann.ac.il/geneannot/ 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. GSTA1 False geneannot genecards.geneloc Gene Location http://genecards.weizmann.ac.il/geneloc/ 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 17503 http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1 False geneloc genecards.genenote Gene Normal Tissue Expression http://genecards.weizmann.ac.il/genenote/ 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. GC06M052656 http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes False genenote genedb GeneDB https://www.genedb.org/ "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the ""Pathogen Genomics"" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed." ^[\w\d\.-]*$ LinJ.20.0070 https://www.genedb.org/gene/$1 True GENEDB 1035 nbdc00469 genedb genedb genedb r3d100010626 P3382 genefarm GeneFarm http://urgi.versailles.inra.fr/Genefarm/ GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. ^\d+$ 4892 sebastien.aubourg@inrae.fr https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 False GENEFARM genefarm genefarm genefarm genepio Genomic Epidemiology Ontology http://genepio.org/ The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. ^\d{7}$ 0001885 damion_dooley@sfu.ca http://purl.obolibrary.org/obo/GENEPIO_$1 False GENEPIO GENEPIO GENEPIO genepio genepio GENEPIO genetree GeneTree http://www.ensembl.org/ Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. ^ENSGT\d+$ ENSGT00550000074763 flicek@ebi.ac.uk http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1 False GENETREE genetree genetree genetree DB-0162 genewiki Gene Wiki http://en.wikipedia.org/wiki/Gene_Wiki The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. ^\d+$ 1017 asu@scripps.edu http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1 False GENEWIKI nbdc00834 genewiki genewiki DB-0180 ncbigene geno Genotype Ontology https://github.com/monarch-initiative/GENO-ontology/ "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" ^\d{7}$ 0000632 mhb120@gmail.com http://purl.obolibrary.org/obo/GENO_$1 https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo False GENO GENO GENO geno geno GENO genpept GenPept https://www.ncbi.nlm.nih.gov/protein The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. ^\w{3}\d{5}(\.\d+)?$ CAA71118.1 https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept False GENPEPT genpept genpept genprop Genome Properties https://www.ebi.ac.uk/interpro/genomeproperties/ Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. ^GenProp\d+$ GenProp0699 https://www.ebi.ac.uk/interpro/genomeproperties/#$1 False GENPROP genprop genprop jcvi.genprop geo NCBI Gene Expression Omnibus https://www.ncbi.nlm.nih.gov/geo/ The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. ^G(PL|SM|SE|DS)\d+$ GDS1234 barrett@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 False GEO 1147 nbdc00080 geo geo geo r3d100010283 geogeo Geographical Entity Ontology https://github.com/ufbmi/geographical-entity-ontology/wiki "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in ""The US declared war on Germany"" vs. the US in ""The plane entered US airspace""." ^\d{9}$ 000000021 hoganwr@gmail.com http://purl.obolibrary.org/obo/GEO_$1 False GEO GEO GEO geogeo geo geo GEO geonames GeoNames https://www.geonames.org The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. ^\d+$ 3532759 https://www.geonames.org/$1 Geomames|Geonamaes False r3d100010245 geonames.feature GeoNames Feature Code https://www.geonames.org/export/codes.html All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes. ADM1 https://www.geonames.org/recent-changes/featurecode/$1/ False gexo Gene Expression Ontology http://www.semantic-systems-biology.org/apo Gene Expression Ontology kuiper@bio.ntnu.no https://www.bio.ntnu.no/ontology/GeXO/gexo.owl https://www.bio.ntnu.no/ontology/GeXO/gexo.obo False GEXO GEXO gexo gfo General Formal Ontology https://www.onto-med.de/ontologies/gfo 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. projects_to heinrich.herre@imise.uni-leipzig.de http://www.onto-med.de/ontologies/gfo.owl#$1 http://www.onto-med.de/ontologies/gfo.owl False GFO GFO ghr Genetics Home Reference https://medlineplus.gov/genetics/condition 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). saddan https://medlineplus.gov/genetics/condition/$1 False giardiadb GiardiaDB https://giardiadb.org/giardiadb/ GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ GL50803_102438 oharb@upenn.edu https://giardiadb.org/giardiadb/app/record/gene/$1 False GIARDIADB nbdc01782 giardiadb giardiadb giardiadb r3d100012458 github GitHub username https://github.com/ GitHub is an online host of Git source code repositories. ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$ biopragmatics/bioregistry https://github.com/$1 False github r3d100010375 P2037 github.issue GitHub Issue https://github.com/ An issue in any public repository on GitHub. biopragmatics/bioregistry/424 https://bioregistry.io/resolve/github/issue/$1 False github.pull GitHub Pull Request https://github.com/ A pull request in any public repository on GitHub. biopragmatics/bioregistry/416 https://bioregistry.io/resolve/github/pull/$1 False gitlab GitLab https://gitlab.com/ GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability. ^.*/.*$ morpheus.lab/morpheus https://gitlab.com/$1 False gitlab glida.gpcr GLIDA GPCR http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors. ^[A-Z-_0-9]+$ ACM1_HUMAN http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1 False GLIDA.GPCR glida.gpcr glida.gpcr glida.ligand GLIDA Ligand http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands. ^L\d+$ L000001 http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1 False GLIDA.LIGAND glida.ligand glida.ligand glycoepitope GlycoEpitope https://www.glycoepitope.jp/epitopes/ GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes. ^EP\d{4}$ EP0311 https://www.glycoepitope.jp/epitopes/$1 False GLYCOEPITOPE nbdc00087 glycoepitope glycoepitope glycomapsdb GlycoMapsDB http://www.glycosciences.de/modeling/glycomapsdb/ A database of GlycoMaps containing 2585 conformational maps. 6819 http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1 False glycomapsdb glycomedb GlycomeDB https://glytoucan.org/ GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. ^\w+$ G77500AY rr@uga.edu https://glytoucan.org/Structures/Glycans/$1 False GLYCOMEDB 2664 nbdc00899 glycomedb glycomedb glycomedb r3d100011527 glytoucan glyconavi GlycoNAVI https://www.noguchi.or.jp/ "GlycoNAVI is a website for carbohydrate research. It consists of the ""GlycoNAVI Database"" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the ""GlycoNAVI tools"" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools." ^GN_[A-Za-z0-9_:]+$ GN_G03681DA issaku@noguchi.or.jp https://glyconavi.org/hub/?id=$1 False nbdc01174 glyconavi glycopost GlycoPOST https://glycopost.glycosmos.org "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their ""raw/processed"" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines." ^GPST[0-9]{6}$ GPST000024 https://glycopost.glycosmos.org/entry/$1 False glycopost glycosciencesdb Glycosciences.DB http://www.glycosciences.de/database/ A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates. ^\d+$ 1 thomas@luetteke-online.de http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1 glycosciences.db False glytoucan GlyTouCan https://glytoucan.org GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. ^G[0-9]{5}[A-Z]{2}$ G00054MO rr@uga.edu https://glytoucan.org/Structures/Glycans/$1 glygen False GLYTOUCAN nbdc02434 glytoucan glytoucan r3d100012388 Glytoucan DB-0254 gmd Golm Metabolome Database http://gmd.mpimp-golm.mpg.de/ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 68513255-fc44-4041-bc4b-4fd2fae7541d kopka@mpimp-golm.mpg.de http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx False GMD gmd gmd r3d100011046 gmd.analyte Golm Metabolome Database Analyte http://gmd.mpimp-golm.mpg.de/ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes. ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 http://gmd.mpimp-golm.mpg.de/Analytes/$1 False GMD.ANALYTE gmd.analyte gmd.analyte gmd.gcms Golm Metabolome Database GC-MS spectra http://gmd.mpimp-golm.mpg.de/ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra. ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 53d583d8-40c6-40e1-9296-23f821cd77a5 http://gmd.mpimp-golm.mpg.de/Spectrums/$1 False GMD.GCMS gmd.gcms gmd.gcms gmd.profile Golm Metabolome Database Profile http://gmd.mpimp-golm.mpg.de/ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 10b38aaf-b977-4950-85b8-f4775f66658d http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1 False GMD.PROFILE gmd.profile gmd.profile gmd.ref Golm Metabolome Database Reference Substance http://gmd.mpimp-golm.mpg.de/ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 8cf84adb-b4db-4807-ac98-0004247c35df http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1 False GMD.REF gmd.ref gmd.ref gmelin Gmelins Handbuch der anorganischen Chemie https://link.springer.com/bookseries/562 The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s. ^[1-9][0-9]{3,6}$ 1466 False 1004 P1578 gnd GND ID https://lobid.org/ 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. ^[0-9X\-]+$ 117145750 https://lobid.org/gnd/$1 False 430 gnd P227 gno Glycan Naming and Subsumption Ontology https://gnome.glyomics.org/ An ontology for glycans based on GlyTouCan, but organized by subsumption. ^(\d{8}|(\w+\d+\w+))$ 10004892 nje5@georgetown.edu http://purl.obolibrary.org/obo/GNO_$1 gnome False GNO GNO gno gno GNO gnomad Genome Aggregation Database https://gnomad.broadinstitute.org 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). 1-55516888-G-GA hrehm@mgh.harvard.edu https://gnomad.broadinstitute.org/variant/$1 False nbdc02561 gnpis GnpIS https://urgi.versailles.inra.fr/gnpis/ GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. ^[A-Za-z0-9]+$ AY109603 urgi-contact@versailles.inra.fr https://urgi.versailles.inra.fr/gnpis/#result/term=$1 False GNPIS gnpis gnpis r3d100012647 gnps.task Global Natural Products Social Molecular Networking Task https://gnps.ucsd.edu/ GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS) ^[a-f0-9]+$ 4b848c342a4f4abc871bdf8a09a60807 mingxun.wang@cs.ucr.edu https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1 False go Gene Ontology http://geneontology.org/ The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. ^\d{7}$ 0032571 suzia@stanford.edu http://purl.obolibrary.org/obo/GO_$1 gobp|gobpid|gocc|goccid|gomf|gomfid False GO GO 572 GO GO 1176 2.16.840.1.113883.6.128 nbdc00074 go go go go GO 272 go r3d100014165 Go DB-0037 P686 go.gpi Gene Product Information Schema http://geneontology.org/docs/gene-product-information-gpi-format/#db-object-id 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. db-object-id http://geneontology.org/docs/gene-product-information-gpi-format/#$1 False go.model Gene Ontology Causal Assembly Model http://www.geneontology.org/gocam 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. 5fce9b7300001250 http://noctua.geneontology.org/editor/graph/gomodel:$1 False go.ref Gene Ontology Database references http://www.geneontology.org/cgi-bin/references.cgi "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of ""GO content"" meetings at which substantial changes in the ontologies are discussed and made." ^\d{7}$ 0000041 https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1 False GO_REF go_ref go.ref go.resource Gene Ontology Registry http://geneontology.org/ A database-specific registry supporting curation in the Gene Ontology CHEBI https://bioregistry.io/metaregistry/go/$1 False go.rule Gene Ontology Rules https://github.com/geneontology/go-site/tree/master/metadata/rules GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio. ^\d{7}$ 0000004 https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md False go goa Gene Ontology Annotation Database https://www.ebi.ac.uk/GOA/ The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ P12345 r.huntley@ucl.ac.uk https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1 False GOA nbdc00468 goa goa goa uniprot goche GO Chemicals https://github.com/geneontology/go-ontology Represent chemical entities having particular CHEBI roles ^\d+$ 25512 https://biopragmatics.github.io/providers/goche/$1 https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl go.chebi|go.chemical|go.chemicals False goeco GO Evidence Code http://geneontology.org/docs/guide-go-evidence-codes/ A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported. IPI False gold Genomes Online Database https://gold.jgi.doe.gov/ The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project. ^[A-Z][a-z][0-9]+$ Gs0000008 tbreddy@lbl.gov https://gold.jgi.doe.gov/resolver?id=$1 False nbdc00483 gold gold r3d100010808 gold.genome GOLD genome http://www.genomesonline.org/cgi-bin/GOLD/index.cgi "- DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes." ^(Gi|Gc)\d+$ Gi07796 http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1 False GOLD.GENOME gold.genome gold.genome gold.meta GOLD metadata http://www.genomesonline.org/cgi-bin/GOLD/index.cgi "- DEPRECATION NOTE - Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples." ^Gm\d+$ Gm00047 http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 False GOLD.META gold.meta gold.meta gold goldbook IUPAC Gold Book Compendium of Chemical Terminology https://goldbook.iupac.org "The Compendium is popularly referred to as the ""Gold Book"", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC ""Colour Books"" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books. Terminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry." ^[A-Z]{1,2}\d{5}$ G02681 https://goldbook.iupac.org/terms/view/$1 False 1884 P4732 google.book Google Books https://books.google.com Search the world's most comprehensive index of full-text books. qafeQTWIWmcC https://books.google.com/books?id=$1 False P675 google.patent Google Patents https://www.google.com/patents/ Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. ^[A-Z]{2,4}\d+([A-Z])?([0-9])?$ US4145692 https://www.google.com/patents/$1 patent False GOOGLE.PATENT Patent google.patent google.patent google.scholar Google Scholar Researcher https://scholar.google.com/ Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. ^[-_0-9A-Za-z]{12}$ PjrpzUIAAAAJ https://scholar.google.com/citations?user=$1 False P1960 gorel GO Relations http://geneontology.org/docs/ontology-relations/ Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. ^\d{7}$ 0002005 http://purl.obolibrary.org/obo/GOREL_$1 ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl False gpcrdb G protein-coupled receptor database http://www.gpcrdb.org/ The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models. ^\w+$ RL3R1_HUMAN david.gloriam@sund.ku.dk https://gpcrdb.org/protein/$1 False GPCRDB nbdc00484 gpcrdb gpcrdb gpcrdb DB-0038 gpcrnava GPCR Natural Variants database http://nava.liacs.nl/ 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. 1150 http://nava.liacs.nl/cgi-bin/nava.py?id=$1 False gnd gpmdb Global Proteome Machine Database http://gpmdb.thegpm.org/ The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. ^GPM\d+$ GPM32310002988 rbeavis@thegpm.org http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1 False GPMDB gpmdb gpmdb graingenes.reference GrainGenes http://wheat.pw.usda.gov A database for Triticeae and Avena references. WGS-95-1333 https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1 False graingenes.symbol GrainGenes http://wheat.pw.usda.gov A database for Triticeae and Avena gene symbols. 1-FEH+w3 http://wheat.pw.usda.gov/report?class=gene;name=$1 False gramene.gene Gramene Gene http://www.gramene.org/ Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. ^GR\:\d+$ GR:0080039 http://www.gramene.org/db/genes/search_gene?acc=$1 GR_GENE False GRAMENE.GENE gramene.gene gramene.gene gramene.growthstage Gramene Growth Stage Ontology http://www.gramene.org/plant_ontology/ Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. ^\d{7}$ 0007133 po-discuss@plantontology.org http://www.gramene.org/db/ontology/search?id=GRO:$1 cpga|gro-cpga True GRAMENE.GROWTHSTAGE GRO-CPGA gro gramene.growthstage gro gramene.po gramene.protein Gramene protein http://www.gramene.org/ Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene. ^\d+$ 78073 http://www.gramene.org/db/protein/protein_search?protein_id=$1 GR_PROTEIN False GRAMENE.PROTEIN gramene.protein gramene.protein gramene.qtl Gramene QTL http://www.gramene.org/ Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene. ^\w+$ CQG5 http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1 GR_QTL False GRAMENE.QTL gramene.qtl gramene.qtl gramene.reference Gramene Reference http://www.gramene.org Literature references in Gramene ^\d+$ 6200 http://www.gramene.org/db/literature/pub_search?ref_id=$1 gramene.ref False gramene.taxonomy Gramene Taxonomy http://www.gramene.org/ Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene. ^\d+$ 013681 https://archive.gramene.org/db/ontology/search?id=GR_tax:$1 False GRAMENE.TAXONOMY gramene.taxonomy gramene.taxonomy grassbase GrassBase https://www.kew.org/data/grasses-syn/index.htm GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species. ^(imp|gen)\d{5}$ imp10873 https://www.kew.org/data/grasses-db/www/$1 False P1832 greengenes 16S rRNA gene database http://greengenes.lbl.gov/ A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ^\d+$ 100000 GLAndersen@lbl.gov http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1 False GREENGENES nbdc01824 greengenes greengenes greengenes r3d100010549 grid Global Research Identifier Database https://www.grid.ac/ International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. ^grid\.[0-9]+\.[a-f0-9]{1,2}$ grid.225360.0 https://www.grid.ac/institutes/$1 False GRID grid grid grin Germplasm Resources Information Network http://www.ars-grin.gov/ 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. 159787 http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1 False grin grin.taxonomy GRIN URL http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. ^\d+$ 19333 http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1 False GRIN.TAXONOMY grin.taxonomy grin.taxonomy P1421 gro Gene Regulation Ontology http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html 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. Lipid vlee@ebi.ac.uk http://www.bootstrep.eu/ontology/GRO#$1 True GRO GRO grsdb G-Rich Sequences Database http://bioinformatics.ramapo.edu/GRSDB2/ GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. ^\d+$ 10142 http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1 False GRSDB grsdb grsdb grsdb gsfa General Standard for Food Additives Online Database http://www.fao.org/gsfaonline "The ""Codex General Standard for Food Additives"" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database." ^\d+$ 174 http://www.fao.org/gsfaonline/additives/details.html?id=$1 FAO/WHO_standards False gsso Gender, Sex, and Sexual Orientation Ontology https://gsso.research.cchmc.org/ The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. ^\d{6}$ 002368 kronkcj@mail.uc.edu http://purl.obolibrary.org/obo/GSSO_$1 False GSSO GSSO gsso gsso gsso GSSO gtex Genotype-Tissue Expression https://www.gtexportal.org The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. ^\w.+$ BRIP1 https://www.gtexportal.org/home/gene/$1 False GTEX gtex gtex gtr Genetic Testing Registry https://www.ncbi.nlm.nih.gov/gtr/ 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 AN0097748 https://www.ncbi.nlm.nih.gov/gtr/conditions/$1 medgen.gtr False gudmap Genitourinary Development Molecular Anatomy Project http://www.gudmap.org/ The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ Q-2958 simon.harding@ed.ac.uk https://gudmap.org/id/$1 False GUDMAP gudmap gudmap r3d100012193 gwascentral.marker GWAS Central Marker https://www.gwascentral.org/markers GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. ^HGVM\d+$ HGVM15354 https://www.gwascentral.org/marker/$1 False GWASCENTRAL.MARKER gwascentral.marker gwascentral.marker gwascentral.phenotype GWAS Central Phenotype https://www.gwascentral.org/phenotypes GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. ^HGVPM\d+$ HGVPM623 https://www.gwascentral.org/phenotype/$1 False GWASCENTRAL.PHENOTYPE gwascentral.phenotype gwascentral.phenotype gwascentral.study GWAS Central Study https://www.gwascentral.org/studies GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. ^HGVST\d+$ HGVST1828 https://www.gwascentral.org/study/$1 False GWASCENTRAL.STUDY gwascentral.study gwascentral.study hgvbase gxa.expt GXA Expt https://www.ebi.ac.uk/gxa/ The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. ^[AEP]-\w{4}-\d+$ E-MTAB-2037 https://www.ebi.ac.uk/gxa/experiments/$1 False GXA.EXPT gxa.expt gxa.expt gxa.gene GXA Gene https://www.ebi.ac.uk/gxa/ The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. ^\w+$ AT4G01080 https://www.ebi.ac.uk/gxa/genes/$1 False GXA.GENE gxa.gene gxa.gene habronattus Habronattus courtship http://www.mesquiteproject.org/ontology/Habronattus/index.html peteremidford@yahoo.com http://purl.obolibrary.org/obo/HABRONATTUS_$1 True HABRONATTUS habronattus hagr.genage The Ageing Gene Database http://genomics.senescence.info/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. 0001 jp@senescence.info http://genomics.senescence.info/genes/details.php?id=$1 False genage hagr.gendr The Dietary Restriction Gene Database http://genomics.senescence.info/diet/ 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 2 jp@senescence.info http://genomics.senescence.info/diet/details.php?id=$1 False gendr hamap High-quality Automated and Manual Annotation of microbial Proteomes https://hamap.expasy.org/ HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. ^MF_\d+$ MF_01400 alan.bridge@isb-sib.ch https://hamap.expasy.org/unirule/$1 False HAMAP 2766 hamap hamap hamap DB-0041 hancestro Human Ancestry Ontology https://ebispot.github.io/hancestro/ Human ancestry ontology for the NHGRI GWAS Catalog ^\d{4}$ 0290 dwelter.ontologist@gmail.com http://purl.obolibrary.org/obo/HANCESTRO_$1 False HANCESTRO HANCESTRO hancestro hancestro HANCESTRO hao Hymenoptera Anatomy Ontology http://hymao.org A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) ^\d{7}$ 0000187 diapriid@gmail.com http://purl.obolibrary.org/obo/HAO_$1 False HAO HAO HAO hao hao HAO hathitrust Hathi Trust Digital Library https://www.hathitrust.org Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world. ^\d+$ 008893080 https://catalog.hathitrust.org/Record/$1 False hba Human Brain Atlas https://human.brain-map.org A controlled vocabulary to support the study of transcription in the human brain ^\d+$ 4005 https://biopragmatics.github.io/providers/hba/$1 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo False hbvar A Database of Human Hemoglobin Variants and Thalassemias http://globin.cse.psu.edu/globin/hbvar This is a relational database of information about hemoglobin variants and mutations that cause thalassemia. 2526 http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1 False hbvar hc.din Health Canada Drug Identification Number https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada. ^\d{8}$ 02069237 False 2.16.840.1.113883.5.1105 hc.npn Health Canada Natural Product Number http://webprod.hc-sc.gc.ca/nhpid-bdipsn/search-rechercheReq.do?lang=eng The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada. ^\d+$ 18125 http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1 False 2.16.840.1.113883.5.1107 hc.trial Health Canada Clinical Trials Database https://health-products.canada.ca/ctdb-bdec Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website] ^\d+$ 239287 https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1 False hcao Human Cell Atlas Ontology https://www.humancellatlas.org Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas. False hcao hco Human Chromosome Ontology https://dbcls.rois.ac.jp/ The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes. ^.+$ MT http://biohackathon.org/resource/hco#$1 False hco hcpcs Healthcare Common Procedure Coding System https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo 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. G8944 Cynthia.Hake@cms.hhs.gov http://purl.bioontology.org/ontology/HCPCS/$1 False HCPCS HCPCS hcvdb Hepatitis C Virus Database Project http://euhcvdb.ibcp.fr/euHCVdb/ the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. ^M\d{5}$ M58335 https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1 False HCVDB hcvdb hcvdb hcv hdl Handle https://www.handle.net/ Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website) ^\d+/.+$ 2381/12775 http://hdl.handle.net/$1 handle False hdr Homeodomain Research http://research.nhgri.nih.gov/apps/homeodomain/web/ The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. ^\d+$ 63 http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1 False HDR hdr hdr 307 hdr hemonc HemOnc Terminology https://hemonc.org/ HemOnc.org is the largest freely available medical wiki of interventions, regimens, and general information relevant to the fields of hematology and oncology. ^\d+$ 15543 False hepro Health Procedure Ontology https://openlhs.github.io/HEPRO/ HEPRO is an ontology of informational entities and processes related to health procedures and health activities. ^\d{7}$ 0000001 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/HEPRO_$1 https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.owl False hesa UK Higher Education Statistics Agency https://www.hesa.ac.uk An identifier for institutions in the United Kingdom, used in GRID and ROR. ^\d+$ 0154 False hgmd Human Gene Mutation Database http://www.hgmd.cf.ac.uk/ac/index.php 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. ^[A-Z_0-9]+$ CALM1 http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 False HGMD 3265 nbdc00097 hgmd hgmd hgnc HUGO Gene Nomenclature Committee http://www.genenames.org The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. ^\d{1,5}$ 16793 elspeth@genenames.org https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 False HGNC HGNC HGNC HGNC 2298 2.16.840.1.113883.6.281 hgnc hgnc hgnc Hgnc DB-0042 P354 hgnc.genefamily HGNC gene family http://www.genenames.org The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. ^\d+$ 2029 https://www.genenames.org/cgi-bin/genefamilies/set/$1 GFAM|HGNC_GROUP|hgnc.family False HGNC.GENEFAMILY hgnc.genefamily hgnc.genefamily hgnc.genegroup hgnc.genegroup HGNC Gene Group https://www.genenames.org The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. ^\d+$ 141 https://www.genenames.org/data/genegroup/#!/group/$1 False hgnc.genegroup hgnc.symbol HGNC gene symbol https://www.genenames.org/ The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. ^[A-Za-z-0-9_]+(\@)?$ DAPK1 https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1 False HGNC.SYMBOL hgnc.symbol hgnc.symbol HgncSymbol P353 hgvs Human Genome Variation Society Nomenclature https://hgvs-nomenclature.org/stable/background/simple/ 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/). NP_003997.1:p.Trp24Cys reecehart@gmail.com http://reg.clinicalgenome.org/allele?hgvs=$1 False 2.16.840.1.113883.6.282 P3331 hinv.locus H-InvDb Locus http://h-invitational.jp/hinv/ahg-db/index.jsp H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view. ^HIX\d{7}(\.\d+)?$ HIX0004394 http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1 False HINV.LOCUS hinv.locus hinv.locus hinv.protein H-InvDb Protein http://h-invitational.jp/hinv/ahg-db/index.jsp H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view. ^HIP\d{9}(\.\d+)?$ HIP000030660 http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1 False HINV.PROTEIN hinv.protein hinv.protein hinv.transcript H-InvDb Transcript http://h-invitational.jp/hinv/ahg-db/index.jsp H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view. ^HIT\d{9}(\.\d+)?$ HIT000195363 http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1 False HINV.TRANSCRIPT hinv.transcript hinv.transcript hipsci Human Induced Pluripotent Stem Cells Initiative https://www.hipsci.org Cell line databases/resources HPSI0114i-bezi_1 https://www.hipsci.org/lines/#/lines/$1 False HipSci hivreagentprogram NIH HIV Reagent Program https://www.hivreagentprogram.org/ Cell line collections (Providers) ARP-1513 https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx False HIVReagentProgram hl7.v2codesystem HL7 V2 Code Systems https://terminology.hl7.org/codesystems-v2.html A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR. ^\d+$ 0778 http://terminology.hl7.org/CodeSystem/v2-$1 False hl7.v3codesystem HL7 V2 Code Systems https://terminology.hl7.org/codesystems-v2.html A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR. ^\w+$ AcknowledgementCondition https://terminology.hl7.org/CodeSystem-v3-$1 False hmdb Human Metabolome Database http://www.hmdb.ca/ The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. ^HMDB\d+$ HMDB00001 david.wishart@ualberta.ca http://www.hmdb.ca/metabolites/$1 HMDB False HMDB 000408 2622 nbdc00909 hmdb hmdb 244 hmdb r3d100011285 Hmdb P2057 hms.lincs.antibody HMS Library of Integrated Network-based Cellular Signatures Antibodies https://lincs.hms.harvard.edu/db/antibodies/ Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. ^8\d{4}$ 80001 https://lincs.hms.harvard.edu/db/antibodies/$1 False hms.lincs.cell HMS LINCS Cell https://lincs.hms.harvard.edu/db/cell/ Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. ^5\d{4}$ 50583 https://lincs.hms.harvard.edu/db/cells/$1 False hms.lincs.compound HMS LINCS Compound https://lincs.hms.harvard.edu/db/sm/ Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. ^1\d{4}-\d{3}$ 10001-101 https://lincs.hms.harvard.edu/db/sm/$1 HMS-LINCS|hmsl_id False hms.lincs.dataset HMS Library of Integrated Network-based Cellular Signatures Datasets https://lincs.hms.harvard.edu/db/datasets/ ^2\d{4}$ 20003 https://lincs.hms.harvard.edu/db/datasets/$1 False hoelzel Hölzel Diagnostika https://www.hoelzel-biotech.com 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. 40592-R001-100 info@hoelzel.de https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1 hölzel False hog Homologous Organ Groups https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc. ^\d{7}$ 0000255 https://biopragmatics.github.io/providers/hog/$1 ftp://ftp.bgee.org/general/ontologies/HOG.obo False hogenom Database of Complete Genome Homologous Genes Families http://pbil.univ-lyon1.fr/databases/hogenom/ HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. ^\w+$ HBG284870 perriere@biomserv.univ-lyon1.fr http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 False HOGENOM nbdc01858 hogenom hogenom hogenom DB-0044 hoip Homeostasis imbalance process ontology https://knowledge.brc.riken.jp/bioresource/ontology/HOIP An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes. ^\d{7}$ 0040379 yuki.yamagata@riken.jp http://purl.bioontology.org/ontology/HOIP/HOIP_$1 https://github.com/yuki-yamagata/hoip/raw/master/hoip_0308.owl False HOIP HOIP hom Homology Ontology https://github.com/BgeeDB/homology-ontology This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. ^\d{7}$ 0000049 bgee@sib.swiss http://purl.obolibrary.org/obo/HOM_$1 False HOM HOM HOM hom hom HOM homd.seq HOMD Sequence Metainformation http://www.homd.org/index.php The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. ^SEQF\d+$ SEQF1003 tchen@forsyth.org http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1 False HOMD.SEQ homd.seq homd.seq homd.seq homd.taxon Human Oral Microbiome Database http://www.homd.org/index.php The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. ^\d+$ 811 tchen@forsyth.org http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1 False HOMD.TAXON homd.taxon homd.taxon homd.taxon homologene HomoloGene https://www.ncbi.nlm.nih.gov/homologene/ HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. ^\d+$ 1000 sayers@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/homologene/$1 False HOMOLOGENE nbdc00101 homologene homologene homologene Homologene P593 horizon_discovery Horizon Discovery cell line collection https://horizondiscovery.com/ Cell line collections (Providers) HD+118-001 https://horizondiscovery.com/en/search?searchterm=$1 False Horizon_Discovery hoso Healthcare Organizations and Services Ontology https://openlhs.github.io/HOSO/ HOSO is an ontology of informational entities and processes related to healthcare organizations and services. ^\d{7}$ 0000001 paul.fabry@usherbrooke.ca False hovergen Homologous Vertebrate Genes Database https://pbil.univ-lyon1.fr/databases/hovergen.php 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. ^HBG\d+$ HBG004341 duret@biomserv.univ-lyon1.fr http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN False HOVERGEN nbdc00284 hovergen hovergen hovergen hp Human Phenotype Ontology http://www.human-phenotype-ontology.org/ The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. ^\d{7}$ 0011140 dr.sebastian.koehler@gmail.com http://purl.obolibrary.org/obo/HP_$1 http://purl.obolibrary.org/obo/hp.obo hpo False HP_O 1937 HPO HP_O 2.16.840.1.113883.6.339 nbdc02559 hpo hp hp hp hp HP P3841 hpa Human Protein Atlas tissue profile information http://www.proteinatlas.org/ The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. ^ENSG\d{11}$ ENSG00000026508 mathias.uhlen@scilifelab.se http://www.proteinatlas.org/$1 False HPA hpa hpa hpa r3d100010931 DB-0046 hpath Histopathology Ontology https://github.com/Novartis/hpath "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. The original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]" ^\d+$ 2000191 carlo.ravagli@novartis.com http://purl.obolibrary.org/obo/MC_$1 https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo MC False hpm.peptide Human Proteome Map Peptide http://www.humanproteomemap.org/index.php The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. ^\d+$ 9606117 http://www.humanproteomemap.org/spectrum.php?pep_id=$1 False HPM.PEPTIDE hpm.peptide hpm.peptide hpm.protein Human Proteome Map http://www.humanproteomemap.org/index.php The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. ^\d+$ 1968 http://www.humanproteomemap.org/protein.php?hpm_id=$1 False HPM.PROTEIN hpm.protein hpm.protein hprd Human Protein Reference Database http://www.hprd.org/ The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. ^\d+$ 00001 pandey@jhmi.edu http://www.hprd.org/protein/$1 False HPRD nbdc00103 hprd hprd 14 hprd r3d100010978 hpscreg Human Pluripotent Stem Cell Registry https://hpscreg.eu/ hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ BCRTi001-A stefanie.seltmann@ibmt.fraunhofer.de https://hpscreg.eu/cell-line/$1 False hPSCreg hpscreg hpscreg r3d100012863 hsapdv Human Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv Life cycle stages for Human ^\d{7}$ 0000194 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/HsapDv_$1 HsapDv False HSAPDV HSAPDV HSAPDV hsapdv hsapdv HsapDv hsdb Hazardous Substances Data Bank https://pubchem.ncbi.nlm.nih.gov/source/hsdb The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. ^\d+$ 5621 https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1 False nbdc00930 P2062 hso Health Surveillance Ontology https://w3id.org/hso "The health Surveillance Ontology (HSO) focuses on ""surveillance system level data"", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance." ^\d{7}$ 0000062 fernanda.dorea@sva.se http://purl.obolibrary.org/obo/HSO_$1 False HSO HSO hso hso HSO hssp Database of homology-derived secondary structure of proteins http://swift.cmbi.kun.nl/swift/hssp/ HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. ^\w{4}$ 102l chris@sanderlab.org ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2 False HSSP hssp hssp hssp htn Hypertension Ontology https://github.com/aellenhicks/htn_owl An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines ^\d{8}$ 00000014 aellenhicks@gmail.com http://purl.obolibrary.org/obo/HTN_$1 False HTN HTN htn htn HTN huge Human Unidentified Gene-Encoded http://www.kazusa.or.jp/huge/ The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. ^KIAA\d{4}$ KIAA0001 ohara@kazusa.or.jp https://www.kazusa.or.jp/huge/gfpage/$1 False HUGE nbdc00104 huge huge huge DB-0049 iao Information Artifact Ontology https://github.com/information-artifact-ontology/IAO/ An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. ^\d{7}$ 0000030 zhengj2007@gmail.com http://purl.obolibrary.org/obo/IAO_$1 http://purl.obolibrary.org/obo/iao.obo False IAO IAO IAO iao iao iao iao IAO icd10 International Classification of Diseases, 10th Revision https://icd.who.int/browse10 "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. Note that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States." ^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\.[0-9]))?))$ C34 info@who.int https://icd.who.int/browse10/2019/en#/$1 ICD|ICD-10|ICD10|ICD10WHO False ICD10 447 ICD ICD10 2611 2.16.840.1.113883.6.3 icd icd icd P494 icd10cm International Classification of Diseases, 10th Revision, Clinical Modification https://www.icd10data.com/ICD10CM ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS). ^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$ F45.21 pbrooks@hcfa.gov https://icd.codes/icd10cm/$1 ICD10CM False ICD10CM ICD10CM 2.16.840.1.113883.6.90 P4229 icd10pcs International Classification of Diseases, 10th Revision, Procedure Coding System https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). 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." 01N50ZZ patricia.brooks2@cms.hhs.gov https://www.findacode.com/code.php?set=ICD10PCS&c=$1 False ICD10PCS ICD10PCS 2.16.840.1.113883.6.4 P1690 icd11 International Classification of Diseases, 11th Revision https://icd.who.int/ Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease. ^[1-9]\d*$ 402558626 https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1 ICD-11 False 2.16.840.1.113883.6.347 nbdc02556 P7807 icd9 International Classification of Diseases, 9th Revision https://www.cdc.gov/nchs/icd/icd9.htm The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics. ^(\d\d\d|V\d\d|E[8-9]\d\d)(\.\d{1,2})?$ 277.9 http://www.icd9data.com/getICD9Code.ashx?icd9=$1 ICD9|ICD9_2005|MTHICD9_2006 False 2.16.840.1.113883.6.42 P493 icd9cm International Classification of Diseases, 9th Revision, Clinical Modification https://www.cdc.gov/nchs/icd/icd9cm.htm ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$ 784 pbrooks@hcfa.gov http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1 IC9CM|ICD9CM|ICD9CM_2005|ICD9CM_2006|ICDCM_2005 False ICD9CM ICD9CM 2.16.840.1.113883.6.2 P1692 icdc Integrated Canine Data Commons https://caninecommons.cancer.gov/#/ The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer. ^\d{6}$ 000009 annika.jahnke-bornemann@uni-hamburg.de https://caninecommons.cancer.gov/#/study/$1 False icdc r3d100010405 icdo International Classification of Diseases for Oncology https://www.who.int/classifications/icd/adaptations/oncology/en/ The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases ^[8-9]\d{3}(/[0-3])?$ 9861/3 http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1 ICD-O|ICDO False 445 2.16.840.1.113883.6.43 icdo P563 iceberg.cime ICEberg cis-integrative and mobilizable element https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_CIME.php?type=alpha&alpha=100 ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements. ^\d+$ 6 hyou@sjtu.edu.cn https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME False iceberg iceberg.element ICEberg integrative and conjugative element https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=alpha&alpha=100 ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. ^\d+$ 100 https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1 iceberg.ice False ICEBERG.ELEMENT iceberg.element iceberg.element iceberg iceberg.family ICEberg family https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_fam.php ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. ^\d+$ 1 hyou@sjtu.edu.cn https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1 False ICEBERG.FAMILY iceberg.family iceberg.family iceberg iceberg.ime ICEberg integrative and mobilizable element https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_IME.php?type=alpha&alpha=100 ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements. ^\d+$ 1 hyou@sjtu.edu.cn https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME False iceberg iceo Integrative and Conjugative Element Ontology https://github.com/ontoice/ICEO A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning. ^\d{7}(_\d)?$ 0000712_1 liumeng94@sjtu.edu.cn http://purl.obolibrary.org/obo/ICEO_$1 False ICEO ICEO iceo iceo ICEO icepo Ion Channel Electrophysiology Ontology https://download.nextprot.org/pub/current_release/controlled_vocabularies/ The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ^\d{7}$ 0000002 pascale.gaudet@isb-sib.ch https://biopragmatics.github.io/providers/icepo/$1 https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo False icf International Classification of Functioning, Disability and Health https://icd.who.int/dev11/l-icf/en The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels. ^\d+$ 326705068 info@who.int http://id.who.int/icd/entity/$1 False ICF ICF 2.16.840.1.113883.6.254 iclc Interlab Cell Line Collection http://www.iclc.it Cell line collections (Providers) ^\w{3}\d+$ ATL98012 http://www.iclc.it/details/det_list.php?line_id=$1 False ICLC icldb Insect Cell Line Database https://entomology.ca.uky.edu/aginsectcellsdatabase 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) 64ba surjeet.arya@uky.edu https://entomology.ca.uky.edu/content/$1 False ICLDB ico Informed Consent Ontology https://github.com/ICO-ontology/ICO The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. ^\d{7}$ 0000066 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/ICO_$1 False ICO ICO ICO ico ico ICO ideal Intrinsically Disordered proteins with Extensive Annotations and Literature https://www.ideal-db.org IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. ^IID\d+$ IID00001 sfukuchi@maebashi-it.ac.jp http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1 False IDEAL nbdc01456 ideal ideal 701 DB-0251 ido Infectious Disease Ontology http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. ^\d{7}$ 0000504 Lindsay.Cowell@utsouthwestern.edu http://purl.obolibrary.org/obo/IDO_$1 False IDO IDO IDO ido ido ido ido IDO idocovid19 The COVID-19 Infectious Disease Ontology https://github.com/infectious-disease-ontology-extensions/ido-covid-19 The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease. ^\d{7}$ 0001191 johnbeverley2021@u.northwestern.edu http://purl.obolibrary.org/obo/COVIDO_$1 https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19 False IDO-COVID-19 IDO-COVID-19 idocovid19 idoden Dengue Fever Ontology https://bioportal.bioontology.org/ontologies/IDODEN An ontology for dengue fever. ^\d{7}$ 0003463 elvira@imbb.forth.gr http://purl.bioontology.org/ontology/IDODEN_$1 False IDODEN IDODEN idog Integrated Resource for Domestic Dog https://ngdc.cncb.ac.cn/idog/ Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses. ^\d+$ 4 baoym@big.ac.cn https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1 False nbdc02480 r3d100012176 idomal Malaria Ontology https://www.vectorbase.org/ontology-browser An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. ^(5?)\d{7}$ 0002350 topalis@imbb.forth.gr http://purl.obolibrary.org/obo/IDOMAL_$1 http://purl.obolibrary.org/obo/idomal.obo True IDOMAL IDOMAL IDOMAL idomal idomal IDOMAL idoo Identifiers.org Ontology http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology Identifiers.org Ontology ^[0-9a-zA-Z]+$ DataCollection http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1 False idoo idoo idot Identifiers.org Terms http://biomodels.net/vocab/idot.rdf Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. ^[A-Za-z]+$ identifierPattern https://biomodels.net/vocab/idot.rdf#$1 False idot idot idot idpo Intrinsically Disordered Proteins Ontology https://www.disprot.org/ontology IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR. ^\d{5}$ 00056 f.quaglia@ibiom.cnr.it https://www.disprot.org/idpo/IDPO:$1 False idr Image Data Resource https://idr.openmicroscopy.org "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image"" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools." ^[0-9]{4}$ 0001 j.a.moore@dundee.ac.uk https://idr.openmicroscopy.org/search/?query=Name:idr$1 False idr r3d100012435 iedb Immune Epitope Database https://www.lji.org/ The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes. ^[0-9]+$ 1038233 rvita@liai.org https://www.iedb.org/reference/$1 False nbdc00924 iedb tied r3d100012702 ieee.author IEEE Xplore author ID https://ieeexplore.ieee.org identifier for an author in IEEE Xplore ^[1-9]\d*$ 37271072100 https://ieeexplore.ieee.org/author/$1 False P6479 ieee.document IEEE Xplore document ID https://ieeexplore.ieee.org identifier for a document in IEEE Xplore ^[1-9]\d*$ 1580791 https://ieeexplore.ieee.org/document/$1 False P6480 ietf.language Internet Engineering Task Force Language Tag http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry Shorthand representations of languages and their subtypes ^\w{2,3}(-\w+)?$ en-GB bcp47 False 2022 P305 iev Event (INOH pathway ontology) http://www.inoh.org The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure. ^\d{7}$ 0000000 http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1 True IEV iev iev igrhcellid Integrated Genomic Resources of human Cell Lines for Identification http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi Cell line databases/resources ACHN http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1 False IGRhCellID igsn International Geo Sample Number http://www.geosamples.org/ IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents. ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$ AU124 jens.klump@csiro.au http://igsn.org/$1 False igsn igsn igsr International Genome Sample Resource https://www.internationalgenome.org/ 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. NA06985 flicek@ebi.ac.uk https://www.internationalgenome.org/data-portal/sample/$1 False IGSR r3d100010180 ihw International Histocompatibility Workshop cell lines https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics. ^IHW\d+$ IHW09326 False IHW illumina.probe Illumina Probe Identifier https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip. ^ILMN_\d+$ ILMN_129894 False imanis Imanis Life Sciences cell line products https://www.imanislife.com/collections/cell-lines/ Cell line collections (Providers) CL070 https://www.imanislife.com/?s=$1 False Imanis imdrf International Medical Device Regulators Forum http://www.imdrf.org/ The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence. False imex International Molecular Exchange https://www.imexconsortium.org/ The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. ^\d+(-\d+)?$ 19210-3 orchard@ebi.ac.uk https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1 False IMEX imex imex 422 imex r3d100010669 img.gene Integrated Microbial Genomes Gene http://img.jgi.doe.gov/ The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. ^\d+$ 638309541 nckyrpides@lbl.gov http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1 False IMG.GENE img.gene img.gene img.gene img.taxon Integrated Microbial Genomes Taxon http://img.jgi.doe.gov/ The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. ^\d+$ 648028003 nckyrpides@lbl.gov http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1 False IMG.TAXON img.taxon img.taxon img.taxon imgt.hla IMGT/HLA human major histocompatibility complex sequence database https://www.ebi.ac.uk/imgt/hla/allele.html IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. ^[A-Z0-9*:]+$ A*01:01:01:01 steven.marsh@ucl.ac.uk https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1 IPD-IMGT/HLA False IMGT.HLA IPD-IMGT/HLA 2773 nbdc00106 imgt.hla imgt.hla imgthla r3d100010804 imgt.ligm ImMunoGeneTics database covering immunoglobulins and T-cell receptors http://www.imgt.org/ IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. ^M\d+$ M94112 marie-paule.lefranc@umontpellier.fr http://www.imgt.org/ligmdb/view?id=$1 False IMGT.LIGM imgt.ligm imgt.ligm imgt.ligm imgt.primerdb IMGT/PRIMER-DB http://imgt.org/IMGTPrimerDB/ The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR). IPP900099 http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList False imgt.primerdb r3d100012535 imotdb Database of Spatially Interacting Motifs in Proteins http://caps.ncbs.res.in/imotdb/ 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. 53784 http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1 True 207 imotdb imr Molecule role (INOH Protein name/family name ontology) http://www.inoh.org MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data. ^\d{7}$ 0000001 curator@inoh.org http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1 True IMR imr imr imsr.apb NHMRC Australian PhenomeBank https://pb.apf.edu.au/phenbank/homePage.html The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID] ^\d+$ 7345 https://pb.apf.edu.au/phenbank/strain.html?id=$1 False IMSR_APB imsr_em European Mouse Mutant Archive https://www.infrafrontier.eu/emma/ Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID] ^\d+$ 11478 d.smedley@qmul.ac.uk https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1 False IMSR_EM imsr_tac Taconic Biosciences https://www.taconic.com/ Supplier of mice for research purposes. [from RRID] 1178 https://scicrunch.org/resolver/RRID:IMSR_TAC_$1 False IMSR_TAC inaturalist.observation iNaturalist Observation https://www.inaturalist.org/observations The identifier for an observation in iNaturalist ^[1-9]\d*$ 36010371 https://www.inaturalist.org/observations/$1 False P5683 inaturalist.place iNaturalist Place https://www.inaturalist.org/places Identifier for a place in iNaturalist ^[1-9]\d*$ 7207 https://www.inaturalist.org/places/$1 False P7471 inaturalist.taxon iNaturalist Taxonomy https://www.inaturalist.org/taxa Identifier for a species in iNaturalist ^[1-9]\d{0,6}$ 21723 https://www.inaturalist.org/taxa/$1 False P3151 inaturalist.user iNaturalist User https://www.inaturalist.org/users Identifier for a user in iNaturalist ^[1-9]\d*$ 1426686 https://www.inaturalist.org/users/$1 False inchi InChI http://www.chemspider.com/ 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. ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$ InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 jmg11@cam.ac.uk http://www.chemspider.com/$1 False INCHI inchi inchi P234 inchikey InChIKey http://www.chemspider.com/ The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])$ RYYVLZVUVIJVGH-UHFFFAOYSA-N http://www.chemspider.com/inchikey=$1 False INCHIKEY inchikey inchikey InchiKey P235 inhand The International Harmonization of Nomenclature and Diagnostic criteria https://www.goreni.org/gr3_nomenclature.php The standard reference for nomenclature and diagnostic criteria in toxicologic pathology. harkemaj@msu.edu False inn International Nonproprietary Names https://www.who.int/teams/health-product-and-policy-standards/inn Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. fluticasone https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1 INN_ID False P2275 innatedb A Knowledge Resource for Innate Immunity Interactions and Pathways http://www.innatedb.ca/ 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. 20021 david.lynn@flinders.edu.au http://www.innatedb.ca/getGeneCard.do?id=$1 False nbdc01870 264 innatedb r3d100010676 ino Interaction Network Ontology https://github.com/INO-ontology/ino he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. ^\d{7}$ 0000003 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/INO_$1 False INO INO ino ino INO insdc Nucleotide Sequence Database https://www.ncbi.nlm.nih.gov/Genbank/ The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4,6}\d{8,10}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ X58356 https://www.ncbi.nlm.nih.gov/nuccore/$1 False INSDC nbdc02567 insdc insdc insdc Insdc insdc.cds INSDC CDS http://getentry.ddbj.nig.ac.jp The coding sequence or protein identifiers as maintained in INSDC. ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ AAA35559 http://getentry.ddbj.nig.ac.jp/getentry/dad/$1 False INSDC.CDS insdc.cds insdc.cds ncbiprotein insdc.gca Genome assembly database - INSDC accessions https://www.ebi.ac.uk/ena/browse/genome-assembly-database The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. ^GCA_[0-9]{9}(\.[0-9]+)?$ GCA_000155495.1 https://www.ebi.ac.uk/ena/data/view/$1 False INSDC.GCA insdc.gca insdc.gca ncbi.assembly insdc.gcf Genome assembly database - RefSeq accessions https://www.ncbi.nlm.nih.gov/ The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage. ^GCF_[0-9]{9}(\.[0-9]+)?$ GCF_000001405 https://www.ncbi.nlm.nih.gov/datasets/genome/$1 insdc.gcf False refseq.gcf ncbi.assembly insdc.run International Nucleotide Sequence Database Collaboration (INSDC) Run https://www.insdc.org/ An experimental run, served thrugh the ENA ^(E|D|S)RR[0-9]{6,}$ ERR436051 https://www.ebi.ac.uk/ena/browser/view/$1 False insdc.sra Sequence Read Archive https://www.ncbi.nlm.nih.gov/sra The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database. ^[SED]R[APRSXZ]\d+$ SRX000007 Hugh.Shanahan@rhul.ac.uk https://www.ncbi.nlm.nih.gov/sra/$1 False INSDC.SRA insdc.sra insdc.sra r3d100010775 intact IntAct protein interaction database https://www.ebi.ac.uk/intact/ IntAct provides a freely available, open source database system and analysis tools for protein interaction data. ^EBI\-[0-9]+$ EBI-2307691 orchard@ebi.ac.uk https://www.ebi.ac.uk/intact/interaction/$1 False INTACT nbdc00507 intact intact 111 intact r3d100010671 Intact DB-0051 intact.molecule IntAct Molecule https://www.ebi.ac.uk/intact/ IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. ^EBI\-[0-9]+$ EBI-366083 https://www.ebi.ac.uk/intact/search?query=$1 False INTACT.MOLECULE intact.molecule intact.molecule integbio Integbio https://integbio.jp/en/ Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about) ^nbdc\d+$ nbdc01071 kwsm@dbcls.rois.ac.jp https://integbio.jp/dbcatalog/en/record/$1 False interfil Human Intermediate Filament Database http://www.interfil.org 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. NM_006262 http://www.interfil.org/details.php?id=$1 False interfil interlex InterLex https://www.fdilab.org InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ^[0-9]+$ 0101963 mmartone@ucsd.edu https://scicrunch.org/scicrunch/interlex/view/ilx_$1 ILX False ilx P696 interpro InterPro http://www.ebi.ac.uk/interpro/index.html InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. ^IPR\d{6}$ IPR016380 interhelp@ebi.ac.uk https://www.ebi.ac.uk/interpro/entry/InterPro/$1 IP|IPR|InterPro False IPR 1133 nbdc00108 interpro interpro ipr interpro r3d100010798 Interpro DB-0052 P2926 iobc Interlinking Ontology for Biological Concepts https://github.com/kushidat/IOBC "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. 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""." 200906038218908385 kushida@biosciencedbc.jp http://purl.jp/bio/4/id/$1 False IOBC IOBC ipi International Protein Index http://www.ebi.ac.uk/IPI 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. IPI00000001 http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default True IPI nbdc00911 ipi irct Iranian Registry of Clinical Trials https://en.irct.ir/ "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage) Note that the website uses a different identifier then the one reported in this semantic space." ^IRCT\d+N\d+$ IRCT20080904001199N7 False ird.segment IRD Segment Sequence http://www.fludb.org/ 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). ^\w+(\_)?\d+(\.\d+)?$ CY077097 richard.scheuermann@nih.gov http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 False IRD.SEGMENT ird.segment ird.segment ird.segment irefweb iRefWeb http://wodaklab.org/iRefWeb/ iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived. ^\d+$ 617102 shoshana@sickkids.ca http://wodaklab.org/iRefWeb/interaction/show/$1 False IREFWEB irefweb irefweb 300 irefweb r3d100012725 iresite Database of experimentally verified IRES structures http://www.iresite.org 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. 322 martin.pospisek@natur.cuni.cz http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1 False nbdc01752 iresite iro Insect Resistance Ontology ^\d{7}$ 0000008 https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1 True isbn International Standard Book Number http://isbndb.com/ The International Standard Book Number (ISBN) is for identifying printed books. ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ 9781584885658 http://isbndb.com/search-all.html?kw=$1 ISBN-10|ISBN-13 False ISBN-13 2634 isbn isbn isbn ised Influenza Sequence and Epitope Database http://influenza.korea.ac.kr ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea. AY209920 False ised isfinder Insertion sequence elements database http://www-is.biotoul.fr/i ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. ^IS\w+(\-\d)?$ ISA1083-2 patricia.siguier@univ-tlse3.fr https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1 False ISFINDER nbdc00510 isfinder isfinder isfinder isni International Standard Name Identifier http://www.isni.org "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC. The mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described." ^[0-9]{15}[0-9X]{1}$ 000000012281955X http://www.isni.org/isni/$1 False 20464 isni isni P213 iso.3166 ISO 3166-1 Country Code https://www.iso.org/iso-3166-country-codes.html An identifier for a country in numeric format per ISO 3166-1 ^\d+$ 554 https://data.who.int/countries/$1 False P299 iso15926 ISO 15926-14 https://15926.org/home/ 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/) activityBoundOf http://standards.iso.org/iso/15926/part14/$1 False isrctn International Traditional Medicine Clinical Trial Registry https://www.isrctn.com/ The ISRCTN registry is a primary clinical trial registry recognised by WHO and ICMJE that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage) ^ISRCTN\d+$ ISRCTN10175490 https://www.isrctn.com/$1 False issn International Standard Serial Number https://portal.issn.org The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. ^\d{4}-\d{3}[\dX]$ 0745-4570 https://portal.issn.org/resource/ISSN/$1 False ISSN issn issn istransbase ISTransbase https://istransbase.scbdd.com/ 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. IST028 oriental-cds@163.com https://istransbase.scbdd.com/database/trans/$1 False itis Integrated Taxonomic Information System https://www.itis.gov/ Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world. ^\d+$ 589462 itiswebmaster@itis.gov https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1 False 17791 nbdc00916 r3d100011213 P815 itmctr International Traditional Medicine Clinical Trial Registry http://itmctr.ccebtcm.org.cn The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website) ^ITMCTR\d+$ ITMCTR2023000002 False ito Intelligence Task Ontology https://openbiolink.github.io/ITOExplorer/ 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. ^\d+$ 01625 matthias.samwald@meduniwien.ac.at https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1 False ITO ITO ito iuphar.family IUPHAR family http://www.guidetopharmacology.org/ The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. ^\d+$ 78 http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1 IUPHARfam False IUPHAR.FAMILY iuphar.family iuphar.family iuphar.family iuphar.ligand Guide to Pharmacology Ligand http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands. ^\d+$ 1755 http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 IUPHAR_LIGAND|IUPHAR_LIGAND_ID False IUPHAR.LIGAND iuphar.ligand iuphar.ligand IupharLigand P595 iuphar.receptor Guide to Pharmacology Target http://www.guidetopharmacology.org/targets.jsp The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. ^\d+$ 101 simon.harding@igmm.ed.ac.uk http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 IUPHAR_GPCR|IUPHARobj False IUPHAR.RECEPTOR iuphar.receptor iuphar.receptor DB-0182 P5458 ivdb Influenza Virus Database http://influenza.psych.ac.cn/ 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. E13035 http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1 False ivdb jax Jackson Laboratories Strain https://www.jax.org/strain Information about the C57BL/6J. Includes genetic background and disease data. ^\d{6}$ 004435 https://www.jax.org/strain/$1 False JAX IMSR_JAX jaxmice JAX Mice http://jaxmice.jax.org/ JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory. ^\d+$ 005012 http://jaxmice.jax.org/strain/$1.html False JAXMICE jaxmice jaxmice jcggdb Japan Consortium for Glycobiology and Glycotechnology Database http://jcggdb.jp/index_en.html JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. ^JCGG-STR\d{6}$ JCGG-STR008690 http://jcggdb.jp/idb/jcggdb/$1 False JCGGDB nbdc01164 jcggdb jcggdb jcm Japan Collection of Microorganisms http://www.jcm.riken.go.jp/ The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. ^\d+$ 17254 http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1 False JCM jcm jcm jcm jcrb JRBC Cell Bank https://cellbank.nibiohn.go.jp Cell line collections (Providers) ^JCRB\d+$ JCRB1355 https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1 False JCRB jcsd Japan Chemical Substance Dictionary http://jglobal.jst.go.jp/en/ The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ J55.713G http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1 False JCSD jcsd jcsd jcsd jgi.proposal Joint Genome Institute Proposals https://genome.jgi.doe.gov/portal/ Identifiers for proposals/projects at the Joint Genome Institute ^\d+$ 502930 sewilson@lbl.gov https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1 False jrct Japan Registry of Clinical Trials https://jrct.niph.go.jp This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website) ^jRCT\w?\d+$ jRCTs041220087 https://jrct.niph.go.jp/en-latest-detail/$1 False jstor Digital archive of scholarly articles http://www.jstor.org/ JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration. ^\d+$ 3075966 http://www.jstor.org/stable/$1 False JSTOR jstor jstor jws JWS Online http://jjj.biochem.sun.ac.za/models/ JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. ^\w+$ achcar11 brettolivier@gmail.com https://jjj.bio.vu.nl/models/$1 False JWS jws jws jws kaggle Kaggle https://kaggle.com Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions. ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$ nasa/kepler-exoplanet-search-results https://www.kaggle.com/$1 False kaggle kaggle r3d100012705 kaken e-Rad researcher number https://nrid.nii.ac.jp/ja/search/?kw= identifier for researchers in Japan used in goverment-based research funding (from 1980s) ^\d{8}$ 00011461 https://nrid.nii.ac.jp/ja/nrid/10000$1 False P9776 kclb Korean Cell Line Bank https://cellbank.snu.ac.kr/english Cell line collections (Providers) 10020.2 https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1 False KCLB kcris Korean Clinical Research Information Service https://cris.nih.go.kr "The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page) Note that the web page that resolves this trial does not correspond to the semantic space" ^KCT\d+$ KCT0008394 False kegg Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ 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. ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$ hsa00190 http://www.kegg.jp/entry/$1 KEGG True KEGG 000409 nbdc00530 kegg kegg 16 DB-0053 kegg.brite KEGG BRITE http://www.genome.jp/kegg/brite.html 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. ko00071 http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1 False nbdc00115 kegg.brite kegg kegg.compound KEGG Compound https://www.genome.jp/kegg/ligand.html KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. ^C\d+$ C12345 kanehisa@kuicr.kyoto-u.ac.jp https://www.kegg.jp/entry/$1 KEGG COMPOUND|KEGG.COMPOUND False KEGG.COMPOUND 2605 nbdc00814 kegg.compound kegg.compound kegg.compound P665 kegg kegg.dgroup KEGG Drug Group http://www.genome.jp/kegg/reaction/ " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups. Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc. Structure - grouped as similar chemical structures having the same skeleton, etc. Target - grouped by drug targets Class - drug classes often representing similar mechanisms of action Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters Chemical groups are often used for identifying essentially the same active ingredients of drugs in different countries." ^DG\d+$ DG00301 KEGG_DGROUP|KEGG_DRUG_GROUP False kegg kegg.disease KEGG Disease http://www.genome.jp/kegg/disease/ 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. ^H\d+$ H00076 http://www.kegg.jp/entry/$1 False KEGG.DISEASE nbdc00813 kegg.disease kegg.disease kegg.disease kegg kegg.drug KEGG Drug https://www.genome.jp/kegg/drug/ KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. ^D\d+$ D00123 kanehisa@kuicr.kyoto-u.ac.jp https://www.kegg.jp/entry/$1 KEGG DRUG|KEGG.DRUG False KEGG.DRUG 2609 nbdc00812 kegg.drug kegg.drug kegg.drug P665 kegg kegg.environ KEGG Environ http://www.genome.jp/kegg/drug/environ.html KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable. ^(ev\:)?E\d+$ ev:E00032 http://www.kegg.jp/entry/$1 KEGG.EDRUG True KEGG.ENVIRON nbdc01059 kegg.environ kegg.environ kegg kegg.enzyme KEGG Enzyme http://www.genome.jp/dbget-bin/www_bfind?enzyme 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. http://www.genome.jp/dbget-bin/www_bget?ec:$1 False kegg eccode kegg.genes KEGG Genes http://www.genome.jp/kegg/genes.html KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. ^\w+:[\w\d\.-]*$ bsu:BSU01340 kanehisa@kuicr.kyoto-u.ac.jp http://www.kegg.jp/entry/$1 False KEGG.GENES kegg.genes kegg.genes kegg.gene P665 kegg kegg.genome KEGG Genome http://www.genome.jp/kegg/catalog/org_list.html KEGG Genome is a collection of organisms whose genomes have been completely sequenced. ^(T0\d+|\w{3,5})$ T06648 kanehisa@kuicr.kyoto-u.ac.jp http://www.kegg.jp/entry/$1 kegg_genome|kegg_genomes False KEGG.GENOME nbdc00816 kegg.genome kegg.genome kegg.genome P665 kegg kegg.glycan KEGG Glycan https://www.genome.jp/kegg/glycan/ KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. ^G\d+$ G00123 kanehisa@kuicr.kyoto-u.ac.jp https://www.kegg.jp/entry/$1 False KEGG.GLYCAN 2613 nbdc00533 kegg.glycan kegg.glycan kegg.glycan kegg kegg.ligand KEGG LIGAND http://www.genome.ad.jp/kegg/docs/upd_ligand.html http://www.genome.jp/dbget-bin/www_bget?cpd:$1 True kegg kegg.metagenome KEGG Metagenome http://www.genome.jp/kegg/catalog/org_list3.html The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. ^T3\d+$ T30002 kanehisa@kuicr.kyoto-u.ac.jp http://www.kegg.jp/entry/$1 False KEGG.METAGENOME kegg.metagenome kegg.metagenome kegg.metagenome kegg kegg.module KEGG Module http://www.kegg.jp/kegg/module.html KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. ^([a-z]{3,5}_)?M\d{5}$ M00002 http://www.kegg.jp/entry/$1 False KEGG.MODULE nbdc01428 kegg.module kegg.module kegg kegg.orthology KEGG Orthology http://www.genome.jp/kegg/ko.html KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. ^K\d+$ K00001 http://www.kegg.jp/entry/$1 False KEGG.ORTHOLOGY kegg.orthology kegg.orthology kegg.orthology kegg kegg.pathway KEGG Pathways Database https://www.genome.jp/kegg/pathway.html KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. ^\w{2,4}\d{5}$ rsk00410 kanehisa@kuicr.kyoto-u.ac.jp https://www.kegg.jp/entry/$1 KEGG-path|KEGG_PATHWAY False KEGG.PATHWAY 2343 kegg.pathway kegg.pathway kegg.pathway P665 kegg kegg.rclass KEGG Reaction Class http://www.genome.jp/kegg/reaction/ KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns. ^RC\d+$ RC00001 KEGG_RCLASS|KEGG_REACTION_CLASS False nbdc00860 kegg kegg.reaction KEGG Reaction https://www.genome.jp/kegg/reaction/ KEGG reaction contains our knowledge on the universe of reactions that are relevant to life. ^R\d+$ R00100 kanehisa@kuicr.kyoto-u.ac.jp https://www.kegg.jp/entry/$1 KEGG_REACTION False KEGG.REACTION 2608 nbdc00818 kegg.reaction kegg.reaction kegg.reaction P665 kegg kerafast Kerafast cell lines https://www.kerafast.com/ Cell line collections (Providers) EJH014 https://www.kerafast.com/Search?SearchTerm="$1" False Kerafast kestrelo KESTREL Ontology https://gitlab.pnnl.gov/kestrel/kestrel_ontology An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains ^\d{7}$ 0000001 lindsey.anderson@pnnl.gov http://purl.obolibrary.org/obo/kestrelo_$1 False knapsack KNApSAcK http://www.knapsackfamily.com/KNApSAcK/ "KNApSAcK provides information on metabolites and the taxonomic class with which they are associated." ^C\d{8}$ C00000001 http://www.knapsackfamily.com/knapsack_core/information.php?word=$1 False KNAPSACK nbdc00545 knapsack knapsack P2064 kupo Kidney and Urinary Pathway Ontology http://www.kupkb.org/ ^\d{7}$ 0001009 True kyinno KYinno cell lines https://www.kyinno.com/ Cell line collections (Providers) KC-0979 https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf False KYinno labo clinical LABoratory Ontology https://github.com/OpenLHS/LABO LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. ^\d{7}$ 0000124 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/LABO_$1 False LABO LABO labo labo LABO langual Langua aLimentaria Thesaurus https://www.langual.org "Langual stands for ""langua alimentaria"" or ""language of food"". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases" ^B\d+$ B2067 https://www.langual.org/langual_thesaurus.asp?termid=$1 False lattes Lattes Platform number https://lattes.cnpq.br number for the Lattes Platform entry on the person or group. Relationship between entry and subject must be supported by a source ^\d{16}$ 0061106995455595 https://lattes.cnpq.br/$1 False P1007 lbctr Lebanon Clinical Trials Registry https://lbctr.moph.gov.lb/ The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage) ^LBCTR\d+$ LBCTR2023015204 False lbo Livestock Breed Ontology http://bioportal.bioontology.org/ontologies/LBO A vocabulary for cattle, chicken, horse, pig, and sheep breeds. ^\d{7}$ 0000487 caripark@iastate.edu https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_$1 https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo False LBO LBO LBO lbo lcsh Library of Congress Subject Headings https://id.loc.gov/authorities Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage) ^\w{1,2}\d{8,10}$ nb2018006591 https://id.loc.gov/authorities/$1 lcnaf|lcnafid False 454 P244 leafsnap Leafsnap http://leafsnap.com/ identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide Amelanchier laevis http://leafsnap.com/species/$1/ False P10538 lei Global LEI Index https://www.gleif.org/ Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland. ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$ HWUPKR0MPOU8FGXBT394 https://www.gleif.org/lei/$1 False lei lei lepao Lepidoptera Anatomy Ontology https://github.com/insect-morphology/lepao The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. ^\d{7}$ 0000005 lagonzalezmo@unal.edu.co http://purl.obolibrary.org/obo/LEPAO_$1 False LEPAO LEPAO lepao lepao LEPAO lgai.cede LG Chemical Entity Detection Dataset (LGCEDe) https://www.lgresearch.ai LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR). ^LGCEDe-S-\d{9}$ LGCEDe-S-000002244 https://s3.us-east-2.amazonaws.com/lg.cede/$1 False lgai.cede lgic Ligand-Gated Ion Channel database https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. ^\w+$ 5HT3Arano https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php True LGIC lgic lgic lgicdb licebase LiceBase https://licebase.org Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. ^[A-Za-z0-9\-\/]+$ EMLSAT00000003403 Inge.Jonassen@uib.no https://licebase.org/?q=$1 False LICEBASE nbdc02217 licebase licebase r3d100013547 ligandbook LigandBook https://ligandbook.org/ Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community. ^[0-9]+$ 785 https://ligandbook.org/package/$1 False ligandbook ligandbook ligandbox LigandBox http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$ D00001 http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1 False LIGANDBOX nbdc00551 ligandbox ligandbox ligandexpo Ligand Expo http://ligand-depot.rutgers.edu/index.html Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. ^(\w){3}$ ABC jwest@rcsb.rutgers.edu http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid False LIGANDEXPO nbdc01864 ligandexpo ligandexpo 154 ligandexpo ligea Cancer cell LInes GEne fusions portAl http://hpc-bioinformatics.cineca.it/fusion/main Polymorphism and mutation databases CCLE_867 http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1 False LiGeA limore Liver Cancer Model Repository https://www.picb.ac.cn/limore/home Cell line databases/resources Li7 https://www.picb.ac.cn/limore/cellLines/single?para=$1 False LIMORE lincs.cell LINCS Cell http://lincsportal.ccs.miami.edu/cells/ The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease. ^(LCL|LDC|ES|LSC|LPC)-\d+$ LCL-2085 http://lincsportal.ccs.miami.edu/cells/#/view/$1 LINCS_LDP False LINCS.CELL LINCS_LDP lincs.cell lincs.cell lincs.data LINCS Data http://lincsportal.ccs.miami.edu/datasets/ The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level). ^[EL]D[SG]-\d+$ LDS-1110 http://lincsportal.ccs.miami.edu/datasets/#/view/$1 False LINCS.DATA lincs.data lincs.data lincs.protein LINCS Protein http://lincs.hms.harvard.edu/db/proteins/ The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. ^\d+$ 200282 https://lincs.hms.harvard.edu/db/proteins/$1 False LINCS.PROTEIN lincs.protein lincs.protein lincs.smallmolecule LINCS Small Molecule http://lincsportal.ccs.miami.edu/SmallMolecules/ The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). ^LSM-\d+$ LSM-6306 http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1 lincs False LINCS.SMALLMOLECULE lincs.smallmolecule lincs.smallmolecule linguist Linguist https://github.com/github/linguist Registry of programming languages for the Linguist program for detecting and highlighting programming languages. ^[a-zA-Z0-9 +#'*]+$ Python https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1 False linguist linkedin LinkedIn personal profile ID https://www.linkedin.com identifier for a person, on the LinkedIn website ^[\w0-9\-&_'’\.]+$ deborahlehr https://www.linkedin.com/in/$1 False P6634 linkml LinkML https://linkml.io/linkml-model/docs/SchemaDefinition/ 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. SchemaDefinition cjmungall@lbl.gov https://w3id.org/linkml/$1 False lipidbank LipidBank http://lipidbank.jp/index.html LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. ^\w+\d+$ BBA0001 e-yasugi@umin.ac.jp http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 False LIPIDBANK 2665 nbdc00126 lipidbank lipidbank lipidbank lipidmaps LIPID MAPS http://www.lipidmaps.org The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ LMPR0102010012 edennis@ucsd.edu http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 LIPID MAPS|LIPID_MAPS_class|LIPID_MAPS_instance False LIPIDMAPS 000564 2625 lipidmaps lipidmaps 503 lipidmaps r3d100012315 Lipidmaps P2063 lipro Lipid Ontology An ontology representation of the LIPIDMAPS nomenclature classification. bakerc@unb.ca http://purl.obolibrary.org/obo/LIPRO_$1 True LIPRO LIPRO LIPRO lipro lncipedia LNCipedia https://lncipedia.org A comprehensive compendium of human long non-coding RNAs SNHG3 pieter.mestdagh@ugent.be False loggerhead Loggerhead nesting http://www.mesquiteproject.org/ontology/Loggerhead/index.html peteremidford@yahoo.com http://purl.obolibrary.org/obo/LOGGERHEAD_$1 True LOGGERHEAD loggerhead loinc Logical Observation Identifiers Names and Codes https://loinc.org/ The international standard for identifying health measurements, observations, and documents. ^(\d|\w)+-\d$ LL379-9 loinc@regenstrief.org https://loinc.org/$1 LNC False LOINC 1897 LOINC 2.16.840.1.113883.6.1 P4338 lonza Lonza https://knowledge.lonza.com Contains information about cells and data sheets related to transfection. ^\d+$ 968 https://knowledge.lonza.com/cell?id=$1 False Lonza loop Loop ID https://loop.frontiersin.org/ identifier for a person, in the Loop database of researcher impact ^[1-9]\d*$ 1859 https://loop.frontiersin.org/people/$1/overview False P2798 loqate The localization and quantitation atlas of the yeast proteome http://www.weizmann.ac.il/molgen/loqate/ The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library 1001 maya.schuldiner@weizmann.ac.il http://www.weizmann.ac.il/molgen/loqate/gene/view/$1 False loqate lotus LOTUS Initiative for Open Natural Products Research https://lotus.naturalproducts.net LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry. ^LTS\d{7}$ LTS0004651 adriano.rutz@ik.me https://lotus.naturalproducts.net/compound/lotus_id/$1 False lpt Livestock Product Trait Ontology https://github.com/AnimalGenome/livestock-product-trait-ontology The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit. ^\d+$ 0000156 caripark@iastate.edu http://purl.obolibrary.org/obo/LPT_$1 https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo False LPT LPT LPT LPT lrg Locus Reference Genomic http://www.lrg-sequence.org/ A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI. ^\d+$ 1 http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml False LRG 2.16.840.1.113883.6.283 nbdc02566 lrg lrg Lrg lspci Laboratory of Systems Pharmacology Compound https://labsyspharm.github.io/lspci/ Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions) ^\d+$ 1 https://labsyspharm.github.io/lspci/$1 False lter Long Term Ecological Research Controlled Vocabulary https://vocab.lternet.edu/vocab/vocab/index.php Ecological terms ^\d+$ 182 https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1 False m4i Metadata4Ing https://w3id.org/nfdi4ing/metadata4ing/ "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. ""Inheritance"" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method × object of research." ^\w+$ Method dorothea.iglezakis@ub.uni-stuttgart.de http://w3id.org/nfdi4ing/metadata4ing#$1 https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.xml False 20402 m4i Q111516803 m4i ma Mouse adult gross anatomy https://github.com/obophenotype/mouse-anatomy-ontology A structured controlled vocabulary of the adult anatomy of the mouse (Mus) ^\d+$ 0002502 Terry.Hayamizu@jax.org http://purl.obolibrary.org/obo/MA_$1 False MA MA MA ma ma ma ma MA ma macie Mechanism, Annotation and Classification in Enzymes https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. ^M\d{4}$ M0001 gemma.l.holliday@gmail.com https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1 False MACIE 2641 macie macie macie maggot Maggot https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/resources/metabolome-platform Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond. ^[A-Za-z0-9]+$ frim1 https://pmb-bordeaux.fr/maggot/metadata/$1 False maggot maizegdb.locus MaizeGDB Locus http://www.maizegdb.org/ MaizeGDB is the maize research community's central repository for genetics and genomics information. ^\d+$ 25011 margaret.woodhouse@usda.gov http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 MaizeGDB False MAIZEGDB.LOCUS nbdc00129 maizegdb.locus maizegdb.locus maizegdb r3d100010795 DB-0058 mamo Mathematical modeling ontology http://sourceforge.net/p/mamo-ontology/wiki/Home/ The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. ^\d{7}$ 0000026 n.lenovere@gmail.com http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1 True MAMO MAMO MAMO mamo mamo mamo mamo MAMO mampol Mammalia Polymorphism Database http://mampol.uab.es 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). MAMpol005339 http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1 False mampol mao Multiple alignment http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment. ^\d{7}$ 0000061 julie@igbmc.u-strasbg.fr http://purl.obolibrary.org/obo/MAO_$1 True MAO mao mao massbank MassBank http://www.massbank.jp MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). ^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$ MSBNK-IPB_Halle-PB000166 tobias.schulze@ufz.de https://massbank.jp/RecordDisplay?id=$1 False MASSBANK nbdc00298 massbank massbank P6689 massive MassIVE https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. ^MSV\d+$ MSV000082131 miw023@ucsd.edu https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1 False MASSIVE massive massive DB-0241 mastodon Mastodon https://mastodon.social address on the Mastodon decentralized social network (the form is 'user@server.domain' without a leading '@') ^[A-Za-z0-9_]+([A-Za-z0-9_\.]+[A-Za-z0-9_]+)?@[\d\w\.\-]+[0-9a-z]+$ jz@mamot.fr https://fedirect.toolforge.org/?id=$1 False P4033 mat Minimal Anatomical Terminology Minimal set of terms for anatomy ^\d{7}$ 0000000 j.bard@ed.ac.uk http://purl.obolibrary.org/obo/MAT_$1 True MAT MAT MAT mat matrixdb MatrixDB http://matrixdb.univ-lyon1.fr/ MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides MULT_4_VAR1_bovine sylvie.ricard-blum@univ-lyon1.fr http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1 False nbdc01222 298 matrixdb r3d100010672 matrixdb.association MatrixDB Association http://matrixdb.univ-lyon1.fr/ MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ P00747__P07355 http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association False MATRIXDB.ASSOCIATION matrixdb.association matrixdb.association mavedb Multiplexed Assays of Variant Effect Database https://www.mavedb.org Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a ^\S+$ 00000011-a alan.rubin@wehi.edu.au https://www.mavedb.org/#/experiments/urn:mavedb:$1 False maxo Medical Action Ontology https://github.com/monarch-initiative/MAxO An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. ^\d{7}$ 0000008 Leigh.Carmody@jax.org http://purl.obolibrary.org/obo/MAXO_$1 False MAXO MAXO maxo maxo maxo MAXO mba Mouse Brain Atlas https://mouse.brain-map.org A controlled vocabulary to support the study of transcription in the mouse brain ^\d+$ 688 chinhda@alleninstitute.org https://biopragmatics.github.io/providers/mba/$1 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo False ABA-AMB mcc Cell Line Ontology [derivative] http://www.molecularconnections.com 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. ThoracicArtery usha@molecularconnections.com http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1 True MCCL mco Microbial Conditions Ontology https://github.com/microbial-conditions-ontology/microbial-conditions-ontology Microbial Conditions Ontology is an ontology... ^\d+$ 0000858 citlalli.mejiaalmonte@gmail.com http://purl.obolibrary.org/obo/MCO_$1 False MCO MCO mco mco MCO mcro Model Card Report Ontology https://github.com/UTHealth-Ontology/MCRO An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). ^\d{7}$ 0000001 muamith@utmb.edu https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1 False MCRO MCRO mcro mcro MCRO mdm Medical Data Models https://medical-data-models.org/ The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. ^\d+$ 4776 bernd.mueller@zbmed.de https://medical-data-models.org/forms/$1 False MDM MDM MDM mdm mdm r3d100013816 meddra Medical Dictionary for Regulatory Activities Terminology http://bioportal.bioontology.org/ontologies/MEDDRA The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). ^\d+$ 10015919 mssohelp@meddra.org http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1 MEDRA|MeDRA|MedDRA|Medical Dictionary for Regulatory Activities False MEDDRA 1237 MEDDRA MEDDRA 2.16.840.1.113883.6.163 nbdc02564 meddra meddra Meddra P3201 medgen Human Medical Genetics https://www.ncbi.nlm.nih.gov/medgen/ MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. ^[CN]*\d{4,7}$ 760050 https://www.ncbi.nlm.nih.gov/medgen/$1 False MedGen nbdc02560 medgen medgen Medgen mediadive.ingredient MediaDive Ingredient https://mediadive.dsmz.de/solutions The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about] ^\d+$ 13 joerg.overmann@dsmz.de https://mediadive.dsmz.de/ingredients/$1 False mediadive.medium MediaDive Medium https://mediadive.dsmz.de/media The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about] ^\d+\w?$ 77 joerg.overmann@dsmz.de https://mediadive.dsmz.de/medium/$1 False mediadive.medium mediadive.solution MediaDive Solution https://mediadive.dsmz.de/solutions The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about] ^S\d+$ S6 joerg.overmann@dsmz.de https://mediadive.dsmz.de/solutions/$1 False medlineplus MedlinePlus Health Topics http://www.nlm.nih.gov/medlineplus/ MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. ^\d+$ 002804 custserv@nlm.nih.gov http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm False MEDLINEPLUS MEDLINEPLUS MEDLINEPLUS 2.16.840.1.113883.6.173 nbdc00836 medlineplus medlineplus merops.clan MEROPS Clan https://www.ebi.ac.uk/merops The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. IA ndr@ebi.ac.uk https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1 False merops merops.entry MEROPS Entry http://merops.sanger.ac.uk/index.htm The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. ^[SCTAGMNUI]\d{2}\.([AB]\d{2}|\d{3})$ I31.952 ndr@ebi.ac.uk https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1 merops.inhibitor False MEROPS.INHIBITOR 2629 merops.inhibitor merops.inhibitor merops merops.family MEROPS Family http://merops.sanger.ac.uk/index.htm The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. ^[SCTAGMNU]\d+$ S1 ndr@ebi.ac.uk https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1 False MEROPS.FAMILY merops.family merops.family merops mesh Medical Subject Headings http://id.nlm.nih.gov/mesh/ MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. ^(C|D)\d{6,9}$ C063233 custserv@nlm.nih.gov https://meshb.nlm.nih.gov/record/ui?ui=$1 MESH|MESHA|MESHC|MESHCS|MESHD|MESHPP|MESH_DESCRIPTOR_UI|MESH_SUPPLEMENTAL_RECORD_UI|MSH|MSH2010_2010_02_22 False MESH 391 MESH MESH MeSH 1177 2.16.840.1.113883.6.177 nbdc00132 mesh mesh mesh Mesh P486 mesh.2012 MeSH 2012 http://www.nlm.nih.gov/mesh/ MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. ^[A-Za-z0-9]+$ 17186 http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded False MESH.2012 mesh.2012 mesh.2012 mesh mesh.2013 MeSH 2013 http://www.nlm.nih.gov/mesh/ MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. ^[A-Za-z0-9]+$ 17165 http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded False MESH.2013 mesh.2013 mesh.2013 mesh mesh.vocab Medical Subject Headings Vocabulary https://hhs.github.io/meshrdf/ Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump term http://id.nlm.nih.gov/mesh/vocab#$1 False mesh metabolights MetaboLights Compound https://www.ebi.ac.uk/metabolights/ MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. ^MTBLS\d+$ MTBLS1 https://www.ebi.ac.uk/metabolights/$1 False METABOLIGHTS MetaboLights nbdc02124 metabolights metabolights r3d100011556 P3890 metacyc.compound Metabolic Encyclopedia of metabolic and other pathways https://metacyc.org MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. ^[A-Za-z0-9+_.%-:]+$ CPD-10330 pkarp@ai.sri.com https://metacyc.org/compound?orgid=META&id=$1 MetaCyc False METACYC.COMPOUND nbdc00907 metacyc.compound metacyc.compound 10 r3d100011294 metacyc.pathway Metabolic Encyclopedia for Pathway/Genome Databases https://metacyc.org "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" 12DICHLORETHDEG-PWY pkarp@ai.sri.com https://metacyc.org/META/NEW-IMAGE?object=$1 False metacyc.reaction MetaCyc Reaction https://metacyc.org MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. ^[A-Za-z0-9+_.%-:]+$ RXN-14904 pkarp@ai.sri.com https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1 False METACYC.REACTION metacyc.reaction metacyc.reaction metanetx.chemical MetaNetX chemical https://www.metanetx.org/ MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components. ^(MNXM\d+|BIOMASS|WATER)$ MNXM1723 https://www.metanetx.org/chem_info/$1 False METANETX.CHEMICAL metanetx.chemical metanetx.chemical metanetx.compartment MetaNetX compartment https://www.metanetx.org/ MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments. ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$ MNXC15 https://www.metanetx.org/comp_info/$1 False METANETX.COMPARTMENT metanetx.compartment metanetx.compartment metanetx.reaction MetaNetX reaction https://www.metanetx.org/ MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. ^(MNXR\d+|EMPTY)$ MNXR101574 https://www.metanetx.org/equa_info/$1 False METANETX.REACTION metanetx.reaction metanetx.reaction metatlas Metabolic Atlas https://metabolicatlas.org A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis. ^(MAM\d{5}\w)|(MAR\d{5})$ MAM01234c mihail.anton@chalmers.se https://metabolicatlas.org/identifier/MetabolicAtlas/$1 False metatlas metatlas.metabolite Metabolic Atlas Metabolite https://metabolicatlas.org A subspace of Metabolic Atlas for compartment-specific records for metabolites. ^MAM\d{5}\w$ MAM01234c mihail.anton@chalmers.se https://metabolicatlas.org/identifier/MetabolicAtlas/$1 False metatlas metatlas.reaction Metabolic Atlas Reaction https://metabolicatlas.org A subspace of Metabolic Atlas for reactions. ^MAR\d{5}$ MAR11851 mihail.anton@chalmers.se https://metabolicatlas.org/identifier/MetabolicAtlas/$1 False metatlas metlin Metabolite and Tandem Mass Spectrometry Database http://masspec.scripps.edu/ The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. ^\d{4}$ 1455 http://metlin.scripps.edu/metabo_info.php?molid=$1 False METLIN metlin metlin r3d100012311 metnetdb Metabolic Network Exchange Database http://www.metnetdb.org/MetNet_db.htm 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. 377369 http://metnetonline.org/browse_pathway2.php?pthID=$1 False 234 metnetdb mex Metabolome Express https://www.metabolome-express.org/ A public place to process, interpret and share GC/MS metabolomics datasets. ^\d+$ 36 https://www.metabolome-express.org/datasetview.php?datasetid=$1 False MEX mex mex mf Mental Functioning Ontology https://github.com/jannahastings/mental-functioning-ontology The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. ^\d{7}$ 0000091 janna.hastings@gmail.com http://purl.obolibrary.org/obo/MF_$1 False MF MF MF mf mf MF mfmo Mammalian Feeding Muscle Ontology https://github.com/rdruzinsky/feedontology The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. ^\d{7}$ 0000208 druzinsk@uic.edu http://purl.obolibrary.org/obo/MFMO_$1 True MFMO MFMO MFMO mfmo mfmo MFMO mfo Medaka fish anatomy and development http://ani.embl.de:8080/mepd/ A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. ^\d{7}$ 0000001 henrich@embl.de http://purl.obolibrary.org/obo/MFO_$1 True MFO MFO MFO mfo mfo mfoem Emotion Ontology https://github.com/jannahastings/emotion-ontology An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. ^\d{6}$ 000204 janna.hastings@gmail.com http://purl.obolibrary.org/obo/MFOEM_$1 False MFOEM MFOEM MFOEM mfoem mfoem MFOEM mfomd Mental Disease Ontology https://github.com/jannahastings/mental-functioning-ontology The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF). ^\d{7}$ 0000046 janna.hastings@gmail.com http://purl.obolibrary.org/obo/MFOMD_$1 False MFOMD MFOMD MFOMD mfomd mfomd MFOMD mge Aclame http://aclame.ulb.ac.be/ ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. ^\d+$ 2 http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1 aclame True ACLAME 2631 nbdc00355 mge mge aclame mgi Mouse Genome Informatics http://www.informatics.jax.org/ The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. ^\d+$ 6017782 joel.richardson@jax.org http://www.informatics.jax.org/accession/MGI:$1 MGD|MGI False MGI MGI 3274 nbdc00568 mgi mgi mgi r3d100010266 MGI DB-0060 P671 mgnify.analysis MGnify Analysis https://www.ebi.ac.uk/metagenomics/ Analyses of microbiome data within MGnify ^MGYA\d+$ MGYA00002270 https://www.ebi.ac.uk/metagenomics/analyses/$1 False mgnify.proj MGnify Project https://www.ebi.ac.uk/metagenomics MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis. ^[A-Z]+[0-9]+$ ERP004492 https://www.ebi.ac.uk/metagenomics/projects/$1 False mgnify.proj mgnify.proj mgnify.samp MGnify Sample https://www.ebi.ac.uk/metagenomics The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. ^[A-Z]+[0-9]+$ SRS086444 https://www.ebi.ac.uk/metagenomics/samples/$1 False mgnify.samp mgnify.samp mi Molecular Interactions Controlled Vocabulary https://github.com/HUPO-PSI/psi-mi-CV The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. ^\d{4}$ 0058 luana.licata@gmail.com http://purl.obolibrary.org/obo/MI_$1 PSI-MI False MI PSIMI MI mi psimi mi mi MI psi.mi miaa Minimal Information About Anatomy ontology True miapa Minimum Anformation About a Phylogenetic Analysis Ontology http://www.evoio.org/wiki/MIAPA "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA." ^\d{7}$ 0000010 hilmar.lapp@duke.edu http://purl.obolibrary.org/obo/MIAPA_$1 False MIAPA MIAPA MIAPA miapa miapa MIAPA micro Ontology of Prokaryotic Phenotypic and Metabolic Characters https://github.com/carrineblank/MicrO An ontology of prokaryotic phenotypic and metabolic characters ^\d{7}$ 0002999 carrine.blank@umontana.edu http://purl.obolibrary.org/obo/MICRO_$1 True MICRO MICRO micro micro MICRO microscope MicroScope http://www.genoscope.cns.fr/agc/microscope MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. ^\d+$ 5601141 cmedigue@genoscope.cns.fr http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1 False MICROSCOPE microscope microscope r3d100012928 microsporidia MicrosporidiaDB http://microsporidiadb.org/micro/ MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ ECU03_0820i oharb@upenn.edu http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 False MICROSPORIDIA microsporidia microsporidia microsporidia millipore Merck Millipore (EMD Millipore) https://www.merckmillipore.com/ Cell line collections (Providers) SCC111 https://www.merckmillipore.com/catalogue/item/$1 False Millipore mimodb MimoDB http://immunet.cn/bdb/ MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. ^\d+$ 1 hj@uestc.edu.cn http://immunet.cn/bdb/index.php/mimoset/$1 False MIMODB mimodb mimodb mimodb minid Minimal Viable Identifier https://fair-research.org Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. ^[A-Za-z0-9]+$ b97957 foster@uchicago.edu https://hdl.handle.net/hdl:20.500.12582/$1 False MINID minid minid minid.test MINID Test https://fair-research.org Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ^[A-Za-z0-9]+$ 3SBPLMKKVEVR https://hdl.handle.net/hdl:20.500.12633/$1 False minid.test mint Molecular Interaction Database https://mint.bio.uniroma2.it The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. ^\d{1,7}$ 6978836 luana.licata@gmail.com https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1 False MINT 2615 mint mint 17 mint r3d100010414 DB-0158 mipmod MIPModDB http://bioinfo.iitk.ac.in/MIPModDB MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. ^\w+$ HOSAPI0399 rsankar@iitk.ac.in http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1 False MIPMOD mipmod mipmod mipmod mir Identifiers.org Registry https://registry.identifiers.org/registry "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or ""PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources." ^\d{8}$ 00100037 https://registry.identifiers.org/registry?query=MIR:$1 False MIR mir mir mirbase miRBase pre-miRNA http://www.mirbase.org/ The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). ^MI\d{7}$ MI0026471 sam.griffiths-jones@manchester.ac.uk http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 False MIRBASE 2642 nbdc00136 mirbase mirbase 210 mirbase r3d100010566 Mirbase P2870 mirbase.family miRBase Families http://www.mirbase.org/ 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. MIPF0000002 http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1 MIRBASE_FAMILY False mirbase.mature miRBase mature miRNA http://www.mirbase.org/ The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. ^MIMAT\d{7}$ MIMAT0046872 http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1 MIRBASEM False MIRBASE.MATURE mirbase.mature mirbase.mature mirbase.mature P2871 mirex mirEX http://comgen.pl/mirex/?page=home mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages. ^\d+(\w+)?$ 165a wmk@amu.edu.pl http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes False MIREX nbdc02064 mirex mirex miriam Identifiers.org namespace https://www.ebi.ac.uk Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain. ^[0-9a-z_:\.-]+$ pubmed n.lenovere@gmail.com https://registry.identifiers.org/registry/$1 identifiers.namespace False 1162 identifiers.namespace miriam.collection MIRIAM Registry collection https://www.ebi.ac.uk/miriam/ MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. ^000\d{5}$ 00000008 https://www.ebi.ac.uk/miriam/main/$1 True MIRIAM.COLLECTION miriam.collection miriam.collection miriam miriam.resource MIRIAM Legacy Registry Identifier https://www.ebi.ac.uk/miriam/ MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. ^001\d{5}$ 00100005 https://www.ebi.ac.uk/miriam/main/resources/$1 True MIRIAM.RESOURCE miriam.resource miriam.resource miriam.resource miriam mirnao microRNA Ontology http://code.google.com/p/mirna-ontology/ An application ontology for use with miRNA databases. topalis@imbb.forth.gr http://purl.obolibrary.org/obo/MIRNAO_$1 True MIRNAO MIRNAO MIRNAO mirnao miRNAO mirnest miRNEST http://rhesus.amu.edu.pl/mirnest/copy/ miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. ^MNEST\d+$ MNEST029358 miszcz@amu.edu.pl http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1 False MIRNEST nbdc01703 mirnest mirnest mirnest miro Mosquito insecticide resistance https://github.com/VEuPathDB-ontology/MIRO Application ontology for entities related to insecticide resistance in mosquitos ^\d{8}$ 40000617 louis@imbb.forth.gr http://purl.obolibrary.org/obo/MIRO_$1 http://purl.obolibrary.org/obo/miro.obo True MIRO MIRO MIRO miro miro MIRO mirtarbase mirTarBase https://mirtarbase.cuhk.edu.cn/ miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. ^MIRT\d{6}$ MIRT000002 ken.sd.hsu@gmail.com https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1 False MIRTARBASE nbdc01217 mirtarbase mirtarbase 715 P2646 mirte miRNA Target Prediction at EMBL http://www.russelllab.org/miRNAs/ This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs miR-1 False mixs Minimal Information about any Sequence https://www.gensc.org/pages/standards/all-terms.html The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample. ^\d{7}$ 0001056 rlwalls2008@gmail.com https://w3id.org/mixs/$1 False MIXS MIXS mlc MLCommons Association https://mlcommons.org/en/ MLCommons Association artifacts, including benchmark results, datasets, and saved models. ^[0-9a-zA-Z\.\-\_]+$ 0.7-123 https://www.mlcommons.org/mlc-id/$1 False mlc mmdb Molecular Modeling Database http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. ^\d{1,5}$ 50885 siqian.he@nih.gov http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1 False MMDB 2667 mmdb mmdb 508 mmdb mmmp.biomaps Melanoma Molecular Map Project Biomaps http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. ^\d+$ 37 http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1 mmmp:biomaps False MMMP:BIOMAPS mmmp:biomaps biomaps mmmp mmo Measurement method ontology https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 A representation of the variety of methods used to make clinical and phenotype measurements. ^\d{7}$ 0000574 jrsmith@mcw.edu http://purl.obolibrary.org/obo/MMO_$1 False MMO MMO MMO mmo mmo MMO mmp.cat MarCat https://mmp.sfb.uit.no/databases/marcat/ MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples. ^MMP\d+.\d+$ MMP743597.11 https://mmp.sfb.uit.no/databases/marcat/#/records/$1 False MMP.CAT mmp.cat mmp.cat mmp.db MarDB https://mmp.sfb.uit.no/databases/mardb/ MarDB includes all sequenced marine microbial genomes regardless of level of completeness. ^MMP\d+.\d+$ MMP02954345.1 https://mmp.sfb.uit.no/databases/mardb/#/records/$1 False MMP.DB mmp.db mmp.db mmp.fun MarFun https://mmp.sfb.uit.no/databases/marfun MarFun is manually curated database for marine fungi which is a part of the MAR databases. ^MMP\d+.\d+$ MMP3888430 https://mmp.sfb.uit.no/databases/marfun/#/records/$1 False mmp.fun mmp.ref MarRef https://mmp.sfb.uit.no/databases/marref/ MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes. ^MMP\d+.\d+$ MMP3312982.2 https://mmp.sfb.uit.no/databases/marref/#/records/$1 False MMP.REF mmp.ref mmp.ref mmrrc Mutant Mouse Resource and Research Centers https://www.mmrrc.org The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. ^\d+$ 70 f.grieder@nih.gov http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 False MMRRC MMRRC mmrrc mmrrc r3d100013715 MMRRC mmsinc MMsINC http://mms.dsfarm.unipd.it/MMsINC 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. MMs00000001 http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=$1 False mmsinc mmsl Multum MediSource Lexicon https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included. ^\d+$ 3355 MMSL_CODE False 2.16.840.1.113883.6.175 mmusdv Mouse Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv Life cycle stages for Mus Musculus ^\d{7}$ 0000066 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/MmusDv_$1 MmusDv False MMUSDV MMUSDV MMUSDV mmusdv mmusdv MmusDv mo Microarray experimental conditions http://mged.sourceforge.net/ontologies/MGEDontology.php The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. ^\w+$ ArrayGroup stoeckrt@pcbi.upenn.edu https://mged.sourceforge.net/ontologies/MGEDontology.php#$1 True MO MO MO mo mo mo mobidb MobiDB http://mobidb.bio.unipd.it MobiDB is a database of protein disorder and mobility annotations. ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$ P10636 silvio.tosatto@unipd.it https://mobidb.org/$1 False MOBIDB nbdc01956 mobidb mobidb 623 DB-0183 uniprot mod Protein modification http://www.psidev.info/MOD The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. ^\d{5}$ 01467 pierre-alain.binz@chuv.ch http://purl.obolibrary.org/obo/MOD_$1 PSI-MOD False PSIMOD MOD PSIMOD mod mod mod mod MOD psi.mod modeldb ModelDB https://modeldb.science ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. ^\d+$ 45539 perry.miller@yale.edu https://modeldb.science/$1 False MODELDB 2669 nbdc02085 modeldb modeldb modeldb r3d100011330 modeldb.concept ModelDB concept https://www.yale.edu Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models. ^\d+$ 3639 https://senselab.med.yale.edu/ModelDB/ModelList?id=$1 False modeldb.concept moid Metadata Management and distribution system for Multiple GNSS Networks https://www.astro.oma.be/en/ M3G stands for “Metadata Management and distribution system for Multiple GNSS Networks”. M3G allows to upload, validate, and distribute GNSS station metadata such as IGS-style site logs, information about local networks, DOIs, nominal data provision, data licenses attached to the daily RINEX data, etc... ^[a-zA-Z0-9]+\.[a-f0-9]{24}$ station.6051b2f8b9142a5b8c676342 https://gnss-metadata.eu/MOID/$1 False moid molbase Molbase http://www.molbase.com/ Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ 128796-39-4 http://www.molbase.com/en/index.php?app=search&search_keyword=$1 False MOLBASE molbase molbase molbase.sheffield MolBase https://winter.group.shef.ac.uk/molbase/ An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students. ^\d+$ 1868 True molmedb MolMeDB http://www.upol.cz/en/ 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. ^[m,M]{2}[0-9]{5}[0-9]*$ MM00040 karel.berka@upol.cz https://molmedb.upol.cz/mol/$1 False molmedb molmovdb Database of Macromolecular Movements http://bioinfo.mbb.yale.edu/MolMovDB/ 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. f665230-5267 http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1 False nbdc00573 molmovdb mondo Mondo Disease Ontology https://monarch-initiative.github.io/mondo A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. ^\d{7}$ 0000001 nicole@tislab.org http://purl.obolibrary.org/obo/MONDO_$1 http://purl.obolibrary.org/obo/mondo.obo False MONDO MONDO MONDO nbdc02563 mondo mondo MONDO Mondo P5270 mop Molecular Process Ontology https://github.com/rsc-ontologies/rxno MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation. ^\d{7}$ 0000079 batchelorc@rsc.org http://purl.obolibrary.org/obo/MOP_$1 https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo False MOP 20466 MOP MOP mop mop MOP morpheus Morpheus model repository https://morpheus.gitlab.io/ "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software. " ^M[0-9]{4,}$ M0001 https://morpheus.gitlab.io/models/$1 False morpheus mosaic MOSAiC Ontology https://ontologies.dataone.org/MOSAiC.html An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io). ^\d{8}$ 00005643 brycemecum@gmail.com https://purl.dataone.org/odo/MOSAIC_$1 https://ontologies.dataone.org/MOSAiC.owl False MOSAIC MOSAIC mp Mammalian Phenotype Ontology https://www.informatics.jax.org/vocab/mp_ontology/ The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. ^\d{7}$ 0005452 pheno@jax.org http://purl.obolibrary.org/obo/MP_$1 False MP MP MP mp mp mp mp MP mp Mp mpath Mouse pathology ontology http://www.pathbase.net A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes ^\d+$ 728 pns12@hermes.cam.ac.uk http://purl.obolibrary.org/obo/MPATH_$1 https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo MPATH False MPATH MPATH MPATH nbdc01568 mpath mpath MPATH mpath mpid Microbial Protein Interaction Database http://www.jcvi.org/mpidb/about.php The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. ^\d+$ 172 jgoll@emmes.com http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1 mpidb False MPID mpid mpid 559 mpi mpio Minimum PDDI Information Ontology https://github.com/MPIO-Developers/MPIO An ontology of minimum information regarding potential drug-drug interaction information. ^\d{7}$ 0000004 mbrochhausen@uams.edu http://purl.obolibrary.org/obo/MPIO_$1 False MPIO MPIO MPIO mpio mpio MPIO mro MHC Restriction Ontology https://github.com/IEDB/MRO The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. ^\d{7}$ 0000634 bpeters@lji.org http://purl.obolibrary.org/obo/MRO_$1 False MRO MRO MRO mro mro MRO ms Mass spectrometry ontology http://www.psidev.info/groups/controlled-vocabularies The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. ^\d{7}$ 1000560 gerhard.mayer@rub.de http://purl.obolibrary.org/obo/MS_$1 False MS MS MS ms ms ms ms MS msigdb Molecular Signatures Database https://www.gsea-msigdb.org The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can ^M\d+$ M1 https://biopragmatics.github.io/providers/msigdb/$1 msig False nbdc02550 msio Metabolomics Standards Initiative Ontology https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies. ^\d{7}$ 0000111 philippe.rocca-serra@oerc.ox.ac.uk http://purl.obolibrary.org/obo/MSIO_$1 False msio mtbd Mouse Tumor Biology Database http://tumor.informatics.jax.org 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. 1374 http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1 False mtbd multicellds MultiCellDS http://multicellds.org/MultiCellDB.php 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. MCDS_S_0000000001 samuel.friedman@cammlab.org http://multicellds.org/MultiCellDB/$1 False multicellds.cell_line MultiCellDS Digital Cell Line http://multicellds.org/MultiCellDB.php MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. ^MCDS_L_[a-zA-Z0-9]{1,10}$ MCDS_L_0000000001 http://multicellds.org/MultiCellDB/$1 False MULTICELLDS.CELL_LINE multicellds.cell_line multicellds.cell_line multicellds multicellds.collection MultiCellDS collection http://multicellds.org/MultiCellDB.php MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). ^MCDS_C_[a-zA-Z0-9]{1,10}$ MCDS_C_0000000001 http://multicellds.org/MultiCellDB/$1 False MULTICELLDS.COLLECTION multicellds.collection multicellds.collection multicellds multicellds.snapshot MultiCellDS Digital snapshot http://multicellds.org/MultiCellDB.php MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. ^MCDS_S_[a-zA-Z0-9]{1,10}$ MCDS_S_0000000001 http://multicellds.org/MultiCellDB/$1 False MULTICELLDS.SNAPSHOT multicellds.snapshot multicellds.snapshot multicellds mvx Manufacturers of Vaccines https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvx The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated. ^\w+$ ASZ https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code=$1 False 2.16.840.1.113883.6.60 mw.project Metabolomics Workbench Project http://www.metabolomicsworkbench.org/ Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). ^PR[0-9]{6}$ PR000001 http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1 False MW.PROJECT mw.project mw.project mw.study Metabolomics Workbench Study http://www.metabolomicsworkbench.org/ Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). ^ST[0-9]{6}$ ST000900 http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1 False MW.STUDY mw.study mw.study myco.lepra MycoBrowser leprae http://mycobrowser.epfl.ch/leprosy.html Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. ^ML\w+$ ML0224 http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1 False MYCO.LEPRA myco.lepra myco.lepra myco.lepra myco.marinum MycoBrowser marinum http://mycobrowser.epfl.ch/marinolist.html Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. ^MMAR\_\d+$ MMAR_2462 http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1 False MYCO.MARINUM myco.marinum myco.marinum myco.marinum myco.smeg MycoBrowser smegmatis http://mycobrowser.epfl.ch/smegmalist.html Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. ^MSMEG\w+$ MSMEG_3769 http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1 False MYCO.SMEG myco.smeg myco.smeg myco.smeg myco.tuber TubercuList knowledge base http://tuberculist.epfl.ch/ Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. ^Rv\d{4}(A|B|c)?$ Rv1908c stewart.cole@epfl.ch http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1 TubercuList False MYCO.TUBER myco.tuber myco.tuber tuberculist DB-0106 mycobank Fungal Nomenclature and Species Bank http://www.mycobank.org/ MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. ^\d+$ 349124 vrobert@unistra.fr http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1 False MYCOBANK nbdc01815 mycobank mycobank mycobank r3d100011222 mzspec Universal Spectrum Identifier http://www.psidev.info/usi The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it. ^.+$ PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 gerhard.mayer@rub.de http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1 False MZSPEC mzspec mzspec n2t Name-to-Thing https://n2t.net An ARK resolver as well as resolver built with common prefixes as in Identifiers.org chebi https://n2t.net/$1: False namerxn NameRXN https://www.nextmovesoftware.com/namerxn.html The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO). 4.2.78 gregory.landrum@phys.chem.ethz.ch False nando Nanbyo Disease Ontology https://nanbyodata.jp/ Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan. ^\d+$ 1200031 kninomiya-mope@g.ecc.u-tokyo.ac.jp https://nanbyodata.jp/disease/NANDO:$1 False NANDO NANDO nando Nando napdi Natural Product-Drug Interaction Research Data Repository https://repo.napdi.org/ The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). ^[0-9]+$ 28 rdb20@pitt.edu https://repo.napdi.org/study/$1 False NAPDI napdi napdi napp Nucleic Acids Phylogenetic Profiling http://napp.u-psud.fr/ NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. ^\d+$ 351 daniel.gautheret@u-psud.fr http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1 False NAPP napp napp napp narcis National Academic Research and Collaborations Information System http://www.narcis.nl NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. ^oai\:cwi\.nl\:\d+$ oai:cwi.nl:4725 http://www.narcis.nl/publication/RecordID/$1 False NARCIS nbdc01862 narcis narcis nasc NASC code http://arabidopsis.info/ The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. ^(\w+)?\d+$ N1899 sean@arabidopsis.org.uk http://arabidopsis.info/StockInfo?NASC_id=$1 False NASC nasc nasc nasc r3d100010906 nbn National Bibliography Number http://nbn-resolving.org/resolve_urn.htm The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. ^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$ urn:nbn:fi:tkk-004781 http://nbn-resolving.org/resolver?identifier=$1&verb=redirect False NBN nbn nbn nbo Neuro Behavior Ontology https://github.com/obo-behavior/behavior-ontology/ An ontology of human and animal behaviours and behavioural phenotypes ^\d{7}$ 0000564 g.gkoutos@bham.ac.uk http://purl.obolibrary.org/obo/NBO_$1 https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo False NBO NBO NBO nbo nbo NBO nbrc NITE Biological Resource Center http://www.nbrc.nite.go.jp/e/index.html NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. ^\d+$ 00001234 http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1 False NBRC nbrc nbrc nbrc ncats.bioplanet National Center for Advancing Translation Sciences BioPlanet https://tripod.nih.gov/bioplanet/ The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays. ^\d+$ 3 ruili.huang@nih.gov https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1 False ncats.drug NCATS Drugs https://drugs.ncats.io/ "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" 44259 https://drugs.ncats.io/drug/$1 inxight|inxight-drugs False ncbi.assembly Assembly https://www.ncbi.nlm.nih.gov/ A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. ^[a-zA-Z0-9_\.]+$ GCF_000005845.2 https://www.ncbi.nlm.nih.gov/datasets/genome/$1 False NCBIAssembly assembly r3d100012688 ncbi.genome NCBI Genome https://www.ncbi.nlm.nih.gov/genome This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations. ^\d+$ 51 https://www.ncbi.nlm.nih.gov/genome/$1 False NCBIGenome 2787 r3d100010785 ncbi.resource NCBI Registry https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources ECOCYC https://bioregistry.io/metaregistry/ncbi/$1 False ncbibook NCBI Bookshelf https://www.ncbi.nlm.nih.gov/books The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. ^NBK\d+$ NBK331 https://www.ncbi.nlm.nih.gov/books/$1 False ncbidrs NCBI Data Repository Service https://www.ncbi.nlm.nih.gov/ This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace. ^[0-9a-fA-F]{32}$ 72ff6ff882ec447f12df018e6183de59 https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1 False ncbidrs ncbigene Entrez Gene https://www.ncbi.nlm.nih.gov/gene Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. ^\d+$ 100010 murphyte@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/gene/$1 EGID|EntrezGene|NCBIGene|NCBI_GeneID|entrez|entrez gene/locuslink|nihgeneid False NCBIGene 1027 2.16.840.1.113883.6.340 nbdc00073 ncbigene ncbigene ncbigene r3d100010650 Ncbigene DB-0118 P351 ncbigi GenInfo Identifier https://www.ncbi.nlm.nih.gov/genbank/sequenceids/ A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number. ^\d+$ 568815597 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1 NCBI_gi|ncbi.gi False NCBIGI 2314 genbank ncbiprotein NCBI Protein https://www.ncbi.nlm.nih.gov/protein The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. ^(\w+\d+(\.\d+)?)|(NP_\d+)$ CAA71118.1 https://www.ncbi.nlm.nih.gov/protein/$1 False NCBIProtein nbdc00636 ncbiprotein ncbiprotein ncbi.protein r3d100010776 ncbitaxon NCBI Taxonomy https://github.com/obophenotype/ncbitaxon The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. ^\d+$ 2170610 schoch2@ncbi.nlm.nih.gov http://purl.obolibrary.org/obo/NCBITaxon_$1 http://purl.obolibrary.org/obo/ncbitaxon.obo NCBI Taxonomy|NCBITaxon|NCBITaxonomyID|NCBI_Taxon_ID|NCBI_taxid|TAX|TaxonomyID|taxid|taxon|taxonomy|uniprot.taxonomy False NCBITAXON NCBITAXON 509 TAXONOMY NCBITAXON NCBI_TaxID 1179 2.16.840.1.113883.6.205 taxonomy taxonomy ncbitaxon ncbitaxon NCBITaxon taxonomy r3d100010415 Taxonomy P685 nci.drug NCI Drug Dictionary ID https://www.cancer.gov/publications/dictionaries/cancer-drug identifier of an entry in the NCI Drug Dictionary beta-carotene https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1 False P11623 ncim NCI Metathesaurus http://ncim.nci.nih.gov/ NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. ^C\d+$ C0026339 http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1 False NCIM ncim ncim ncit NCI Thesaurus https://github.com/NCI-Thesaurus/thesaurus-obo-edition NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. ^C\d+$ C138986 haendel@ohsu.edu http://purl.obolibrary.org/obo/NCIT_$1 http://purl.obolibrary.org/obo/ncit.obo NCI|NCI2004_11_17|NCIT|NCIT_Thesaurus|NCIThesaurus|NCITm|NCITt|NCI_Thesaurus|NCIt|NCit|ncithesaurus False NCIT NCIT NCIT NCIt 2.16.840.1.113883.6.206 nbdc02651 ncit ncit ncit ncit NCIT ncit P1748 ncro Non-Coding RNA Ontology http://omnisearch.soc.southalabama.edu/w/index.php/Ontology An ontology for non-coding RNA, both of biological origin, and engineered. ^\d{7}$ 0002927 huang@southalabama.edu http://purl.obolibrary.org/obo/NCRO_$1 http://purl.obolibrary.org/obo/ncro.owl https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo False NCRO NCRO NCRO ncro ncro NCRO ndc National Drug Code http://www.accessdata.fda.gov/scripts/cder/ndc/ The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. ^\d+\-\d+\-\d+$ 0002-1975-61 http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1 False NDC 2.16.840.1.113883.6.69 ndc ndc P3640 nddf National Drug Data File https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements. ^\d{6}$ 002678 cs@firstdatabank.com http://purl.bioontology.org/ontology/NDDF/$1 False NDDF NDDF 2.16.840.1.113883.6.208 ndex Network Data Exchange https://www.ndexbio.org The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge. aa78a43f-9c4d-11eb-9e72-0ac135e8bacf rpillich@ucsd.edu https://www.ndexbio.org/viewer/networks/$1 False r3d100012690 ndfrt National Drug File - Reference Terminology https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]. ^N[0-9]{10}$ N0000001662 michael.lincoln@va.gov https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NDFRT&code=$1 NUI|ndf-rt False NDFRT NDFRT 2.16.840.1.113883.6.209 NDF-RT ndfrt P2115 nembase Nematode & Neglected Genomics http://www.nematodes.org 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. NBC00001 http://www.nematodes.org/nembase4/cluster.php?cluster=$1 True nembase nemo Neuroscience Multi-Omic BRAIN Initiative Data https://www.nemoarchive.org This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects. ^[a-z]{3}-[a-km-z0-9]{7}$ smp-m3w9hbe https://assets.nemoarchive.org/$1 False nemo nemo2 Neural ElectroMagnetic Ontology http://aimlab.cs.uoregon.edu/NEMO/web/index.html 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. 0000196 gfrishkoff@gsu.edu http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1 False NEMO NEMO neurolex NIF Standard Ontology: Neurolex https://github.com/SciCrunch/NIF-Ontology The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). ^\d+$ 4 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_$1 NLX|nlx False NEUROLEX neurolex neurolex neurolex nif neuromorpho NeuroMorpho http://neuromorpho.org/index.jsp NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. ^\w+$ Rosa2 Ascoli@gmu.edu http://neuromorpho.org/neuron_info.jsp?neuron_name=$1 False NEUROMORPHO 2657 neuromorpho neuromorpho neuromorpho neuronames NeuroNames http://braininfo.rprc.washington.edu/ BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it. ^\d+$ 268 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1 neuroname False P4394 neurondb NeuronDB http://senselab.med.yale.edu/NeuronDB/ NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments. ^\d+$ 265 http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1 False NEURONDB 2656 neurondb neurondb neurondb neurovault.collection NeuroVault Collection http://neurovault.org Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images. ^[1-9][0-9]*$ 3304 https://neurovault.org/collections/$1 False NEUROVAULT.COLLECTION neurovault.collection neurovault.collection neurovault.image NeuroVault Image http://neurovault.org Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images. ^[1-9][0-9]*$ 58788 https://neurovault.org/images/$1 False NEUROVAULT.IMAGE neurovault.image neurovault.image nextdb Nematode Expression Pattern DataBase http://nematode.lab.nig.ac.jp/ NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones. ^[A-Za-z0-9]+$ 6b1 http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1 False NEXTDB nbdc00594 nextdb nextdb nextdb nextprot nextProt https://www.nextprot.org/ neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases. ^NX_\w+$ NX_O00165 monique.zahn@sib.swiss https://www.nextprot.org/db/entry/$1 NXP False NEXTPROT nbdc02107 nextprot nextprot DB-0161 nextprot.family neXtProt family https://www.nextprot.org/ "NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. (Developed by the SIB Swiss Institute of Bioinformatics)" ^\d+$ 01406 https://www.nextprot.org/term/FA-$1 NXPFA False nfdi4chem.ontocape Ontology for computer aided process engineering https://www.avt.rwth-aachen.de/cms/AVT/Forschung/Software/~ipts/OntoCape/ OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources. True nfdi4chem.osmo Ontology for simulation, modelling, and optimization https://zenodo.org/record/5237774#.YXq72hxCRGo OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/) True ngbo Next Generation Biobanking Ontology https://github.com/Dalalghamdi/NGBO Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management. ^\d{7}$ 6000122 dal.alghamdi92@gmail.com http://purl.obolibrary.org/obo/NGBO_$1 False NGBO NGBO ngbo ngbo NGBO ngl NASA GeneLab https://genelab-data.ndc.nasa.gov/genelab/ NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA. ^GLDS-\d+$ GLDS-141 https://genelab-data.ndc.nasa.gov/genelab/accession/$1 False NGL ngl ngl nhcdr NINDS Human Cell and Data Repository https://stemcells.nindsgenetics.org Cell line collections (Providers) ND50028 https://stemcells.nindsgenetics.org?line=$1 False NHCDR niaest NIA Mouse cDNA Project http://lgsun.grc.nia.nih.gov/cDNA/ A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones. ^\w\d{4}\w\d{2}(\-[35])?$ J0705A10 dawood@helix.nih.gov http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1 False NIAEST niaest niaest niaest niaid.chemdb NIAID ChemDB ID http://chemdb.niaid.nih.gov ID in NIAID ChemDB 059486 http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1 False P2065 nif.cell NIF Cell http://neuinfo.org/ Neuronal cell types smtifahim@gmail.com http://purl.obolibrary.org/obo/NIF_CELL_$1 True NIFCELL NIF_CELL NIFCELL nif_cell nif nif.dysfunction NIF Dysfunction http://neuinfo.org/ smtifahim@gmail.com http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1 True NIF_DYSFUNCTION nif_dysfunction nif nif.ext NIF Standard Ontology: External https://github.com/SciCrunch/NIF-Ontology "NIFEXT covers IRIs that were ""external"" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed." ^\d+$ 7123 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nifext_$1 NIFEXT False nif nif.grossanatomy NIF Gross Anatomy http://neuinfo.org/ smtifahim@gmail.com http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1 True NIF_GROSSANATOMY nif_grossanatomy nif nif.std NIF Standard Ontology https://github.com/SciCrunch/NIF-Ontology NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing. ^BAMSC\d+$ BAMSC981 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/$1 NIFSTD False NIFSTD NIFSTD nif nihhesc NIH Human Embryonic Stem Cell Registry https://grants.nih.gov/stem_cells/registry/current.htm 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) NIHhESC-10-0083 https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1 False NIHhESC nihreporter.project NIH RePORTER https://reporter.nih.gov/ RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding. ^\d+$ 10343835 https://reporter.nih.gov/project-details/$1 False nist NIST Chemistry WebBook https://webbook.nist.gov/chemistry/ 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. NIST|NIST Chemistry WebBook False nist.codata NIST/CODATA ID http://physics.nist.gov/cuu/Constants/index.html identifier for a physical constant c http://physics.nist.gov/cgi-bin/cuu/Value?$1 False P1645 nkos Networked Knowledge Organization Systems/Services/Structures http://w3id.org/nkos "NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet. Knowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. 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)." alignedWith http://w3id.org/nkos/$1 False nlfff NLFFF Database https://nlfff.dataset.deepsolar.space/en/ Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database ^[0-9]+$ 345201101230312003 http://database.deepsolar.space:18080/dbs/nlfff/$1 False nlfff nlm National Library of Medicine Catalog https://www.ncbi.nlm.nih.gov/nlmcatalog Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings. ^\d+$ 101775319 https://www.ncbi.nlm.nih.gov/nlmcatalog/$1 False 528 nlx.anat NeuroLex Anatomy https://scicrunch.org/scicrunch/interlex/dashboard NLXANAT covers anatomy terms. Almost all terms are also in Uberon. ^\d+$ 090201 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1 False nif nlx.br NIF Standard Ontology: Brain Regions https://github.com/SciCrunch/NIF-Ontology NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999). ^\d+$ 145 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_br_$1 NLXBR False nif nlx.cell NIF Standard Ontology: Cell Types https://github.com/SciCrunch/NIF-Ontology NLXCELL conatins cell types with a focus on neuron types. ^\d+$ 091005 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1 NLXCELL False nif nlx.chem NIF Standard Ontology: Chemical https://github.com/SciCrunch/NIF-Ontology NLXCHEM covers chemicals. Most classes are also in ChEBI. ^\d+$ 090801 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1 NLXCHEM False nif nlx.dys NeuroLex Dysfunction https://scicrunch.org/scicrunch/interlex/dashboard NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc. ^\d+$ 20090602 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1 False nif nlx.func NIF Standard Ontology: Cognitive Function https://github.com/SciCrunch/NIF-Ontology NLXFUNC covers terms for cognitive function. ^\d+$ 90801 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_func_$1 NLXFUNC False nif nlx.inv NIF Standard Ontology: Investigations https://github.com/SciCrunch/NIF-Ontology NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis. ^\d+$ 90901 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1 NLXINV False nif nlx.mol NIF Standard Ontology: Molecules https://github.com/SciCrunch/NIF-Ontology NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system. ^\d+$ 90806 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1 NLXMOL False nif nlx.oen NIF Standard Ontology: OEN Terms in Neurolex https://github.com/SciCrunch/NIF-Ontology NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results). ^\d+$ 0001000 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/oen_$1 NLXOEN False nif nlx.org NIF Standard Ontology: Organisms https://github.com/SciCrunch/NIF-Ontology NLXORG covers organisms. ^\d+$ 090701 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1 NLXORG False nif nlx.qual NIF Standard Ontology: Qualities https://github.com/SciCrunch/NIF-Ontology NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO). ^\d+$ 100810 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1 NLXQUAL False nif nlx.res NIF Standard Ontology: Digital Resources https://github.com/SciCrunch/NIF-Ontology NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites ^\d+$ 090924 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_res_$1 NLXRES False nif nlx.sub NIF Standard Ontology: Subcellular Entities https://github.com/SciCrunch/NIF-Ontology NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO). ^\d+$ 090803 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1 NLXSUB|nif_subcellular False nif nmdc National Microbiome Data Collaborative https://microbiomedata.org/ An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem. ^.{2,}$ y3ax-8bq3-60 donny@polyneme.xyz https://w3id.org/nmdc/$1 False nmdc nmpdr National Microbial Pathogen Data Resource http://www.nmpdr.org 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. fig|306254.1.peg.183 http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1 True nmpdr nmr NMR-instrument specific component of metabolomics investigations http://msi-ontology.sourceforge.net/ nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. ^\d+$ 1000003 schober@imbi.uni-freiburg.de https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?short_form=NMR:$1 https://nmrml.org/cv/stable/nmrCV.owl nmrcv True NMR NMR NMR nmr nmr nmr nmrcv nmr nmrshiftdb2 NMRShiftDB structure https://nmrshiftdb.nmr.uni-koeln.de NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. ^[0-9]+$ 234 stefan.kuhn@dmu.ac.uk https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1 NMRShiftDB False nmrshiftdb2 r3d100010316 P9405 noaa NOAA Fisheries Species Directory https://www.fisheries.noaa.gov/species-directory Identifier for a species on the noaa fisheries website ^[a-z]+(\-[a-z]+)*$ long-finned-pilot-whale https://www.fisheries.noaa.gov/species/$1 False P6049 noaa.cameo CAMEO Chemicals ID https://cameochemicals.noaa.gov CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazards—such as explosions or toxic fumes. ^\d*$ 19757 https://cameochemicals.noaa.gov/chemical/$1 False P11931 nomen A nomenclatural ontology for biological names https://github.com/SpeciesFileGroup/nomen NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. ^\d{7}$ 0000295 diapriid@gmail.com http://purl.obolibrary.org/obo/NOMEN_$1 False NOMEN NOMEN nomen nomen NOMEN noncodev3 NONCODE v3 http://www.noncode.org/ NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. ^\d+$ 377550 biozy@ict.ac.cn http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1 False NONCODEV3 noncodev3 noncodev3 noncode noncodev4.gene NONCODE v4 Gene http://www.bioinfo.org/NONCODEv4/ NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions. ^NONHSAG\d{5}$ NONHSAG00001 http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1 False NONCODEV4.GENE noncodev4.gene noncodev4.gene noncodev4.rna NONCODE v4 Transcript http://www.bioinfo.org/NONCODEv4/ NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts. ^NONHSAT\d{6}$ NONHSAT000001 http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1 False NONCODEV4.RNA noncodev4.rna noncodev4.rna norine Nonribosomal Peptides Database http://bioinfo.lifl.fr/norine/ Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings. ^NOR\d+$ NOR00681 maude.pupin@univ-lille.fr http://bioinfo.lifl.fr/norine/result.jsp?ID=$1 False NORINE norine norine norine novus Novus Biologicals https://www.novusbio.com A vendor of antibodies and other biologics nb100-56351 https://www.novusbio.com/products/$1 False npass Natural Product Activity and Species Source Database http://bidd.group/NPASS/ "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data. " ^NPC\d+$ NPC139585 False npm Node Package Manager https://www.npmjs.com A repository of software packages written in Javascript, TypeScript, and related. @biopragmatics/curies https://www.npmjs.com/package/$1 False npo NanoParticle Ontology https://bioportal.bioontology.org/ontologies/NPO An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy. ^\d+$ 1731 nathan.baker@pnnl.gov http://purl.bioontology.org/ontology/npo#NPO_$1 False NPO NPO nrfc National Repository of Fish Cell Lines https://mail.nbfgr.res.in/nrfc/index.php The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage) ^NRFC\d+$ NRFC051 False NRFC nsc USA National Service Center Number https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data Identifier used by the Cancer Chemotherapy National Service Center. ^\d+$ 27223 https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1 False 000565 nsf.award National Science Foundation Award https://www.nsf.gov/awards/about.jsp Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research. ^\d+$ 1458400 https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1 False nsrrc National Swine Resource and Research Center http://www.nsrrc.missouri.edu/ Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID] ^\d+$ 0005 https://nsrrc.missouri.edu/nsrrc$1info/ False NSRRC nucc.characteristic National Uniform Claim Committee Characteristic https://nucc.org/index.php/code-sets-mainmenu-41/provider-characteristics-mainmenu-39 The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan. ^\d(\d|\w)$ 2A False nucc.taxonomy National Uniform Claim Committee Taxonomy https://taxonomy.nucc.org "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." ^\d{3}\w(\w|\d_)\d{4}X$ 207LH0002X False nucleardb NucleaRDB http://www.receptors.org/nucleardb/ 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. ^\w+\_\w+$ prgr_human vriend@cmbi.ru.nl http://www.receptors.org/nucleardb/proteins/$1 nuclearbd False NUCLEARBD nbdc00599 nuclearbd nuclearbd nucleardb nucleotide Nucleotide https://www.ncbi.nlm.nih.gov/ The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. ^[a-zA-Z0-9_\.]+$ 880798137 https://www.ncbi.nlm.nih.gov/nuccore/$1 False nbdc00600 nucleotide insdc nxr National Xenopus Resource http://www.mbl.edu/xenopus/ National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID] ^\d+$ 0024 https://scicrunch.org/resolver/RRID:NXR_$1 False NXR nztcs New Zealand Threat Classification System https://nztcs.org.nz/ identifier for species classified under the New Zealand Threat Classification System ^[1-9]\d{3,7}$ 11061 https://nztcs.org.nz/nztcs-species/$1 False P9889 oa Web Annotation Ontology http://www.w3.org/ns/oa The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture. sourceDateStart http://www.w3.org/ns/oa#$1 False OA oa OA oa oa oae Ontology of Adverse Events https://github.com/OAE-ontology/OAE/ The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. ^\d{7}$ 0002959 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OAE_$1 False OAE OAE OAE oae oae OAE oarcs Ontology of Arthropod Circulatory Systems https://github.com/aszool/oarcs OArCS is an ontology describing the Arthropod ciruclatory system. ^\d{7}$ 0000029 mjyoder@illinois.edu http://purl.obolibrary.org/obo/OARCS_$1 False OARCS OARCS OARCS oarcs oarcs OARCS oba Ontology of Biological Attributes https://github.com/obophenotype/bio-attribute-ontology A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO. ^(VT)?\d{7}$ 0000001 cjmungall@lbl.gov http://purl.obolibrary.org/obo/OBA_$1 False OBA OBA OBA OBA oba oba OBA oban Open Biomedical Annotations https://github.com/EBISPOT/OBAN It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub] ^\w+$ provenance http://purl.org/oban/$1 https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.owl False OBAN obci Ontology for Biomarkers of Clinical Interest https://github.com/clinical-biomarkers/OBCI The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects. ^\d+$ 000000001 dan5@georgetown.edu http://purl.obolibrary.org/obo/OBCI_$1 https://proteininformationresource.org/staff/nataled/OBCI/obci.owl False obcs Ontology of Biological and Clinical Statistics https://github.com/obcs/obcs OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI) ^\d{7}$ 0000121 jiezhen@med.umich.edu http://purl.obolibrary.org/obo/OBCS_$1 False OBCS OBCS OBCS obcs obcs obcs OBCS obi Ontology for Biomedical Investigations http://obi-ontology.org The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). ^\d{7}$ 0400109 bpeters@lji.org http://purl.obolibrary.org/obo/OBI_$1 https://github.com/obi-ontology/obi/raw/master/views/obi.obo False OBI OBI OBI obi obi obi obi OBI obi obib Ontology for Biobanking https://github.com/biobanking/biobanking The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. ^\d{7}$ 0000389 jmwhorton@uams.edu http://purl.obolibrary.org/obo/OBIB_$1 False OBIB OBIB OBIB obib obib OBIB obo Open Biological and Biomedical Ontologies http://www.obofoundry.org/ The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies. uberon nicolas.matentzoglu@gmail.com http://purl.obolibrary.org/obo/$1 False OBO nbdc00305 obo oboinowl OBO in OWL https://github.com/geneontology/go-ontology/tree/master/contrib This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties ^\w+$ hasDbXref cjmungall@lbl.gov http://www.geneontology.org/formats/oboInOwl#$1 http://www.geneontology.org/formats/oboInOwl.owl http://www.geneontology.org/formats/oboInOwl.obo oboformat|oio False oboInOwl oboinowl obv Austrian Library Network https://www.obvsg.at/ The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections. ^AC[0-9]{8}$ AC00963334 https://permalink.obvsg.at/$1 False 20430 obv occ OpenCitations Corpus https://w3id.org/oc/corpus The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law. ^[a-z][a-z]/[0-9]+$ br/1 https://w3id.org/oc/corpus/$1 False occ occ occo Occupation Ontology https://github.com/Occupation-Ontology/OccO An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union. ^\d+$ 00000001 zhengj2007@gmail.com http://purl.obolibrary.org/obo/OCCO_$1 False OCCO OCCO occo OCCO oci Open Citation Identifier http://opencitations.net Each OCI (Open Citation Identifier) has a simple structure: oci:-, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first is the identifier for the citing bibliographic resource, while the second is the identifier for the cited bibliographic resource. ^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$ 01027931310-01022252312 https://w3id.org/oc/oci/$1 False OCI oci oci ocid Ontology Concept Identifiers https://ontochem.com/ "'ocid' stands for ""Ontology Concept Identifiers"" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology." ^[0-9]{12}$ 190000021540 https://ocid.ontochem.com/prefname?ocid=$1 False ocid oclc Online Computer Library Center WorldCat https://www.oclc.org/en/about.html The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information. ^[0-9]+$ 634515043 https://www.worldcat.org/oclc/$1 False OCLC oclc oclc odam Open Data for Access and Mining https://metabolome.cgfb.u-bordeaux.fr/ Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed. ^[A-Za-z0-9]+$ frim1 http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1 False odam odamexplorer ODAM Data explorer https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/ "ODAM (Open Data for Access and Mining) is an Experimental data table management software (EDTMS) to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines. ODAM allows datasets to be explored and then extracted in whole or in part as needed. For more information/explanation, see ODAM User's Guide : https://inrae.github.io/ODAM/" ^[A-Za-z][A-Za-z0-9]+$ frim1 https://pmb-bordeaux.fr/dataexplorer/?ds=$1 False odam.explorer odc.sci Open Data Commons for Spinal Cord Injury https://odc-sci.org The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data. ^[0-9]*$ 602 jgrethe@ucsd.edu https://odc-sci.org/data/$1 False odc.sci r3d100014071 odc.tbi Open Data Commons for Traumatic Brain Injury https://odc-tbi.org The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data. ^[0-9]*$ 408 https://odc-tbi.org/data/$1 False odc.tbi odor Odor Molecules DataBase http://senselab.med.yale.edu/OdorDB OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors ^\d+$ 74 http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5 False ODOR odor odor odrl Open Digital Rights Language Ontology http://www.w3.org/ns/odrl/2 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. assetConcepts http://www.w3.org/ns/odrl/2/$1 False odrl oecd.template OECD Harmonised Templates https://www.oecd.org/ehs/templates/ The Organisation for Economic Co-operation and Development (OECD) Harmonised Templates (OHTs) are standard data formats for reporting information used for the risk assessment of chemicals, mainly studies done on chemicals to determine their properties or effects on human health and the environment, but also for storing data on use and exposure. ^\d+\.\d+$ 74.186 False ogg The Ontology of Genes and Genomes https://bitbucket.org/hegroup/ogg 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. ^\d+$ 3000887619 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OGG_$1 False OGG OGG OGG ogg ogg OGG ogi Ontology for genetic interval https://code.google.com/archive/p/ontology-for-genetic-interval/ "OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is ""the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture."" Related paper: 1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology) Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf) Yu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF) " ^\d{7}$ 0000019 linikujp@gmail.com http://purl.obolibrary.org/obo/OGI_$1 OGI.owl True OGI OGI OGI ogi ogi OGI ogms Ontology for General Medical Science https://github.com/OGMS/ogms "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology." ^\d{7}$ 0000031 baeverma@jcvi.org http://purl.obolibrary.org/obo/OGMS_$1 http://purl.obolibrary.org/obo/ogms.obo ogms/OMRE False OGMS 216 OGMS OGMS ogms ogms OGMS ogsf Ontology of Genetic Susceptibility Factor https://github.com/linikujp/OGSF An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. ^\d{7}$ 0000025 linikujp@gmail.com http://purl.obolibrary.org/obo/OGSF_$1 True OGSF OGSF OGSF ogsf ogsf OGSF ohd Oral Health and Disease Ontology https://purl.obolibrary.org/obo/ohd/home The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies. ^\d{7}$ 0000006 wdduncan@gmail.com http://purl.obolibrary.org/obo/OHD_$1 False OHD OHD OHD ohd ohd OHD ohmi Ontology of Host-Microbiome Interactions https://github.com/ohmi-ontology/ohmi OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions. ^\d{7}$ 0000460 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OHMI_$1 False OHMI OHMI OHMI ohmi ohmi OHMI ohpi Ontology of Host Pathogen Interactions https://github.com/OHPI/ohpi OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration). ^\d+$ 9001411 edong@umich.edu http://purl.obolibrary.org/obo/OHPI_$1 False OHPI OHPI ohpi ohpi OHPI oid ISO Object Identifier http://www.oid-info.com/introduction.htm OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes. ^[\d.]+$ 2.16.840 http://oid-info.com/get/$1 False oid oid olatdv Medaka Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv Life cycle stages for Medaka ^\d{7}$ 0000210 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/OlatDv_$1 True OLATDV OLATDV OLATDV olatdv olatdv OlatDv om Ontology of units of Measure https://github.com/HajoRijgersberg/OM The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging Dimension hajo.rijgersberg@wur.nl http://www.ontology-of-units-of-measure.org/resource/om-2/$1 False OM OM OM om oma.grp OMA Group https://omabrowser.org/cgi-bin/gateway.pl OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs. ^[A-Z]+$ LCSCCPN https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1 False OMA.GRP oma.grp oma.grp oma.hog OMA HOGs https://omabrowser.org Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ 0459895 https://omabrowser.org/oma/hog/HOG:$1 False oma.hog oma.protein OMA Protein https://omabrowser.org/cgi-bin/gateway.pl OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. ^[A-Z0-9]{5}\d+$ HUMAN16963 https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1 False OMA.PROTEIN oma.protein oma.protein OmaProtein omia Online Mendelian Inheritance in Animals https://omia.org Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia' prefix is used for phenes, either across species (omia:001000) or in a specific species (omia:001000-9615) ^\d{6}(-\d+)?$ 001000 imke.tammen@sydney.edu.au https://omia.org/phene/omia:$1 OMIA False OMIA nbdc00153 omia omia omia omia.variant OMIA variants https://omia.org Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia.variant' prefix is used for genetic variants associated with phenes listed in OMIA ^\d+$ 1710 imke.tammen@sydney.edu.au https://omia.org/variant/omia.variant:$1 False OMIA nbdc00153 omiabis Ontologized MIABIS https://github.com/OMIABIS/omiabis-dev An ontological version of MIABIS (Minimum Information About BIobank data Sharing) ^\d{7}$ 0001079 mbrochhausen@gmail.com http://purl.obolibrary.org/obo/OMIABIS_$1 True OMIABIS OMIABIS OMIABIS omiabis omiabis OMIABIS omid OpenCitations Meta Identifier http://opencitations.net/ Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted. ^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$ br/0601 https://w3id.org/oc/meta/$1 False omid omim Online Mendelian Inheritance in Man https://omim.org/ Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. ^\d+$ 603903 ahamosh@jhmi.edu https://omim.org/MIM:$1 OMIM|mim False OMIM OMIM OMIM 1153 2.16.840.1.113883.6.174 nbdc00154 mim mim omim DB-0062 P492 omim.ps OMIM Phenotypic Series https://www.omim.org/phenotypicSeriesTitles/all A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome. ^\d+$ 214100 ahamosh@jhmi.edu https://omim.org/MIM:PS$1 MIMPS|OMIMPS|PS|mim.ps False omim omit Ontology for MicroRNA Target http://omit.cis.usouthal.edu/ The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). ^\d{7}$ 0000069 huang@southalabama.edu http://purl.obolibrary.org/obo/OMIT_$1 https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo OMIT False OMIT OMIT OMIT omit omit omit omit OMIT omo OBO Metadata Ontology https://github.com/information-artifact-ontology/ontology-metadata An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). ^\d{7}$ 0003003 cjmungall@lbl.gov http://purl.obolibrary.org/obo/OMO_$1 False OMO OMO omo omo OMO omon Overview of Medical Research in the Netherlands https://onderzoekmetmensen.nl/en The new national clinical trials registry of the Netherlands ^\d{5}$ 53367 https://onderzoekmetmensen.nl/en/trial/$1 False omop Observational Medical Outcomes Partnership https://www.ohdsi.org/data-standardization/the-common-data-model/ The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format. ^\d+$ 1 https://athena.ohdsi.org/search-terms/terms/$1 OMOP False omp Ontology of Microbial Phenotypes http://microbialphenotypes.org An ontology of phenotypes covering microbes ^\d{7}$ 0005067 jimhu@tamu.edu http://purl.obolibrary.org/obo/OMP_$1 False OMP OMP OMP omp omp OMP omrse Ontology for Modeling and Representation of Social Entities https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. ^\d{8}$ 00000022 hoganwr@gmail.com http://purl.obolibrary.org/obo/OMRSE_$1 https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo False OMRSE OMRSE OMRSE omrse omrse OMRSE omx.dataset OncoMX Dataset https://data.oncomx.org OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX. ^\d+$ 000059 https://data.oncomx.org/OMX_$1 False oncotree OncoTree http://oncotree.mskcc.org 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. BLL http://oncotree.mskcc.org/api/tumorTypes/search/code/$1 False one Ontology for Nutritional Epidemiology https://github.com/cyang0128/Nutritional-epidemiologic-ontologies An ontology to standardize research output of nutritional epidemiologic studies. ^\d{7}$ 0001021 chenyangnutrition@gmail.com http://purl.obolibrary.org/obo/ONE_$1 False ONE ONE one one ONE ons Ontology for Nutritional Studies https://github.com/enpadasi/Ontology-for-Nutritional-Studies An ontology for description of concepts in the nutritional studies domain. ^\d{7}$ 0000060 francesco.vitali@ibba.cnr.it http://purl.obolibrary.org/obo/ONS_$1 False ONS ONS ONS ons ons ONS ontie Ontology for Immune Epitopes https://ontology.iedb.org/ The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes. ^\d{7}$ 0000001 bpeters@lji.org https://ontology.iedb.org/ontology/ONTIE_$1 https://raw.githubusercontent.com/IEDB/ONTIE/master/ontie.owl False ontoavida Ontology for Avida digital evolution platform https://gitlab.com/fortunalab/ontoavida "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. OntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA). More information can be found at https://obofoundry.org/ontology/ontoavida.html" ^\d{8}$ 00000001 fortuna@ebd.csic.es http://purl.obolibrary.org/obo/ONTOAVIDA_$1 False ONTOAVIDA ONTOAVIDA ontoavida ontoavida ONTOAVIDA ontoneo Obstetric and Neonatal Ontology http://ontoneo.com The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. ^\d{8}$ 00000098 fernanda.farinelli@gmail.com http://purl.obolibrary.org/obo/ONTONEO_$1 False ONTONEO ONTONEO ONTONEO ontoneo ontoneo ONTONEO oostt Ontology of Organizational Structures of Trauma centers and Trauma systems https://github.com/OOSTT/OOSTT The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). ^\d{8}$ 00000099 mbrochhausen@gmail.com http://purl.obolibrary.org/obo/OOSTT_$1 False OOSTT OOSTT OOSTT oostt oostt OOSTT opb Ontology of Physics for Biology http://bioportal.bioontology.org/ontologies/OPB The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. ^\d+$ 00573 maxneal@gmail.com https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1 False OPB OPB OPB opb opb opb openalex OpenAlex https://openalex.org/ OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other. ^[WAICV]\d{2,}$ W2741809807 hpiwowar@gmail.com https://openalex.org/$1 False openwemi openWEMI Vocabulary https://dcmi.github.io/openwemi/ openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item. ^\w+$ Endeavor kcoyle@kcoyle.net https://dcmi.github.io/openwemi/ns#$1 False opl Ontology for Parasite LifeCycle https://github.com/OPL-ontology/OPL The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. ^\d{7}$ 0000319 zhengj2007@gmail.com http://purl.obolibrary.org/obo/OPL_$1 False OPL OPL OPL opl opl opl OPL opm Orientations of Proteins in Membranes Database http://opm.phar.umich.edu/ The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. ^[0-9][A-Za-z0-9]{3}$ 1h68 http://opm.phar.umich.edu/protein.php?pdbid=$1 False OPM opm opm opmi Ontology of Precision Medicine and Investigation https://github.com/OPMI/opmi OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. ^\d{7}$ 0000101 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OPMI_$1 False OPMI OPMI opmi opmi OPMI orcid Open Researcher and Contributor https://orcid.org ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ 0000-0003-4423-4370 w.simpson@orcid.org https://orcid.org/$1 ORCID|ORCiD False 2021 ORCID orcid orcid P496 ordb Olfactory Receptor Database http://senselab.med.yale.edu/OrDB/ The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs). ^\d+$ 8497 http://senselab.med.yale.edu/ORDB/Data/$1 False ORDB ordb ordb 65 ordb oridb.sacch OriDB Saccharomyces http://cerevisiae.oridb.org/index.php OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae. ^\d+$ 1 http://cerevisiae.oridb.org/details.php?id=$1 False ORIDB.SACCH oridb.sacch oridb.sacch oridb.schizo OriDB Schizosaccharomyces http://pombe.oridb.org/index.php OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe. ^\d+$ 1 http://pombe.oridb.org/details.php?id=$1 False ORIDB.SCHIZO oridb.schizo oridb.schizo ornaseq Ontology of RNA Sequencing http://kim.bio.upenn.edu/software/ornaseq.shtml An application ontology designed to annotate next-generation sequencing experiments performed on RNA. ^\d{7}$ 0000010 safisher@upenn.edu http://purl.obolibrary.org/obo/ORNASEQ_$1 http://purl.obolibrary.org/obo/ornaseq.obo False ORNASEQ ORNASEQ ornaseq ornaseq ORNASEQ orphanet Orphanet http://www.orpha.net/consor/ Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases. ^\d+$ 85163 bliemsl@xs4all.nl http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1 http://www.orphadata.org/data/ORDO/ordo_orphanet.owl ORPHA False Orphanet nbdc01422 orphanet orphanet orphanet DB-0068 P1550 orphanet.ordo Orphanet Rare Disease Ontology https://www.ebi.ac.uk/ols4/ontologies/ordo "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)." ^C?\d+$ C023 ordo.orphanet@inserm.fr http://www.orpha.net/ORDO/Orphanet_$1 http://www.orphadata.org/data/ORDO/ordo_orphanet.owl ordo False ordo ORPHANET.ORDO ORDO ORDO orphanet.ordo orphanet.ordo ordo orth Orthology Ontology https://github.com/qfo/OrthologyOntology 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. HomologyRelation jfernand@um.es http://purl.org/net/orth#$1 https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl False ORTH ORTH orth orthodb OrthoDB https://www.orthodb.org OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups ^\w+$ Q9P0K8 evgeny.zdobnov@unige.ch http://cegg.unige.ch/orthodb/results?searchtext=$1 False ORTHODB orthodb orthodb orthodb DB-0143 uniprot oryzabase.gene Oryzabase Gene http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information. ^\d+$ 117 http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1 False ORYZABASE.GENE oryzabase.gene oryzabase.gene oryzabase.mutant Oryzabase Mutant http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information. ^\d+$ 21393 http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1 False ORYZABASE.MUTANT oryzabase.mutant oryzabase.mutant oryzabase.reference Oryzabase Reference http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. ^\d+$ 42840 https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1 False oryzabase.reference oryzabase.reference oryzabase.stage Oryzabase Stage http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information. ^\d+$ 34 http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1 False ORYZABASE.STAGE oryzabase.stage oryzabase.stage oryzabase.strain Oryzabase Strain http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information. ^\d+$ 1 http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1 False ORYZABASE.STRAIN oryzabase.strain oryzabase.strain osf Open Science Framework ID https://osf.io ID in osf.io ^[a-z0-9]{5}$ 2u4tf https://osf.io/$1 False P7238 oslc OASIS Open Services for Lifecycle Collaboration Core Vocabulary http://open-services.net/ns/core Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains. Property jamsden@us.ibm.com http://open-services.net/ns/core#$1 False oslc osti.article Office of Scientific and Technical Information (OSTI) https://www.osti.gov/ The U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) is the main metadata archive for permanent storage of registered [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service) (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord) is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services)) and can be alternatively used as the main product identifier endpoint when [searching OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below). OSTI.GOV is the primary registry and search tool for all Department of Energy (DOE) funded science, technology, and engineering research and development (R&D) results and the organizational hub for information about the DOE Office of Scientific and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761 - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761 - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761 **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/ - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/ ^\d+$ 1668761 https://www.osti.gov/biblio/$1 False P3894 otl Oryza Tag Line http://oryzatagline.cirad.fr/ Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information. ^A[A-Z]+\d+$ AADB12 guiderdoni@cirad.fr http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1 False OTL otl otl otl otol Open Tree of Life https://tree.opentreeoflife.org Identifier for an entity in open tree of life ^[1-9]\d*$ 3905431 https://tree.opentreeoflife.org/taxonomy/browse?id=$1 False P9157 ovae Ontology of Vaccine Adverse Events http://www.violinet.org/ovae/ OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ^\d{7}$ 0000609 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OVAE_$1 False OVAE OVAE OVAE ovae ovae OVAE owl Web Ontology Language https://www.w3.org/TR/owl-features/ Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. Ontology rmrich5@gmail.com http://www.w3.org/2002/07/owl#$1 https://triplydb.com/w3c/owl/download.trig.gz False owl nbdc00307 owl owl owl owlstar Ontological Interpretations for Web Property Graphs https://linkml.io/owlstar/ This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub] ^\w+$ AllSomeInterpretation cjmungall@lbl.gov http://w3id.org/owlstar/$1 False p3db.protein P3DB Protein http://www.p3db.org/ Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites. ^\d+$ 70 http://www.p3db.org/protein.php?id=$1&ref=0 False P3DB.PROTEIN p3db.protein p3db.protein p3db p3db.site P3DB Site http://www.p3db.org/ Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins. ^\d+$ 65 http://www.p3db.org/phosphosite.php?id=$1&ref=0 False P3DB.SITE p3db.site p3db.site packagist Packagist https://packagist.org A repository of software packages written in PHP. florianv/swap https://packagist.org/packages/$1 False pactr Pan African Clinical Trials Registry https://pactr.samrc.ac.za/ The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage) ^PACTR\d+$ PACTR202304525632216 False paleodb Paleobiology Database http://paleodb.org/ 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. ^\d+$ 83088 http://fossilworks.org/?a=taxonInfo&taxon_no=$1 False PALEODB paleodb paleodb paleodb pandit Protein and Associated NucleotideDomains with Inferred Trees http://www.ebi.ac.uk/goldman-srv/pandit PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. PF00004 http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1 False nbdc00607 pandit r3d100011232 pfam panorama Panorama Public https://panoramaweb.org 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. FxnI151FMs brendanx@uw.edu https://panoramaweb.org/$1.url False panther.family PANTHER Family http://www.pantherdb.org/ The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families. ^PTHR\d{5}(\:SF\d{1,3})?$ PTHR12345 pdthomas@usc.edu http://www.pantherdb.org/panther/family.do?clsAccession=$1 False PANTHER.FAMILY panther.family panther.family panther DB-0069 panther panther.node PANTHER Node http://pantree.org/ The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes. ^PTN\d{9}$ PTN000000026 http://www.pantree.org/node/annotationNode.jsp?id=$1 False PANTHER.NODE panther.node panther.node panther panther.pathway PANTHER Pathway http://www.pantherdb.org/ The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. ^P\d{5}$ P00024 http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1 False PANTHER.PATHWAY 1161 panther.pathway panther.pathway panther panther.pthcmp PANTHER Pathway Component http://www.pantherdb.org/ "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation." ^(G|P|U|C|S)\d{5}$ P00266 http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1 False PANTHER.PTHCMP panther.pthcmp panther.pthcmp panther pao Plant Anatomy Ontology http://www.plantontology.org jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/PAO_$1 True PAO pao pass2 Protein Alignment organised as Structural Superfamily http://caps.ncbs.res.in/pass2 The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. ^\d+$ 46977 http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1 True PASS2 nbdc02108 pass2 pass2 pass2 pathbank PathBank https://pathbank.org PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. ^(SMP|PW)\d+$ SMP0000219 https://pathbank.org/view/$1 False Pathbank pathguide Pathguide http://pathguide.org Pathguide contains information about 325 biological related resources and molecular interaction related resources. ^\d+$ 49 gary.bader@utoronto.ca http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1 False nbdc00608 pathguide pathoplant PathoPlant® http://www.pathoplant.de 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. MO000027 http://www.pathoplant.de/detail.php?accNo=$1 False 333 pathoplant pathwaycommons Pathway Commons http://www.pathwaycommons.org/pc/ Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. ^\d+$ 485991 chris@sanderlab.org http://www.pathwaycommons.org/pc/record2.do?id=$1 False PATHWAYCOMMONS pathwaycommons pathwaycommons pathwaycommons r3d100012731 DB-0253 pato Phenotype And Trait Ontology https://github.com/pato-ontology/pato/ PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. ^\d{7}$ 0001998 g.gkoutos@gmail.com http://purl.obolibrary.org/obo/PATO_$1 False PATO PATO PATO PATO pato pato pato pato PATO pato pav Provenance, Authoring, and Versioning Vocabulary https://pav-ontology.github.io/pav/ PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. ^[a-z][a-zA-Z]+$ authoredBy stian@soiland-reyes.com http://purl.org/pav/$1 False PAV pav PAV pav paxdb.organism PaxDb Organism http://pax-db.org/ PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species. ^\d+$ 9606 http://pax-db.org/#!species/$1 False PAXDB.ORGANISM paxdb.organism paxdb.organism paxdb.protein PaxDb Protein http://pax-db.org/ PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels. ^\d+$ 977869 http://pax-db.org/#!protein/$1 False PAXDB.PROTEIN paxdb.protein paxdb.protein pazar Pazar Transcription Factor http://www.pazar.info/ The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors. ^TF\w+$ TF0001053 wyeth@cmmt.ubc.ca http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1 False PAZAR nbdc00611 pazar pazar 521 pazar pba Primate Brain Atlas https://www.blueprintnhpatlas.org/ A controlled vocabulary to support the study of transcription in the primate brain ^\d+$ 128011350 https://biopragmatics.github.io/providers/pba/$1 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo False pcl Provisional Cell Ontology https://github.com/obophenotype/provisional_cell_ontology Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties. ^\d{7}$ 0011124 davidos@ebi.ac.uk http://purl.obolibrary.org/obo/PCL_$1 False PCL PCL pcl pcl PCL pco Population and Community Ontology https://github.com/PopulationAndCommunityOntology/pco The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. ^\d{7}$ 0000021 rlwalls2008@gmail.com http://purl.obolibrary.org/obo/PCO_$1 http://purl.obolibrary.org/obo/pco.obo False PCO PCO PCO PCO PCO pco pco PCO pd_st Platynereis stage ontology http://4dx.embl.de/platy henrich@embl.de http://purl.obolibrary.org/obo/PD_ST_$1 True PD_ST pd_st pdb PDB Structure https://www.wwpdb.org/ The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. ^[0-9][A-Za-z0-9]{3}$ 2gc4 harukin@protein.osaka-u.ac.jp https://www.wwpdb.org/pdb?id=$1 RCSB_PDB|pdbe|pdbj|wwpdb False PDB 1127 nbdc00613 pdb pdb 398 pdbj r3d100010910 Pdb DB-0172 P638 pdb-ccd Chemical Component Dictionary https://www.ebi.ac.uk/pdbe-srv/pdbechem/ The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. ^\w{1,3}$ AB0 berman@rcsb.rutgers.edu https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 pdbechem False PDB-CCD pdb-ccd pdb-ccd ccd PdbCcd pdb.ligand pdb.ligand PDB ligand http://www.pdb.org/ The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands. ^[A-Za-z0-9]+$ TRQ http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1 PDB_CHEM_ID False PDB.LIGAND pdb.ligand pdb.ligand 169 pdbligand P3636 pdbsum PDBsum; at-a-glance overview of macromolecular structures http://www.ebi.ac.uk/pdbsum PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them. 1kfv roman@ebi.ac.uk https://www.ebi.ac.uk/pdbsum/$1 False nbdc00308 461 pdbsum DB-0119 pdb pdc.study Proteomic Data Commons https://pdc.cancer.gov/pdc The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public. ^PDC\d+$ PDC000351 https://pdc.cancer.gov/pdc/study/$1 False pdro The Prescription of Drugs Ontology https://github.com/OpenLHS/PDRO An ontology to describe entities related to prescription of drugs ^\d{7}$ 0010039 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/PDRO_$1 False PDRO PDRO PDRO pdro pdro PDRO pdumdv Platynereis Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv Life cycle stages for Platynereis dumerilii ^\d{7}$ 0001410 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/PdumDv_$1 PdumDv True PDUMDV PDUMDV PDUMDV pdumdv pdumdv PdumDv peco Plant Experimental Conditions Ontology http://planteome.org/ A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. ^\d{7}$ 0007114 jaiswalp@science.oregonstate.edu https://browser.planteome.org/amigo/term/PECO:$1 https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo False PECO PECO PECO PECO peco peco PECO ped Protein Ensemble Database https://proteinensemble.org/ The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. ^PED\d{5}$ PED00037 zhangzhang@big.ac.cn https://proteinensemble.org/$1 False nbdc02490 ped ped.ensemble Protein Ensemble Database ensemble https://proteinensemble.org/ The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. ^PED\d{5}e\d{3}$ PED00017e001 https://proteinensemble.org/$1 False ped.ensemble ped peff PSI Extended File Format https://www.psidev.info/peff ^\d{7}$ 0001011 https://biopragmatics.github.io/providers/peff/$1 https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo True pennsieve Pennsieve https://discover.pennsieve.io "Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a ""peer""-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs. " ^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a https://discover.pennsieve.io/package/$1 False ps pepbank PepBank Peptide Database http://pepbank.mgh.harvard.edu/ 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. 21877 http://pepbank.mgh.harvard.edu/interactions/details/$1 True 235 pepbank peptideatlas PeptideAtlas http://www.peptideatlas.org/ The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. ^PAp[0-9]{8}$ PAp00000009 edeutsch@systemsbiology.org https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1 False PEPTIDEATLAS 2626 nbdc01812 peptideatlas peptideatlas peptideatlas r3d100010889 DB-0071 peptideatlas.dataset PeptideAtlas Dataset https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas. ^PASS\d{5}$ PASS01237 http://www.peptideatlas.org/PASS/$1 False peptideatlas.dataset peptideatlas.dataset perkinelmer PerkinElmer cell line collection https://www.perkinelmer.com/ Cell line collections (Providers) SCC111 https://www.perkinelmer.com/searchresult?searchName=$1 False PerkinElmer peroxibase Peroxibase http://peroxibase.toulouse.inra.fr/ Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. ^\d+$ 5282 dunand@lrsv.ups-tlse.fr http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1 False PEROXIBASE nbdc01869 peroxibase peroxibase peroxibase DB-0072 pesticideinfo PesticideInfo chemical ID https://www.pesticideinfo.org chemical in the database supplied by Pesticide Action Network North America ^PRI\d*$ PRI10 https://www.pesticideinfo.org/chemical/$1 False P11949 pesticides Alan Wood's Pesticides http://www.alanwood.net/pesticides The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients. derivatives%2Fthiocyclam%20hydrochloride http://www.alanwood.net/pesticides/$1.html False pfam Pfam https://www.ebi.ac.uk/interpro/ The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. ^PF\d{5}$ PF11779 agb@ebi.ac.uk https://www.ebi.ac.uk/interpro/entry/pfam/$1 PF False PFAM 1138 nbdc00163 pfam pfam pfam r3d100012850 Pfam DB-0073 P3519 pfam.clan Pfam Clans https://pfam.xfam.org Higher order grouping of Pfam families ^CL\d+$ CL0192 https://www.ebi.ac.uk/interpro/set/pfam/$1 False 2758 pfr Proteoform Atlas http://repository.topdownproteomics.org/proteoforms Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets. ^\d+$ 1001 http://repository.topdownproteomics.org/proteoforms/$1 TDR False r3d100012385 pgdso Plant Growth and Development Stage http://www.plantontology.org po-discuss@plantontology.org http://purl.obolibrary.org/obo/PGDSO_$1 True PGDSO pgdso pgs Polygenic Score Catalog http://pgscatalog.org The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation. ^PGS[0-9]{6}$ PGS000018 https://www.pgscatalog.org/pgs/$1 False pgs pgx Progenetix https://progenetix.org/ "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt ""neoplasm"" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs." ^\w{3,15}[-_]\w[\w.-]{3,128}$ pgxbs-kftva5zv mbaudis@me.com https://progenetix.org/services/ids/$1 Progenetix False PGX Progenetix pgx pgx r3d100012820 pharmacodb.cell PharmacoDB Cells https://pharmacodb.ca/cell_lines 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. 22RV1_12_2019 https://pharmacodb.ca/cell_lines/$1 False PharmacoDB pharmacodb.dataset PharmacoDB Datasets https://pharmacodb.ca/datasets Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset. ^\d+$ 1 https://pharmacodb.ca/datasets/$1 False pharmacodb.tissue PharmacoDB Tissues https://pharmacodb.ca/tissues Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue. ^\d+$ 13 https://pharmacodb.ca/tissues/$1 False pharmgkb.disease PharmGKB Disease http://www.pharmgkb.org/ The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. ^PA\d+$ PA447218 teri.klein@stanford.edu http://www.pharmgkb.org/disease/$1 False PHARMGKB.DISEASE 2651 pharmgkb.disease pharmgkb.disease pharmgkb.disease P7001 pharmgkb.drug PharmGKB Drug http://www.pharmgkb.org/ The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. ^PA\d+$ PA448710 teri.klein@stanford.edu http://www.pharmgkb.org/drug/$1 False PHARMGKB.DRUG 2652 pharmgkb.drug pharmgkb.drug pharmgkb.drug P7001 pharmgkb.gene PharmGKB Gene http://www.pharmgkb.org/ The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. ^PA\w+$ PA131 teri.klein@stanford.edu http://www.pharmgkb.org/gene/$1 False PHARMGKB.GENE PHARMGKB pharmgkb.gene pharmgkb.gene pharmgkb.gene DB-0074 P7001 pharmgkb.pathways PharmGKB http://www.pharmgkb.org/ "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies." ^PA\d+$ PA146123006 teri.klein@stanford.edu http://www.pharmgkb.org/pathway/$1 False PHARMGKB.PATHWAYS 2650 pharmgkb.pathways pharmgkb.pathways pharmgkb.pathways P7001 pharmvar Pharmacogene Variation Consortium https://www.pharmvar.org 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. CYP2A6 agaedigk@cmh.edu https://www.pharmvar.org/gene/$1 False pharmvar hgnc.symbol phenolexplorer Phenol-Explorer http://www.phenol-explorer.eu/foods/ Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. ^\d+$ 75 http://phenol-explorer.eu/foods/$1 False PHENOLEXPLORER phenolexplorer phenolexplorer r3d100012197 phenx PhenX Toolkit https://www.phenxtoolkit.org/ A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants. ^\d+$ 130502 yingqin@rti.org https://www.phenxtoolkit.org/protocols/view/$1 phenxtoolkit False PHENX PHENX nbdc02244 phipo Pathogen Host Interaction Phenotype Ontology https://github.com/PHI-base/phipo Ontology of species-neutral phenotypes observed in pathogen-host interactions. ^\d{7}$ 0000001 alayne.cuzick@rothamsted.ac.uk http://purl.obolibrary.org/obo/PHIPO_$1 False PHIPO PHIPO phipo phipo PHIPO phosphopoint.kinase PhosphoPoint Kinase http://kinase.bioinformatics.tw/ PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information. ^\w+$ AURKA http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1 False PHOSPHOPOINT.KINASE phosphopoint.kinase phosphopoint.kinase phosphopoint.protein PhosphoPoint Phosphoprotein http://kinase.bioinformatics.tw/ PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information. ^\w+$ AURKA http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0 False PHOSPHOPOINT.PROTEIN phosphopoint.protein phosphopoint.protein phosphosite.curation PhosphoSite Curation https://www.phosphosite.org PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications. ^\d+$ 34665743 https://www.phosphosite.org/curatedInfoAction.action?record=$1 False phosphosite.protein PhosphoSite Protein http://www.phosphosite.org/homeAction.do PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database. ^\d{5}$ 12300 http://www.phosphosite.org/proteinAction.do?id=$1 False PHOSPHOSITE.PROTEIN phosphosite.protein phosphosite.protein phosphosite.residue PhosphoSite Residue http://www.phosphosite.org/homeAction.do PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence. ^\d+$ 2842 http://www.phosphosite.org/siteAction.do?id=$1 False PHOSPHOSITE.RESIDUE phosphosite.residue phosphosite.residue phosphosite.sitegroup PhosphoSite Site Group https://www.phosphosite.org Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur. ^\d+$ 447860 False phrr Philippine Health Research Registry https://registry.healthresearch.ph 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] 4195 https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1 False phylomedb PhylomeDB http://phylomedb.org/ PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins. ^\w+$ Phy000CLXM_RAT toni.gabaldon@crg.eu http://phylomedb.org/?seqid=$1 False PHYLOMEDB nbdc01764 phylomedb phylomedb phylomedb DB-0144 phytozome.locus Plant Genome Network http://www.phytozome.net/ Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information. ^[A-Za-z0-9]+$ Glyma0021s00410 http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1 JGI Phytozome False PHYTOZOME.LOCUS phytozome.locus phytozome.locus pibase Database of structurally defined protein interfaces http://salilab.org/pibase 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. 21692 http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1 False 183 pibase pictar PicTar https://pictar.mdc-berlin.de/ hsa-let-7a pictar-vert True pid.pathway NCI Pathway Interaction Database: Pathway http://pid.nci.nih.gov/ The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information. ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$ eff796f3-6195-11e5-8ac5-06603eb7f303 schaefec@mail.nih.gov http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1 pid False PID.PATHWAY 2344 pid.pathway pid.pathway 119 pid pigqtldb Animal Genome Pig QTL https://www.animalgenome.org/QTLdb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs. ^\d+$ 14 https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 False PIGQTLDB pigqtldb pigqtldb pigqtldb qtldb pina Protein Interaction Network Analysis http://cbg.garvan.unsw.edu.au/pina/ Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ Q13485 wujm@bjmu.edu.cn http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1 False PINA pina pina 348 uniprot piroplasma PiroplasmaDB http://piroplasmadb.org/ PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^TA\d+$ TA14985 http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 False PIROPLASMA piroplasma piroplasma pirsf PIR Superfamily Classification System https://pir.georgetown.edu/ The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. ^PIRSF\d{6}$ PIRSF000100 wuc@udel.edu https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 False PIRSF 1136 pirsf pirsf pirsf DB-0079 pkdb PK-DB https://www.hu-berlin.de/?set_language=en&cl=en PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ^PKDB[0-9]{5}$ PKDB00198 konigmatt@googlemail.com https://pk-db.com/data/$1 False pkdb plana Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology https://github.com/obophenotype/planaria-ontology PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea. ^\d{7}$ 0000001 smr@stowers.org http://purl.obolibrary.org/obo/PLANA_$1 False PLANA PLANA PLANA plana plana PLANA planp Planarian Phenotype Ontology https://github.com/obophenotype/planarian-phenotype-ontology Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. ^\d+$ 0000001 smr@stowers.org http://purl.obolibrary.org/obo/PLANP_$1 False PLANP PLANP planp planp PLANP planttfdb Plant Transcription Factor Database http://planttfdb.cbi.pku.edu.cn The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors. ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$ Ath_AT1G01030.1 gaog@mail.cbi.pku.edu.cn http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1 False PLANTTFDB planttfdb planttfdb 497 planttfdb r3d100011301 plasmodb PlasmoDB http://plasmodb.org/plasmo/ AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ PF11_0344 oharb@upenn.edu http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 ApiDB_PlasmoDB False PLASMODB nbdc01783 plasmodb plasmodb 514 plasmodb r3d100011569 plo Plasmodium Life Cycle http://www.sanger.ac.uk/Users/mb4/PLO/ mb4@sanger.ac.uk http://purl.obolibrary.org/obo/PLO_$1 True PLO plo pmap.cutdb CutDB http://cutdb.burnham.org The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). ^\d+$ 25782 adam@burnham.org http://cutdb.burnham.org/relation/show/$1 False PMAP.CUTDB pmap.cutdb pmap.cutdb pmap.cutdb pmap.substratedb SubstrateDB http://substrate.burnham.org/ The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates. ^\d+$ 1915 eroshkin@burnham.org http://substrate.burnham.org/protein/annotation/$1/html False PMAP.SUBSTRATEDB pmap.substratedb pmap.substratedb pmap.substratedb pmc PubMed Central http://europepmc.org/ PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature. ^PMC\d+(\.\d+)?$ PMC3084216 beck@ncbi.nlm.nih.gov http://europepmc.org/articles/$1 PMC|PMCID False PMCID pmc pmc pmc P932 pmdb Protein Model Database https://bioinformatics.cineca.it/PMDB/ The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. ^PM\d{7}$ PM0012345 https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1 False PMDB pmdb pmdb pmdb pmp Protein Model Portal http://www.proteinmodelportal.org/ The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers. ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ Q0VCA6 torsten.schwede@unibas.ch http://www.proteinmodelportal.org/query/uniprot/$1 False PMP pmp pmp 438 pmp uniprot pmr Physical Medicine and Rehabilitation https://www.auckland.ac.nz/en.html Resource for the community to store, retrieve, search, reference, and reuse CellML models. ^[a-z0-9]{32,32}$ ebf69ca24298b28b2361e7d43eb52d6c laia.subirats@gmail.com https://models.physiomeproject.org/exposure/$1 False PMR PMR pmr pmr.workspace Physiome Model Repository workspace https://www.auckland.ac.nz/en.html Workspace (Git repository) for modeling projects managed by the Physiome Model Repository ^[a-zA-Z0-9_\-]+(/.*?)?$ modularmassactionprimer https://models.physiomeproject.org/workspace/$1 False pmr.workspace po Plant Ontology http://browser.planteome.org/amigo The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. ^\d+$ 0009089 jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/PO_$1 False PO PO PO PO 1180 po po po po PO po pocketome Pocketome http://www.pocketome.org/sfSearch.cgi?act=browseall Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries. ^[A-Za-z_0-9]+$ 1433C_TOBAC_1_252 ikufareva@ucsd.edu http://www.pocketome.org/files/$1.html False POCKETOME pocketome pocketome 537 polbase PolBase http://polbase.neb.com/ Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity. ^[A-Za-z-0-9]+$ 19-T4 lreha@ualberta.ca https://polbase.neb.com/polymerases/$1#sequences False POLBASE nbdc02079 polbase polbase pombase PomBase https://www.pombase.org/ PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. ^S\w+(\.)?\w+(\.)?$ SPCC13B11.01 vw253@cam.ac.uk https://www.pombase.org/gene/$1 PomBase False PomBase nbdc00332 pombase pombase pombase r3d100011478 DB-0031 P6245 poro Porifera Ontology https://github.com/obophenotype/porifera-ontology An ontology describing the anatomical structures and characteristics of Porifera (sponges) ^\d{7}$ 0000550 robert.thacker@stonybrook.edu http://purl.obolibrary.org/obo/PORO_$1 False PORO PORO PORO poro poro PORO ppdb Pesticide Properties DataBase https://sitem.herts.ac.uk/aeru/ppdb/ PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. ^\d+$ 1484 ppdb@gifu-u.ac.jp https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm False nbdc01041 ppo Plant Phenology Ontology https://github.com/PlantPhenoOntology/PPO An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. ^\d{7}$ 0002058 rlwalls2008@gmail.com http://purl.obolibrary.org/obo/PPO_$1 False PPO PPO PPO PPO ppo ppo PPO ppr Europe PMC Preprints https://europepmc.org/Preprints Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000. ^PPR\d+$ PPR103739 https://europepmc.org/article/ppr/$1 False pr Protein Ontology http://proconsortium.org The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. ^(?:\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\d+)?)$ 000000024 dan5@georgetown.edu http://purl.obolibrary.org/obo/PR_$1 PR|PRO False PR PR PR PR nbdc01630 pr pr pr pr PR pr DB-0181 P4926 prefixcommons Prefix Commons https://prefixcommons.org A registry of life science prefxes ChEBI https://bioregistry.io/metaregistry/prefixcommons/$1 False pride PRIDE Controlled Vocabulary https://github.com/PRIDE-Utilities/pride-ontology The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays. ^\d{7}$ 0000006 yperez@ebi.ac.uk http://purl.obolibrary.org/obo/PRIDE_$1 True PRIDE PRIDE nbdc00630 pride pride pride pride r3d100010137 DB-0130 pride.project PRIDE Project https://www.ebi.ac.uk/pride/ The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects. ^P(X|R)D\d{6}$ PXD000440 https://www.ebi.ac.uk/pride/archive/projects/$1 False PRIDE.PROJECT PRIDE pride.project pride.project prints PRINTS compendium of protein fingerprints http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. ^PR\d{5}$ PR00001 teresa.k.attwood@manchester.ac.uk http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off sprint False PRINTS nbdc00039 prints prints sprint DB-0082 probesanddrugs Probes and Drugs https://www.probes-drugs.org The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation. ^PD\d{6}$ PD000596 ctibor.skuta@img.cas.cz https://www.probes-drugs.org/compound/$1 False P11199 probonto Probability Distribution Ontology http://probonto.org ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities. ^(c|k)\d{7}$ c0000005 pierre.grenon@ifomis.uni-saarland.de http://www.probonto.org/ontology#PROB_$1 False PROBONTO probonto probonto probonto proco Process Chemistry Ontology https://github.com/proco-ontology/PROCO PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry. ^\d{7}$ 0000001 wes_schafer@merck.com http://purl.obolibrary.org/obo/PROCO_$1 False PROCO PROCO proco proco PROCO prodom ProDom http://prodom.prabi.fr/prodom/current/html/home.php ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. ^PD\d+$ PD10000 Daniel.Kahn@toulouse.inra.fr http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1 False PRODOM nbdc00174 prodom prodom prodom proglyc ProGlycProt http://www.proglycprot.org/ ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. ^[A-Z]C\d{1,3}$ AC119 http://www.proglycprot.org/detail.aspx?ProId=$1 False PROGLYC proglyc proglyc propreo Proteomics data and process provenance http://lsdis.cs.uga.edu/projects/glycomics/propreo/ A comprehensive proteomics data and process provenance ontology. protein satyasahoo@ieee.org http://purl.obolibrary.org/obo/PROPREO_$1 True PROPREO PROPREO PROPREO propreo propreo prosite PROSITE https://www.expasy.org/prosite/ PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. ^PS\d{5}$ PS00001 Ioannis.Xenarios@unil.ch https://prosite.expasy.org/$1 False PROSITE nbdc00241 prosite prosite prosite Prosite DB-0084 P4355 protclustdb ProtClustDB https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. ^\w+$ O80725 klimke@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1 False PROTCLUSTDB protclustdb protclustdb protclustdb protcom Database of protein-protein complexes http://www.ces.clemson.edu/compbio/protcom 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). 12e8LH http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1 True 242 protcom proteomicsdb.peptide ProteomicsDB Peptide https://www.proteomicsdb.org/#peptideSearch ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein. ^\d+$ 53504 https://www.proteomicsdb.org/#human/proteinDetails/$1 False PROTEOMICSDB.PEPTIDE proteomicsdb.peptide proteomicsdb.peptide proteomicsdb.protein ProteomicsDB Protein https://www.proteomicsdb.org/#human ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins. ^\d+$ 53504 https://www.proteomicsdb.org/#human/proteinDetails/$1/summary False PROTEOMICSDB.PROTEIN proteomicsdb.protein proteomicsdb.protein protonet.cluster ProtoNet Cluster http://www.protonet.cs.huji.ac.il/ ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information. ^\d+$ 4349895 michall@cc.huji.ac.il http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1 False PROTONET.CLUSTER protonet.cluster protonet.cluster protonet.cluster protonet.proteincard ProtoNet ProteinCard http://www.protonet.cs.huji.ac.il/ ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. ^\d+$ 16941567 michall@cc.huji.ac.il http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1 False PROTONET.PROTEINCARD protonet.proteincard protonet.proteincard protonet.proteincard prov PROV Namespace https://www.w3.org/ns/prov The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web. Activity http://www.w3.org/ns/prov#$1 False PROV prov prov prov prov pscdb Protein Structural Change Database http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion. ^\d+$ 051 mota@i.nagoya-u.ac.jp http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html False PSCDB nbdc01636 pscdb pscdb psdo Performance Summary Display Ontology https://github.com/Display-Lab/psdo "Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01). Landis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf" ^\d{7}$ 0000055 zachll@umich.edu http://purl.obolibrary.org/obo/PSDO_$1 False PSDO PSDO psdo psdo PSDO pseudogene PseudoGene http://www.pseudogene.org This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase. PGOHUM00000289843 mark@gersteinlab.org http://tables.pseudogene.org/[?species_name]/$1 pseudogene.org False pseudo nbdc00178 pseudogene pseudomonas Pseudomonas Genome Database http://www.pseudomonas.com/ The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation. ^P\w+$ PSEEN0001 http://www.pseudomonas.com/feature/show/?locus_tag=$1 False PSEUDOMONAS pseudomonas pseudomonas psipar Protein Affinity Reagents https://www.psidev.info/psi-par Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms. ^\d+$ 0116 https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1 True PSIPAR psipar psipar pso Plant Stress Ontology https://github.com/Planteome/plant-stress-ontology The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. ^\d{7}$ 0000013 cooperl@oregonstate.edu http://purl.obolibrary.org/obo/PSO_$1 False PSO PSO PSO pso pso PSO pspub Phenoscape Publication https://wiki.phenoscape.org/wiki/Curation_workflow Documentation of the Phenoscape Curation Workflow False pubchem.bioassay NCBI PubChem database of bioassay records https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. ^\d+$ 1018 pruitt@ncbi.nlm.nih.gov https://pubchem.ncbi.nlm.nih.gov/bioassay/$1 pubchem.aid|pubchem.assay False PUBCHEM.BIOASSAY 2638 nbdc00640 pubchem.bioassay pubchem.bioassay pubchem.bioassay pubchem pubchem.cell PubChem Cell Line https://pubchem.ncbi.nlm.nih.gov Cell Lines in PubChem ^\d+$ 31 https://pubchem.ncbi.nlm.nih.gov/cell/$1 False pubchem pubchem.classification PubChem Classification https://pubchem.ncbi.nlm.nih.gov/classification/ The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records. ^\d+$ 87 https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1 False pubchem pubchem.compound PubChem CID https://pubchem.ncbi.nlm.nih.gov/ PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records. ^\d+$ 100101 bolton@ncbi.nlm.nih.gov https://pubchem.ncbi.nlm.nih.gov/compound/$1 CID|DSSTox_CID|PUBCHEM_CID|PubChem_Compound_CID|Pubchem|pubchem_id False PUBCHEM.COMPOUND PubChem 000140 2639 nbdc02626 pubchem.compound pubchem.compound 361 pubchem.compound r3d100010129 PubchemCompound P662 pubchem pubchem.element PubChem Element https://pubchem.ncbi.nlm.nih.gov/periodic-table PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number. ^\d+$ 1 https://pubchem.ncbi.nlm.nih.gov/element/$1 False pubchem pubchem.substance PubChem Substance ID (SID) https://pubchem.ncbi.nlm.nih.gov/ PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records. ^\d+$ 100101 https://pubchem.ncbi.nlm.nih.gov/substance/$1 DSSTox_Generic_SID False PUBCHEM.SUBSTANCE 000141 nbdc00642 pubchem.substance pubchem.substance pubchem.substance PubchemSubstance P2153 pubchem publons.publication Publons publication https://publons.com identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID) 18466622 https://publons.com/publon/$1 False P3431 publons.researcher Publons Researcher https://publons.com/researcher Database of researchers to track publications, citation metrics, peer reviews, and journal editing work. ^\d+$ 1981638 https://publons.com/researcher/$1 False P3829 pubmed PubMed https://www.ncbi.nlm.nih.gov/PubMed/ PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. ^\d+$ 16333295 beck@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/pubmed/$1 MEDLINE|PMID|PubMed|pmid False PUBMED PubMed 000302 1187 nbdc00179 pubmed pubmed pubmed Pubmed P698 puro Publishing Roles Ontology http://www.sparontologies.net/ontologies/pro 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. RoleInTime silvio.peroni@unibo.it http://purl.org/spar/pro/$1 False pw Pathway ontology http://rgd.mcw.edu/rgdweb/ontology/search.html The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions. ^\d{7}$ 0000423 gthayman@mcw.edu http://purl.obolibrary.org/obo/PW_$1 https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo False PW PW PW pw pw pw pw PW pw P7333 pwo Publishing Workflow Ontology http://www.sparontologies.net/ontologies/pwo An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity. Workflow silvio.peroni@unibo.it http://purl.org/spar/pwo/$1 False pwo px ProteomeXchange http://www.proteomexchange.org/ The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. ^(R)?PXD\d{6}$ PXD000500 http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1 False PX px px pypi PyPI https://www.python.org/psf/ The Python Package Index (PyPI) is a repository for Python packages. ^[a-zA-Z_][a-zA-Z0-9\-_]+$ numpy https://pypi.org/project/$1 False pypi qb The data cube vocabulary https://www.w3.org/TR/vocab-data-cube This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI). ^\w+$ Observation richard@cyganiak.de http://purl.org/linked-data/cube#$1 False qb qb qtldb Animal Genome QTL https://www.animalgenome.org/QTLdb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent. ^\d+$ 4685 https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 False qtldb qudt Quantities, Units, Dimensions, and Types Ontology https://qudt.org Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types. baseDimensionEnumeration http://qudt.org/schema/qudt#$1 False QUDT 18206 QUDT qudt qudt radiomics Radiomics Ontology http://www.radiomics.org/RO 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] LK99 alberto.traverso@maastro.nl http://www.radiomics.org/RO/$1 False RO radlex RSNA Informatics RadLex https://radlex.org "A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research. RadLex provides the foundation for vital data resources used in radiology: - The LOINC/RSNA Radiology Playbook - RadElement Common Data Elements -RadReport Radiology Reporting Templates The development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project." ^RID\d+$ RID1 radlex-feedback@lists.rsna.org https://radlex.org/RID/$1 False RADLEX RADLEX 2.16.840.1.113883.6.256 rapdb.locus RAP-DB Locus https://rapdb.dna.affrc.go.jp/ Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB. ^Os\S+g\d{7}$ Os01g0883800 https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1 irgsp False rapdb.locus rapdb.transcript Rice annotation Project database https://rapdb.dna.affrc.go.jp/ Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB. ^Os\S+t\d{7}-\d{2}$ Os01t0883800-02 https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1 False rapdb.transcript rapdb ratmap Rat Genome Database http://ratmap.org 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 5 http://ratmap.org/Showgene.php?gene_stable_id=$1 True ratmap rbk Rebuilding a Kidney https://www.rebuildingakidney.org/ (Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ Q-2958 oxburl@mmc.org https://www.rebuildingakidney.org/id/$1 False RBK rbk rbk rbo Radiation Biology Ontology https://github.com/Radiobiology-Informatics-Consortium/RBO RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. ^\d{6,8}$ 00000105 daniel.c.berrios@nasa.gov http://purl.obolibrary.org/obo/RBO_$1 False RBO RBO rbo rbo RBO rcb RIKEN Bioresource Center Cell Bank https://cell.brc.riken.jp/en/rcb Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center. ^RCB\d+$ RCB0002 atsushi.yoshiki@riken.jp https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1 False RCB IMSR_RBRC rdf Resource Description Framework http://www.w3.org/1999/02/22-rdf-syntax-ns This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts type rmrich5@gmail.com http://www.w3.org/1999/02/22-rdf-syntax-ns#$1 False rdf rdf rdf rdfa RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting http://www.w3.org/ns/rdfa 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/) PrefixOrTermMapping ivan@w3.org http://www.w3.org/ns/rdfa#$1 False rdfa rdfa rdfs RDF Schema https://www.w3.org/TR/rdf-schema/ RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary. label danbri@w3.org http://www.w3.org/2000/01/rdf-schema#$1 https://triplydb.com/w3c/rdfs/download.trig.gz False RDFS rdfs RDFS rdfs rdfs rdfs rdo RGD Disease Ontology https://ratmine.mcw.edu/ontology/disease/ Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. ^\d{7}$ 9002859 http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1 https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo False re3data re3data https://datacite.org Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines. ^r3d\d{9,9}$ r3d100010772 https://www.re3data.org/repository/$1 False 822 re3data reactome Reactome https://www.reactome.org/ The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology. ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$ R-BTA-418592 deustp01@med.nyu.edu https://reactome.org/content/detail/$1 RE|REACT|reactome.pathway False REACTOME 000411 1155 nbdc00185 reactome reactome 103 reactome r3d100010861 ReactomePathway P3937 reaxys Reaxys https://www.reaxys.com Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier. ^\d+$ 1257009 Beilstein|Reaxys False 1003 P1579 rebase REBASE Enzyme Number http://rebase.neb.com/rebase/ REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. ^\d+$ 101 roberts@neb.com http://rebase.neb.com/rebase/enz/$1.html False REBASE 2325 nbdc00648 rebase rebase 72 rebase r3d100012171 DB-0089 P4866 rebec Brazilian Registry of Clinical Trials https://ensaiosclinicos.gov.br Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant. ^RBR-\w+$ RBR-6qvdftm https://ensaiosclinicos.gov.br/rg/$1 False receptome.family Human Plasma Membrane Receptome Families http://www.receptome.org The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database. 5.1 http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1 False hpmr redfly Regulatory Elements Database for Drosophila http://redfly.ccr.buffalo.edu REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). 8 http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1 True 265 redfly refseq Reference Sequence Collection https://www.ncbi.nlm.nih.gov/projects/RefSeq/ The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\d+)|(NZ_[A-Z]{2,4}\d+))(\.\d+)?$ NP_012345 pruitt@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/protein/$1 REFSEQ_PROT False RefSeq 1098 2.16.840.1.113883.6.280 nbdc00187 refseq refseq refseq r3d100010285 DB-0117 ncbiprotein reo Reagent Ontology https://github.com/tis-lab/reagent-ontology The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs. ^\d{7}$ 0000079 matt@tislab.org http://purl.obolibrary.org/obo/REO_$11 https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl False REO repeatsdb.protein RepeatsDB Protein https://repeatsdb.org/ RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database. ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$ P29894 https://repeatsdb.org/protein/$1 False repeatsdb.protein uniprot repeatsdb.structure RepeatsDB Structure https://repeatsdb.org/ RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database. ^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$ 2gc4E https://repeatsdb.org/structure/$1 False repeatsdb.structure repec Peruvian Clinical Trial Registry https://ensayosclinicos-repec.ins.gob.pe/en/ The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website) ^\d+-\d+(-[A-Z])?$ 046-19 https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1 False reproduceme REPRODUCE-ME Ontology https://w3id.org/reproduceme/research 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. MicrobeamManipulation sheeba.samuel@uni-jena.de https://w3id.org/reproduceme#$1 False REPRODUCE-ME REPRODUCE-ME reproduceme researchgate.profile ResearchGate profile ID https://www.researchgate.net identifier for a person, used by ResearchGate profiles ^[0-9A-Za-z_-]+$ Rita-Heuser https://www.researchgate.net/profile/$1 False P2038 resid Protein covalent bond https://proteininformationresource.org/resid/ The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. ^AA\d{4}$ AA0001 john.garavelli@ebi.ac.uk https://proteininformationresource.org/cgi-bin/resid?id=$1 True RESID 2619 resid resid resid resid reto Regulation of Transcription Ontology http://www.semantic-systems-biology.org/apo Regulation of Transcription vladimir.n.mironov@gmail.com https://www.bio.ntnu.no/ontology/ReTO/reto.owl https://www.bio.ntnu.no/ontology/ReTO/reto.obo False RETO RETO reto rex Physico-chemical process https://www.ebi.ac.uk/chebi/ An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. ^\d{7}$ 0000512 chebi-help@ebi.ac.uk http://purl.obolibrary.org/obo/REX_$1 http://purl.obolibrary.org/obo/rex.owl True REX REX REX rex rex REX rex chebi rexo Regulation of Gene Expression Ontology http://www.semantic-systems-biology.org/apo Regulation of Gene Expression kuiper@bio.ntnu.no https://www.bio.ntnu.no/ontology/ReXO/rexo.owl https://www.bio.ntnu.no/ontology/ReXO/rexo.obo False REXO REXO rexo rfam Rfam database of RNA families https://rfam.org/ The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. ^RF\d{5}$ RF00230 apetrov@ebi.ac.uk https://rfam.org/family/$1 False RFAM 2356 nbdc00654 rfam rfam rfc Internet Standard -- IETF Request for Comments https://www.ietf.org/ Legacy site for IETF RFC proposals ^\d+$ 5013 https://tools.ietf.org/rfc/rfc$1 False rfc rgap Rice Genome Annotation Project http://rice.plantbiology.msu.edu/ This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data. LOC_Os02g13300 http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=$1 True rgap rgd Rat Genome Database http://rgd.mcw.edu/ Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes. ^\d{4,}$ 7499841 jrsmith@mcw.edu http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1 RGD False RGD RGD RGD RGD 2620 nbdc00188 rgd rgd 267 rgd r3d100010417 RGD Rgd DB-0091 P3853 rgd.qtl Rat Genome Database qTL http://rgd.mcw.edu/ Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes. ^\d+$ 1354581 http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1 False RGD.QTL rgd.qtl rgd.qtl rgd.strain Rat Genome Database strain http://rgd.mcw.edu/ Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology. ^\d+$ 5688061 http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1 False RGD.STRAIN rgd.strain rgd.strain rhea Rhea, the Annotated Reactions Database https://www.rhea-db.org/ " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants. Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB." ^\d{5}$ 12345 anne.morgat@sib.swiss https://www.rhea-db.org/rhea/$1 RHEA False RHEA 2644 nbdc02083 rhea rhea 310 rhea r3d100010891 Rhea ribocentre Ribocentre https://www.ribocentre.org/ Ribocentre is designed to contain comprehensive information of all natural ribozymes. ^[a-zA-Z0-9-]+$ hammer huanglin36@mail.sysu.edu.cn https://www.ribocentre.org/docs/$1 ribocenter False ricecyc Rice Metabolic Pathways http://www.gramene.org/pathway/ricecyc.html 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 PWY-1042 http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1 False 227 ricecyc ricegap Rice Genome Annotation Project http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines. ^LOC\_Os\d{1,2}g\d{5}$ LOC_Os02g13300 http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1 False RICEGAP ricegap ricegap ricenetdb.compound RiceNetDB Compound http://bis.zju.edu.cn/ricenetdb RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping. ^OSC\d{4}$ OSC1416 http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1 False RICENETDB.COMPOUND ricenetdb.compound ricenetdb.compound ricenetdb.gene RiceNetDB Gene http://bis.zju.edu.cn/ricenetdb/ RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping. ^LOC\_Os\d{1,2}g\d{5}\.\d$ LOC_Os01g49190.1 http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1 False RICENETDB.GENE ricenetdb.gene ricenetdb.gene ricenetdb.mirna RiceNetDB miRNA http://bis.zju.edu.cn/ricenetdb RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping. ^osa-miR\d{3,5}[a-z]{0,1}$ osa-miR446 http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1 False RICENETDB.MIRNA ricenetdb.mirna ricenetdb.mirna ricenetdb.protein RiceNetDB Protein http://bis.zju.edu.cn/ricenetdb/ RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping. ^LOC\_Os\d{1,2}g\d{5}$ LOC_Os01g49190 http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1 False RICENETDB.PROTEIN ricenetdb.protein ricenetdb.protein ricenetdb.reaction RiceNetDB Reaction http://bis.zju.edu.cn/ricenetdb RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping. ^OSR\d{4}$ OSR0818 http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1 False RICENETDB.REACTION ricenetdb.reaction ricenetdb.reaction rism RISM Online https://rism.digital/ RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project. ^[a-z]+/[0-9]+$ people/11035 https://rism.online/$1 False rism rna_sstrand RNA SSTRAND http://www.rnasoft.ca/sstrand 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. CRW_00469 http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1 False rna_sstrand rnacentral RNACentral https://rnacentral.org/ RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. ^URS[0-9A-F]{10}(\_\d+)?$ URS0000759CF4 bsweeney@ebi.ac.uk https://rnacentral.org/rna/$1 LNCRNADB False RNACENTRAL 3856 nbdc01215 rnacentral rnacentral P8697 rnajunction Database of RNA Junctions and Kissing loop Structures http://rnajunction.abcc.ncifcrf.gov 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. 8668 ygyingli@ncsu.edu https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1 False rnajunction rnaloops RNAloops https://rnaloops.cs.put.poznan.pl Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank. ^\d+$ 91792 Maciej.Antczak@cs.put.poznan.pl https://rnaloops.cs.put.poznan.pl/search/details/$1 False rnamod The RNA Modification Database http://rna.rega.kuleuven.be/rnamods/ A comprehensive listing of post-transcriptionally modified nucleosides from RNA - ^\d{3}$ 051 http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1 False rnamods RNA Modification Database http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. ^\d{3}$ 101 http://mods.rna.albany.edu/mods/modifications/view/$1 False RNAMODS rnamods rnamods rnamods rnao RNA ontology https://github.com/bgsu-rna/rnao Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. ^\d{7}$ 0000128 BatchelorC@rsc.org http://purl.obolibrary.org/obo/RNAO_$1 True RNAO RNAO RNAO rnao rnao RNAO rnao rnavdb RNA Virus Database http://virus.zoo.ox.ac.uk/rnavirusdb/ 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. 164750 http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1 False rvd ro Relation Ontology https://oborel.github.io/ The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. ^(HOM)?\d{7}$ 0002533 cjmungall@lbl.gov http://purl.obolibrary.org/obo/RO_$1 RO_proposed_relation|obo_rel|oborel False RO RO RO OBOREL ro ro ro ro RO ro P3590 roleo Role Ontology http://sourceforge.net/projects/roleo The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles. ^\d{7}$ 0000002 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/RoleO_$1 True ROLEO ROLEO roleo ror Research Organization Registry https://ror.org "ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations. ROR is jointly operated by California Digital Library, Crossref, and Datacite." ^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$ 03yrm5c26 maria.gould@ucop.edu https://ror.org/$1 https://w3id.org/rorio/rorio.owl False 20474 ror ror rouge Rodent Unidentified Gene-Encoded Large Proteins http://www.kazusa.or.jp/rouge/ The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. ^m\w+$ mKIAA4200 ohara@kazusa.or.jp https://www.kazusa.or.jp/rouge/gfpage/$1 False ROUGE nbdc00672 rouge rouge rouge DB-0092 rpcec Cuban Registry of Clinical Trials https://rpcec.sld.cu/en/home The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage) ^RPCEC\d+$ RPCEC00000423 https://rpcec.sld.cu/en/trials/$1 False rrid Research Resource Identification https://rrid.site "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch." ^[a-zA-Z]+.+$ AB_262044 bandrow@gmail.com https://scicrunch.org/resolver/RRID:$1 False RRID rrid rrid rrrc Rat Resource and Research Center http://www.rrrc.us/ Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID] ^\d+$ 961 https://www.rrrc.us/Strain/?x=$1 False RRRC rs Rat Strain Ontology http://rgd.mcw.edu/rgdweb/search/strains.html Ontology of rat strains ^\d{7}$ 0001807 sjwang@mcw.edu http://purl.obolibrary.org/obo/RS_$1 https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo False RS RS RS rs rs RS rs rtecs Registry of Toxic Effects of Chemical Substances https://www.cdc.gov/niosh/rtecs/ RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments. ^AB\d+$ AB1925000 vep1@cdc.gov False 000566 rubygems RubyGems https://rubygems.org A repository of software packages written in Ruby. bel https://rubygems.org/gems/$1 False runbiosimulations runBioSimulations https://icahn.mssm.edu/ runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive. ^[0-9a-z]{24,24}$ 5fde96bdc5f1aa9ff0cce18a https://run.biosimulations.org/simulations/$1 False runbiosimulations rxno Name Reaction Ontology https://github.com/rsc-ontologies/rxno RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization. ^\d{7}$ 0000253 batchelorc@rsc.org http://purl.obolibrary.org/obo/RXNO_$1 https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo False RXNO RXNO RXNO rxno rxno RXNO P2106 rxnorm RxNorm https://www.nlm.nih.gov/research/umls/rxnorm/ RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary. ^[0-9]{1,7}$ 221058 custserv@nlm.nih.gov https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1 RXCUI False RXNORM RXCUI RXNORM 2.16.840.1.113883.6.88 P3345 s_mart_db The S/MAR transaction DataBase http://smartdb.bioinf.med.uni-goettingen.de/ 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. SM0000020 http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1 False nbdc00674 47 s_mart_db sabiork.compound SABIO-RK Compound http://sabiork.h-its.org/ SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information. ^\d+$ 75 http://sabiork.h-its.org/newSearch?q=$1 False sabiork.compound sabiork.compound sabiork.ec SABIO-RK EC Record http://sabiork.h-its.org/ SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$ 2.7.1.1 ulrike.wittig@h-its.org http://sabiork.h-its.org/newSearch?q=ecnumber:$1 False SABIORK.EC sabiork.ec sabiork.ec sabiork.ec eccode sabiork.kineticrecord SABIO Reaction Kinetics http://sabiork.h-its.org/ SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information. ^\d+$ 5046 ulrike.wittig@h-its.org http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1 False SABIORK.KINETICRECORD sabiork.kineticrecord sabiork.kineticrecord sabiork.kinetic sabiork.reaction SABIO-RK Reaction http://sabiork.h-its.org/ SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. ^\d+$ 75 ulrike.wittig@h-its.org http://sabiork.h-its.org/reacdetails.jsp?reactid=$1 SABIO-RK False SABIORK.REACTION 2309 sabiork.reaction sabiork.reaction 226 sabiork.reaction r3d100011052 DB-0177 sael Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List True salk Salk Institute for Biological Studies https://www.salk.edu/ Scientific research institute for neuroscience, genetics, immunology, plant biology and more. ^\d{6}$ 037727 https://abrc.osu.edu/stocks/number/SALK_$1 False salmon Salmon Ontology https://github.com/DataONEorg/sem-prov-ontologies/ An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms. ^\d+$ 00000674 brycemecum@gmail.com https://purl.dataone.org/odo/SALMON_$1 False SALMON SALMON sao Subcellular Anatomy Ontology http://ccdb.ucsd.edu/CCDBWebSite/sao.html SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. ^\d+$ 5277619 slarson@ncmir.ucsd.edu http://uri.neuinfo.org/nif/nifstd/sao$1 True SAO SAO SAO sao sao sasap The State of Alaska's Salmon and People Ontology https://github.com/DataONEorg/sem-prov-ontologies An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. ^\d+$ 00000101 brycemecum@gmail.com https://purl.dataone.org/odo/SASAP_$1 False SASAP SASAP sasbdb Small Angle Scattering Biological Data Bank http://www.sasbdb.org/ Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$ SASDAX8 a.kikhney@embl-hamburg.de http://www.sasbdb.org/data/$1 False SASBDB sasbdb sasbdb r3d100012273 DB-0258 sbo Systems Biology Ontology http://www.ebi.ac.uk/sbo/ The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort. ^\d{7}$ 0000485 sheriff@ebi.ac.uk http://purl.obolibrary.org/obo/SBO_$1 http://purl.obolibrary.org/obo/sbo.obo False SBO SBO SBO sbo sbo sbo sbo SBO sbo scdo Sickle Cell Disease Ontology https://scdontology.h3abionet.org/ An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. ^\d{7}$ 0000728 giant.plankton@gmail.com http://purl.obolibrary.org/obo/SCDO_$1 False SCDO SCDO scdo scdo SCDO schem Selventa Chemicals https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt Selventa legacy chemical namespace used with the Biological Expression Language ^A\d{4}$ A0001 https://biopragmatics.github.io/providers/schem/$1 False schema Schema.org https://schema.org 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. Person johardi@stanford.edu https://schema.org/$1 schemaorg False SCHEMAORG SCHEMA schema schemaorg_http schema scholia.resource Scholia Registry https://scholia.toolforge.org/ A frontend to Wikidata doi https://bioregistry.io/metaregistry/scholia/$1 False sciflection Sciflection https://sciformation.com/sciflection.html Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$ 5ede4273-b26c-4ea4-adb7-3ce294ab3397 https://sciflection.com/$1 False sciflection r3d100013413 sciprofiles SciProfiles ID https://sciprofiles.com/ numerical identifier for an author in SciProfiles by MDPI ^[1-9]\d*$ 118021 https://sciprofiles.com/profile/$1 False P8159 scomp Selventa Complexes https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt Selventa legacy complex namespace used with the Biological Expression Language ^C\d{4}$ C0001 https://biopragmatics.github.io/providers/scomp/$1 False scop Structural Classification of Proteins - Unique Identifier https://scop.berkeley.edu SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.). ^\d+$ 47419 JMChandonia@lbl.gov http://scop.berkeley.edu/sunid=$1 scop.sun|scop.sunid False SCOP 1042 scop scop scop scop.sccs SCOP(e) concise classification string https://scop.berkeley.edu 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. a.39.1.1 JMChandonia@lbl.gov http://scop.berkeley.edu/sccs=$1 False 1041 scop.sid Structural Classification of Protein - Stable Domain Identifier https://scop.berkeley.edu " 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." d4akea1 JMChandonia@lbl.gov http://scop.berkeley.edu/sid=$1 False 1039 scopus Scopus Researcher https://www.scopus.com "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. Delivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts and humanities, Scopus features smart tools to track, analyze and visualize research." ^\d+$ 56305849200 https://www.scopus.com/authid/detail.uri?authorId=$1 scopus.author False P1153 scopus.affiliation Scopus affiliation ID http://info.sciencedirect.com/scopus/scopus-in-detail/tools/affiliationidentifier identifier for an organisation in author affiliations per Scopus 60025709 https://www.scopus.com/affil/profile.uri?afid=$1 False P1155 scopus.publication Scopus Publication https://www.scopus.com/ identifier for a source/publication venue (journal, conference, etc) in Scopus ^[1-9]\d{0,11}$ 16129 https://www.scopus.com/sourceid/$1 False P1156 scopus.work Scopus Work https://www.scopus.com/ unique academic work identifier assigned in Scopus bibliographic database ^2-s2\.0-\d+$ 2-s2.0-0030770923 http://www.scopus.com/record/display.url?origin=inward&eid=$1 scopus.eid False P1154 scoro Scholarly Contributions and Roles Ontology http://www.sparontologies.net/ontologies/scoro An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator). IntellectualContribution silvio.peroni@unibo.it http://purl.org/spar/scoro/$1 False scoro scpd Saccharomyces cerevisiae promoter database http://rulai.cshl.edu/SCPD/ Database containing promotor sequences found in Saccharomyces cerevisiae. CDC2 http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1 True 130 scpd scr SciCrunch Registry https://scicrunch.org/browse/resourcedashboard The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources. ^\d+$ 022586 abandrowski@ncmir.ucsd.edu http://scicrunch.org/resolver/SCR_$1 scicrunch False nbdc01937 SCR scretf ScerTF http://stormo.wustl.edu/ScerTF/ ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor. ^\w+$ RSC3 http://stormo.wustl.edu/ScerTF/details/$1 False SCRETF scretf scretf sdap Structural Database of Allergenic Proteins http://fermi.utmb.edu/SDAP SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes. 610 http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1 False sdap sdbs Spectral Database for Organic Compounds http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra. ^\d+$ 4544 http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1 False SDBS nbdc01520 sdbs sdbs sdgio Sustainable Development Goals Interface Ontology https://github.com/SDG-InterfaceOntology/sdgio An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators. ^\d{8}$ 00020134 pier.buttigieg@awi.de http://purl.unep.org/sdg/SDGIO_$1 https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl False SDGIO sdgio SDGIO sdis Selventa Diseases https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt Selventa legacy disease namespace used with the Biological Expression Language ^D\d{4}$ D0001 https://biopragmatics.github.io/providers/sdis/$1 False sedml.format SED-ML data format http://sed-ml.org/ Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML). ^[a-z]+(\..*?)?$ csv https://sed-ml.org/urns.html#format:$1 False sedml.format sedml.language SED-ML model format http://sed-ml.org/ Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML). ^[a-z]+(\..*?)?$ sbml.level-3.version-2 https://sed-ml.org/urns.html#language:$1 False sedml.language seed The SEED; http://seed-viewer.theseed.org/seedviewer.cgi This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. ^\w+$ Biotin_biosynthesis http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1 False SEED seed seed seed.compound SEED Compound http://modelseed.org/ This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. ^cpd\d+$ cpd15380 http://modelseed.org/biochem/compounds/$1 False SEED.COMPOUND seed.compound seed.compound seed.reaction SEED Reactions http://modelseed.org/biochem/reactions/ ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions. ^rxn\d+$ rxn00001 http://modelseed.org/biochem/reactions/$1 False seed.reaction seed.reaction seinet Southwestern Environmental Information Network https://swbiodiversity.org/seinet/index.php A vocabulary about species to support the environmental research community in Arizona and New Mexico ^\d+$ 762 https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1 False P6209 semapv Semantic Mapping Vocabulary https://mapping-commons.github.io/semantic-mapping-vocabulary/ The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata. LexicalMatching nicolas.matentzoglu@gmail.com https://w3id.org/semapv/vocab/$1 https://raw.githubusercontent.com/mapping-commons/semantic-mapping-vocabulary/main/semapv.owl False 20428 semion Semion author ID https://www.semion.io identifier of an author or reviewer, in Semion ^\d+$ 22132778 https://www.semion.io/Author/$1 False P7671 senso Sensitive Data Ontology https://github.com/DataONEorg/sem-prov-ontologies The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing. ^\d+$ 00000003 brycemecum@gmail.com http://purl.dataone.org/odo/SENSO_$1 False SENSO SENSO seo Scientific Event Ontology https://w3id.org/seo SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops. Symposium https://w3id.org/seo#$1 False seo sep Sample processing and separation techniques https://psidev.info/sepcv A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. ^\d{5,6}$ 00073 psidev-gps-dev@lists.sourceforge.net http://purl.obolibrary.org/obo/SEP_$1 https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo True SEP SEP SEP sep SEP sep sepio Scientific Evidence and Provenance Information Ontology https://github.com/monarch-initiative/SEPIO-ontology An ontology for representing the provenance of scientific claims and the evidence that supports them. ^\d{7}$ 0000048 mhb120@gmail.com http://purl.obolibrary.org/obo/SEPIO_$1 False SEPIO SEPIO SEPIO sepio sepio SEPIO sfam Selventa Families https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt Selventa legacy protein family namespace used with the Biological Expression Language ^F\d{4}$ F0001 https://biopragmatics.github.io/providers/sfam/$1 False sgd Saccharomyces Genome Database https://www.yeastgenome.org/ The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$ S000002493 cherry@genome.stanford.edu https://www.yeastgenome.org/locus/$1 False SGD 2632 nbdc00202 sgd sgd sgd r3d100010419 Sgd DB-0095 P3406 sgd.pathways Saccharomyces genome database pathways http://pathway.yeastgenome.org/ Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). ^PWY\w{2}\-\d{3}$ PWY3O-214 Karen.Christie@jax.org http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1 False SGD.PATHWAYS sgd.pathways sgd.pathways sgd.pathways sgn Sol Genomics Network http://solgenomics.net/ The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. ^\d+$ 0001 lam87@cornell.edu http://solgenomics.net/phenome/locus_display.pl?locus_id=$1 False SGN nbdc02414 sgn sgn 433 sgn r3d100012078 sh Shapes Constraint Language https://www.w3.org/TR/shacl/ A language for validating RDF graphs against a set of conditions NodeShape dr.shorthair@pm.me http://www.w3.org/ns/shacl#$1 https://triplydb.com/w3c/sh/download.trig.gz shacl False sh sh shareloc ShareLoc https://shareloc.xyz ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc. ^\d{6}$ 000004 https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1 False shareloc sharkipedia.species Sharkipedia Species https://www.sharkipedia.org/ Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone. ^\d+$ 983 creeas@gmail.com https://www.sharkipedia.org/species/$1 False sharkipedia sharkipedia.trait Sharkipedia Trait https://www.sharkipedia.org/ Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone. ^\d+$ 13 creeas@gmail.com https://www.sharkipedia.org/traits/$1 False sharkipedia sharkipedia.trend Sharkipedia Trend https://www.sharkipedia.org/ Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone. ^\d+$ 3447 creeas@gmail.com https://www.sharkipedia.org/trends/$1 False sharkipedia sheepqtldb Animal Genome Sheep QTL https://www.animalgenome.org/QTLdb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs. ^\d+$ 19803 https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 False SHEEPQTLDB sheepqtldb sheepqtldb sheepqtldb qtldb shex Shape Expression Vocabulary http://www.w3.org/ns/shex# The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces. ^\w+$ TripleExpression gregg@greggkellogg.net http://www.w3.org/ns/shex#$1 False shex shibase ShiBASE http://www.mgc.ac.cn/ShiBASE/ The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format. SDY2614 http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1 True shibase sibo Social Insect Behavior Ontology https://github.com/obophenotype/sibo Social Behavior in insects ^\d{7}$ 0000509 cjmungall@lbl.gov http://purl.obolibrary.org/obo/SIBO_$1 True SIBO SIBO SIBO sibo sibo SIBO sider.drug SIDER Drug http://sideeffects.embl.de/ SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER. ^\d+$ 2244 http://sideeffects.embl.de/drugs/$1 False SIDER.DRUG sider.drug sider.drug sider.effect SIDER Side Effect http://sideeffects.embl.de/ SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER. ^C\d+$ C0017565 http://sideeffects.embl.de/se/$1 False SIDER.EFFECT sider.effect sider.effect umls sigmaaldrich Sigma Aldrich https://www.sigmaaldrich.com Sigma Aldrich is a life sciences supply vendor. HPA000698 https://www.sigmaaldrich.com/US/en/product/sigma/$1 False 236 signaling-gateway Signaling Gateway http://www.signaling-gateway.org/molecule The Signaling Gateway provides information on mammalian proteins involved in cellular signaling. ^A\d{6}$ A001094 kenan@ucsd.edu http://www.signaling-gateway.org/molecule/query?afcsid=$1 False SIGNALING-GATEWAY signaling-gateway signaling-gateway 87 signaling-gateway signor Signaling Network Open Resource https://signor.uniroma2.it/ SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. ^SIGNOR\-[A-Z]+\d+$ SIGNOR-C41 gianni.cesareni@torvergata.it https://signor.uniroma2.it/relation_result.php?id=$1 SIGNOR False signor 599 DB-0206 signor.relation SIGNOR Relation https://signor.uniroma2.it Identifiers for relationships between proteins and complexes, along with their type and provenance ^SIGNOR-\d+$ SIGNOR-252737 False signor sio Semanticscience Integrated Ontology https://github.com/micheldumontier/semanticscience The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. ^\d{6}$ 000912 michel.dumontier@gmail.com https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form=$1 False SIO SIO SIO SIO sio sio sio SIO siren Scientific Information Retrieval and Exchange Network https://www.langual.org/langual_indexed_datasets.asp A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods ^F\d+$ F11903 patrice.buche@inrae.fr SUBSET_SIREN False SIREN sisu Sequencing Initiative Suomi http://www.sisuproject.fi/ 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. ^[0-9]+:[0-9]+$ 17:41223048 hannele.laivuori@helsinki.fi http://search.sisuproject.fi/#/variant/$1 False SISU sisu sisu sitex SitEx http://www-bionet.sscc.ru/sitex/ SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments. ^\d+$ 1000 imedvedeva@celgene.com http://www-bionet.sscc.ru/sitex/index.php?siteid=$1 False SITEX sitex sitex sitex skip Stemcell Knowledge and Information Portal https://skip.stemcellinformatics.org/en/ SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine. ^SKIP\d+$ SKIP001214 https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1 False SKIP skm Stress Knowledge Map http://www.nib.si/eng/ Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ^rx[0-9]{5}$ rx00408 https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary False skm skos Simple Knowledge Organization System https://www.w3.org/2004/02/skos/ SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web prefLabel alistair.miles@linacre.ox.ac.uk http://www.w3.org/2004/02/skos/core#$1 False skos skos skos skos skos skosxl Simple Knowledge Organization System eXtension for Labels http://www.w3.org/2008/05/skos-xl# 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. literalForm http://www.w3.org/2008/05/skos-xl#$1 False skosxl skosxl slctr Sri Lanka Clinical Trials Registry https://slctr.lk/ The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage) ^SLCTR/\d{4}/\d+$ SLCTR/2023/010 False slkbase SUM Breast Cancer Cell Line Knowledge Base https://sumlineknowledgebase.com/ Cell line databases/resources ^\d+$ 3618 https://sumlineknowledgebase.com/?page_id=$1 False SLKBase slm SwissLipid http://www.swisslipids.org/#/ SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions. ^\d+$ 000000341 swisslipids@isb-sib.ch https://www.swisslipids.org/#/entity/SLM:$1 swisslipid|swisslipids False SWISSLIPID nbdc02026 slm swisslipid slm 687 r3d100012603 Swisslipids DB-0197 P8691 slso Space Life Sciences Ontology https://github.com/nasa/LSDAO 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. 0000000 daniel.c.berrios@nasa.gov http://purl.obolibrary.org/obo/SLSO_$1 False SLSO SLSO slso SLSO smart Simple Modular Architecture Research Tool http://smart.embl-heidelberg.de/ The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures. ^SM\d{5}$ SM00015 chris.ponting@ed.ac.uk http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1 False SMART nbdc00682 smart smart smart Smart DB-0097 smid C. elegans Small Molecule Identifier Database https://smid-db.org/ SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. ^\d+$ 137 https://smid-db.org/smid/$1 SMID-DB False smiles Simplified molecular-input line-entry system https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions. ^[A-Za-z0-9+\-\*=#$:().>/\\\[\]%]+$ CC2(C)C\1CCC(C)/C=C/12 tim.vandermeersch@gmail.com https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip False P233 smpdb Small Molecule Pathway Database https://smpdb.ca/ The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. ^SMP\d+$ SMP0000219 david.wishart@ualberta.ca https://smpdb.ca/view/$1 SMP False SMPDB 2659 nbdc00908 smpdb smpdb 311 smpdb snap Snapshot http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf 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. Quality http://www.ifomis.org/bfo/1.1/snap#$1 False 494 snap snctp Swiss National Clinical Trials Portal https://kofam.ch/en/snctp-portal The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage] SNCTP000005580 False snomedct SNOMED CT (International Edition) http://www.snomedbrowser.com/ SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc. ^(\w+)?\d+$ 284196006 custserv@nlm.nih.gov http://snomed.info/id/$1 SCTID|SCTID_2010_1_31|SNOMECT|SNOMED|SNOMEDCT|SNOMEDCTCT|SNOMEDCTCT_2018_03_01|SNOMEDCTCT_2019_03_01|SNOMEDCT_2005_07_31|SNOMEDCT_2010_1_31|SNOMEDCT_2020_03_01|SNOMEDCT_US|SNOMEDCT_US_2015_03_01|SNOMEDCT_US_2016_03_01|SNOMEDCT_US_2018_03_01|SNOMEDCT_US_2018_09_01|SNOMEDCT_US_2019_03_01|SNOMEDCT_US_2019_09_01|SNOMEDCT_US_2020_03_01|SNOMEDCT_US_2020_09_01|SNOMEDCT_US_2021_03_01|SNOMEDCT_US_2021_07_31|SNOMEDCT_US_2021_09_01|SNOMEDCT_US_2022_07_31|SNOMEDCT_US_2022_09_01|SNOMEDCT_US_2022_12_31|SNOMEDCT_US_2023_02_28|SNOMEDCT_US_2023_03_01|SNOMEDCT_US_2023_09_01|SNOMEDCT_US_2023_10_01|SNOMEDCT_US_2023_11_01|SNOMED_CT|SNOMED_CT_US_2018_03_01|SNOWMEDCT|SNOWMEDCT_US|SNOWMEDCT_US_2018_03_01 False SNOMEDCT SNOMEDCT SNOMEDCT 2.16.840.1.113883.6.96 snomedct snomedct snomed snomedct P5806 snornabase snoRNABase https://www-snorna.biotoul.fr/ "A comprehensive database of human H/ACA and C/D box snoRNAs." SR0000178 http://www-snorna.biotoul.fr/plus.php?id=$1 False nbdc00323 snornalbmedb snp2tfbs SNP to Transcription Factor Binding Sites https://ccg.epfl.ch/snp2tfbs/ SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome. ^rs[0-9]+$ rs11603840 https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1 False snp2tfbs dbsnp snp500cancer SNP500Cancer http://snp500cancer.nci.nih.gov 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. TP53-47 http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1 True snp500cancer so Sequence types and features ontology http://www.sequenceontology.org/ The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. ^\d{7}$ 0001157 keilbeck@genetics.utah.edu http://purl.obolibrary.org/obo/SO_$1 https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo False SO SO SO SO so so so so SO so sopharm Suggested Ontology for Pharmacogenomics http://www.loria.fr/~coulet/sopharm2.0_description.php 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. adrien.coulet@loria.fr http://purl.obolibrary.org/obo/SOPHARM_$1 True SOPHARM SOPHARM SOPHARM sopharm soybase SoyBase http://soybase.org/ SoyBase is a repository for curated genetics, genomics and related data resources for soybean. ^\w+(\-)?\w+(\-)?\w+$ BARC-013845-01256 Jacqueline.Campbell@usda.gov http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1 False SOYBASE nbdc01817 soybase soybase 44 soy r3d100010846 span Span http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality. False spbase SpBase http://spbase.org 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. SPU_000001 http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1 True nbdc00686 spbase spd Spider Ontology http://research.amnh.org/atol/files/ An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). ^\d{7}$ 0000001 ramirez@macn.gov.ar http://purl.obolibrary.org/obo/SPD_$1 http://purl.obolibrary.org/obo/spd.obo False SPD SPD SPD spd spd SPD spdo P4537 spdx Software Package Data Exchange License https://spdx.org/licenses The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception. ^[0-9A-Za-z\-.]+$ CC-BY-1.0 https://spdx.org/licenses/$1 False spdx spdx sphn Swiss Personalized Health Network Schema https://www.sphn.ch The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/). ^\S+$ Allergy Sabine.Oesterle@sib.swiss https://biomedit.ch/rdf/sphn-ontology/sphn#$1 https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.owl False spike.map SPIKE Map http://www.cs.tau.ac.il/~spike/ SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps. ^spike\d{5}$ spike00001 Yossih@tauex.tau.ac.il http://www.cs.tau.ac.il/~spike/maps/$1.html False SPIKE.MAP spike.map spike.map spike splash Spectra Hash Code http://mona.fiehnlab.ucdavis.edu/ The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance. ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$ splash10-0zq2000000-77302b0326a418630a84 http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1 False SPLASH splash splash splicenest SpliceNest http://splicenest.molgen.mpg.de/ 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. Hs635 http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1 True splicenest spp Signaling Pathways Project https://www.signalingpathways.org/index.jsf The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways. ^10.\w{4}/\w{10}$ 10.1621/vwN2g2HaX3 nmckenna@bcm.edu https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1 False spp r3d100013650 srao FAIRsharing Subject Ontology https://github.com/FAIRsharing/subject-ontology The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies. ^\d{7}$ 0000400 allyson.lister@oerc.ox.ac.uk http://www.fairsharing.org/ontology/subject/SRAO_$1 https://raw.githubusercontent.com/FAIRsharing/subject-ontology/master/releases/SRAO.owl False srao fairsharing ssbd.dataset System Science of Biological Dynamics dataset https://ssbd.riken.jp Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. ^\d+$ 1 sonami@riken.jp https://ssbd.riken.jp/database/dataset/$1 False ssbd.project System Science of Biological Dynamics project https://ssbd.riken.jp Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. ^\d+$ 1 https://ssbd.riken.jp/database/project/$1 False ssrn.article Social Science Research Network Article https://ssrn.com identifier for an article/paper at the SSRN 1667659 https://ssrn.com/abstract=$1 False P893 ssrn.author Social Science Research Network Author https://ssrn.com identifier for an author at the Social Science Research Network ^[1-9]\d{0,6}$ 112517 https://ssrn.com/author=$1 False P3747 sssom Simple Standard for Sharing Ontological Mappings https://w3id.org/sssom "SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as ""sssom:mapping_justification"" are defined in the sssom namespace." ^[A-Za-z_]+$ mapping_justification nicolas.matentzoglu@gmail.com https://w3id.org/sssom/$1 False sstoss Sequence-Structural Templates of Single-member Superfamilies http://caps.ncbs.res.in/SSTOSS/index.htm 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. 01.01.005 http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1 True sstoss stap Statistical Torsional Angles Potentials http://psb.kobic.re.kr/STAP/refinement/ STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). ^[0-9][A-Za-z0-9]{3}$ 1a24 bhsung@kribb.re.kr http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1 False STAP stap stap stato The Statistical Methods Ontology http://stato-ontology.org/ STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. ^\d{7}$ 0000288 proccaserra@gmail.com http://purl.obolibrary.org/obo/STATO_$1 False STATO STATO STATO stato stato stato STATO stitch Search Tool for Interactions of Chemicals http://stitch.embl.de/ STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. ^\w{14}$ BQJCRHHNABKAKU bork@embl.de http://stitch.embl.de/interactions/$1 False STITCH stitch stitch 313 stitch r3d100012165 stn FDA Submission Tracking Number https://www.fda.gov/media/128698/download The pre-IND tracking number for submissions to the FDA 125768 False storedb Store DB https://www.storedb.org/ STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. ^(STUDY|FILE|DATASET)\d+$ STUDY1040 PNS12@cam.ac.uk https://www.storedb.org/?$1 False STOREDB nbdc02191 storedb storedb r3d100011049 storedb.dataset STOREDB at University of Cambridge https://www.storedb.org/ Datasets inside StoreDB ^\d+$ 1251 https://www.storedb.org/?STOREDB:DATASET$1 True storedb storedb.file STOREDB at University of Cambridge https://www.storedb.org/ File inside StoreDB ^\d+$ 12929 https://www.storedb.org/store_v3/download.jsp?fileId=$1 False storedb storedb.study STOREDB at University of Cambridge https://www.storedb.org/ Study inside StoreDB ^\d+$ 1174 https://www.storedb.org/store_v3/study.jsp?studyId=$1 False storedb string Search Tool for Retrieval of Interacting Genes/Proteins http://string.embl.de/ "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable." ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$ P53350 bork@embl.de http://string.embl.de/interactions/$1 False STRING 2302 nbdc00690 string string 93 string r3d100010604 DB-0141 uniprot sty UMLS Semantic Types Ontology https://lhncbc.nlm.nih.gov/semanticnetwork/ UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. ^T\d{3}$ T039 support@bioontology.org https://uts.nlm.nih.gov/uts/umls/semantic-network/$1 UMLSSG|umls.st|umls.sty False STY STY STY STY P11955 subtilist Bacillus subtilis genome sequencing project http://genolist.pasteur.fr/SubtiList/ "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments." ^BG\d+$ BG11523 antoine.danchin@normalesup.org http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1 False SUBTILIST subtilist subtilist subtilist subtiwiki SubtiWiki http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon." ^BSU\d{5}$ BSU29180 jstuelk@gwdg.de http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1 False SUBTIWIKI nbdc00693 subtiwiki subtiwiki subtiwiki sugarbind SugarBind http://sugarbind.expasy.org/ The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands. ^[A-Za-z]+\/[0-9]+$ lectins/172 frederique.lisacek@isb-sib.ch http://sugarbind.expasy.org/$1 False SUGARBIND SUGARBIND SUGARBIND nbdc02224 sugarbind sugarbind supfam SUPERFAMILY http://supfam.org/SUPERFAMILY/ SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. ^\w+$ SSF57615 pandura@mrc-lmb.cam.ac.uk http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1 False SUPFAM supfam supfam superfamily DB-0155 sweetrealm Semantic Web for Earth and Environment Technology Ontology https://bioportal.bioontology.org/ontologies/SWEET 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). ANOVA http://sweetontology.net/matrMineral/$1 https://raw.githubusercontent.com/EnvironmentOntology/envo/master/src/envo/sources/sweetrealm.obo False SWEET swh Software Heritage https://archive.softwareheritage.org Software Heritage is the universal archive of software source code. ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$ 1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d https://archive.softwareheritage.org/browse/swh:$1 False SWH swh swh swiss-model SWISS-MODEL Repository https://swissmodel.expasy.org The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences. ^\w+$ P23298 help-swissmodel@unibas.ch https://swissmodel.expasy.org/repository/uniprot/$1 False SWISS-MODEL swiss-model swiss-model swissmodel r3d100010605 uniprot swissregulon SwissRegulon http://swissregulon.unibas.ch A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. ^[A-Za-z0-9]+$ AHR erik.vannimwegen@unibas.ch http://swissregulon.unibas.ch/query/$1 False SWISSREGULON nbdc02225 swissregulon swissregulon swo Software ontology https://github.com/allysonlister/swo The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. ^\d{7}$ 0000144 allyson.lister@oerc.ox.ac.uk http://purl.obolibrary.org/obo/SWO_$1 https://raw.githubusercontent.com/allysonlister/swo/master/swo.owl https://raw.githubusercontent.com/allysonlister/swo/master/swo.obo False SWO SWO SWO swo swo SWO swo swrl A Semantic Web Rule Language Combining OWL and RuleML https://www.w3.org/2003/11/swrl# SWRL enables Horn-like rules to be combined with an OWL knowledge base. Variable http://www.w3.org/2003/11/swrl#$1 False swrl symp Symptom Ontology http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases. ^\d{7}$ 0019171 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/SYMP_$1 SYMP False SYMP SYMP SYMP symp symp SYMP symptom P8656 synapse Synapse Data Repository https://sagebionetworks.org Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. ^[0-9]*\.*[0-9]*$ 41455251.1 https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn$1 False nbdc02162 synapse r3d100011894 syoid Gemina Symptom Ontology True t3db Toxin and Toxin Target Database http://www.t3db.org/ Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. ^T3D\d+$ T3D0001 david.wishart@ualberta.ca http://www.t3db.org/toxins/$1 False T3DB 2662 t3db t3db 326 t3db r3d100012189 t4fs terms4FAIRskills https://github.com/terms4fairskills/FAIRterminology A terminology for the skills necessary to make data FAIR and to keep it FAIR. ^\d{7}$ 0000127 allyson.lister@oerc.ox.ac.uk http://purl.obolibrary.org/obo/T4FS_$1 False T4FS T4FS t4fs t4fs T4FS tads Tick Anatomy Ontology https://www.vectorbase.org/ontology-browser The anatomy of the Tick, Families: Ixodidae, Argassidae ^\d{7}$ 0000547 dsonensh@odu.edu http://purl.obolibrary.org/obo/TADS_$1 http://purl.obolibrary.org/obo/tads.obo True TADS TADS TADS tads tads TADS tahe Terminology of Anatomy of Human Embryology pierre.sprumont@unifr.ch http://purl.obolibrary.org/obo/TAHE_$1 True TAHE tahe tahh Terminology of Anatomy of Human Histology pierre.sprumont@unifr.ch http://purl.obolibrary.org/obo/TAHH_$1 True TAHH tahh tair.gene TAIR Gene http://arabidopsis.org/index.jsp The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus. ^\d{7}$ 2200934 aisling.doyle9@gmail.com http://arabidopsis.org/servlets/TairObject?accession=Gene:$1 False TAIR.GENE tair.gene tair.gene tair.gene tair tair.locus The Arabidopsis Information Resource http://arabidopsis.org/index.jsp The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS. ^\d+$ 2200950 aisling.doyle9@gmail.com http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1 False TAIR.LOCUS tair.locus tair.locus tair.locus tair.protein TAIR Protein http://arabidopsis.org/index.jsp The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept ^\d{10}$ 1009107926 aisling.doyle9@gmail.com http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1 False TAIR.PROTEIN tair.protein tair.protein tair.protein tao Teleost Anatomy Ontology http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa ^\d{7}$ 0000086 wasila.dahdul@usd.edu http://purl.obolibrary.org/obo/TAO_$1 TAO_RETIRED True TAO TAO TAO tao tao tao tarbase TarBase http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used. ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)$ hsa-let-7a-2-3p http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1 False TARBASE nbdc02102 tarbase tarbase 283 taxrank Taxonomic rank vocabulary https://github.com/phenoscape/taxrank A vocabulary of taxonomic ranks (species, family, phylum, etc) ^\d{7}$ 0000001 balhoff@renci.org http://purl.obolibrary.org/obo/TAXRANK_$1 False TAXRANK TAXRANK TAXRANK TAXRANK taxrank taxrank TAXRANK taxrank tcb Tick Cell Biobank https://www.pirbright.ac.uk/tick-cell-lines-views-page Cell line collections ^\d+$ 2966 https://www.pirbright.ac.uk/node/$1 False TCB tccd The Cell Cycle DB http://www.itb.cnr.it/cellcycle Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle TP53 http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1 True tccd tcdb Transporter Classification Database https://www.tcdb.org The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally. ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$ 5.A.1.1.1 msaier@ucsd.edu http://www.tcdb.org/search/result.php?tc=$1 TC False TCDB 2756 tcdb tcdb 104 tcdb DB-0135 P7260 tctr Thai Clinical Trials Registry https://www.thaiclinicaltrials.org The TCTR was estabished in 2009 and has been operated by Clinical Research Collaboration Network (CRCN), an organization under the Medical Research Foundation, which is a non-profit organization, and financially supported by Thailand Center of Excellence for Life Sciences (TCELS). CRCN has been retitled the Medical Research Network (MedResNet) since June 15, 2012. (from homepage) ^TCTR\d+$ TCTR20230429001 https://www.thaiclinicaltrials.org/show/$1 False te Terminologia Embryologica https://ifaa.unifr.ch/ 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] E5.11.2.0.0.0.4 False P1693 tfclass Classification of Transcription Factors in Mammalia http://tfclass.bioinf.med.uni-goettingen.de 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.. 2.1.1 edgar.wingender@edgar-wingender.de http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1 False 666 tgd Tetrahymena Genome Database http://ciliate.org/index.php/ The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature. ^TTHERM\_\d+$ TTHERM_00648910 http://ciliate.org/index.php/feature/details/$1 False TGD tgd tgd tgd tgma Mosquito gross anatomy ontology https://www.vectorbase.org/ontology-browser A structured controlled vocabulary of the anatomy of mosquitoes. ^\d{7}$ 0000984 topalis@imbb.forth.gr http://purl.obolibrary.org/obo/TGMA_$1 http://purl.obolibrary.org/obo/tgma.obo True TGMA TGMA TGMA tgma tgma TGMA tgma tgn Getty Thesaurus of Geographic Names https://www.getty.edu/research/tools/vocabularies/tgn/ TGN is a structured vocabulary currently containing around 1,106,000 names and other information about places. Names for a place may include names in the vernacular language, English, other languages, historical names, names and in natural order and inverted order. Among these names, one is flagged as the preferred name. TGN is a thesaurus, compliant with ISO and NISO standards for thesaurus construction; it contains hierarchical, equivalence, and associative relationships. Note that TGN is not a GIS (Geographic Information System). While many records in TGN include coordinates, these coordinates are approximate and are intended for reference only. The focus of each TGN record is a place. There are around 912,000 places in the TGN. In the database, each place record (also called a subject) is identified by a unique numeric ID. Linked to the record for the place are names, the place's parent or position in the hierarchy, other relationships, geographic coordinates, notes, sources for the data, and place types, which are terms describing the role of the place (e.g., inhabited place and state capital). The temporal coverage of the TGN ranges from prehistory to the present and the scope is global. The TGN is a hierarchical database; its trees branch from a root called Top of the TGN hierarchies (Subject_ID: 1000000). Currently there are two TGN facets, World and Extraterrestrial Places. Under the facet World, places are arranged in hierarchies generally representing the current political and physical world, although some historical nations and empires are also included. There may be multiple broader contexts, making the TGN polyhierarchical. The primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public. ^\d+$ 1023371 http://vocab.getty.edu/page/tgn/$1 True 109 th Terminologia Histologica https://ifaa.unifr.ch/ The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia] ^H\d\.\d{2}\.\d{2}\.\d\.\d{5}$ H3.03.00.0.00007 False P1694 thermofisher Thermo Fisher Scientific https://www.thermofisher.com ThermoFisher is a life sciences supply vendor. ^\w+$ OSR00185W https://www.thermofisher.com/antibody/product/$1 False tigrfam TIGR protein families http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. ^TIGR\d+$ TIGR00010 https://www.ncbi.nlm.nih.gov/cdd?term=$1 False TIGRFAM 1141 tigrfam tigrfam tigrfams time Time Ontology in OWL https://www.w3.org/TR/owl-time/ Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. 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. DateTimeDescription dr.shorthair@pm.me http://www.w3.org/2006/time#$1 False TIME TIME time time tkg Tohoku University cell line catalog http://www2.idac.tohoku.ac.jp/dep/ccr/ Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells. ^\d+$ 0221 http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html False TKG tngb Telethon Network of Genetic Biobanks http://biobanknetwork.telethon.it/ Cell line collections (Providers) ^\d+$ 67035 http://biobanknetwork.telethon.it/Sample/View?sampleId=$1 False TNGB to Plant Trait Ontology http://browser.planteome.org/amigo A controlled vocabulary to describe phenotypic traits in plants. ^\d{7}$ 0000630 jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/TO_$1 False TO TO TO PTO to to TO pto togoid TogoID Ontology https://togoid.dbcls.jp/ontology 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/) AffyProbeset ktym@dbcls.jp https://togoid.dbcls.jp/#$1 False togovar TogoVar https://grch38.togovar.org/ TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them. ^tgv[0-9]+$ tgv139393198 https://grch38.togovar.org/variant/$1 False nbdc02359 togovar Togovar tokue TOKU-E Cell-culture Database http://cell-lines.toku-e.com Cell line databases/resources http://cell-lines.toku-e.com/Cell-Lines_$1.html True TOKU-E tol Tree of Life Web Project http://tolweb.org/tree/ "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things." ^\d+$ 98034 http://tolweb.org/$1 tol.webproj False 400 TOL tol tol P5221 topdb Topology Data Bank of Transmembrane Proteins http://topdb.enzim.hu/ The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. ^[A-Z0-9]+$ AP00378 http://topdb.enzim.hu/?m=show&id=$1 False TOPDB 2789 topdb topdb topdb topfind TopFind https://topfind.clip.msl.ubc.ca TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ Q9UKQ2 chris.overall@ubc.ca http://clipserve.clip.ubc.ca/topfind/proteins/$1 False TOPFIND topfind topfind r3d100012721 uniprot toxoplasma ToxoDB http://toxodb.org/toxo/ ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ TGME49_053730 http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 False TOXOPLASMA toxoplasma toxoplasma trans Pathogen Transmission Ontology https://github.com/DiseaseOntology/PathogenTransmissionOntology The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. ^\d{7}$ 0000024 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/TRANS_$1 False TRANS TRANS TRANS trans trans TRANS pt transportdb TransportDB http://www.membranetransport.org TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available. MMP0523 http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1 False 105 transportdb transyt Transport Systems Tracker https://www.bio.di.uminho.pt/ The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes. ^T[A-Z]\d{7}$ TR0000001 https://transyt.bio.di.uminho.pt/reactions/$1 False transyt tred Transcriptional Regulatory Element Database http://rulai.cshl.edu/TRED Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present. 21552 http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1 True 167 tred treebase TreeBASE http://treebase.org/ TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc. ^TB[1,2]?:[A-Z][a-z]?\d+$ TB2:S1000 rutgeraldo@gmail.com http://purl.org/phylo/treebase/phylows/study/$1?format=html False TREEBASE nbdc01882 treebase treebase treebase r3d100010170 treefam TreeFam http://www.treefam.org/ TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. ^\w{1,2}\d+$ TF101014 Fab.Schreiber@gmail.com http://www.treefam.org/family/$1 False TREEFAM nbdc01596 treefam treefam treefam DB-0185 tricdb tricdb http://www.biomeddb.org/ Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine. ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$ 1eec8393-e598-41ed-9d8b-6d5b0db94470 http://biomeddb.org/Disease/Details?DISEASEID=$1 False tricdb trichdb TrichDB http://trichdb.org/trichdb/ TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ TVAG_386080 oharb@pcbi.upenn.edu http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 False TRICHDB nbdc01785 trichdb trichdb r3d100012461 tritrypdb TriTrypDB http://tritrypdb.org/tritrypdb/ TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+(\.)?\w+(\.)?\w+$ Tb927.8.620 oharb@pcbi.upenn.edu http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 False TRITRYPDB nbdc01786 tritrypdb tritrypdb r3d100011479 trnadbce tRNA Gene Database http://trna.nagahama-i-bio.ac.jp "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." 265912 http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1 False nbdc00720 trnadbce tsc Tetrahymena Stock Center https://tetrahymena.vet.cornell.edu/ Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID] ^SD\d+$ SD00043 https://tetrahymena.vet.cornell.edu/display.php?stockid=$1 False TSC ttd.drug TTD Drug http://bidd.nus.edu.sg/group/ttd/ttd.asp The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. ^DAP\d+$ DAP000773 http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1 False TTD.DRUG 2653 ttd.drug ttd.drug ttd.target TTD Target http://bidd.nus.edu.sg/group/ttd/ttd.asp The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. ^TTDS\d+$ TTDS00056 http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1 False TTD.TARGET 2654 ttd.target ttd.target tto Teleost taxonomy ontology https://github.com/phenoscape/teleost-taxonomy-ontology An ontology covering the taxonomy of teleosts (bony fish) ^\d+$ 1058367 balhoff@renci.org http://purl.obolibrary.org/obo/TTO_$1 False TTO TTO TTO tto tto TTO tto txpo Toxic Process Ontology https://toxpilot.nibiohn.go.jp/ "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms. In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp" ^\d{7}$ 0002066 yuki.yamagata@riken.jp http://purl.obolibrary.org/obo/TXPO_$1 False TXPO TXPO txpo txpo TXPO uberon Uber Anatomy Ontology http://uberon.org Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. ^\d+$ 2005080 cjmungall@lbl.gov http://purl.obolibrary.org/obo/UBERON_$1 http://purl.obolibrary.org/obo/uberon/basic.obo UBERON|Uber-anatomy ontology|Uberon False UBERON UBERON UBERON UBERON uberon uberon uberon uberon UBERON Uberon P1554 ubio.namebank uBio NameBank http://www.ubio.org "NameBank is a ""biological name server"" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context." ^\d+$ 2555646 http://www.ubio.org/browser/details.php?namebankID=$1 False UBIO.NAMEBANK ubio.namebank ubio.namebank ubprop Uberon Property UBPROP|UBREL True ucas UK Universities and Colleges Admissions Service https://www.ucas.com An identifier for institutions in the United Kingdom, used in GRID and ROR. ^\w\d+$ N21 False ucsc UCSC Genome Browser https://genome.ucsc.edu/ 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. uc001rvw.5 max@soe.ucsc.edu ftp://hgdownload.cse.ucsc.edu/goldenPath/$1 False UCSC DB-0139 P2576 ucum Unified Code for Units of Measure https://ucum.org 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. aBq dr.shorthair@pm.me https://units-of-measurement.org/$1 False 1895 2.16.840.1.113883.6.8 ucum ukprn UK Provider Reference Number https://www.ukrlp.co.uk identifier for an educational organization issued by the UK Register of Learning Providers ^[1-9]\d*$ 10007835 https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L ukprns False P4971 umbbd.compound UM-BBD compound http://umbbd.ethz.ch/ The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information. ^c\d+$ c0001 http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1 UM-BBD_compID False UMBBD.COMPOUND umbbd.compound umbbd.compound P8121 umbbd umbbd.enzyme EAWAG Biocatalysis/Biodegradation Database http://umbbd.ethz.ch/ The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information. ^e\d+$ e0333 http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1 UM-BBD_enzymeID False UMBBD.ENZYME umbbd.enzyme umbbd.enzyme umbbd umbbd.pathway EAWAG Biocatalysis/Biodegradation Database http://umbbd.ethz.ch/ The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information. ^\w+$ ala http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1 UM-BBD_pathwayID False UMBBD.PATHWAY umbbd.pathway umbbd.pathway umbbd umbbd.reaction EAWAG Biocatalysis/Biodegradation Database http://umbbd.ethz.ch/ The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information. ^r\d+$ r0001 http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1 UM-BBD_reactionID False UMBBD.REACTION umbbd.reaction umbbd.reaction umbbd umbbd.rule EAWAG Biocatalysis/Biodegradation Database http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules. ^bt\d+$ bt0001 http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1 UM-BBD_ruleID False UMBBD.RULE umbbd.rule umbbd.rule umbbd uminctr University hospital Medical Information Network Clinical Trial Registry https://www.umin.ac.jp/ctr/index.htm An additional Japanese clinical trial registry ^UMIN\d+$|^C\d+$ UMIN000049383 False nbdc01470 umls Unified Medical Language System Concept Unique Identifier https://www.nlm.nih.gov/research/umls 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. ^C\d+$ C2584994 https://uts.nlm.nih.gov/uts/umls/concept/$1 UMLS|UMLS CUI|UMLS_CUI|umls.cui False 20052 UMLS 1181 2.16.840.1.113883.6.86 umls umls P2892 umls.aui Unified Medical Language System Atomic Unique Identifier https://www.nlm.nih.gov/research/umls An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus. ^A\d+$ A0118748 UMLS_ICD9CM_2005_AUI False unichem UniChem compound https://chembl.gitbook.io/unichem/downloads identifier of a compound in the UniChem database ^\d+$ 161671 https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1 False P11089 unigene UniGene http://www.ncbi.nlm.nih.gov/unigene A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. ^\d+$ 4900 http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1 True UNIGENE nbdc00220 unigene unigene unigene r3d100010774 unii Unique Ingredient Identifier https://precision.fda.gov/uniisearch The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information. ^[A-Z0-9]+$ 3G6A5W338E https://precision.fda.gov/uniisearch/srs/unii/$1 False UNII 000563 unii unii P652 unimod Unimod protein modification database for mass spectrometry http://www.unimod.org/ Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). ^\d+$ 1200 jcottrell@matrixscience.com http://www.unimod.org/modifications_view.php?editid1=$1 False UNIMOD 3757 unimod unimod unimod uniparc UniProt Archive https://www.ebi.ac.uk/uniparc/ The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases. ^UPI[A-F0-9]{10}$ UPI000000000A apweiler@ebi.ac.uk https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1 False UNIPARC 2392 uniparc uniparc uniparc r3d100011519 unipathway.compound UniPathway Compound http://www.grenoble.prabi.fr/obiwarehouse/unipathway UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds. ^UPC\d{5}$ UPC04349 http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1 False UNIPATHWAY.COMPOUND unipathway.compound unipathway.compound unipathway.reaction UniPathway Reaction http://www.grenoble.prabi.fr/obiwarehouse/unipathway UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions. ^UCR\d{5}$ UCR00226 http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1 False UNIPATHWAY.REACTION unipathway.reaction unipathway.reaction uniprot UniProt Protein http://www.uniprot.org The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ P0DP23 apweiler@ebi.ac.uk http://purl.uniprot.org/uniprot/$1 SwissProt|UP|UniProt|UniProtKB|Uniprot ID|uniprot/swiss-prot False UP UniProtKB UniProtKB 3021 nbdc00221 uniprot uniprot uniprot r3d100011521 Uniprot P352 uniprot.arba Association-Rule-Based Annotator https://www.uniprot.org/arba Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system. ^ARBA\d+$ ARBA00000001 https://www.uniprot.org/arba/$1 arba False uniprot.chain UniProt Chain https://www.uniprot.org This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein. ^PRO_[0-9]{10}$ PRO_0000016681 http://purl.uniprot.org/annotation/$1 UPPRO False uniprot.chain uniprot uniprot.core Uniprot Core Ontology http://purl.uniprot.org/core/ Properties and classes used for protein annotation certain http://purl.uniprot.org/core/$1 False uniprot uniprot.disease UniProt Diseases https://www.uniprot.org/diseases/ The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary. ^DI-\d{5}$ DI-04240 https://www.uniprot.org/diseases/$1 https://rest.uniprot.org/diseases/stream?compressed=true&format=obo&query=%28%2A%29 DI|SP_DI False P11430 uniprot uniprot.isoform UniProt Isoform http://www.uniprot.org/ The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information. ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$ Q5BJF6-3 http://purl.uniprot.org/isoforms/$1 UPISO False UNIPROT.ISOFORM uniprot.isoform uniprot.isoform uniprot uniprot.journal UniProt journal https://www.uniprot.org/journals identifier for a scientific journal, in the UniProt database ^\d{4}$ 3546 https://www.uniprot.org/journals/$1 False P4616 uniprot.keyword UniProt Keywords http://www.uniprot.org/keywords/ UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries. ^KW-\d{4}$ KW-1273 https://www.uniprot.org/keywords/$1 https://rest.uniprot.org/keywords/stream?compressed=true&fields=id%2Cname%2Ccategory%2Cgene_ontologies&format=tsv&query=%28%2A%29 SP_KW|UniProtKB-KW|uniprot.keyword|uniprot.kw False uniprot.kw uniprot uniprot.location UniProt Subcellular Locations https://www.uniprot.org/locations/ The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms. ^SL-\d+$ SL-0002 https://www.uniprot.org/locations/$1 https://rest.uniprot.org/locations/stream?compressed=true&format=obo&query=%28%2A%29 SP_SL|UPLOC|UniProtKB-SubCell False uniprot uniprot.mnemonic UniProt https://www.uniprot.org/ The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. This entry represents UniProt mnemonics which combine an alphanumeric representation the protein name and a species identification code representing the biological source of the protein. ^[A-Z0-9]{1,10}_[A-Z0-9]{1,5}$ BRAF_HUMAN https://www.uniprot.org/uniprotkb/$1 False UniprotMnemonic uniprot.proteome UniProt Proteomes https://www.uniprot.org/proteomes UniProt provides proteome sets of proteins whose genomes have been completely sequenced. ^UP\d{9}$ UP000005640 https://www.uniprot.org/proteomes/$1 False uniprot uniprot.ptm UniProt Post-Translational Modification https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format ^PTM-\d{4}$ PTM-0450 https://biopragmatics.github.io/providers/uniprot.ptm/$1 PTM False uniprot uniprot.resource UniProt Resource https://www.uniprot.org/database/ The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources. ^DB-\d{4}$ DB-0174 https://www.uniprot.org/database/$1 uniprot.database|uniprot.db False uniprot uniprot.tissue Tissue List https://www.uniprot.org/docs/tisslist.txt The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified. ^TS-\d{4}$ TS-0285 https://www.uniprot.org/tissues/$1 False TISSUELIST tissuelist tissuelist uniprot uniprot.var UniProt Variants https://web.expasy.org/variant_pages The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species. ^\d+$ 068078 http://purl.uniprot.org/annotation/VAR_$1 SP_VAR|UPVAR|UniProtKB_VAR False uniprot uniref UniRef https://www.uniprot.org/ The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view. ^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$ UniRef90_P00750 https://www.uniprot.org/uniref/$1 False 2346 uniref r3d100011518 unirule UniRule https://www.uniprot.org/unirule/ 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. UR000124451 https://www.uniprot.org/unirule/$1 False unists Database of Sequence Tagged Sites https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. ^\d+$ 456789 https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1 False UNISTS 2389 unists unists unists unite Molecular database for the identification of fungi http://unite.ut.ee/ UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa. ^UDB\d{6}$ UDB000691 urmas.koljalg@ut.ee http://unite.ut.ee/bl_forw.php?nimi=$1 False UNITE 2390 nbdc01905 unite unite unite r3d100011316 unpd Universal Natural Products Database http://pkuxxj.pku.edu.cn/UNPD/ True uo Units of measurement ontology https://github.com/bio-ontology-research-group/unit-ontology Ontology of standardized units ^\d{7}$ 0000080 g.gkoutos@gmail.com http://purl.obolibrary.org/obo/UO_$1 False UO UO UO UO uo uo uo uo UO uo upa Unipathway https://github.com/geneontology/unipathway A manually curated resource for the representation and annotation of metabolic pathways ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$ UCR00513 Anne.Morgat@sib.swiss http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1 https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo UPa|unipathway|unipathway.pathway True UPA UNIPATHWAY UPA 2645 upa upa UPA 414 unipathway upheno Unified Phenotype Ontology https://github.com/obophenotype/upheno The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. vasilevs@ohsu.edu http://purl.obolibrary.org/obo/UPHENO_$1 False UPHENO UPHENO UPHENO upheno upheno UPHENO uspto United States Patent and Trademark Office http://patft.uspto.gov/netahtml/PTO/index.html The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement. ^(\d{1,2},?\d{3},?\d{3}|(PP|RE|AI|RX)\d{2},?\d{3}|(D|T|H|X)\d{3},?\d{3})$ 4145692 http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1 False USPTO uspto uspto utrdb UTRdb https://utrdb.cloud.ba.infn.it/utrdb/index_107.html A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. ^([3-5][A-Z])\w+[^A-Z][0-9]$ 5UTR_107_ENST00000517291.2 https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1 False nbdc00730 utrdb vac Vaccine Adjuvant Compendium https://vac.niaid.nih.gov The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs. ^\d+$ 15 https://vac.niaid.nih.gov/view?id=$1 False validatordb ValidatorDB https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ Database of validation results for ligands and non-standard residues in the Protein Data Bank. ^[A-Za-z0-9\/]+$ 2h6o david.sehnal@gmail.com https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1 False VALIDATORDB nbdc02174 validatordb validatordb pdb vandf Veterans Administration National Drug File https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. ^\d+$ 4019477 michael.lincoln@med.va.gov http://purl.bioontology.org/ontology/VANDF/$1 False VANDF VANDF 2.16.840.1.113883.6.229 vann A vocabulary for annotating vocabulary descriptions https://vocab.org/vann/ This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes. usageNote nospam@iandavis.com https://vocab.org/vann/#$1 False vann vann vario Variation Ontology http://variationontology.org The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. ^\d+$ 0376 mauno.vihinen@med.lu.se http://purl.obolibrary.org/obo/VariO_$1 True VARIO VARIO VARIO VARIO vario vario vario vario VariO vbase2 Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse http://www.vbase2.org/vbase2.php The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. ^\w+$ humIGHV025 wmueller@gbf.de http://www.vbase2.org/vgene.php?id=$1 False VBASE2 nbdc01897 vbase2 vbase2 vbase2 vbo Vertebrate Breed Ontology https://github.com/monarch-initiative/vertebrate-breed-ontology Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names. ^\d{7}$ 0000038 Sabrina@tislab.org http://purl.obolibrary.org/obo/VBO_$1 False VBO VBO vbo vbo VBO vbrc Viral Bioinformatics Resource Center http://vbrc.org/ The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. ^\d+$ 35742 http://vbrc.org/gene_detail.asp?gene_id=$1 False VBRC vbrc vbrc vbrc vcell VCell Published Models https://health.uconn.edu/ Models developed with the Virtual Cell (VCell) software prorgam. ^\d{5,}$ 201022999 https://vcell.org/biomodel-$1 False vcell vdrc Vienna Drosophila Resource Center http://stockcenter.vdrc.at/control/main Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID] ^\d+$ 100291 https://shop.vbc.ac.at/vdrc_store/$1.html False VDRC vectorbase Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens https://www.vectorbase.org/ VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host. ^\D{4}\d{6}(\-\D{2})?$ ISCW007415 d.e.starns@liv.ac.uk https://vectorbase.org/gene/$1 False VECTORBASE nbdc01909 vectorbase vectorbase vectorbase r3d100010880 vega Vertebrate Genome Annotation Database https://vega.archive.ensembl.org/index.html A repository for high-quality gene models produced by the manual annotation of vertebrate genomes. OTTHUMG00000169812 jla1@sanger.ac.uk http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1 VEGA False vega r3d100012575 vegbank VegBank http://vegbank.org/ VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. ^VB\.[A-Za-z][A-Za-z]\..*$ VB.Ob.3736.GRSM125 http://vegbank.org/cite/$1 False vegbank r3d100010153 venom Veterinary Nomenclature https://venomcoding.org/ The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems. ^\d+$ 12969 DBrodbelt@RVC.AC.UK False vfb Virtual Fly Brain https://VirtualFlyBrain.org An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster. ^[0-9a-zA-Z]{8}$ 00000001 r.court@ed.ac.uk http://virtualflybrain.org/reports/$1 False vfb vfb r3d100011373 vfdb.gene VFDB Gene http://www.mgc.ac.cn/VFs/ VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes. ^\w+$ VFG2154 http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1 False VFDB.GENE vfdb.gene vfdb.gene vfdb.genus VFDB Genus http://www.mgc.ac.cn/VFs/ VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus. ^\w+$ Chlamydia http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1 False VFDB.GENUS vfdb.genus vfdb.genus vgnc Vertebrate Gene Nomenclature Committee https://vertebrate.genenames.org The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee. ^\d{1,9}$ 3792 stweedie@ebi.ac.uk https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1 False VGNC nbdc02624 vgnc Vgnc DB-0226 vhog Vertebrate Homologous Organ Group Ontology http://bgee.unil.ch "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 ""historical homology"". Each mapping has been manually reviewed, and we provide confidence codes and references when available." ^\d{7}$ 0000411 bgee@isb-sib.ch http://purl.obolibrary.org/obo/VHOG_$1 ftp://ftp.bgee.org/general/ontologies/vHOG.obo VHOG_RETIRED True VHOG VHOG VHOG vhog vhog viaf VIAF ID http://viaf.org The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web. ^\d+$ 75121530 http://viaf.org/viaf/$1 False 2053 viaf viaf P214 vido The Virus Infectious Disease Ontology https://github.com/infectious-disease-ontology-extensions/ido-virus The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc. ^\d{7}$ 0001114 johnbeverley2021@u.northwestern.edu http://purl.obolibrary.org/obo/VIDO_$1 https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl False VIDO VIDO vido VIDO violinnet ViolinNet Defunct vaccine information source from the He Lab ^\d+$ 4140 http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1 violinID|violinId True P1925 viperdb VIPERdb http://viperdb.scripps.edu/ 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. 2c6s https://viperdb.org/Info_Page.php?VDB=$1 False nbdc00835 viperdb r3d100012362 pdb vipr Virus Pathogen Resource http://www.viprbrc.org/brc/home.do?decorator=vipr The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information. ^[A-Za-z 0-9]+$ BeAn 70563 rscheuermann@jcvi.org http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena False VIPR vipr vipr r3d100011931 viralzone ViralZone http://www.expasy.org/viralzone/ ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures. ^\d+$ 992 Philippe.Lemercier@sib.swiss https://viralzone.expasy.org/$1 vz False VIRALZONE nbdc02226 viralzone viralzone vz r3d100013314 virgen VirGen http://bioinfo.ernet.in/virgen/virgen.html 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. AY321118 False virgen virmirdb Vir-Mir db http://alk.ibms.sinica.edu.tw A database containing predicted viral miRNA candidate hairpins. 11002 http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1 False virmirdb ncbitaxon viroligo VirOligo http://viroligo.okstate.edu 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. BM0456 http://viroligo.okstate.edu/main.php?vid=$1 False viroligo virsirna VIRsiRNA http://crdd.osdd.net/servers/virsirnadb The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region. ^virsi\d+$ virsi1909 http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1 False VIRSIRNA virsirna virsirna virushostdb Virus-HostDB https://www.genome.jp/virushostdb/ Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-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. 438782 ogata@kuicr.kyoto-u.ac.jp https://www.genome.jp/virushostdb/$1 False nbdc02395 virushostdb ncbitaxon vita Virus' miRNA target http://vita.mbc.nctu.edu.tw/ 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. AB016785 http://vita.mbc.nctu.edu.tw/search.php?acc=$1 False vita vmc Variation Modelling Collaboration True vmhgene VMH Gene https://www.vmh.life/ The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. ^[0-9]+\.[0-9]+$ 8639.1 https://www.vmh.life/#gene/$1 False vmhgene vmhmetabolite VMH metabolite https://www.vmh.life/ The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. ^[a-zA-Z0-9_\(\_\)\[\]]+$ h2o https://www.vmh.life/#metabolite/$1 False VMHMETABOLITE vmhmetabolite vmhmetabolite vmhreaction VMH reaction https://www.vmh.life/ The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. ^[a-zA-Z0-9_\(\_\)\[\]]+$ HEX1 https://www.vmh.life/#reaction/$1 False VMHREACTION vmhreaction vmhreaction vo Vaccine Ontology https://violinet.org/vaccineontology The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities. ^\d{7}$ 0000093 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/VO_$1 False VO VO VO vo vo VO vo P1928 voc4cat A vocabulary for the catalysis disciplines https://nfdi4cat.github.io/voc4cat/ Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science. ^\d{7,}$ 0000123 nikolaos.moustakas@catalysis.de https://w3id.org/nfdi4cat/voc4cat_$1 False void Vocabulary of Interlinked Datasets http://vocab.deri.ie/void 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. feature http://rdfs.org/ns/void#$1 False void void void vsao Vertebrate Skeletal Anatomy Ontology https://www.nescent.org/phenoscape/Main_Page Vertebrate skeletal anatomy ontology. ^\d{7}$ 0000183 wasila.dahdul@usd.edu http://purl.obolibrary.org/obo/VSAO_$1 VSAO_RETIRED True VSAO VSAO VSAO vsao vsao vao vsdb Veterinary Substances DataBase https://sitem.herts.ac.uk/aeru/vsdb Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source. ^\d+$ 1868 https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm False vsmo Ontology for vector surveillance and management https://code.google.com/archive/p/vector-surveillance-and-management-ontology/ 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. 0000000 lars.eisen@colostate.edu http://purl.obolibrary.org/obo/VSMO_$1 https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.owl https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.obo False vso Vital Sign Ontology https://bioportal.bioontology.org/ontologies/VSO The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ^\d{7}$ 0000041 albertgoldfain@gmail.com https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1 False VSO VSO vso vso vt Vertebrate trait ontology https://github.com/AnimalGenome/vertebrate-trait-ontology The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. ^\d{7}$ 0000685 caripark@iastate.edu http://purl.obolibrary.org/obo/VT_$1 https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo False VT VT VT VT vt vt VT vt vto Vertebrate Taxonomy Ontology https://github.com/phenoscape/vertebrate-taxonomy-ontology Comprehensive hierarchy of extinct and extant vertebrate taxa. ^\d{7}$ 9008500 balhoff@renci.org http://purl.obolibrary.org/obo/VTO_$1 False VTO VTO VTO vto vto VTO vuid Veterans Health Administration (VHA) unique identifier https://www.va.gov/health The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year. ^\d+$ 4007166 False wb.rnai WormBase RNAi https://www.wormbase.org/ 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. ^WBRNAi\d{8}$ WBRNAi00086878 https://www.wormbase.org/species/c_elegans/rnai/$1 False WB.RNAI wb.rnai wb.rnai wbbt C. elegans Gross Anatomy Ontology https://github.com/obophenotype/c-elegans-gross-anatomy-ontology Ontology about the gross anatomy of the C. elegans ^\d{7}$ 0001290 raymond@caltech.edu http://purl.obolibrary.org/obo/WBbt_$1 WBbt False WBBT WBbt WB-BT wbbt wbbt WBbt wbbt wbls C. elegans development ontology https://github.com/obophenotype/c-elegans-development-ontology Ontology about the development and life stages of the C. elegans ^\d{7}$ 0000690 cgrove@caltech.edu http://purl.obolibrary.org/obo/WBls_$1 WBls False WBLS WBLS WB-LS wbls wbls WBls wbls wbphenotype C. elegans phenotype https://github.com/obophenotype/c-elegans-phenotype-ontology Ontology about C. elegans and other nematode phenotypes ^\d{7}$ 0000983 cgrove@caltech.edu http://purl.obolibrary.org/obo/WBPhenotype_$1 WBPhenotype False WBPHENOTYPE WBPhenotype WB-PHENOTYPE wbphenotype wbphenotype WBPhenotype wbphenotype webelements Web Elements https://www.webelements.com/ Browser for the periodic table of the elements ^\w+$ chromium https://www.webelements.com/$1 False wgs84 WGS84 Geo Positioning https://www.w3.org/2003/01/geo/wgs84_pos A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum latitude http://www.w3.org/2003/01/geo/wgs84_pos#$1 False geo wicell WiCell Research Institute Cell Collection https://www.wicell.org Cell line collections (Providers) ai10e-kctd13b https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true False WiCell wikidata Wikidata https://www.wikidata.org/ Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic. ^(Q|P)\d+$ Q47475003 vrandecic@gmail.com http://www.wikidata.org/entity/$1 WD_Entity|wd False 1940 WIKIDATA Wikidata 000567 wikidata wikidata wikidata.property Wikidata Property https://www.wikidata.org "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines. Wikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. " ^P\d+$ P4355 https://www.wikidata.org/wiki/Property:$1 False WD_Prop wikidata wikigenes WikiGenes http://www.wikigenes.org/ WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process. ^\d+$ 3771877 http://www.wikigenes.org/e/gene/e/$1.html False WIKIGENES wikigenes wikigenes ncbigene wikipathways WikiPathways http://www.wikipathways.org/ WikiPathways is a database of biological pathways maintained by and for the scientific community. ^WP\d{1,5}(\_r\d+)?$ WP732 egon.willighagen@gmail.com http://www.wikipathways.org/instance/$1 False WIKIPATHWAYS 3952 nbdc02116 wikipathways wikipathways 237 wikipathways r3d100013316 Wikipathways P2410 wikipathways.vocab WikiPathways Ontology http://www.wikipathways.org An ontology supporting data modeling in WikiPathways DataNode egon.willighagen@gmail.com https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1 False WIKIPATHWAYS WIKIPATHWAYS wikipedia.en Wikipedia http://en.wikipedia.org/wiki/Main_Page Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay. ^\S+$ SM_UB-81 http://en.wikipedia.org/wiki/$1 wikipedia False WIKIPEDIA.EN wikipedia.en wikipedia.en wikipedia worfdb C. elegans ORFeome cloning project http://worfdb.dfci.harvard.edu/ WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends). ^\w+(\.\d+)$ T01B6.1 http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1 False WORFDB nbdc00738 worfdb worfdb worfdb world2dpage The World-2DPAGE database http://world-2dpage.expasy.org/repository/ 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. 0020 https://world-2dpage.expasy.org/repository/$1 True world2dpage DB-0121 worldavatar.compchem Computational Chemistry Ontology https://como.ceb.cam.ac.uk/preprints/223/ 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/) http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl False worldavatar.kin Ontology for Chemical Kinetic Reaction Mechanisms http://www.theworldavatar.com/ontokin/ Represents chemical kinetic reaction mechanisms. ElementNumber http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1 http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl False wormbase WormBase https://www.wormbase.org/ WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities. ^WB[A-Z][a-z]+\d+$ WBGene00000001 todd@wormbase.org https://www.wormbase.org/get?name=$1 WB|WB_REF|wb|wormbase False WormBase 1805 nbdc00740 wb wb 426 wormbase r3d100010424 WB-STRAIN:WBStrain DB-0110 P3860 wormpep Wormpep https://www.wormbase.org/db/seq/protein Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. ^CE\d{5}$ CE28239 https://www.wormbase.org/db/seq/protein?name=$1 False WORMPEP wormpep wormpep wormpep worms WoRMS-ID for taxa http://www.marinespecies.org/ The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts. ^\d+$ 146421 leen.vandepitte@vliz.be http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1 False 720 WORMS worms worms P850 wos Web of Science ID (work) https://www.webofscience.com unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix) 000177759000002 https://www.webofscience.com/wos/woscc/full-record/WOS:$1 wosid|wosuid False P8372 wos.researcher ResearcherID https://access.clarivate.com/login?app=wos identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829 ^[A-Z]{1,3}-\d{4}-(19|20)\d\d$ B-5720-2018 https://www.webofscience.com/wos/author/record/$1 False P1053 wwf.ecoregion World Wildlife Fund Ecoregion https://www.worldwildlife.org/biomes WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. ^AT\d+$ AT1402 https://www.worldwildlife.org/ecoregions/$1 WWF False P1294 xao Xenopus Anatomy Ontology http://www.xenbase.org/anatomy/xao.do?method=display XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. ^\d{7}$ 0004486 Erik.Segerdell@cchmc.org http://purl.obolibrary.org/obo/XAO_$1 False XAO 581 XAO XAO xao xao XAO P4495 xco Experimental condition ontology https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. ^\d{7}$ 0000780 jrsmith@mcw.edu http://purl.obolibrary.org/obo/XCO_$1 False XCO XCO XCO xco xco XCO xco xenbase Xenbase https://www.xenbase.org/ Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. ^XB\-\w+\-\d+$ XB-GENE-922462 troy_pells@yahoo.ca https://www.xenbase.org/entry/$1 Xenbase False Xenbase 2738 xenbase xenbase xenbase r3d100011331 DB-0129 ximbio Ximbio https://ximbio.com Cell line collections (Providers) ^\d+$ 151022 https://ximbio.com/reagent/$1 False Ximbio xl Cross-linker reagents ontology http://www.psidev.info/groups/controlled-vocabularies A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. psidev-ms-vocab@lists.sourceforge.net True XL XL xl XL xlmod HUPO-PSI cross-linking and derivatization reagents controlled vocabulary http://www.psidev.info/groups/controlled-vocabularies A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. ^\d{5}$ 00050 gerhard.mayer@rub.de http://purl.obolibrary.org/obo/XLMOD_$1 False XLMOD XLMOD xlmod xlmod XLMOD xmetdb Xenobiotics Metabolism Database https://xmetdb.org Metabolites in the Xenobiotics Metabolism Database. ^\d+$ 171 http://www.xmetdb.org/xmetdb/protocol/$1 True xml Extensible Markup Language https://www.w3.org/TR/xml/ 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. lang http://www.w3.org/XML/1998/namespace#$1 False xml xpo Xenopus Phenotype Ontology https://github.com/obophenotype/xenopus-phenotype-ontology XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. ^\d+$ 0100002 Erik.Segerdell@cchmc.org http://purl.obolibrary.org/obo/XPO_$1 False XPO XPO xpo xpo XPO xsd XML Schema Definition http://www.w3.org/2001/XMLSchema This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language. decimal http://www.w3.org/2001/XMLSchema#$1 False xsd xsd xsd xuo XUO True ydpm Yeast Deletion and the Mitochondrial Proteomics Project http://www-deletion.stanford.edu/YDPM/ The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. ^Y[A-Z]{2}\d+[CW]$ YAL001C http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1 False YDPM ydpm ydpm ydpm yeastintron Yeast Intron Database v4.3 http://intron.ucsc.edu/yeast4.3/ The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]. ^[A-Z0-9]+$ SNR17A http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1 False YEASTINTRON yeastintron yeastintron yeastract Yeast Searching for Transcriptional Regulators and Consensus Tracking http://www.yeastract.com 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. YBR125c isacorreia@tecnico.ulisboa.pt http://www.yeastract.com/view.php?existing=locus&orfname=$1 False 205 yeastract yetfasco YeTFasCo http://yetfasco.ccbr.utoronto.ca/ The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. ^\w+\_\d+(\.\d+)?$ YOR172W_571.0 http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1 False YETFASCO yetfasco yetfasco ygob Yeast Genome Order Browser http://wolfe.gen.tcd.ie/ygob YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes. ADH1 http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1 True ygob hgnc.symbol yid Yeast Intron Database v3 http://compbio.soe.ucsc.edu/yeast_introns.html The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]. ^[A-Z0-9]+$ SNR17A http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1 False YID yid yid ymdb Yeast Metabolome Database http://www.ymdb.ca The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). ^YMDB\d+$ YMDB00001 david.wishart@ualberta.ca http://www.ymdb.ca/compounds/$1 False 388 r3d100012733 ypo Yeast Phenotype Ontology http://www.yeastgenome.org/ cherry@genome.stanford.edu http://purl.obolibrary.org/obo/YPO_$1 True YPO ypo yrcpdr YRC PDR http://www.yeastrc.org/pdr/ The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. ^\d+$ 2673500 mriffle@u.washington.edu http://yeastrc.org/pdr/viewProtein.do?id=$1 False YRCPDR yrcpdr yrcpdr yrc r3d100010975 zazuko Zazuko Prefix Server https://prefix.zazuko.com/ 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 ) frbr ktk@netlabs.org https://prefix.zazuko.com/prefix/$1: False zea Maize gross anatomy http://www.maizemap.org/ Maize gross anatomy ^\d{7}$ 0015177 Leszek@missouri.edu http://purl.obolibrary.org/obo/ZEA_$1 True ZEA ZEA ZEA zea zea zeco Zebrafish Experimental Conditions Ontology https://github.com/ybradford/zebrafish-experimental-conditions-ontology Ontology of Zebrafish Experimental Conditions ^\d{7}$ 0000171 ybradford@zfin.org http://purl.obolibrary.org/obo/ZECO_$1 False ZECO ZECO ZECO zeco zeco ZECO zenodo.record Zenodo https://zenodo.org Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts. ^\d+$ 4390079 lars.holm.nielsen@cern.ch https://zenodo.org/record/$1 zenodo False nbdc02187 r3d100010468 P4901 zfa Zebrafish anatomy and development ontology https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources ZFA description. ^\d{7}$ 0005926 van_slyke@zfin.org http://purl.obolibrary.org/obo/ZFA_$1 ZFA_RETIRED False ZFA ZFA ZFA zfa zfa ZFA zfa zfin Zebrafish Information Network Gene http://zfin.org ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN. ^ZDB\-\w+\-\d+\-\d+$ ZDB-GENE-041118-11 dhowe@zfin.org http://zfin.org/$1 ZFIN False ZFIN nbdc00746 zfin zfin zfin r3d100010421 ZIRC DB-0113 P3870 zfs Zebrafish developmental stages ontology https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources Developmental stages of the Zebrafish ^\d{7}$ 0000050 van_slyke@zfin.org http://purl.obolibrary.org/obo/ZFS_$1 False ZFS ZFS ZFS zfs zfs ZFS zinc ZINC is not Commercial http://zinc15.docking.org/ ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. ^(ZINC)?\d+$ ZINC1084 http://zinc15.docking.org/substances/$1 False ZINC zinc zinc r3d100010372 P2084 zp Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phenotype-ontology The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. ^\d+$ 0019030 ybradford@zfin.org http://purl.obolibrary.org/obo/ZP_$1 False ZP ZP ZP zp zp ZP