"false"^^ . "^\\d+$"^^ . . . "NLXCELL conatins cell types with a focus on neuron types."^^ . "http://leafsnap.com/species/$1/"^^ . . . "pmc" . . . . . . "http://purl.obolibrary.org/obo/OCCO_$1"^^ . "community care" . . "intact.molecule" . "genomics" . "^\\d{7}$"^^ . . "true"^^ . "false"^^ . "interaction" . . "https://biomodels.net/vocab/idot.rdf#"^^ . . "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist="^^ . . "false"^^ . . . . "https://athena.ohdsi.org/search-terms/terms/$1"^^ . "transyt" . "Spectral Database for Organic Compounds" . "ama-cpt" . . . . . "LBCTR2023015204"^^ . . . "false"^^ . . . . . . . "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1"^^ . . . . . "biology" . . "biomedical science" . . "Upinder S. Bhalla" . . "Online Mendelian Inheritance in Man" . . "https://umgear.org/p?id=$1"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . "false"^^ . . . . "https://www.kaggle.com/"^^ . . . . . "https://www.atcc.org/products/"^^ . "3403"^^ . . "SNP500Cancer" . "bmrb.restraint" . "^(\\d{8}|(\\w+\\d+\\w+))$"^^ . "Medical Action Ontology" . . . . "https://arxiv.org/abs/"^^ . . "https://w3id.org/nmdc/$1"^^ . . "NINDS Human Cell and Data Repository" . "https://bioregistry.io/metaregistry/prefixcommons/"^^ . "pubchem.compound" . . "pathway" . . . "seed" . "EC" . "dbSNP Reference SNP number" . . . "0400109"^^ . "false"^^ . "https://models.physiomeproject.org/exposure/$1"^^ . . . "NCBI Registry" . . "https://purl.dataone.org/odo/SASAP_$1"^^ . "genecards" . "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . . . . . . . . "obi" . "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"^^ . . "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?"^^ . . . "false"^^ . . "https://tools.ietf.org/rfc/rfc"^^ . . "https://prefix.zazuko.com/$1:$2" . "MicrosporidiaDB" . . . . "182"^^ . . "characterisation data heat" . "medicine" . . . . "wosuid" . . . . . . . . "false"^^ . "Phenotype And Trait Ontology" . "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants."^^ . . . . "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."^^ . . . "Identifier for a place in iNaturalist"^^ . "Daniel Gautheret" . "sequence annotation" . . "http://purl.obolibrary.org/obo/AEO_$1"^^ . . "human genetics" . . . "comparative genomics" . "199/2168"^^ . . "NIST Chemistry WebBook" . . . . . . . . "false"^^ . . . "http://rest.bmrb.wisc.edu/bmrb/$1/html"^^ . . "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID="^^ . "ensemblglossary" . . . . . . . "^\\d{7}$"^^ . . . "ASPL0000349247"^^ . "0000040"^^ . "lincs.data" . . . . "false"^^ . . . . . . . "chemical entity" . . . . . . . "mutant mouse strain" . . . "bcrj" . . . "ZFIN" . . . "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)"^^ . "Mouse gross anatomy and development, timed" . "ChEMBL database of bioactive drug-like small molecules - Cell lines section" . "ASPL0000349247"^^ . . "http://purl.uniprot.org/uniprot/"^^ . . . "iev" . "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."^^ . . . . "4DNESWX1J3QU"^^ . . "false"^^ . . . . . "http://purl.obolibrary.org/obo/GOREL_$1"^^ . "LipidBank" . . . . _:N5b392927e055404abdb4f9a091809e81 "Edd Wilder-James" . . . . . . "false"^^ . . "false"^^ . . . . . "FlyBase Controlled Vocabulary" . . . . "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."^^ . . . "false"^^ . . "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."^^ . "biozy@ict.ac.cn" . . "Minimum PDDI Information Ontology" . . "development" . "http://www.kegg.jp/entry/$1"^^ . "resource metadata" . . "H00076"^^ . "rebase" . . . . . . "plant phenotypes and traits" . . . . . . "cell biology" . . "miRBase pre-miRNA" . . . . . . . . . "iRefWeb" . "ontology" . "knowledge and information systems" . . . . "false"^^ . "translational medicine" . "patient care" . . . . "ctd.chemical" . . "The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals."^^ . . "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . . "wos.researcher" . . . . . . . "pgs" . . "false"^^ . . . . . . "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible."^^ . . . . . "National Center for Biotechnology Information Registry" . . "^.{2,}$"^^ . "Ontology for the Anatomy of the Insect SkeletoMuscular system" . . . . . "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . . . . "Database of protein-protein complexes" . . . . "bspo" . . . "degradome" . . . . "false"^^ . "false"^^ . . "http://www.pantree.org/node/annotationNode.jsp?id="^^ . "http://lincsportal.ccs.miami.edu/cells/#/view/$1"^^ . "false"^^ . "ontology" . "https://www.authorea.com/users/$1"^^ . "0007807"^^ . . "hathitrust" . "obv" . "https://www.drugbank.ca/categories/$1"^^ . . "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^ . . . . "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . . . "protonet.cluster" . . . . "https://www.pharmvar.org/gene/"^^ . "^[\\w\\-:,]{3,64}$"^^ . "publishing" . "false"^^ . . "HPSI0114i-bezi_1"^^ . "^\\d+$"^^ . . . "https://www.deciphergenomics.org/syndrome/"^^ . . . . "genome" . "Amphibian gross anatomy" . . "true"^^ . . . . . . "basic research" . "https://www.kegg.jp/entry/"^^ . . . . . . . . . . . "emea" . . "http://purl.obolibrary.org/obo/ECO_$1"^^ . . . . "alzheimer's disease" . . "bootstrep" . . "GiardiaDB" . "http://purl.bioontology.org/ontology/IDODEN_"^^ . "false"^^ . . . . "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"^^ . . . . . . . . . . . "pathway model" . . "XB-GENE-922462"^^ . . . . . "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . . . . "^[AEP]-\\w{4}-\\d+$"^^ . "genomics" . . . "transcriptomics" . . "gmd.profile" . "TAIR Gene" . . . "strain" . "false"^^ . . "anatomy" . . "http://metlin.scripps.edu/metabo_info.php?molid=$1"^^ . . . . . . "https://lov.linkeddata.es/dataset/lov/vocabs/$1" . . . "disease" . "aeo" . "^\\d{7}$"^^ . . "doap" . "false"^^ . . "0000019"^^ . . . . . . "^\\d+$"^^ . "https://pathbank.org/view/$1"^^ . "https://www.ebi.ac.uk/ega/studies/$1"^^ . . . . "ontology" . . . . "chemistry" . . "cooperl@oregonstate.edu" . "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. "^^ . . "SIDER Drug" . "https://pypi.org/project/"^^ . "GR_QTL" . . . . . . . . "4779"^^ . . . "82"^^ . . "false"^^ . . . . "glycopost" . . . . . . "false"^^ . "5.A.1.1.1"^^ . . . . "RepeatsDB Protein" . . "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. "^^ . "https://cropontology.org/rdf/CO_338:$1"^^ . . . . "http://edamontology.org/data_"^^ . _:N48711611788a42118df926abee2adc7e "vlee@ebi.ac.uk" . "https://www.hipsci.org/lines/#/lines/$1"^^ . . . . . "citlalli.mejiaalmonte@gmail.com" . . "DisProt" . . . . . . . "oceanography" . "http://purl.unep.org/sdg/SDGIO_"^^ . "MSMEG_3769"^^ . "animal genetics" . "0745-4570"^^ . . . "structural biology" . . "disease" . . . . . . . . . . "http://purl.obolibrary.org/obo/CL_"^^ . "false"^^ . . . . "https://www.ebi.ac.uk/metabolights/"^^ . . . . . "Complex Portal" . . "phylogenetics" . "kegg.brite" . . . . "http://purl.obolibrary.org/obo/ECTO_$1"^^ . . "rgd.qtl" . . "ontology" . . . "false"^^ . . "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term="^^ . . "obo" . . . . . . . . . "false"^^ . . . . . . . "90000018"^^ . . . . "http://www.ncbi.nlm.nih.gov/clinvar?term="^^ . . . . . "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name="^^ . "http://purl.obolibrary.org/obo/UO_$1"^^ . . "false"^^ . "00000001"^^ . "neurovault.collection" . . . . . "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . "chemistry" . . . "The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)"^^ . . "^\\d+$"^^ . "numpy"^^ . . "CranioMaxilloFacial ontology" . "re3data" . "HGNC_GROUP" . "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . "https://panoramaweb.org/$1.url"^^ . . . . "ExAC Variant" . . "https://hamap.expasy.org/unirule/"^^ . "^[0-9a-z]{24,24}$"^^ . . . . . "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."^^ . . "false"^^ . . "0000066"^^ . . . . . "https://europepmc.org/article/CBA/$1"^^ . . . . "comparative genomics" . . . "pmr.workspace" . "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1"^^ . "Cell Version Control Repository" . . . . . . "nih initiative" . . . "https://cropontology.org/rdf/CO_333:$1"^^ . . . . . . "Ontology"^^ . . "^\\d+$"^^ . . "^[A-Za-z 0-9]+$"^^ . . . "OMIT" . "antibodies" . . "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1"^^ . "atsushi.yoshiki@riken.jp" . . . . "00000003"^^ . "drug report" . "ontology" . "AD834"^^ . . "00011461"^^ . . "radiology" . . "epidemiology" . "false"^^ . . . "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"^^ . "0000013"^^ . . . . "disease phenotype" . . "Gramene protein" . . "study design" . . . "Friend of a Friend" . "141"^^ . . . . . . . . "21552"^^ . . . . "VMH reaction" . . . "life sciences" . "human disease model" . "false"^^ . . . "^T[A-Z]\\d{7}$"^^ . . . . "http://purl.obolibrary.org/obo/PPO_"^^ . . "life science" . "http://www.pocketome.org/files/$1.html"^^ . "Medical Subject Headings Vocabulary" . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models."^^ . . . . "Genetic Testing Registry" . "bioregistry.registry" . "https://lincs.hms.harvard.edu/db/cells/"^^ . . . . "false"^^ . . . . . "elspeth@genenames.org" . "https://www.ncbi.nlm.nih.gov/research/cog/pathway/"^^ . . "Selventa Chemicals" . "glycomapsdb" . "genome" . . . "Spencer L. Liem" . "geno" . . . "100810"^^ . . . . . . . "Regulation of Gene Expression"^^ . "classyfire" . . "This collection contains various brain atlases from the Allen Institute." . "TreeFam" . "informatics" . _:Ndaf89a6d2d0e49adbd980a31067be76b . "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^ . "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . "AgentIdentifierScheme"^^ . . . "genefarm" . . . . . "uspto" . . . "http://gmd.mpimp-golm.mpg.de/Analytes/"^^ . "^\\d{7}$"^^ . "kegg.enzyme" . "SwissLipid" . . . . "nathan.baker@pnnl.gov" . . . "expression data" . "^\\d{7}$"^^ . "https://www.sharkipedia.org/species/"^^ . . "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."^^ . . . . . . . "false"^^ . . . "annotation" . . "surjeet.arya@uky.edu" . . . "knockout" . "experimentally determined" . . "life science" . . "Wikipedia" . . . . . . "https://www.webelements.com/$1"^^ . "Variants in dbVar."^^ . . "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^ . . "Ontology for MicroRNA Target" . . "Jakob Voß" . "0000210"^^ . . . . . "http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1"^^ . . . . "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"^^ . . . . "infection" . . "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"^^ . . . "NA06985"^^ . . . . "mutant" . _:Nda4b00b3f12f4bfd971f6d6f4b0a245e . . . . . . . . . . "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n"^^ . . "neuroscience" . "PMID" . . . . . . . "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . . . . . . "INSDC CDS" . . . . . "^\\d+$"^^ . "http://aims.fao.org/aos/agrovoc/c_$1"^^ . "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId="^^ . "false"^^ . "sgn" . . "chemistry" . . "WD_Entity" . "ribonucleic acid" . . . . . . "metabolites" . . . . . . . "genomics" . . . "agb@ebi.ac.uk" . "inchi" . . "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . . . "modeling and simulation" . . "https://biocomputeobject.org/BCO_$1"^^ . . . "Beet Ontology ontology" . "^\\w+$"^^ . . . . . . "http://genome.crg.es/datasets/abs2005/entries/$1.html"^^ . _:Nf2d21872f7394647b8dfa7a0fb81329b "chebi-help@ebi.ac.uk" . . "http://purl.obolibrary.org/obo/CTENO_"^^ . . . "sequence annotation" . "Minimal Information about any Sequence" . "human" . "^PA\\d+$"^^ . . . "tropicalis" . . . "^jRCT\\w?\\d+$"^^ . . "https://flybase.org/reports/FBrf"^^ . . . "anatomy" . . . "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . . . "125768"^^ . . . . . . . "^\\w+$"^^ . . . "obo" . "curies"^^ . "preclinical studies" . . . "http://hawaii.eagle-i.net/i/$1"^^ . . . . "Gene"^^ . . "person" . . "false"^^ . . . "MultiCellDS Digital snapshot" . "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms"^^ . "sequence" . . "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1"^^ . "Australian New Zealand Clinical Trials Registry" . . . . "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."^^ . . . "mgiglio@som.umaryland.edu" . . . . . . . . . . "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . . "http://purl.org/oban/$1"^^ . . "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#"^^ . . . . . . . "false"^^ . "http://www.signaling-gateway.org/molecule/query?afcsid="^^ . . "Structural Classification of Protein - Stable Domain Identifier" . . "https://packagist.org/packages/$1"^^ . "false"^^ . . . "mass spectrum" . . . . "true"^^ . . . . . . "^\\d+$"^^ . . "0001707"^^ . "moid" . . "^\\d+$"^^ . . . . . . . . . . . "false"^^ . . . "false"^^ . "life science" . "dna" . . "4390079"^^ . . . "https://nsrrc.missouri.edu/nsrrc$1info/"^^ . . "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains."^^ . . "^\\d{7}$"^^ . "46"^^ . "https://registry.identifiers.org/registry/$1" . "hgnc.symbol" . "bgee@sib.swiss" . "orchard@ebi.ac.uk" . "^\\d+$"^^ . "ontology" . "https://go.drugbank.com/salts/"^^ . "0000199"^^ . . "ror" . "false"^^ . . . . . . . . . . . . . "rcb" . . . "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . "environmental material" . . . . . "National Drug Data File" . "1537"^^ . "true"^^ . . . "false"^^ . . . "https://doi.org/$1"^^ . "ontology" . "^\\d+(\\w+)?$"^^ . _:N43f83568a25046bf8a71ecab5ee22c10 "hajo.rijgersberg@wur.nl" . . . . . . "false"^^ . . . . . . . . . "statistics" . . . . . . "nuclearbd" . . . . . . "false"^^ . . . . . "3305"^^ . "MeSH 2013" . . . . . . . . "pictar" . . . . "genome-wide association study" . . . . "false"^^ . "Cell Biolabs cell line products" . "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^ . . . "https://www.ebi.ac.uk/pride/archive/projects/"^^ . . "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."^^ . . . _:N59ec4859e5af4b8a8c7745d7bd426805 "helpdesk@cropontology-curationtool.org" . "CAS Registry Number" . "lbctr" . . . "ontology" . . . "InChIKey" . "98346"^^ . . "http://purl.obolibrary.org/obo/AERO_$1"^^ . . . "^\\w+$"^^ . . . "false"^^ . . "^HBG\\d+$"^^ . "http://purl.bioontology.org/ontology/VANDF/$1"^^ . "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."^^ . "A vocabulary about species to support the environmental research community in Arizona and New Mexico"^^ . . . . "statistics" . . . "molecular dynamics" . "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."^^ . . "kaken" . "regulation" . . . . . "HUMAN16963"^^ . . . "false"^^ . "http://purl.org/spar/pwo/$1"^^ . "https://bioregistry.io/chemspider:"^^ . "health science" . "Close to 5K Categorizations for drugs, similar to ATCC."^^ . . "dggr" . "bsu:BSU01340"^^ . . . "^\\d{7}$"^^ . "2029"^^ . . . "International Classification of Diseases, 9th Revision, Clinical Modification" . . . "https://easychair.org/cfp/topic.cgi?tid="^^ . . . "^\\d{4}$"^^ . . "iECABU_c1320"^^ . . "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."^^ . "molecular entity" . . . . . . . "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1"^^ . . . . "gramene.reference" . . . . . . . . "ird.segment" . . "histology" . . . "biology" . "Berkeley Drosophila Genome Project EST database" . "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."^^ . "domain" . . . "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1"^^ . . . . . "^CLPUB\\d+$"^^ . . "proteomics" . . . . . . . "intervention design" . . "true"^^ . "https://biopragmatics.github.io/providers/goche/"^^ . . . . "Environmental Molecular Sciences Laboratory Project" . "civic.mpid" . . . . . . . "false"^^ . . "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'."^^ . "ontology" . . . . . "Korean Cell Line Bank" . . "Epidemiology Ontology" . "The S/MAR transaction DataBase" . . . "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . . "^.*/.*$"^^ . . . . "data coordination" . "comparative genomics" . . . "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."^^ . . . . . . . . . . "http://purl.org/spar/c4o/$1"^^ . . "ontology and terminology" . . "https://www.clinicaltrials.gov/study/$1"^^ . . . . . . . . . "sabiork.compound" . "0000000"^^ . "AOPWiki (Stressor)" . . "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . . "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . . . . . "false"^^ . . "https://www.xenbase.org/entry/$1"^^ . . "false"^^ . "obo" . . "Hazardous Substances Data Bank" . . . . . "https://cropontology.org/rdf/CO_330:"^^ . . . . . . . . "grassbase" . . . "chemistry" . . "^\\d{7}$"^^ . "GWAS Central Marker" . . "druzinsk@uic.edu" . . "false"^^ . . "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/"^^ . "nif.ext" . "GnpIS" . . "0001"^^ . . "identifiers.namespace" . . "TDR" . . . . . . "ontology" . "false"^^ . . . "https://eol.org/pages/$1"^^ . "sasap" . "obo" . . . "treefam" . "molecules" . "molecular biology" . . . . . . . . . "behavior" . . . . . . . . . . "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^ . . "http://purl.obolibrary.org/obo/IAO_"^^ . . "YMDB00001"^^ . "https://biopragmatics.github.io/providers/goche/$1"^^ . . . . . "false"^^ . . "https://www.ebi.ac.uk/intact/search?query="^^ . "botany" . . "22-46615880-T-C"^^ . . . "UniProt Isoform" . . . "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . "brenda.ligandgroup" . . . "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^ . . "genome" . "false"^^ . . "http://purl.unep.org/sdg/SDGIO_$1"^^ . . . "co_357" . . "PubChem Cell Line" . "^\\w+$"^^ . . . . "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^ . "true"^^ . "casspc" . . . . . "false"^^ . "An identifier for a country in numeric format per ISO 3166-1"^^ . "Tuan Amith" . . . . "kerafast" . . . "false"^^ . "life science" . "mathematics" . . . . "http://purl.obolibrary.org/obo/CARO_"^^ . . . "phylogeny" . . . "GLIDA Ligand" . . . "CAID" . . . . "false"^^ . . "false"^^ . . . . "genome" . . "sigmaaldrich" . . . . . . . . . . "botany" . . . . . . "Jian Huang" . "^(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+)?)$"^^ . "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."^^ . _:N1076b2d9be5147cf89a9a0301e03ce05 "Qiong Gu" . "http://www.cellresource.cn/cellsearch.aspx?sc=1&where="^^ . . . "data model" . "https://cropontology.org/rdf/CO_343:"^^ . "http://purl.obolibrary.org/obo/EHDA_"^^ . . . "ssrn.article" . "https://www.clinicaltrialsregister.eu/ctr-search/search?query="^^ . . . . . . . "ddinter.drug" . . "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)"^^ . . . . "https://comptox.epa.gov/dashboard/"^^ . . . . . "Joachim Kopka" . "life cycle stage" . . . . "Integrated Resource for Domestic Dog" . . . . . "https://biopragmatics.github.io/providers/icepo/$1"^^ . "https://www.gwascentral.org/study/$1"^^ . "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue."^^ . . . "NONHSAT000001"^^ . "MolBase" . "false"^^ . "hog" . . . . . "inaturalist.place" . . . "dictybase.est" . . . "^\\S+$"^^ . "http://cerevisiae.oridb.org/details.php?id=$1"^^ . . "biology" . . "^S\\w+(\\.)?\\w+(\\.)?$"^^ . . "http://virtualflybrain.org/reports/"^^ . . . . "clinvar.record" . "bioinformatics" . . "life science" . _:N32a7802dd61f4d89a5051c6f2cc5c28d "LOINC Support" . . . . . . . . "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."^^ . . "genetics" . . . "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1"^^ . . . "false"^^ . "jla1@sanger.ac.uk" . . . . "https://publons.com/publon/"^^ . . . . "https://biopragmatics.github.io/providers/peff/$1"^^ . "Pan African Clinical Trials Registry" . . . "false"^^ . . "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis."^^ . "glida.gpcr" . "An experimental run, served thrugh the ENA"^^ . . . "ctgov" . "metascience" . "^MAM\\d{5}\\w$"^^ . "^\\d+$"^^ . "ontology" . . "Cell line collections (Providers)"^^ . . . . . . . . "LG Chemical Entity Detection Dataset (LGCEDe)" . . . . . "https://disprot.org/"^^ . . . . . . . . . "http://purl.obolibrary.org/obo/DINTO_"^^ . . . . "pesticideinfo" . . . . "Fabrice Legeai" . . . . "owl" . . "http://purl.obolibrary.org/obo/ZECO_"^^ . . "protein" . "https://civicdb.org/links/gene/"^^ . "obo" . . . "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."^^ . . . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code="^^ . . . "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."^^ . . "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."^^ . . . "obo" . "pharmgkb.drug" . "SNOMEDCT_US_2023_03_01" . . . . . . . . "edgar.wingender@edgar-wingender.de" . "proteins" . "http://aber-owl.net" . . . . . "Interlab Cell Line Collection" . . . . "shareloc" . . . "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."^^ . . . . "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."^^ . . "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . . "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion."^^ . . . "ikufareva@ucsd.edu" . "BioCatalogue Service" . . . "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query="^^ . . "protein" . . . . . . . . . . . . . . . . "OMIMPS" . "^[A-Za-z_0-9]+$"^^ . . . . . . "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."^^ . "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.\n\nODAM allows datasets to be explored and then extracted in whole or in part as needed.\n\nFor more information/explanation, see ODAM User's Guide : https://inrae.github.io/ODAM/"^^ . . . . . . . "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . . "NXPFA" . . . "dsm4" . . . . "Sabrina@tislab.org" . . "https://stemcells.nindsgenetics.org?line="^^ . . "http://w3id.org/nkos/$1"^^ . "ontology" . . "imedvedeva@celgene.com" . . "KEGG DRUG" . . . . . "DUO is an ontology which represent data use conditions."^^ . "http://igsn.org/"^^ . . . . "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . "natural language processing" . "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"^^ . . . . "SPIKE Map" . . "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . . . . . "Collembola Anatomy Ontology" . . . "false"^^ . . . . . . "pharmacogenomics" . "https://www.iedb.org/reference/"^^ . . . "neurophysiology" . . . . "genome" . . . "NIF Standard Ontology: OEN Terms in Neurolex" . "Genetic and Rare Diseases Information Center" . . "c0000005"^^ . . . "drug" . . "Genome assembly database - RefSeq accessions" . . "https://registry.identifiers.org/registry?query=MIR:$1"^^ . "physiology" . "http://purl.obolibrary.org/obo/PCO_"^^ . . . "insertion" . . "ontology" . "^DAP\\d+$"^^ . . . . . . . . "Sequence types and features ontology" . "food" . "pathway" . . _:Nc2bec7c24f884185b2e565c05857a9af . "KEGG Orthology" . . "plant" . . "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."^^ . . . . . . . . . . "obo" . "false"^^ . . . "http://purl.obolibrary.org/obo/AGRO_$1"^^ . . . "http://www.chemspider.com/inchikey=$1"^^ . . "Degradome Database" . . . . . "bsweeney@ebi.ac.uk" . "^(T0\\d+|\\w{3,5})$"^^ . . . . . . "false"^^ . "70"^^ . . "noncodev4.rna" . "true"^^ . . "000017"^^ . . . . . "31253.11.sciencedb.j00001.00123"^^ . . . "cardiology" . "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . "RxNorm" . "Idan Gabdank" . . "classification" . . . . "A repository of software packages written in Rust."^^ . . . "pharmacy" . "Collection"^^ . . . . "provides for" . . . . . . . . . "4685"^^ . . "^\\d{7}$"^^ . . . . "Datanator Reaction" . "oryzabase.strain" . "Affymetrix Probeset" . "CIViC Molecular Profile" . . "ClinVar Submission" . "vocabularies" . "false"^^ . . "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes."^^ . . . . "^2\\d{4}$"^^ . "241"^^ . . "erm" . . . "6978836"^^ . "chebi" . "gene" . "https://www.uniprot.org/uniprotkb/$1"^^ . "Human Gene Mutation Database" . "Genetics Home Reference" . "Ax1"^^ . . . . "http://www.w3.org/ns/odrl/2/$1"^^ . . "spar" . "alan.bridge@isb-sib.ch" . . "bioinformatics" . . . . "An ontology to support comparative effectiveness researchers studying claims data."^^ . "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."^^ . . "https://www.biozol.de/en/product/$1"^^ . . . . "false"^^ . "protein" . "https://cropontology.org/rdf/CO_365:$1"^^ . "plant phenotypes and traits" . "Dataset"^^ . "cell" . "disease" . . "80001"^^ . "ontology" . . . . "M94112"^^ . . "https://cordis.europa.eu/article/id/$1"^^ . "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . . . "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."^^ . . . . "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)"^^ . . . . "Decentralized Biomedical Ontology" . "http://qudt.org/schema/qudt#"^^ . "genome" . "false"^^ . "ppdb@gifu-u.ac.jp" . . "Babelon" . "RNACentral" . . "gene" . . . "false"^^ . . "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."^^ . "obo" . . "https://drugs.ncats.io/drug/$1"^^ . . "https://aopwiki.org/events/$1"^^ . "Metabolites in drugbank"^^ . . . . "protein" . "GCF_000005845.2"^^ . "knowledge representation" . . "^\\d+$"^^ . . "Cephalopod Ontology" . . . . "ontology" . . "behavior" . "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."^^ . "Proteomic Data Commons" . . . . "protein" . . . . "1.1.1.1"^^ . . "4"^^ . . . . "drosophila" . "Basic Formal Ontology" . "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^ . . . . . "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue="^^ . . . . . . . "nfdi4chem.osmo" . _:N00fbffe88ffd4a7ca35a8319997b0f2c "helpdesk@cropontology-curationtool.org" . . . . "^\\w\\d+$"^^ . . . . . . . . . "nrfc" . . "Jeffrey Wong" . "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."^^ . "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"^^ . . . . "teri.klein@stanford.edu" . . . "http://hdl.handle.net/"^^ . . "hemonc" . . . . "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."^^ . . "https://viralzone.expasy.org/$1"^^ . . "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^ . . "CO_325" . "taxonomy" . "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . . "NeuroLex Dysfunction" . . . . . . "https://biopragmatics.github.io/providers/hog/$1"^^ . . . "COL3A1"^^ . . . "^HGVST\\d+$"^^ . "EC number" . . . . "Search the world's most comprehensive index of full-text books."^^ . . "Clinical Trials Ontology" . . . . "^\\d+$"^^ . . . . "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters."^^ . "life science" . "structural biology" . . "146421"^^ . . . . "^\\d+$"^^ . . "protein" . "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."^^ . "life science" . . "AKR-270"^^ . "http://www.vbase2.org/vgene.php?id="^^ . . . "Carrine Blank" . "Product number for the European Medicines Agency"^^ . "^\\d{7}$"^^ . "Data Object Service" . . "^\\d+$"^^ . . "false"^^ . . "cognitive neuroscience" . "AB" . . . "1001"^^ . . "^\\d{7}$"^^ . "ordo.orphanet@inserm.fr" . . . . . "Teri E Klein" . . . . . . . . . "ontology" . "https://www.probes-drugs.org/compound/$1"^^ . . . "phipo" . . "The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF." . "false"^^ . . . . . . "RPCEC00000423"^^ . . "disease" . . "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]"^^ . . . "https://odc-sci.org/data/$1"^^ . "http://ctdbase.org/detail.go?type=chem&acc="^^ . . "tokue" . . . "rare disease" . "Entrez Gene" . . . . . "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . . . . "frbrer" . "https://dblp.org/pid/$1"^^ . . "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature="^^ . "^[1-9]\\d*$"^^ . . . "lectins/172"^^ . . . "http://viaf.org/viaf/$1"^^ . . . . "oridb.sacch" . . . . . . . "chemidplus" . . . . "medicine" . "ontology" . . "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . "genomics" . . "100010"^^ . . "https://www.mlcommons.org/mlc-id/$1"^^ . . "diseasesdb" . . . . "false"^^ . . "Will Simpson" . . "cell biology" . "subject agnostic" . . . . . . . "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id="^^ . . "hgnc.genefamily" . . "Steven E. Wilson" . "ontology" . . . . "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . . . "^[A-Za-z_0-9]+$"^^ . . . . . . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/GSSO_"^^ . . "Units of measurement ontology" . . "true"^^ . . . "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . . . "help@emdatabank.org" . "^\\d+$"^^ . . "https://mips.helmholtz-muenchen.de/corum/?id="^^ . . . . . "false"^^ . _:Nd4dc91a8bb1b4baa908fd11571ec0cba "Frédérick Giasson" . "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."^^ . . . . . . "ricenetdb.compound" . . . "swo" . "siren" . . . "false"^^ . "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . . "https://meshb.nlm.nih.gov/record/ui?ui="^^ . "Bio-Pesticides DataBase" . . . "laia.subirats@gmail.com" . . "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . . . . . . "mutant mouse strain" . . . . "imsr_tac" . . . "Medical Data Models" . . "emap" . . . "^\\d+$"^^ . "hsdb" . "http://ratmap.org/Showgene.php?gene_stable_id=$1"^^ . . "dc.elements" . "identifier for an author at the Social Science Research Network"^^ . . . . "virology" . . . . . . "false"^^ . "deepak.unni3@lbl.gov" . "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_"^^ . "obo" . "AY209920"^^ . . . . "teresa.k.attwood@manchester.ac.uk" . . . "hao" . "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . "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."^^ . . . "http://www.alanwood.net/pesticides/$1.html"^^ . . "NeuroLex Anatomy" . "signaling" . "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . . . . . . . . . . . . . . . . . . . "https://www.arraymap.org/pgx:$1"^^ . "EAWAG Biocatalysis/Biodegradation Database" . . . . . "http://purl.obolibrary.org/obo/PPO_$1"^^ . "false"^^ . . . . . . . "http://edamontology.org/operation_"^^ . . . . . . . . . . . . . "spar" . "life cycle stage" . . . . "Simple Knowledge Organization System" . . . "dna" . "EOL Secretariat" . . . . "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations."^^ . . . "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No="^^ . "clustering" . "https://easychair.org/cfp/"^^ . "https://metazoa.ensembl.org/id/$1"^^ . . . "funderregistry" . "veterinary medicine" . "OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . "https://cropontology.org/rdf/CO_323:"^^ . . "^\\d+$"^^ . "botany" . . "UniProt Post-Translational Modification" . . . "general & upper" . . . . . "false"^^ . . . "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^ . . . "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . . . . . . . . "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1"^^ . . . "ontology" . . . . . . . . "E-cyanobacterium entity" . . . . "1667659"^^ . . "https://swbiodiversity.org/seinet/taxa/index.php?taxon="^^ . "person" . . "hancestro" . "Human Cell Atlas Ontology" . . . . . . "false"^^ . . . "051"^^ . . "Janna Hastings" . . . . . "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . . . "https://scicrunch.org/resolver/RRID:NXR_"^^ . . "Malachi Griffith" . . . . "https://www.kegg.jp/entry/"^^ . . . . "life science" . "http://purl.obolibrary.org/obo/CHEBI_"^^ . . "^\\d+$"^^ . "TriTrypDB" . . . . "Conferences in EasyChair"^^ . "ontology" . "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession)." . "https://herv.img.cas.cz/s/"^^ . "Cell line collections (Providers)"^^ . . . . . . "rna" . . . "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . "BP100000"^^ . . . . "https://www.metanetx.org/equa_info/"^^ . . . . . "13"^^ . . . . . . . "Consensus CDS" . . . . "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID="^^ . . "http://purl.org/cerif/frapo/$1"^^ . . . . . . "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"^^ . . . . . . . . . "PyPI" . . . "uniprot.journal" . "^DDInter\\d+$"^^ . . "0000252"^^ . "^S\\d+$"^^ . "00573"^^ . "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID="^^ . "http://purl.obolibrary.org/obo/OBCI_$1"^^ . "false"^^ . . . "http://sweetontology.net/matrMineral/$1"^^ . "gene" . . . . . "Yeast Deletion and the Mitochondrial Proteomics Project" . . "life science" . "Matthias König" . . . . . "https://w3id.org/faircookbook/$1"^^ . . "food" . . . . "biocarta.pathway" . "identifier for a scientific journal, in the UniProt database"^^ . "false"^^ . . "hovergen" . . . . . "lncipedia" . "Ioannis Xenarios" . "true"^^ . "cheminformatics" . "centrally registered identifier" . . . . . . "biomedical science" . . "gene" . . . . . . "SR0000178"^^ . "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)"^^ . . . . . "http://purl.org/spar/pwo/"^^ . . . "http://purl.jp/bio/4/id/$1"^^ . "http://classyfire.wishartlab.com/tax_nodes/C"^^ . . "true"^^ . . "computer science" . . "^\\d(\\d|\\w)$"^^ . . . . "Assembling the Fungal Tree of Life - Category" . "false"^^ . "UniProt Variants" . . . . . . . . "false"^^ . . . . . "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3"^^ . . . "report" . . . . "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."^^ . "gold standard" . . . "^\\d{7}$"^^ . . "sweetrealm" . "adeans@psu.edu" . "splash" . . . . "zfa" . . . . . . . . . . "http://isbndb.com/search-all.html?kw=$1"^^ . . " The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies.\n\nIn 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)"^^ . "bco" . . . "disease" . "https://bioregistry.io/dashr.expression:"^^ . "false"^^ . . . . . . . . "has URI prefix" . . . . "^\\d+$"^^ . "ontology" . . . . . "Regulation of Transcription Ontology" . . "life science" . "molmedb" . "^OSC\\d{4}$"^^ . "ontology" . . . "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value="^^ . "false"^^ . "linguistics" . . . "uniprot.chain" . . "nucleotide" . "431472"^^ . "Authenticus ID" . "false"^^ . . "functional genomics" . . . . . "kegg.compound" . . "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"^^ . "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^ . . . . . . . "false"^^ . "^EGAD\\d{11}$"^^ . . . . . . "exposure" . . . "^\\d{7}$"^^ . . . "mba" . . . "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1"^^ . . . "citation" . . . . . "Lindsey N. Anderson" . . . "https://bioregistry.io/flybrain.ndb:"^^ . "OpenCitations Meta Identifier" . . . "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . "^\\w{1,3}$"^^ . . . . . . "^TF\\w+$"^^ . "feolo@ncbi.nlm.nih.gov" . . . . . . "https://gnomad.broadinstitute.org/variant/$1"^^ . . "false"^^ . . . "Mammalian Phenotype Ontology" . "false"^^ . "National Bibliography Number" . "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . "pharmacogenomics" . . . . . . . . . . . "nkos" . "agriculture" . . "ligea" . "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."^^ . . . "nhcdr" . . "repeatsdb.protein" . . . . "Open Researcher and Contributor" . . "https://scicrunch.org/resolver/RRID:NXR_$1"^^ . "fbsp" . . . "gfo" . . . . "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1"^^ . . . "PTPN1"^^ . . "https://hub.docker.com/u/$1"^^ . "A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis."^^ . . "NCI Data Commons Framework Services" . "morphology" . . . . . . . "MNXM1723"^^ . . "small molecule" . . . . "isrctn" . "phenotype" . . . . . . . "The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format."^^ . . "https://pdc.cancer.gov/pdc/study/"^^ . "resource metadata" . . "AA0001"^^ . . "^\\d+$"^^ . . "annotation" . "http://www.w3.org/ns/rdfa#"^^ . "dna" . . . . . "genomics" . . . . "https://licebase.org/?q="^^ . "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^ . . "false"^^ . . . . "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082"^^ . . . "MarRef" . . _:N1076b2d9be5147cf89a9a0301e03ce05 . . . . . . "genome" . "Jaime Huerta-Cepas" . "Chemical Information Ontology" . "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^ . "gomf" . "chemical" . "repository" . . . . . . . . . . . "trnadbce" . . . "biological sample" . . "^\\d+$"^^ . . "001"^^ . "wormbase" . "https://commonchemistry.cas.org/detail?cas_rn="^^ . "cattleqtldb" . "https://lincs.hms.harvard.edu/db/sm/$1"^^ . . . "false"^^ . "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER."^^ . . . . . . . "KEGG.COMPOUND" . . . . . "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . "false"^^ . . . "strain" . . . . . . "A representation of the variety of methods used to make clinical and phenotype measurements."^^ . "interaction" . "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas="^^ . . "biochemistry" . . "phosphosite.curation" . . . . . . . "obo" . . "ontology" . . "plant breeding" . . . "true"^^ . . . "biomedical science" . "^\\d{7}$"^^ . . . . "https://w3id.org/oc/oci/$1"^^ . . . . "people" . . . . . "false"^^ . "plant phenotypes and traits" . . "CAPS-DB" . "Elementary Multiperspective Material Ontology" . "https://biopragmatics.github.io/providers/icepo/"^^ . . . . . . . "https://www.pesticideinfo.org/chemical/"^^ . "fypo" . "faseb list" . . . "polbase" . "RL3R1_HUMAN"^^ . "Identifier for a species on the noaa fisheries website"^^ . . . . "dietary restriction" . . "^\\d{7}$"^^ . "data model" . . "enzymology" . . "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"^^ . . "metascience" . "http://dictybase.org/gene/$1"^^ . . . . . . . "^[A-Za-z0-9]+$"^^ . "https://www.nextprot.org/term/FA-"^^ . "24801"^^ . . . . . . . . . "Plant Growth and Development Stage" . "^spike\\d{5}$"^^ . "false"^^ . "agriculture" . "https://rnaloops.cs.put.poznan.pl/search/details/"^^ . "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."^^ . "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object="^^ . . . "Description of a Project" . . "mimodb" . . . "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."^^ . . . "http://data.food.gov.uk/codes/foodtype/id/$1"^^ . . "sdap" . "true"^^ . "https://www.ncbi.nlm.nih.gov/nucleotide/"^^ . "UniProt journal" . "http://www.proteinmodelportal.org/query/uniprot/$1"^^ . . "microbiology" . "botany" . "food" . "nbdc01071"^^ . . "0000411"^^ . . "^\\w+$"^^ . . . . "ruili.huang@nih.gov" . "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . "^\\d{7}$"^^ . . . "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . . . "MolMeDB" . . . "life cycle stage" . . "bibo" . . "mhb120@gmail.com" . . "TGME49_053730"^^ . "earth science" . "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites."^^ . . "^\\d+$"^^ . . "^\\d+$"^^ . . . . . "The cell line vocabulary inside FlyBase"^^ . . . "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"^^ . . . "patient care" . . "bibliography" . . . "obo" . . "Life cycle stages for Platynereis dumerilii"^^ . "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . "loggerhead" . . . "genbase" . "kegg.genome" . "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^ . . . . . . "ontology" . "FB" . "false"^^ . "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . . . . "https://tetrahymena.vet.cornell.edu/display.php?stockid="^^ . . . "semantic web" . "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"^^ . . "gene" . "life science" . "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases."^^ . "Ilene Karsch-Mizrachi" . "https://flowrepository.org/id/$1"^^ . "protein" . "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . . . . "metabolomics" . "openalex" . . . . "https://www.inaturalist.org/users/$1"^^ . "bactibase" . "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki."^^ . "^\\w{14}$"^^ . "278"^^ . . . "http://www.bioguo.org/AnimalTFDB/family.php?fam="^^ . "ucas" . . . "health science" . . . "^\\d+$"^^ . "radiology" . . "0000001"^^ . "ordb" . "https://osf.io/$1"^^ . "rsankar@iitk.ac.in" . "longevity" . "obo" . "LNCRNADB" . . . . . . . "false"^^ . . . . "structrual bioinformatics" . . "false"^^ . . . . "^[0-9]+$"^^ . "false"^^ . . "dna" . . . "embryonic stem cell line" . "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."^^ . "AAC"^^ . . . . "0376"^^ . . "^\\d{7}$"^^ . "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC="^^ . . "^\\d+$"^^ . "https://prefix.cc/$1" . . . . . . . . . . . . . . "protein" . . "taxonomy" . . "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id="^^ . . . . . . . "https://www.pombase.org/gene/$1"^^ . . "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."^^ . "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . . "uniprot.var" . . . "http://purl.obolibrary.org/obo/PD_ST_"^^ . "NIH Human Embryonic Stem Cell Registry" . . "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."^^ . . . . . "functional genomics" . "https://data.4dnucleome.org/experiment-set-replicates/"^^ . . . . "iso.3166" . . "false"^^ . "https://flybase.org/reports/$1"^^ . . "ontology" . . "gene" . "http://ctdbase.org/detail.go?type=gene&acc="^^ . "false"^^ . . . . . . "Healthcare Common Procedure Coding System" . . "pancreatic islet" . . "SNOMED_CT" . . . . . . . . . . . . "^\\d{4,}$"^^ . . . . . . . . "^\\d{7}$"^^ . . "PMC3084216"^^ . . . . . . . "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"^^ . "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line="^^ . "http://bigg.ucsd.edu/models/universal/reactions/"^^ . "C34"^^ . "pancreatic development" . . . "dblp.author" . "http://www.hgmd.cf.ac.uk/ac/gene.php?gene="^^ . . _:Na743319970e34828867a0aede14ed149 "slarson@ncmir.ucsd.edu" . "epidemiology" . "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser."^^ . "organ" . . . . . . "^\\d+$"^^ . . . "dockerhub.user" . . . . "false"^^ . . . "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$"^^ . "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."^^ . "human" . "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."^^ . . . "http://purl.obolibrary.org/obo/TRANS_$1"^^ . . "true"^^ . . "https://flowrepository.org/id/"^^ . "^\\d{4}-\\d{3}[\\dX]$"^^ . . . "OSR0818"^^ . "genome" . . . . "experimental measurement" . . . . "SNOMEDCT_US_2018_09_01" . "identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/)"^^ . . . "ndfrt" . . . . . "Wojciech M. Karlowski" . . . "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . "experiment" . . "true"^^ . . . "^B\\d{5}$"^^ . . . . . "Crates.io" . . "anatomy" . "https://ngdc.cncb.ac.cn/genbase/search/gb/"^^ . . . . . . "david.lynn@flinders.edu.au" . . . . . "^SL-\\d+$"^^ . "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"^^ . "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^ . . . "biology" . . "^\\d{7}$"^^ . . "false"^^ . . . . . "rs" . . "https://omia.org/phene/omia:$1"^^ . "The cBioPortal for Cancer Genomics" . . . . . . "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid="^^ . . "structural biology" . . "http://ddinter.scbdd.com/ddinter/interact/$1"^^ . "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."^^ . . . . . "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID="^^ . . "co_336" . "protein" . . "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . . "128011350"^^ . . . . . . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1="^^ . . . "http://purl.obolibrary.org/obo/OARCS_$1"^^ . "^RCB\\d+$"^^ . . . . . . "pdc.study" . "dialnet.article" . . . "https://bioregistry.io/bmrb:"^^ . "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning."^^ . "hms.lincs.dataset" . "obo" . _:N65fdd5987bbe4da98cc0b92134f8f123 "helpdesk@cropontology-curationtool.org" . "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."^^ . "240-17-488-3-4-12"^^ . "citation" . . "https://www.ebi.ac.uk/gxa/genes/"^^ . "The localization and quantitation atlas of the yeast proteome" . "eroshkin@burnham.org" . . "false"^^ . . "genome" . . "SUBSET_SIREN" . . . . . "1cukA01"^^ . "biochemistry" . "pathways" . . "uniprot.db" . "Dr Paul Schofield" . . . . "ecology" . . "http://database.deepsolar.space:18080/dbs/nlfff/"^^ . . "fcb" . . "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NDFRT&code=$1"^^ . "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."^^ . . "researcher" . . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"^^ . . . "false"^^ . . . . . . "animal breeding" . . "disease" . . . . "http://sideeffects.embl.de/drugs/"^^ . . . "^\\d+$"^^ . . "obo" . "life science" . "obo" . . . "urn:nbn:fi:tkk-004781"^^ . . "chemistry" . . "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."^^ . . . . . . . . . "IUPHAR_LIGAND" . "NIF Standard Ontology: Cell Types" . . "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"^^ . "International Nonproprietary Names" . . . . "NIF Standard Ontology: Cognitive Function" . . "https://purl.dataone.org/odo/SALMON_"^^ . "14362"^^ . . "clinical veterinary medicine" . "^AS\\d{6}$"^^ . . . . "S000002493"^^ . . . . "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified."^^ . "invertebrate" . . . . . . "diagnosis" . . "AGROVOC" . . "statistics" . . "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/"^^ . "ontology" . . "^\\d+$"^^ . . . "false"^^ . . "false"^^ . . "linguistics" . . . "lepao" . . . . . "554"^^ . . . . "https://bioregistry.io/imgt.primerdb:"^^ . . "http://purl.obolibrary.org/obo/COVOC_$1"^^ . "ugis@ebi.ac.uk" . . "obo" . . "https://ligandbook.org/package/"^^ . . . . . "phylogenomics" . . . . "bibliography" . . . "https://horizondiscovery.com/en/search?searchterm=$1"^^ . . . . "functional genomics" . "dclunie@dclunie.com" . "Sylvie Ricard-Blum" . . . "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia."^^ . . "post-translational modification" . "clinical data" . _:Na54c46d2f8d6435e94dffc1381b16104 "Bgee team" . "false"^^ . "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"^^ . . . _:Na54c46d2f8d6435e94dffc1381b16104 . . "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule="^^ . "false"^^ . . "https://comptox.epa.gov/dashboard/$1"^^ . "mavedb" . . "491187"^^ . . . . . "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . . "reaction data" . . . . . "http://purl.obolibrary.org/obo/PDRO_"^^ . . "322"^^ . "^\\d{7}$"^^ . . "ontology" . "Sol Genomics Network" . . . . "^\\d+$"^^ . . "ontology" . . . "false"^^ . "cells" . "true"^^ . "https://flybase.org/reports/FBtc$1"^^ . . "false"^^ . . "http://purl.obolibrary.org/obo/EMAP_$1"^^ . . "jwest@rcsb.rutgers.edu" . . . "Bibliographic Reference Ontology" . . "deepak.unni3@gmail.com" . "rna" . . . . . . "rnao" . . "C0020004/4992"^^ . "organic molecular chemistry" . . . . . . . "http://www.hprd.org/protein/$1"^^ . . . "https://scicrunch.org/resolver/RRID:BCBC_$1"^^ . "^[dp]\\.[a-z0-9]{8}$"^^ . . . "Pigeonpea ontology" . . "http://purl.obolibrary.org/obo/CLYH_"^^ . . . "International Classifications of Diseases" . . . "obo" . "swissregulon" . . . . . "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1"^^ . . . "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/"^^ . . . . . . . "false"^^ . . . . . "https://www.wormbase.org/get?name="^^ . . . . . "anatomy" . "ICARDA - TDv5 - Sept 2018"^^ . . . . . . "http://purl.org/spar/biro/$1"^^ . . . . "https://bioregistry.io/pscdb:"^^ . "false"^^ . . . . . . . "https://www.merckmillipore.com/catalogue/item/"^^ . "Alvin Walker" . "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects."^^ . "Richard Boyce" . . . . . "262393"^^ . . . "https://w3id.org/semapv/vocab/"^^ . "The Behaviour Change Intervention Ontology" . . . "neurophysiology" . . . "68513255-fc44-4041-bc4b-4fd2fae7541d"^^ . . "has local unique identifier example" . . "^\\d+$"^^ . "http://scop.berkeley.edu/sunid=$1"^^ . . . . "C_AA001108.1"^^ . . . . "rdf" . "biomaterial manufacture" . . "0778"^^ . . . . . "International repository of Adverse Outcome Pathways."^^ . . . "Gerald Guala" . "disease" . . "https://senselab.med.yale.edu/ModelDB/ModelList?id=$1"^^ . "An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io)."^^ . . . "https://bioregistry.io/kyinno:"^^ . "pierre.grenon@ifomis.uni-saarland.de" . "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."^^ . "http://www.w3.org/ns/activitystreams#$1"^^ . . . "jgraybeal@stanford.edu" . . . . "Logical Observation Identifiers Names and Codes" . "false"^^ . "^\\d{7}$"^^ . "3000045"^^ . . . . . . "person" . . . . "conferences" . . . . . . "^PACTR\\d+$"^^ . "relationships" . . . . . . "http://purl.obolibrary.org/obo/LIPRO_"^^ . "^NCT\\d{8}$"^^ . . . "genetic disorder" . "http://www.bioassayontology.org/bao#BAO_"^^ . "cryptodb" . . "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."^^ . . "ICD-10" . "https://drugs.ncats.io/drug/"^^ . . . . . . "data model" . . . . . . . . . . . . . . . "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id="^^ . "false"^^ . . . . "assay" . . "16"^^ . . . . . . "Web Annotation Ontology" . "false"^^ . . "http://purl.obolibrary.org/obo/REX_$1"^^ . . "nsv3875336"^^ . "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^ . . . . . . "ssbd.dataset" . . "reactions" . . . . . . "Ontology about the development and life stages of the C. elegans"^^ . "controlled vocabularies" . . . . . . "alignedWith"^^ . . . . . . "18"^^ . "identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829"^^ . . "cbioportal" . "ehda" . "https://biopragmatics.github.io/providers/peff/"^^ . "amphx" . . "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$"^^ . "https://w3id.org/babelon/"^^ . "false"^^ . "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."^^ . . . . "SFB_COVID19_MW286762"^^ . "molecular entity" . . "Prefix Commons" . "pier.buttigieg@awi.de" . . . . . . . "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/"^^ . "S7000002168151102"^^ . "DSMZCellDive" . . . . . "dialnet.author" . . "false"^^ . . . . . "India Clinical Trials Registry" . . . "^\\d+$"^^ . . . . "IC9CM" . . "sov:WRfXPg8dantKVubE3HX8pw"^^ . . . "http://purl.obolibrary.org/obo/VIDO_$1"^^ . . "false"^^ . "false"^^ . . . . . . . . . "false"^^ . "NCBI_taxid" . "omit" . "61467"^^ . . "TCTR20230429001"^^ . . "^\\d{6}$"^^ . . "biomedical science" . "Database of Genotypes and Phenotypes" . . . . . "1455"^^ . "http://www.innatedb.ca/getGeneCard.do?id="^^ . "hrehm@mgh.harvard.edu" . . "The RNA Modification Database" . . "0000773"^^ . . "Wheat ontology" . "cryopreservation" . . . . . . . "https://icd.who.int/browse10/2019/en#/"^^ . "obo" . . . . . . "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^ . . . . "https://civicdb.org/links/sources/"^^ . . "https://web.expasy.org/cellosaurus/" . "Citlalli Mejía-Almonte" . "Image Data Resource" . . . "Hathi Trust Digital Library" . . "http://www.cathdb.info/cathnode/$1"^^ . . "ChEMBL" . "hms.lincs.cell" . "brain regions" . . "Anvil" . "CORDIS Project" . "Handle" . "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^ . "Toxin and Toxin Target Database" . "PDBsum; at-a-glance overview of macromolecular structures" . . . . "ontology" . . . . . _:Ne2526672e8524864bdd1de7582f1adb9 . . . . . . . "FAIRsharing Organization" . . "https://www.ncbi.nlm.nih.gov/sra/$1"^^ . . "ontology" . . "maizegdb.locus" . "pathway" . . "E. coli Metabolite Database" . . . . . . "307"^^ . . "http://purl.obolibrary.org/obo/MFMO_$1"^^ . . . . "^\\d{7}$"^^ . "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . "life science" . "expression data" . "botany" . . . . "agriculture" . "Kristian Axelsen" . "false"^^ . "^KIAA\\d{4}$"^^ . "glyconavi" . . "https://bioregistry.io/ipi:"^^ . "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."^^ . . "obo" . "omrse" . . "selventa" . "Conrad L Schoch" . "Ensembl Gene" . . "true"^^ . . . . . "genome" . "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_"^^ . . . . "^\\d+$"^^ . . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id="^^ . . "taxonomy" . . . . . . . . . . "life science" . . "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . "Publons publication" . . . . . . "^CHEMBL\\d+$"^^ . "0000091"^^ . "conference" . . . "clo" . . . . . . "true"^^ . . "false"^^ . . . . . . . . . . . . . "https://onderzoekmetmensen.nl/en/trial/"^^ . "^\\w+$"^^ . . "msig" . "https://dcmi.github.io/openwemi/ns#$1"^^ . . . . . . . . . . . . . "Description of Plant Viruses" . . . . . . "EB0170"^^ . . . . . . . . . "anatomy" . "false"^^ . . "life sciences" . . "chemical" . . "00000021"^^ . "biomedical science" . . . . "https://semanticscience.org/resource/CHEMINF_$1" . . "microbial" . "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."^^ . . "protein" . . "EU Clinical Trials" . . . . . . "https://cropontology.org/rdf/CO_321:$1"^^ . "Ribocentre" . . . "hl7.v2codesystem" . "FAIR* Reviews Ontology" . . . "ndex" . "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.\n\nOGMS 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."^^ . . "pathway" . . "Franziska B. Grieder" . . . . . . "Tick Cell Biobank" . "ssbd.project" . . "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."^^ . . . "statistics" . . "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . . . . . . . . . "sdis" . . . . "Abcam" . . "^BAMSC\\d+$"^^ . "life science" . "ontology" . "molecular interaction" . . . . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid="^^ . "taxonomic classification" . . "dsm5" . "reactome.pathway" . . . "00000011-a"^^ . . . . "hoso" . . . "WormBase RNAi" . . . . . . . . "Wyeth W. Wasserman" . . . . . . . . . _:N0d2a53c4b87d4b6da6e666b19afae7de . . . . "GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group."^^ . . . . . "^([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+)$"^^ . . "cgrove@caltech.edu" . "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an="^^ . "classification" . "structure" . "obo" . . . . "false"^^ . "huang@southalabama.edu" . . . . "https://biomedit.ch/rdf/sphn-ontology/sphn#"^^ . "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"^^ . . "Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system."^^ . . . "https://bioregistry.io/cubedb:"^^ . . . . . "civic.tid" . "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary."^^ . . . . . . . . "jaiswalp@science.oregonstate.edu" . . . . . "UM-BBD compound" . . "^\\d+$"^^ . . "https://biopragmatics.github.io/providers/hba/"^^ . . "genomics" . . . . . . "IPI00000001"^^ . . "false"^^ . "dna" . . "Gene Ontology Rules" . . . . . "medicine" . "Research Resource Identifiers" . "anatomy" . "biomedical science" . "Collection" . . . "pseudogene" . . "knowledge and information systems" . . "22132778"^^ . . "small molecule" . "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."^^ . . "https://web.expasy.org/abcd/ABCD_"^^ . . . . . . "zenodo" . . "551115"^^ . . "gene" . . "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."^^ . . . . . "https://cells.ebisc.org/"^^ . . "http://purl.org/spar/pro/$1"^^ . . "0000095"^^ . "^[A-Za-z][A-Za-z0-9]+$"^^ . . . "false"^^ . . . . . . . . . "0000435"^^ . . . . . "DockerHub User" . . . . . . . "cancer" . "anatomy" . . . . . "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . . . "http://purl.obolibrary.org/obo/GOREL_"^^ . . . "false"^^ . . "https://www.ebi.ac.uk/biomodels/$1"^^ . "http://www.weizmann.ac.il/molgen/loqate/gene/view/"^^ . . . "Bioregistry Schema" . . "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release."^^ . "model" . . "SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops."^^ . "amalik@ebi.ac.uk" . "mathematical model" . . . . "subject agnostic" . "http://bioportal.bioontology.org/ontologies/"^^ . . . . . . . "protein" . . . . . "Jeremy D. Glasner" . . . . "http://viroligo.okstate.edu/main.php?vid="^^ . . "molecular chemistry" . . . "false"^^ . . . . . . . . . . . . . . . . . . "false"^^ . . . . . "pactr" . . "false"^^ . . . . . . "biocuration" . "vendor" . . . "Eric W. Deutsch" . . . . . . "false"^^ . "true"^^ . . . . . . "nlx.inv" . "life science" . "These resources represent software repositories" . "^\\d{7}$"^^ . . "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . "maggot" . "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1" . . "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . . "vaccine" . . . "http://purl.obolibrary.org/obo/XPO_$1"^^ . . . "genetic resource" . . "Zach Landis-Lewis" . . "biology" . . "false"^^ . "data model" . "https://www.phenxtoolkit.org/protocols/view/$1"^^ . . . . . . . "http://www.ebi.ac.uk/astd/geneview.html?acc=$1"^^ . . . "DragonDB Allele" . "dispositions" . . "https://www.ebi.ac.uk/gxa/experiments/"^^ . . . . . "OMOP" . . . . . "bcgo" . . "0000339"^^ . . "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code="^^ . . . . . "Drosophila Genomics Resource Center" . "false"^^ . . . . . . . . . . . . . "https://w3id.org/sssom/$1"^^ . "VIRsiRNA" . "sewilson@lbl.gov" . "true"^^ . . . . . "life science" . _:N266cd1ebb1ed494dbf7cdcc48ad91b13 . . . . . . . . . "false"^^ . . . . "https://swissmodel.expasy.org/repository/uniprot/"^^ . "https://biopragmatics.github.io/providers/hog/"^^ . . . . . . . "centrally registered identifier" . "https://bioregistry.io/vipr:"^^ . . . "http://mods.rna.albany.edu/mods/modifications/view/"^^ . . "https://www.ncbi.nlm.nih.gov/research/cog/cog/"^^ . "TF101014"^^ . "1755"^^ . . . "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . . "neuromorpho" . . . "measurement" . . . "ontology" . "David Starns" . "A10BA02"^^ . . . "00000101"^^ . "metadata" . "^VB\\.[A-Za-z][A-Za-z]\\..*$"^^ . . "0000062"^^ . . "^[A-Z]+[0-9]+$"^^ . . . "biology" . "lincs" . . . . "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#"^^ . . . . _:N1b02f412632046809bbb9ec4bc2c4457 . . . . "David N. Orloff" . "Nicole Vasilevsky" . . . "0000000"^^ . . . "neuroscience" . . . . . . . "Agronomy Ontology" . "collagenmutdb" . . "The Ontology of Genes and Genomes" . "fly" . "Edison Ong" . . "GPM32310002988"^^ . "10020.2"^^ . "http://mirbase.org/cgi-bin/mature.pl?mature_acc="^^ . "classification" . . . . . . "https://cropontology.org/rdf/CO_370:"^^ . "false"^^ . "disease" . . "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."^^ . . "false"^^ . "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"^^ . . . "life science" . . . "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature."^^ . "subject agnostic" . "Genomics of Drug Sensitivity in Cancer" . "Animal Genome Cattle QTL" . . . "study design" . "panorama" . . . . . . "data management" . . . . . . "1668761"^^ . . . "^[0-9]+$"^^ . "http://purl.obolibrary.org/obo/LPT_$1"^^ . . . "chebi"^^ . . . "nawrocke@ncbi.nlm.nih.gov" . . "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"^^ . . "life science" . . . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id="^^ . . . "http://oid-info.com/get/$1" . "Cell line collections (Providers)"^^ . . . . . "0000423"^^ . . . "false"^^ . "genome" . "uminctr" . . . . . . . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information."^^ . . "protein complexes" . "^[a-z_A-Z]+$"^^ . . . . . "obo" . . . . "academy" . . . "protocol" . "chembl.cell" . . . . . . "^osa-miR\\d{3,5}[a-z]{0,1}$"^^ . "phenotype" . "^\\d{7}$"^^ . "data integration" . . . "biomedical science" . . . . "dictyBase" . . . . "diet" . "assays" . . "http://purl.obolibrary.org/obo/PGDSO_$1"^^ . . . . . . "0000400"^^ . "sequence" . "mirex" . "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"^^ . "A vocabulary for the catalysis disciplines" . . . "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed."^^ . . . . . "false"^^ . . . "true"^^ . . "false"^^ . "mathematics" . "fishbase.species" . . "ontology" . "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^ . . . "RSNA Informatics RadLex" . "meddra" . . "false"^^ . . . . . . "S1"^^ . "false"^^ . "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest."^^ . "protein" . . . . . . . . . . . . . . . . . . "Polymorphism and mutation databases"^^ . . "biomedical science" . . . . . . "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc."^^ . . "Marc_Ciriello@hms.harvard.edu" . "transcriptomics" . "^\\d+$"^^ . . . . "Proteomics data and process provenance" . . . "NLXOEN" . . . . "fish" . . . . . . "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid="^^ . "53367"^^ . "10001-101"^^ . "Cell line databases/resources"^^ . . . "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"^^ . . "oclc" . . . . . . . . . . . "200-003-9"^^ . . "ontology" . . "go.rule" . "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."^^ . "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . . . "biology" . . . . . . . . _:Na6fbbb8732324d569f2999091c91b2a5 . "http://id.who.int/icd/entity/$1"^^ . "EDAM Ontology" . . . . . . . "Alan Wood's Pesticides" . "http://vita.mbc.nctu.edu.tw/search.php?acc=$1"^^ . . "SoyBase" . . . . . "UMLS_CUI" . "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."^^ . . . "obo" . . "https://bioregistry.io/fbol:"^^ . . . "affy.probeset" . "citation" . . . "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . . . . . . . "^\\d{7}$"^^ . . "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . . . . . "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^ . . "http://viaf.org/viaf/"^^ . . . "pathway" . . . . . "true"^^ . . . "transgenic" . . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id="^^ . . "hoganwr@gmail.com" . . . "345201101230312003"^^ . "protein" . . "agriculture" . "genome" . "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."^^ . . "autdb" . . "agriculture" . . . "kyinno" . . "https://lincs.hms.harvard.edu/db/datasets/$1"^^ . . "enzyme" . . "bto" . . . . "false"^^ . "yongqunh@med.umich.edu" . "http://www.pharmgkb.org/disease/$1"^^ . . . "false"^^ . . . "Q-2958"^^ . "proteomics" . "https://www.cbioportal.org/study/summary?id=$1"^^ . . . . . . . . . . "cell lines" . . . . . . "1948"^^ . . . "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."^^ . . "100291"^^ . . "catalog" . . "BioContext contains modular JSON-LD contexts for bioinformatics data." . . . "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"^^ . "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . "Statistical Torsional Angles Potentials" . . . "Assembly" . . . . . . . "PhenX Toolkit" . "metadata" . "https://lotus.naturalproducts.net/compound/lotus_id/"^^ . . "MT"^^ . "anatomy" . "chemistry" . . . "https://pharmacodb.ca/cell_lines/"^^ . . . . . "protein" . . "https://www.e-cyanobacterium.org/bcs/entity/"^^ . . . . . . "sequence" . . . . "Discourse Elements Ontology" . . . . . . . . . "http://purl.obolibrary.org/obo/SBO_$1"^^ . . . "interaction" . . . . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid="^^ . "nb100-56351"^^ . . "radiomics" . "false"^^ . . . . . . . . "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^ . . . . "data model" . "William Hogan" . "https://prosite.expasy.org/"^^ . . . . . . . . . "funcbase.fly" . . "life science" . . . . . . . "false"^^ . . . . "SNOMECT" . " 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.\n\nRhea 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."^^ . "crates" . . . . "biology" . . . . . . . . "natural product" . "PjrpzUIAAAAJ"^^ . . "sequence" . . . . . . . . . "ncbi.gi" . . "https://vac.niaid.nih.gov/view?id=$1"^^ . "rpillich@ucsd.edu" . . "KEGG_REACTION" . "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . "^\\d+$"^^ . . . . "obo" . . . . "tigrfam" . "Zebrafish Information Network Gene" . "phenotype" . "false"^^ . . . "Pier Luigi Buttigieg" . . "https://www.datanator.info/metabolite/$1"^^ . . "ICD9_2005" . "Raja Mazumder" . "LDS-1110"^^ . . . "structural biochemistry" . . . . "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . . "Sample processing and separation techniques" . . . . "^\\d{7}$"^^ . "RoleInTime"^^ . "https://labsyspharm.github.io/lspci/$1"^^ . . . . "biomedical science" . . . "GlycoMapsDB" . . . . . . . . . . . "Plant Stress Ontology" . . . . . "false"^^ . . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_"^^ . . "Metabolomics Workbench Project" . . "Radiation Biology Ontology" . . "^\\d{9,9}$"^^ . . "phosphosite.protein" . . "w3c rec" . . . "drugbank.category" . . . "^\\w+$"^^ . "novus" . "^MCDS_C_[a-zA-Z0-9]{1,10}$"^^ . . "ontology" . "spike.map" . "false"^^ . . . "identifier of an author or reviewer, in Semion"^^ . . . . . . . . "biochemistry" . . . . "Identifiers.org Registry" . . "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."^^ . . . "true"^^ . . . . . "HBG004341"^^ . "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . "cell types" . . "^[A-Z0-9]+$"^^ . . . "jesper.friis@sintef.no" . "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes."^^ . . . . . . . . . "https://www.webofscience.com/wos/woscc/full-record/WOS:"^^ . . . . . "allergen" . "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$"^^ . . "toxicology" . . "1"^^ . "Sharkipedia Trend" . . "protein" . . . "Intrinsically Disordered proteins with Extensive Annotations and Literature" . . . . . "ontology" . "obo" . . . . . "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . "https://dgrc.bio.indiana.edu/product/View?product=$1"^^ . . . "ontology" . . "0000003"^^ . . "person" . "^[A-Z]+$"^^ . "molecular infection biology" . . . "stock" . . . "false"^^ . "CC-BY-1.0"^^ . . "https://e-cyanobacterium.org/bcs/rule/$1"^^ . . . . "true"^^ . "data transformation" . . . . "false"^^ . . . . "Database of experimentally verified IRES structures" . . "http://www.bootstrep.eu/ontology/GRO#$1"^^ . "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot="^^ . "^\\d+$"^^ . "cell replacement" . "Molecular Process Ontology" . "virology" . . . . . "Dialnet book ID" . . . "https://gen3.theanvil.io/ga4gh/drs/v1/objects/"^^ . . . . . . "annotation" . . . . . . "20003"^^ . . "microbiology" . "disease" . . "narcis.fernandez@gmail.com" . . . "false"^^ . "interoperability" . "false"^^ . "http://pathguide.org" . "food" . "Stress Knowledge Map" . . . . . "kronkcj@mail.uc.edu" . . . "https://bioregistry.io/pesticides:"^^ . . . . "SNOMEDCT_US_2022_07_31" . "obo" . "true"^^ . "false"^^ . "lcnaf" . . . . "Higher order grouping of Pfam families"^^ . . "lipidmaps" . "lipidomics" . "false"^^ . "MobiDB" . "pseudogene.org" . . . . "G00123"^^ . . . "^\\d{6}$"^^ . "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"^^ . . "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^ . "http://mods.rna.albany.edu/mods/modifications/view/$1"^^ . . . "taxonomy" . "rfam" . . . . . "16129"^^ . . . . . . . "0000015"^^ . . . "false"^^ . . . "scoro" . . . "https://nanbyodata.jp/disease/NANDO:"^^ . "http://edamontology.org/data_$1"^^ . "life science" . . "false"^^ . . "subject agnostic" . "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid="^^ . . . . "https://www.langual.org/langual_thesaurus.asp?termid="^^ . "PdumDv" . . . "false"^^ . . . . . . "true"^^ . . "identifier of a journal in Dialnet"^^ . "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1"^^ . . . . . . "false"^^ . "John Westbrook" . . . . "^\\d{4}$"^^ . . . . "http://purl.obolibrary.org/obo/OPMI_$1"^^ . . . . . "false"^^ . . . . . "false"^^ . . "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. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"^^ . "https://www.re3data.org/repository/$1"^^ . . "^\\d+$"^^ . . . . "7123"^^ . "African Population Ontology" . "https://purl.dataone.org/odo/SASAP_"^^ . . . . "true"^^ . "^\\d+$"^^ . . . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$"^^ . . "http://thebiogrid.org/$1"^^ . . "b97957"^^ . . "true"^^ . "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas."^^ . "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."^^ . . . "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."^^ . "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."^^ . "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."^^ . . "JGI Phytozome" . "false"^^ . . . . . "developmental biology" . . "classification" . . . "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata."^^ . "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."^^ . . "https://www.jax.org/strain/"^^ . . . "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"^^ . . . . . . . . . "^\\d+$"^^ . . . "UniProt provides proteome sets of proteins whose genomes have been completely sequenced."^^ . . . "taxonomy" . . . "obo" . "^\\d+$"^^ . "mirTarBase" . . . "false"^^ . . "numerical identifier for an author in SciProfiles by MDPI"^^ . "https://biosimulators.org/simulators/"^^ . "ga4ghdos" . "false"^^ . "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts."^^ . "model" . . . . "eukaryotic" . . "^BG\\d+$"^^ . . . . . "Yongqun Oliver He" . . "false"^^ . "w3c rec" . . "false"^^ . . "morbidity" . "whimar@ohsu.edu" . . . "taxonomy" . . "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."^^ . . "tk2@ebi.ac.uk" . . . . . . . "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$"^^ . . . . . "589462"^^ . "http://lisanwanglab.org/DASHR/entry/$1"^^ . "life science" . . . . . "life science" . "leen.vandepitte@vliz.be" . . "structure" . . . "gene expression" . . "topalis@imbb.forth.gr" . . . . . . . . . . . . "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . . . . "false"^^ . . . . . . "mesh.2012" . "Deepak Unni" . . "false"^^ . . "https://www.cellbiolabs.com/search?keywords=$1"^^ . "biomedical science" . . "ontology" . "https://www.discoverx.com/?post_type=product&s=$1"^^ . . . . . . . . . "BioKC" . "0000590"^^ . . "annotation" . "evolutionary biology" . . "false"^^ . . "^\\d+$"^^ . . "Neil D Rawlings" . . "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . . "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract)."^^ . "Cell Signaling Technology Pathways" . "AHR"^^ . . . . "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples."^^ . "http://purl.obolibrary.org/obo/GALLONT_"^^ . "classification" . . . . "^.*?--%3E.*?$"^^ . . . . "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^ . "false"^^ . "sty" . . "https://foodb.ca/foods/$1"^^ . . "https://biopragmatics.github.io/providers/schem/$1"^^ . . . . . "https://sciflection.com/"^^ . "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."^^ . "https://coicatalogue.uc.pt/index.php?t=specimen&COINumber=$1"^^ . "vaccine" . . . . . . "omics" . . . "http://purl.obolibrary.org/obo/BCO_"^^ . . . . . "charprot" . "life science" . "https://www.cellbankaustralia.com/$1.html"^^ . "BiGG Model" . "^[A-Za-z_0-9]+$"^^ . "Animal Genome QTL" . . . "https://cropontology.org/rdf/CO_365:"^^ . "gene" . . "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$"^^ . . . "gold standard" . . . . . "1"^^ . . "Tb927.8.620"^^ . . . "repository" . "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n"^^ . "https://bioregistry.io/hssp:"^^ . "world2dpage" . . "biology" . . "http://purl.obolibrary.org/obo/GAZ_"^^ . . "omia.variant" . "mouse strain" . "^\\d+$"^^ . . . "EDAM Topic" . . . . . . . . . "genetics" . "false"^^ . . . . "slime-mould" . . . . . . . . . "genome" . . "https://cropontology.org/rdf/CO_322:"^^ . . "signaling" . "5277619"^^ . . "creeas@gmail.com" . . "genome" . . "schema" . . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/RNAO_$1"^^ . "structural biology" . . . . . "https://licebase.org/?q=$1"^^ . "Ensembl Bacteria" . . . "p.buttigieg@gmail.com" . "https://gnss-metadata.eu/MOID/$1"^^ . . . . . . "1981638"^^ . "https://www.gtexportal.org/home/gene/"^^ . "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1"^^ . . "D00001"^^ . "TBK Reddy" . . . . . "Legacy site for IETF RFC proposals"^^ . . . . . . "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . . . "social science" . "Sean May" . "botany" . "The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated."^^ . . "^[A-Za-z0-9]+$"^^ . "plant anatomy" . . "clinical trials" . . . . "https://www.uniprot.org/diseases/"^^ . . . "Chlamydia"^^ . "https://bioregistry.io/genecards.genenote:"^^ . . "^\\d{7}$"^^ . "https://www.ebi.ac.uk/miriam/main/resources/$1"^^ . . "ecology" . "https://www.addexbio.com/productdetail?pid="^^ . . "false"^^ . "ontology" . . . . . . "^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$"^^ . . . "https://bioregistry.io/vsdb:"^^ . . "https://metacyc.org/META/NEW-IMAGE?object=$1"^^ . . . . . "http://www.whocc.no/atc_ddd_index/?code="^^ . . . . . . "gene expression" . . . . . . "https://civicdb.org/links/drugs/"^^ . "obo" . . . "^[0-9]+$"^^ . "FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors."^^ . . "genome" . . . . . "false"^^ . "00000268"^^ . . . . . . "NIF Standard Ontology: Brain Regions" . "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . "0001021"^^ . . . "^[0-9]+$"^^ . . "ido" . "4019477"^^ . "^\\d+$"^^ . . . . "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . . . "agriculture" . "^MIMAT\\d{7}$"^^ . "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_"^^ . "drug interaction" . . . "FBbi" . . "genome" . . "environmental science" . . "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . . . . . . . . . . . "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."^^ . "biomedical science" . . "http://elm.eu.org/elms/elmPages/$1.html"^^ . "20021"^^ . "false"^^ . "Pazar Transcription Factor" . "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information."^^ . . . . "OECD Harmonised Templates" . "^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . . . "Foundational Model of Anatomy" . "http://ascl.net/$1"^^ . . . . "https://www.ncbi.nlm.nih.gov/protein/"^^ . . . "expression" . . "Traits and phenotypes of flowering plants occurring in digitized Floras"^^ . "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research)."^^ . . . . "dermo" . "false"^^ . "dna" . . . . . . "^\\d{7}$"^^ . . . . "experimental measurement" . . "022586"^^ . . . . "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"^^ . "genome" . . . . . . . . . "^\\d{6}$"^^ . "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]"^^ . . . "Dorothea Iglezakis" . . . "ArchDB" . . . . "genetics" . "BRAF"^^ . . "ontology" . "diagnosis" . "Yang Chai" . . . "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$"^^ . "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."^^ . . "3"^^ . . "https://github.com/biolink/biolink-model" . "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."^^ . "1000"^^ . "false"^^ . . "https://biomodels.net/vocab/idot.rdf#$1"^^ . . . . . "gene" . . "biology" . "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . "iceberg.family" . . . "Common Bean ontology" . "gene" . . "Bob Thacker" . "0000390"^^ . "A type for entries in the Bioregistry's registry." . "https://pypi.org/project/$1"^^ . "DepMap Cell Lines" . "bel" . . "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."^^ . "ontology" . . "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."^^ . . . "genetic" . . . . . . . "allele" . "http://topdb.enzim.hu/?m=show&id=$1"^^ . . . . "http://en.wikipedia.org/wiki/$1"^^ . "0000121"^^ . . . . "interfil" . "tarbase" . "false"^^ . . . . . . . . . . "^\\d{7}$"^^ . "ddc" . . . . "ychai@usc.edu" . "^MSV\\d+$"^^ . . "^\\d+$"^^ . . "ArrayGroup"^^ . . "RiceNetDB Reaction" . "EAWAG Biocatalysis/Biodegradation Database" . . "PXD000440"^^ . . . . . . "Xenbase" . . . "https://w3id.org/aio/"^^ . "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. "^^ . "ribocenter" . . . "CryptoDB" . . "pathway" . . . . "Cancer cell LInes GEne fusions portAl" . . "Sergio José Rodríguez Méndez" . "Cellular Phenotypes" . "273"^^ . . . . . "https://ecocyc.org/gene?id=$1"^^ . . . . . . "gard" . . . . . "Paolo Romano" . "^[1-9]\\d*$"^^ . . "^[0-9a-z_-]+$"^^ . . "mfmo" . . . . . . . . . . . "ERM00000044"^^ . "Human Brain Atlas" . . . "false"^^ . . "fisheries science" . . "sébastien Aubourg" . . "Paul David Neil Hebert" . "false"^^ . "GlycoPOST" . . "baseDimensionEnumeration"^^ . . "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset."^^ . . . . "Gene Regulation Ontology" . "pmp" . . . . "false"^^ . "fair" . "identifierPattern"^^ . . . "ResearchGate profile ID" . . "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way."^^ . . "virology" . "PGS000018"^^ . "^[A-Z0-9]+$"^^ . "https://aopwiki.org/aops/"^^ . "^[0-9X\\-]+$"^^ . . "recombinase" . . "food" . . "imaging" . "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump"^^ . . . . . "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . "eolife" . . . . . "developmental biology" . . . "structure" . . "r0001"^^ . . . . "Human Chromosome Ontology" . . . "gxa.expt" . . "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . . . "jakkbl@gmail.com" . "false"^^ . . . . . "obo" . "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."^^ . . "lpt" . . . . "NCBI Gene Expression Omnibus" . . "false"^^ . "ontology" . "embryonic stem cell" . . "plant" . "sam.griffiths-jones@manchester.ac.uk" . . . "http://purl.obolibrary.org/obo/MFOEM_$1"^^ . . "Sharkipedia Trait" . "cell_biolabs" . "ena.embl" . . "^\\d+$"^^ . . "easychair.topic" . . . "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" . . . "https://www.brenda-enzymes.de/ligand.php?brenda_group_id="^^ . "false"^^ . "linkml" . . . . . "genes" . "DASHR expression" . "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."^^ . . . "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^ . . . . . . "rat" . . . . . "^\\S+$"^^ . _:N022b298b5b8a4c60bc6d754421090013 "custserv@nlm.nih.gov" . . . . "obo" . . "Laurent Duret" . . "protein interaction" . . "^\\d+$"^^ . . "catalog" . . . "MEDLINE" . "genepio" . "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1"^^ . "chemistry" . . "https://cropontology.org/rdf/CO_326:$1"^^ . "false"^^ . "ArachnoServer" . . . . "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."^^ . . . "study design" . . . "admin@envipath.org" . . "marie-paule.lefranc@umontpellier.fr" . "64ba"^^ . "oboformat" . "Citation Typing Ontology" . . . . . "https://glytoucan.org/Structures/Glycans/$1"^^ . "false"^^ . "sequence variant" . "International Classification of Diseases, 11th Revision" . . . "https://www.ebi.ac.uk/ena/browser/view/"^^ . . "genpept" . "hsapdv" . . "0000890"^^ . . "false"^^ . . "taxonomic classification" . . . "false"^^ . "ABC"^^ . "^BE\\d{7}$"^^ . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . . "false"^^ . . "taxonomy" . "reproduction" . . "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"^^ . "National Uniform Claim Committee Characteristic" . "false"^^ . "SitEx" . . . . . "laevis" . . . . . . "Cell line collections (Providers)"^^ . "https://trialsearch.who.int/Trial2.aspx?TrialID="^^ . "rna" . . "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id="^^ . "developmental biology" . . . "An ontology to represent genomics cohort attributes."^^ . . "6017782"^^ . "edam.operation" . "NP_012345"^^ . . . "0000630"^^ . . "ontology" . . "0000204"^^ . "http://purl.obolibrary.org/obo/CDNO_"^^ . . . "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."^^ . . "cell culture" . . . . "https://www.ncbi.nlm.nih.gov/protein/"^^ . . . "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . "obo" . "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."^^ . . . . . "kcris" . "botany" . . . . . . . "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."^^ . . . . "http://purl.obolibrary.org/obo/MFOMD_"^^ . . . . "http://aber-owl.net/ontology/$1" . "00007294"^^ . . . . "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^ . "false"^^ . . . . . . "false"^^ . . . . . . "Human Protein Reference Database" . "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"^^ . . . "life science" . "^\\d{7}$"^^ . . "mark@gersteinlab.org" . "structure" . . . . "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"^^ . . . . "^\\d{7}$"^^ . . . . "oma.grp" . "bioactivities" . . . "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . "false"^^ . "Beta Cell Genomics Ontology" . . "Stephen Fisher" . "https://www.scopus.com/affil/profile.uri?afid=$1"^^ . . "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."^^ . . . . "https://trialsearch.who.int/Trial2.aspx?TrialID=$1"^^ . . . "citation" . . . . . "urmas.koljalg@ut.ee" . . . . "dna" . . . "kegg_genome" . "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data."^^ . . . . "false"^^ . . "clinvar" . . "phenotype" . . . . "apid.interactions" . . "cath.superfamily" . . "rbo" . . . . "false"^^ . . . "false"^^ . . . . "https://data.bloodpac.org/ga4gh/drs/v1/objects/"^^ . "false"^^ . "Mouse adult gross anatomy" . . . . "false"^^ . . "insdc.run" . "Database of homology-derived secondary structure of proteins" . . "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . . . . . "ARP-1513"^^ . . . "E-MEXP-1712"^^ . . . . . "TA14985"^^ . "nif.grossanatomy" . . . "https://github.com/$1"^^ . "clement.jonquet@inrae.fr" . "OntoBee" . "58788"^^ . . . "3771992"^^ . . . "https://www.ebi.ac.uk/ols4/ontologies/fma/terms?obo_id=FMA:"^^ . "https://aftol.umn.edu/glossary?category="^^ . . "dpo" . . "cell biology" . . . . "simon.harding@igmm.ed.ac.uk" . . "Spider Ontology" . . . "anne.morgat@sib.swiss" . . . . . "James C. Hu" . . . "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . "http://fossilworks.org/?a=taxonInfo&taxon_no="^^ . . . "ecosystem" . . . . "6819"^^ . . "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"^^ . . . "vbrc" . "http://purl.obolibrary.org/obo/PR_"^^ . . . . . "biomedical science" . . "experiment" . . . "ulrike.wittig@h-its.org" . . "^[0-9]+$"^^ . "github.pull" . "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."^^ . . . . . . . . "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]."^^ . . "^MMAR\\_\\d+$"^^ . . . "Harshad Hegde" . . "rr@uga.edu" . . "Antibody Registry" . "bibliography" . "https://publons.com/researcher/"^^ . "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\"."^^ . "pdumdv" . "E00002"^^ . "gene" . "jRCTs041220087"^^ . "protein" . . . . "00000532"^^ . . . "http://www.imgt.org/ligmdb/view?id="^^ . . "biomedical science" . . "Studies in dbVar."^^ . . "https://data.oncomx.org/OMX_$1"^^ . "spdx" . . "ontology" . "PF11779"^^ . "https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip"^^ . . . "metatlas" . . _:Nd8c5865333bf40c4acb6cd21189c49f2 "helpdesk@cropontology-curationtool.org" . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$"^^ . "false"^^ . . . "cdno" . "YBR125c"^^ . . "6038"^^ . "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . . "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."^^ . . "bioinformatics" . "false"^^ . "true"^^ . "https://archive.softwareheritage.org/browse/swh:$1"^^ . "ontology" . . . . . . "ontology" . . . "^\\d+$"^^ . . . . . . "https://dialnet.unirioja.es/servlet/autor?codigo=$1"^^ . . . . "life science" . "wb" . . "MIRIAM Legacy Registry Identifier" . "zfin" . "ccle.cell" . . "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^ . . "0000111"^^ . . . . . "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^ . . . . . . . . "^\\d{8}$"^^ . "NLXFUNC" . "https://bioregistry.io/dragondb.locus:"^^ . "ontology" . . "ncro" . . "^\\d+$"^^ . "false"^^ . . "geogeo" . . . . . . . . "sickle cell disease" . . . "false"^^ . . "http://www.icd9data.com/getICD9Code.ashx?icd9="^^ . "ensembl.bacteria" . . "http://purl.obolibrary.org/obo/MA_"^^ . . "senso" . . . "urgi-contact@versailles.inra.fr" . "false"^^ . "false"^^ . . . . . . . . . . "anatomy" . . . . . . . . "TripleExpression"^^ . . "mass spectrum" . . "itmctr" . "Costal and Marine Ecological Classification Standard" . . . . . . . . . "false"^^ . . . . . "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources." . "co_320" . . "long-finned-pilot-whale"^^ . "19210-3"^^ . . "ecao" . . "disease" . . . . "^\\d+$"^^ . . . "immunology" . . "J0705A10"^^ . . "^\\d{7}$"^^ . . "scop.sunid" . . . . . . . "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."^^ . . . "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."^^ . . "false"^^ . . . "life science" . "genomics" . . "false"^^ . . . "Jianmin Wu" . "xeni.kechagioglou@lifewatch.eu" . . . . "https://www.thaiclinicaltrials.org/show/"^^ . . . . "timrobertson100@gmail.com" . . "plasmid" . . . . . . . . . "biomedical science" . "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . "http://purl.obolibrary.org/obo/VHOG_$1"^^ . "^\\d{7}$"^^ . . . "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname="^^ . . "9606"^^ . . "0010316"^^ . "288"^^ . . "1000000"^^ . . . . . "cpd15380"^^ . . . "http://purl.obolibrary.org/obo/ERO_$1"^^ . "gene expression" . . . . "mobidb" . . . . . "life science" . . . "life science" . . . "https://terminology.hl7.org/CodeSystem-v3-$1"^^ . . . . . . . . . "Biocompute Object" . . . . . "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."^^ . . . "https://www.osti.gov/biblio/$1"^^ . . . . . . "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."^^ . "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"^^ . . "http://purl.obolibrary.org/obo/XLMOD_$1"^^ . . "false"^^ . . . . . "KEGG.DRUG" . . "protein" . . . . . "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID="^^ . . . "Drug Target Ontology" . . . . "STUDY1040"^^ . . . . . "http://vegbank.org/cite/"^^ . "culture" . . . . . . "obo" . . . "Paula Duek Roggli" . . "https://www.grid.ac/institutes/$1"^^ . . "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^ . "anatomy" . . . "d.a59037e8"^^ . "life science" . . "0000069"^^ . "Paul Fabry" . "0000004"^^ . "Benjamin M. Gyori" . "hescriva@obs-banyuls.fr" . "frim1"^^ . "cba" . "false"^^ . "false"^^ . . "^oai\\:cwi\\.nl\\:\\d+$"^^ . . . "0100011"^^ . . . . . . "hpiwowar@gmail.com" . . . "mgnify.analysis" . . . "C. elegans ORFeome cloning project" . . . "^DB-\\d{4}$"^^ . "vmhreaction" . . "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene="^^ . . "obo" . . . "ecn" . "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . "^\\d+$"^^ . . . . . . . . "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."^^ . "https://bdsc.indiana.edu/stocks/"^^ . . . "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."^^ . "http://purl.obolibrary.org/obo/MAT_$1"^^ . "funding bodies" . . . . "biomedical science" . . "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).\n\nLandis-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"^^ . . . . . . . . . . . . . . "false"^^ . . . "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1"^^ . . "false"^^ . "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . . . . . . . . . . . "The reviewer of a prefix" . . "gene" . . "http://swissregulon.unibas.ch/query/"^^ . "GrainGenes" . "ucsc" . "0000001"^^ . . "metabolite" . "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . "obo" . . . "confident.series" . . "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."^^ . "ccle" . . . . . . . "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."^^ . . . . . "pseudomonas" . . . . . . "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."^^ . "citation" . "bioresource" . . "ASRP1423"^^ . "Echinobase" . "structure" . . . . _:Nf01bdac05851415dbc25fd25427c1837 . . "true"^^ . . . . . "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo="^^ . "false"^^ . . "2.1.1"^^ . . . . . "false"^^ . . "tcb" . . . . . . "https://sumlineknowledgebase.com/?page_id=$1"^^ . . "Rachael P. Huntley" . . "Human Reference Atlas Common Coordinate Framework Ontology" . "DDB_G0267522"^^ . . . . . . "https://bioregistry.io/pocketome:"^^ . . . . "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"^^ . . . "Reagent Ontology" . . . "817732"^^ . . "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^ . "botany" . "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . "biology" . . . . _:N05d5bf61592043b6848a7935da52a0ea . . . . . . "https://e-cyanobacterium.org/models/model/"^^ . . . . "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species."^^ . "environmental science" . . . . "https://discover.pennsieve.io/package/"^^ . "gemet" . "life science" . . . "^\\d{7}$"^^ . . . . . "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . "H3.03.00.0.00007"^^ . "false"^^ . . . "Properties and classes used for protein annotation"^^ . . . "true"^^ . . . . "Search Tool for Retrieval of Interacting Genes/Proteins" . . "^\\d+$"^^ . . "comparative genomics" . "diagnosis" . . "true"^^ . . . "bmeldal@ebi.ac.uk" . "wdduncan@gmail.com" . . "^\\d+$"^^ . . "mmrrc" . "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . _:N900d7c1024bd4e4f985fd8917ddd2241 "NLM Customer Service" . . "structure" . . . . . "snoRNABase" . . . . "Amelanchier laevis"^^ . "structure" . . . "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."^^ . . . "worm" . "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid="^^ . . "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"^^ . . . "PELNAW"^^ . . . "OriDB Schizosaccharomyces" . . . . . "computer science" . . "GWAS Central Phenotype" . "^\\d+$"^^ . . . . . "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.\n"^^ . . . "4900"^^ . "annethessen@gmail.com" . "PSI-MOD" . . . "false"^^ . "https://www.re3data.org/repository/"^^ . "social and behavioural science" . . "proteins" . . . . "ontology" . . . . "Daniel Sonenshine" . "0000003"^^ . . . . . "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."^^ . . . . "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."^^ . . . .