"0002989"^^ . . "npm" . "Human Proteome Map" . . "admin@envipath.org" . . . . . "false"^^ . . . . "false"^^ . . . "false"^^ . . . . "false"^^ . "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^ . . . "0001079"^^ . "^([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])$"^^ . "SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes."^^ . . . "gnd" . "https://prosite.expasy.org/"^^ . . . . "gramene.reference" . . "dbprobe" . . "http://purl.obolibrary.org/obo/RNAO_"^^ . . . . . . . . . . . . "daml.pt" . . . . "DG00301"^^ . "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"^^ . . . . "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."^^ . "biogrid" . . "epidemiology" . "environmental science" . . "http://www.t3db.org/toxins/$1"^^ . . "ECGOntology" . . . . "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations."^^ . . . . "protein" . . "dna" . . . "International Standard Name Identifier" . . . . . . "OASIS Open Services for Lifecycle Collaboration Core Vocabulary" . "biomedical science" . . . . . . . . "MMP743597.11"^^ . . . "^[A-Z]{2}\\d+$"^^ . . "UPI000000000A"^^ . . "https://www.cellbiolabs.com/search?keywords="^^ . . . . . . "merops.inhibitor" . . "The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]"^^ . . . "structure" . . . . "fabrice.legeai@rennes.inra.fr" . "Fiona M McCarthy" . . "om" . . . . _:Nef9d6d95346440a1beac024ba7c57e91 "helpdesk@cropontology-curationtool.org" . . "CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC."^^ . . "^C\\d+$"^^ . . . "false"^^ . "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . . "false"^^ . . "gene" . . "ontology" . . . "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^ . . . "F-SNP" . "Open Science Framework ID" . "^\\d+$"^^ . "http://emmo.info/emmo/cif-core#"^^ . . . . . "https://www.iedb.org/assay/$1"^^ . . "NLFFF Database" . . . "Unified Code for Units of Measure" . . . . . . . . . "protein" . "https://www.thermofisher.com/antibody/product/$1"^^ . "false"^^ . . "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . . "Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000."^^ . "ICD10" . . "obo" . "transcript" . . . . "https://registry.bio2kg.org/resource/$1" . "ddanat" . . "Human Phenotype Ontology" . . "https://deims.org/networks/$1"^^ . . . . . . "dna" . "0000001"^^ . "^\\d+$"^^ . "ontology" . "Amphibian taxonomy" . . . . . . . "2"^^ . "dna" . . . . "identifier for a person, in the Loop database of researcher impact"^^ . "^\\d+$"^^ . . . . . "^\\d{6}$"^^ . "https://www.disprot.org/$1"^^ . . . . "luana.licata@gmail.com" . . . . "isni" . . . . . . . . . . . . . . . . . "mircoRNA Gene Database is a collection of animal microRNA genes. This database allows researchers to analyze mircoRNA properties like secondary structure and features in a phylogenetic context."^^ . "citlalli.mejiaalmonte@gmail.com" . "https://data.bloodpac.org/ga4gh/drs/v1/objects/"^^ . "http://purl.org/spar/doco/$1"^^ . "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes."^^ . . . "1968"^^ . . "^[A-Z0-9]+$"^^ . . . _:Nd66f42c5411c4a318ce1416d173110db . "false"^^ . . "^\\d\\w+$"^^ . . . . . . . "Pathguide contains information about 325 biological related resources and molecular interaction related resources."^^ . . . "plant phenotypes and traits" . "phylogeny" . "KEGG.EDRUG" . "14362"^^ . . . . . . . . . "pathway" . "mpio" . . "virology" . . "http://purl.obolibrary.org/obo/ICO_"^^ . "life science" . "medical imaging" . "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^ . . "Metabolic Encyclopedia for Pathway/Genome Databases" . . . . . . . . . . . "https://www.ncbi.nlm.nih.gov/nlmcatalog/"^^ . "protein" . "^ACYPI\\d{6}(-RA)?$"^^ . . "troy_pells@yahoo.ca" . "https://biosimulators.org/simulators/"^^ . . . "^\\w+$"^^ . . "0007114"^^ . . "Spectral Database for Organic Compounds" . . . "anatomy" . . . . "KEGG Environ" . . "cytology" . . "true"^^ . "plant breeding" . "28789"^^ . . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes."^^ . "false"^^ . "false"^^ . . "life science" . . . "^\\d+$"^^ . "https://www.ebi.ac.uk/chembl/compound/inspect/"^^ . . . "false"^^ . "0009089"^^ . . . . . . "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."^^ . . "false"^^ . . . "Insect Resistance Ontology" . . "10001-101"^^ . "http://www.wikidata.org/entity/$1" . . "MedlinePlus Health Topics" . "46946"^^ . . . . . "false"^^ . "^\\d+$"^^ . "NIF Standard Ontology: Brain Regions" . . "egon.willighagen@gmail.com" . "https://prefix.zazuko.com/prefix/$1:" . . "648028003"^^ . "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1"^^ . "Event (INOH pathway ontology)" . "0000632"^^ . . . "01467"^^ . . . . . . . "life cycle" . . . . "HOSO is an ontology of informational entities and processes related to healthcare organizations and services."^^ . . . "0000947"^^ . . . . "computational biology" . . . . "structure" . . "false"^^ . . . "centrally registered identifier" . "bioinformatics" . . . "electroencephalography" . . "http://uri.neuinfo.org/nif/nifstd/nlx_chem_"^^ . "re3data" . "pandura@mrc-lmb.cam.ac.uk" . . "^\\d{8}$"^^ . . . . "^\\d+$"^^ . "protein" . "false"^^ . "ontology" . . "mpath" . "https://www.disprot.org/idpo/IDPO:$1"^^ . "false"^^ . . "https://scicrunch.org/resolver/RRID:BCBC_$1"^^ . . "https://w3id.org/oc/corpus/$1"^^ . . "proteomics" . _:N6a6323aa9606436298cdc45138bb0a17 . "obo" . "sequence annotation" . . . "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^ . . "false"^^ . . "false"^^ . . . . . . "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . . . . "natural product" . "phenotype" . . "cell_model_passport" . . . . . "SNOMEDCT_2010_1_31" . . "ReviewVersion"^^ . "hc.trial" . . "http://metnetonline.org/browse_pathway2.php?pthID="^^ . "gene" . "cmedigue@genoscope.cns.fr" . . . . . . "phenotype" . "ido" . . "T3D0001"^^ . "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . . . "glenn.king@imb.uq.edu.au" . "enzyme" . "https://cropontology.org/rdf/CO_341:"^^ . . "FeatureOfInterest"^^ . "statistics" . . "false"^^ . "https://cropontology.org/rdf/CO_370:"^^ . . "iuphar.ligand" . "Signaling Pathways Project" . . "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"^^ . . "David Linke" . . . . "Activities in DEIMS SDR"^^ . "false"^^ . . . "life sciences" . . "dna" . "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data."^^ . "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . . . . . . "CASRAI Contributor Roles Taxonomy" . "https://www.ebi.ac.uk/ega/studies/$1"^^ . "Identifiers.org Registry" . . . . . "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks."^^ . . "developmental biology" . "^tgv[0-9]+$"^^ . "pigqtldb" . . . . . "SUBSET_SIREN" . . "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="^^ . . . "An ontology for dengue fever."^^ . . . . "CL070"^^ . . "false"^^ . "https://cropontology.org/rdf/CO_366:$1"^^ . "false"^^ . "dpbo" . . "cardiology" . . . "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^ . "biomedical science" . "https://sciflection.com/"^^ . "https://civicdb.org/links/evidence/"^^ . "drsanv0" . . . . . . "small molecule" . . . . . "biomedical science" . _:Nd66f42c5411c4a318ce1416d173110db "zimmerly@ucalgary.ca" . . . . "development" . . . . "DockerHub User" . . . . . . . "https://chemprosquare.idrblab.net/data/probe/details/"^^ . "anatomy" . . . . . . . . . . . "ricenetdb.mirna" . . . . . . . . "1001"^^ . . . . . . . "faseb list" . . . . . "^\\d+$"^^ . "false"^^ . "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. "^^ . . "An ontology to standardize research output of nutritional epidemiologic studies."^^ . . . "https://web.expasy.org/cellosaurus/" . . "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"^^ . . . "jwest@rcsb.rutgers.edu" . "A database of GlycoMaps containing 2585 conformational maps."^^ . "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"^^ . . "Yongqunh He" . . "subject agnostic" . . . . . . . . . "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . . . . "sweetrealm" . . . . "life science" . "botany" . "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . "Plant Anatomy Ontology" . "https://www.webofscience.com/wos/author/record/"^^ . . . . "person" . "medicine" . "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity."^^ . "false"^^ . "false"^^ . "craniofacial phenotype" . "dna" . . "4447"^^ . . . "^\\d+$"^^ . . . . . "pdbj" . "^\\d+$"^^ . . "occo" . . . . . "evolutionary biology" . . . "A repository of software packages written in PHP."^^ . . . . . . "false"^^ . . . "insdc.gca" . "https://www.arabidopsis.org/locus?accession=$1"^^ . . "^FCB\\d{3}$"^^ . . . "genetic construct" . . "ENSG00000136147"^^ . . _:Naceb801cb270407194aa4a0ac4c3af42 "edd@usefulinc.com" . . . "true"^^ . . . . . . "A collection of ontologies relevant for chemistry.\n\nThe NFDI program deploys a [custom instance](https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1) of the Ontology Lookup Service (OLS) that provides the ontologies in this list.\n\nA further analysis of the metadata landscape of the ontologies in this list can be found [here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat).\n\nOntoCompChem and OntoKin appear on the NFDI4Cat list but have not yet been registered in the Bioregistry because the resources are missing/incomplete such that they do not meet minimum Bioregistry metadata standards. These might be added in the future if additional metadata can be found." . . "001000"^^ . "virus" . "00000014"^^ . "antweb" . . . . "BioDeep Database" . "http://purl.obolibrary.org/obo/OBIB_$1"^^ . "ontology" . . . "false"^^ . . . . "false"^^ . . . . . . . "annotation" . "variants" . "^\\d{7}$"^^ . . "fobi" . "Li7"^^ . . . "The Organisation for Economic Co-operation and Development (OECD) Harmonised Templates (OHTs) are standard data formats for reporting information used for the risk assessment of chemicals, mainly studies done on chemicals to determine their properties or effects on human health and the environment, but also for storing data on use and exposure."^^ . . . . "0000041"^^ . "ProteomeXchange" . . . . "^\\d{7}$"^^ . "UPLOC" . . "^\\d+$"^^ . . . . . . . . . "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]"^^ . . "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u"^^ . "synthetic biology" . . . "http://purl.obolibrary.org/obo/NIF_CELL_"^^ . . . . . . . . . . . "https://bioregistry.io/hovergen:"^^ . . . . . . . "https://doulix.com/biomodules/"^^ . . "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."^^ . . . . . "GLDS-141"^^ . "https://senselab.med.yale.edu/ModelDB/ModelList?id=$1"^^ . . . "genetics" . . . . "rare disease" . . . . . . . . . . "agriculture" . "protein" . . . "false"^^ . . . "mirtarbase" . "http://icd9cm.chrisendres.com/index.php?action=search&srchtext="^^ . . . . . "^\\d+$"^^ . . "prosite" . "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_"^^ . "has responsible" . . . . . "life science" . . "^\\d{7}$"^^ . . "https://cropontology.org/rdf/CO_323:$1"^^ . . . . . "http://bactibase.hammamilab.org/"^^ . . . . . "phenotype" . . "enzyme" . . . . . . . "morbidity" . "openWEMI Vocabulary" . . . . . . "^\\d{10}$"^^ . "life science" . . . . "Peter D. Karp" . . "Trushar Shah" . . . . . "comparative genomics" . . "ontology" . . "^[A-Z]+[A-Z-0-9]{2,}$"^^ . . . . . . . "EC-CODE" . "subject agnostic" . . "A10BA02"^^ . . . . "https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_"^^ . . "ontology" . . . . . . . . . "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^ . "^\\d{7}$"^^ . . "cthoyt@gmail.com" . "https://nztcs.org.nz/nztcs-species/"^^ . "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id="^^ . . . . . "http://purl.obolibrary.org/obo/GAZ_"^^ . "SNP500Cancer" . . "geonames" . "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." . . "^PM\\d{7}$"^^ . . "pathways" . "obo" . . "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1"^^ . "BloodPAC" . . . "https://w3id.org/sulo/$1"^^ . "sider.drug" . "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other."^^ . . . . "genomics" . "drug" . . "10343835"^^ . "hinv.protein" . . "protein" . "dsm4" . "https://www.grid.ac/institutes/"^^ . "false"^^ . . "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"^^ . . "rat" . "spar" . . "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."^^ . . "ontology" . . . "Martin Pospíšek" . . . . "nemo2" . "GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match."^^ . "KEGG Orthology" . "true"^^ . "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules."^^ . "moid" . . . "NIF Standard Ontology: External" . . . "Bill Duncan" . "kegg.brite" . . "patient care" . "ec" . . "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1"^^ . . "Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver."^^ . . . . . . . . . . "TP53-47"^^ . "http://www.tcdb.org/search/result.php?tc=$1"^^ . . "bigg.compartment" . . . _:N08af7157802e4fe1a36022ee8ba15c2f "sschurer@med.miami.edu" . . "INSDC CDS" . "biodolphin" . . "mavedb" . "false"^^ . . "experimental measurement" . "^([0-9A-F]{4}-){2}[0-9A-F]{4}$"^^ . . . "interaction" . "The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class ‘dietary nutritional component’ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe ‘analytical methods’ for quantification, ‘physical properties’ or ‘dietary function’. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the ‘nutritional component concentration’ class may be used to represent quantification of components described in the ‘dietary nutritional component’ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) ‘Food product by organism’, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum."^^ . . . . . "omics" . "http://purl.obolibrary.org/obo/EHDAA_"^^ . . . . . "^\\d{7}$"^^ . "BatchelorC@rsc.org" . . . . "chemical" . . . "https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?curie=NMR:$1"^^ . "Darwin Core Terms" . "Haruki Nakamura" . "D001151"^^ . "psipar" . "^rs\\d+$"^^ . . . "The cell line vocabulary inside FlyBase"^^ . . . . . . "40135"^^ . . . . "https://scicrunch.org/resolver/RRID:AGSC_$1"^^ . "structural biology" . . "4.2.78"^^ . . . . "animal physiology" . . . "genetics" . "life science" . . "molecular biology" . . . . "A person" . . _:N162037c0c5e841c8ad3e24ff5b417396 . "false"^^ . "Identifier of an object from the ASTD database."^^ . "life science" . . . "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible." . "187021"^^ . . . . . . "ontology" . . . . "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns."^^ . "AT1G73965"^^ . . . "H-InvDb Transcript" . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene."^^ . "Metabolomics Standards Initiative Ontology" . "FaceBase Data Repository" . . . . "false"^^ . . . "^\\d+$"^^ . "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used."^^ . . "konigmatt@googlemail.com" . . . . . "Plant Genome Network" . . . . "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . . . . . . . "https://mycobrowser.epfl.ch/genes/"^^ . "The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)"^^ . "0000184"^^ . . "suzia@stanford.edu" . . "Ana Rath" . . . "alan.bridge@isb-sib.ch" . . "Pazar Transcription Factor" . . . . . . "transgenic" . . . "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies"^^ . "^IHW\\d+$"^^ . . . . . "issn" . . . "Genomics of Drug Sensitivity in Cancer" . . . "canal"^^ . . . . "http://www.pseudomonas.com/feature/show/?locus_tag="^^ . . . . "plant phenotypes and traits" . . "CHEBIID" . . "ontology" . "topalis@imbb.forth.gr" . "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^ . "phenotype" . "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . . . "omo" . . "0000013"^^ . "http://purl.obolibrary.org/obo/HSO_"^^ . . . . . "https://www.merriam-webster.com/dictionary/$1"^^ . "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis."^^ . "https://bitbucket.org/"^^ . "dna" . "false"^^ . . . "http://www.pseudomonas.com/feature/show/?locus_tag=$1"^^ . . . . . . . . "genomics" . . "goeco" . . _:N7735554169874ebcad108460d8ad0f99 "Onard Mejino" . "Creative Commons Rights Expression Language" . . "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID="^^ . "http://purl.obolibrary.org/obo/MPIO_"^^ . . "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences."^^ . . "^\\d{7}$"^^ . . . . "bioinformatics" . "European Bank for induced pluripotent Stem Cells" . "FundRef" . "phenotype" . . . "biology" . "nlx.dys" . . "https://w3id.org/dpv#$1"^^ . . "genome" . . . . "false"^^ . . "FlyBase_Cell_line" . "A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . . "PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2"^^ . . . "nucleotide" . . "co_334" . "biology" . . . "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^ . "obo" . . "true"^^ . . . "https://www.datanator.info/metabolite/"^^ . "http://uri.neuinfo.org/nif/nifstd/nifext_"^^ . "MarkerDB" . . . . "false"^^ . "CHEBI"^^ . "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact."^^ . "iedb.reference" . "http://purl.obolibrary.org/obo/CLYH_$1"^^ . . "0000404"^^ . . . "reagent" . "Yoshiharu Y. Yamamoto" . "The tRNA Gene DataBase Curated by Experts \"tRNADB-CE\" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones."^^ . . "Online Computer Library Center WorldCat" . . . "true"^^ . . "false"^^ . "data model" . . . . . "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . . . . . "loop" . . . "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^ . "Online Mendelian Inheritance in Man" . "Ontology of Physics for Biology" . "idoo" . . "rna" . . "cell reprogramming" . . "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name="^^ . . . . . . . "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^ . "frederique.lisacek@isb-sib.ch" . . . . "subject agnostic" . . "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information."^^ . "regulation" . "Rice Metabolic Pathways" . . . . . "ontology" . "false"^^ . . "false"^^ . "agriculture" . "A representation of the periodic table of the elements in OWL, with both elements and a hierarchical classification. This is from the DARPA Agent Markup Language (DAML) project, which has been inactive since the mid 2000's."^^ . . . . . "http://modelseed.org/biochem/reactions/"^^ . "NCT" . "Ontology of Host Pathogen Interactions" . . . . . . "http://purl.obolibrary.org/obo/VariO_"^^ . . "TTHERM_00648910"^^ . . . "synbip.pss" . . . "icechem" . . "false"^^ . . . "false"^^ . . . "version control" . . "https://www.imanislife.com/?s=$1"^^ . . "^\\d{7}$"^^ . . "ccdc" . "Leigh.Carmody@jax.org" . "MESHC" . . . . . "structure" . . . . . . "LOC_Os01g49190.1"^^ . . "false"^^ . . "obo" . "rna sequencing" . "Bioregistry Schema" . . . "^[a-z_A-Z0-9]+(\\[[c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y]\\])?$"^^ . . . "http://www.bioassayontology.org/bao#BAO_"^^ . . . . "ConfIDent Event" . . . "co_320" . . "false"^^ . . "sbalu@ebi.ac.uk" . "glycomics" . . . "sheeba.samuel@uni-jena.de" . . . "xao" . "molecular dynamics" . . . "An ontology of physico-chemical methods and properties."^^ . "mass spectrum" . "Mike Cherry" . "computational biology" . . "UniProt journal" . . . . . . . . . "ac" . . "false"^^ . . . "AAC"^^ . "DECIPHER CNV Syndromes" . . . . "enzyme" . "false"^^ . "Adriano Mari" . . . . "3403"^^ . . . "molecules" . . . "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."^^ . . . . . "centrally registered identifier" . . . . "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . . "owl" . . . . . . . . . "david.lynn@flinders.edu.au" . . . . "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^ . . "^\\d{7}$"^^ . . "molecules" . . . . "biodiversity" . . "ISTransbase is a highly reliable and accessible database that focuses on inhibitors and substrates of drug transporters, offering a wealth of vital information encompassing experimental methods, transport parameters, and references."^^ . "FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge."^^ . "TAB-884"^^ . . . "https://vcell.org/biomodel-"^^ . "life science" . "botany" . . . . . . "http://physics.nist.gov/cgi-bin/cuu/Value?$1"^^ . . . . . "false"^^ . "structural biology" . . . "bone" . . "https://phytochem.nal.usda.gov/phytochem/chemicals/show/"^^ . "ontology" . . "The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections."^^ . . . "identifier for a physical constant"^^ . . . "false"^^ . "Johannes B. Goll" . . "000001"^^ . . . . "MmusDv" . . . "nanoparticle" . . . . "http://vocab.getty.edu/page/tgn/"^^ . . "obo" . "ontology" . . . "http://exac.broadinstitute.org/gene/"^^ . "false"^^ . "https://civicdb.org/links/molecular_profile/"^^ . "false"^^ . . . . . . "rna" . . "Abdomen"^^ . . "false"^^ . . . . . . . . . . . "agriculture" . . . " http://edamontology.org" . . . . . . . "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^ . . . "BlastRules (identifiers starting with the “NBR” prefix) are a type of evidence for functional classification of proteins based on BLAST (Basic Local Alignment Search Tool). A BlastRule consists of one or more 'model' proteins with known biological function, and BLAST identity and coverage cutoffs. Any protein aligning to a model protein above the cutoffs is considered a BlastRule hit. [from homepage]"^^ . "false"^^ . . . . . . . . . . . . . "genetics" . "livestock" . . "go.gpi" . . "https://cropontology.org/rdf/CO_334:"^^ . . . . . "https://cropontology.org/rdf/CO_331:$1"^^ . "http://www.onto-med.de/ontologies/gfo.owl#$1"^^ . . . . "^\\d+$"^^ . . . "true"^^ . "dialnet.author" . . . . . "pkdb" . "Publons publication" . "Pierre Baldi" . . . . . . . . "biochemistry" . "Colorectal Cancer Atlas" . "0001056"^^ . "fish" . . _:N920933e26da64a52ba1a715b160061bc . . . "http://purl.jp/bio/4/id/"^^ . . "false"^^ . . . . "ontology" . . "NIF Cell" . "false"^^ . "deims.location" . . "bioinformatics" . "false"^^ . . "dlxb" . . "cgd" . . "false"^^ . . . . . . "taxonomy" . . "genome" . . "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . "pavel.hobza@uochb.cas.cz" . . . . "7123"^^ . . "http://purl.obolibrary.org/obo/CLAO_"^^ . . . . . "FunderRegistry" . . . . . . "radiomics" . . "Codon Usage Tabulated from GenBank" . "http://en.wikipedia.org/wiki/$1"^^ . . . . . . . . . . . . . . . "protein" . "cdna" . . . . . "slime-mould" . . . "File inside StoreDB"^^ . "birgit.kersten@thuenen.de" . . . . "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"^^ . . . . "plant phenotypes and traits" . "plant phenotypes and traits" . . . "machine learning" . "https://scholar.google.com/citations?user="^^ . . . . . "http://addgene.org/$1"^^ . . "life cycle stage" . "cell line" . . "false"^^ . "Mammalian Phenotype Ontology" . . . "pandey@jhmi.edu" . . . . "vfdb.gene" . . . . "ontology" . . . "MetaboLights Compound" . . . . . . "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.."^^ . "life science" . "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-"^^ . "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites."^^ . "https://books.google.com/books?id="^^ . "LINCS Data" . . . . "false"^^ . . . "dcid" . . . "w3c rec" . . . . . . . . . . . . . . . "8668"^^ . . "^\\d{7}$"^^ . . . . . . "^ZDB\\-\\w+\\-\\d+\\-\\d+$"^^ . . . . "Identifiers for the protein scaffolds of synthetic binding proteins (SBP), detailing their structural frameworks and roles in facilitating SBP function."^^ . . "microRNA Gene Database" . . "^[A-Z0-9]{6,7}$"^^ . . . . "http://purl.obolibrary.org/obo/DRON_$1"^^ . "BioLegend is a life sciences supply vendor."^^ . . . . "regulation" . . "ontology" . "Immune Epitope Database Epitopes" . . . . . . "true"^^ . . "rouge" . . "Toni Gabaldón" . . . "proteomics" . "sael" . "Physiome Model Repository workspace" . . . . . . . . . . "mcc" . . . "^EBI\\-[0-9]+$"^^ . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"^^ . "SNP to Transcription Factor Binding Sites" . . . "apdavis3@ncsu.edu" . . . "togovar" . "Locus Reference Genomic" . "https://data.4dnucleome.org/biosources/$1"^^ . . "false"^^ . . "1000000"^^ . "https://www.phosphosite.org/curatedInfoAction.action?record="^^ . "life science" . . . "Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance"^^ . . "http://exac.broadinstitute.org/gene/$1"^^ . . . . "ama-cpt" . . . "Core Ontology for Biology and Biomedicine" . . . . . . . "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1"^^ . . . "https://w3id.org/nmdc/"^^ . . "microbial ecology" . "Protein Structural Change Database" . . . "The cBioPortal for Cancer Genomics" . _:N4f2dacaced1b47daa7675d633ebdf89a "Crop Ontology Helpdesk" . "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^ . . . . "cognition" . . "developmental biology" . . . . "http://phylomedb.org/?seqid=$1"^^ . . "https://www.re3data.org/repository/$1"^^ . "0000111"^^ . "storedb.dataset" . . . . "The Echinoderm Anatomy and Development Ontology" . . . . . . . . "http://purl.obolibrary.org/obo/MIRNAO_"^^ . "genome" . "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data."^^ . . . . . . . . . "false"^^ . "https://www.ebi.ac.uk/pdbsum/$1"^^ . "false"^^ . "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse."^^ . "^[0-9]+(LR)?$"^^ . "false"^^ . . "Semion author ID" . "egon.willighagen@maastrichtuniversity.nl" . "http://www.radiomics.org/RO/$1"^^ . "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert="^^ . "mathematics" . . "protein structure" . . . . "genome" . . "The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world."^^ . "small molecule" . . . . . . . . . . . . "MicroScope" . . . . . "bibo" . . . . "Progenetix" . "human" . . "orthologous" . . "https://scicrunch.org/resolver/RRID:AGSC_"^^ . . . . "obci" . _:N0062499e39e142ee87957c7f094e9cf7 "cellsemantics@gmail.com" . . . . "https://www.glycoepitope.jp/epitopes/$1"^^ . . . "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories."^^ . "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets"^^ . . . . "neurovault.image" . "http://www.w3.org/2004/02/skos/core#$1"^^ . "scientist" . . . . . . "genome" . . . . "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^ . . . "P53350"^^ . . "http://purl.obolibrary.org/obo/VT_"^^ . "uberon" . "computational biology" . "paralogous" . "iso15926" . . . "^[0-9]+$"^^ . . . "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl="^^ . . . . . "CCDS12976"^^ . . . . . "^\\d{7}$"^^ . . . . . . . . "0000079"^^ . . . . . . . "https://vocab.org/vann/#$1"^^ . . "false"^^ . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_dys_"^^ . . . "284196006"^^ . . "data integration" . . "ChEMBL" . . . . "Pierre-Marie Allard" . . "epcc" . . . . . . . . . . "https://www.genenames.org/data/genegroup/#!/group/$1"^^ . "Cathy Wu" . . "SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases."^^ . . "data model" . . "TCTR20230429001"^^ . "SABIO Reaction Kinetics" . . "^\\d{7}$"^^ . "http://sabiork.h-its.org/newSearch?q=$1"^^ . "epidemiology" . . . "http://purl.obolibrary.org/obo/NOMEN_"^^ . . "subject agnostic" . "Collection"^^ . "https://www.wormbase.org/species/c_elegans/rnai/$1"^^ . . . . . . . "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/"^^ . . "NIF Standard Ontology: Subcellular Entities" . "bb0754dd-7e69-4b29-b348-3f8017f73d6b"^^ . . "https://www.genome.jp/virushostdb/"^^ . "Ximbio" . "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology."^^ . "C6155"^^ . . "NASA Open Science Data Repository Hardware" . "728"^^ . . . "^\\d+$"^^ . . "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^ . . . . . "^\\d+$"^^ . "phylogenetics" . "https://mycobrowser.epfl.ch/genes/$1"^^ . . "Dutch Research Council File Number" . "LL379-9"^^ . . . . . . . "mammalian" . "Teresa K. Attwood" . "Nathan Edwards" . "^\\d{6}$"^^ . "http://purl.obolibrary.org/obo/CHIRO_$1"^^ . . . "hagr.gendr" . . . . "ArrayExpress" . . "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis="^^ . . "rdf" . "biochemistry" . . . . "General Formal Ontology" . "false"^^ . "imex" . "Identifiers for space-related data from studies that investigate biological and health responses of terrestrial life to spaceflight"^^ . . "systems biology" . . "database" . "http://purl.obolibrary.org/obo/HOM_"^^ . "0000081"^^ . . "molbase" . "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . . . . . . "SMP0000219"^^ . . "data_1664"^^ . "SSF57615"^^ . . . "Synthetic Binding Protein" . "academy" . . . . "classyfire" . "gc" . . "http://purl.obolibrary.org/obo/CLYH_"^^ . . . . . "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort."^^ . . . . "stefanie.seltmann@ibmt.fraunhofer.de" . . . . "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. "^^ . . . "c3abdc60-49f1-49db-81fe-863b7dbb21d3"^^ . . . . "https://www.inaturalist.org/observations/$1"^^ . . "^ENSG\\d{11}$"^^ . . . "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions."^^ . . . "life science" . . "genomics" . . . "gnomad" . . . . . . . . "obo" . . "asteraceaegd.plant" . . . . "ATC_code" . "^\\d+$"^^ . . "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . . "http://purl.obolibrary.org/obo/ONTONEO_"^^ . . "Rat Genome Database qTL" . "GLIDA GPCR" . . . . . "data management" . . "false"^^ . "mba" . "^[0-9a-z_-]+$"^^ . . "http://purl.bioontology.org/ontology/HCPCS/"^^ . "https://bioregistry.io/registry/$1"^^ . . "glida.ligand" . "^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$"^^ . "Jie Zheng" . "encode" . . . . "http://purl.obolibrary.org/obo/CMF_"^^ . "https://biodolphin.chemistry.gatech.edu/detail/"^^ . "NCBI Probe database Public registry of nucleic acid reagents" . . _:Nf5506d4f4bbc4a948d01fceca090af87 "Tom Brennan" . "Sequence Read Archive" . . "cells" . . . . . "report" . "^[0-9a-f\\-]+$"^^ . "^\\d{3}$"^^ . "ttd.drug" . "Open Data Commons for Traumatic Brain Injury" . "sustainability" . "cheminformatics" . . . "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val="^^ . . . "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder."^^ . . . . "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d"^^ . . "botany" . "obo" . . . . . "BioContext" . . "mo" . "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."^^ . "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . "life science" . . . . "false"^^ . "knowledge representation" . . . "Laia Subirats" . "wbls" . . . . . "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"^^ . "Identifiers for immune receptors, representing receptor complexes or groups studied for their interactions with antigens or epitopes."^^ . "Mechanism, Annotation and Classification in Enzymes" . "NLXCHEM" . "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"^^ . . . "Citation Typing Ontology" . "Hsa-Let-7-P2a3"^^ . "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source."^^ . . . "anatomy" . "Epilepsy and Seizure Ontology" . . . "false"^^ . "microbe-host interaction phenotype" . "genome" . . "https://www.checklistbank.org/dataset/3LR/taxon/$1"^^ . . . . . . "small molecule" . "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID="^^ . . . . "Protein and Associated NucleotideDomains with Inferred Trees" . "false"^^ . "CADAFLAT00006211"^^ . . . "biokc" . "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . . . "biomedical science" . . "virushostdb" . . . "Kyoto Encyclopedia of Genes and Genomes" . . "https://biocomputeobject.org/BCO_"^^ . . . "17503"^^ . . . . "https://www.homd.org/genome/genome_description?gid="^^ . . "2023-503698-40-00"^^ . "ChEBI Integrated Role Ontology" . . "^\\d+$"^^ . "addiehl@buffalo.edu" . . . . . "ontology" . . . "http://emmo.info/emmo/cif-core#$1"^^ . "^AT[1-5]G\\d{5}(\\.\\d+)?$"^^ . "^YMDB\\d+$"^^ . . . "obo" . . "SNCTP000005580"^^ . "a.39.1.1"^^ . _:Nfbab19d7fc574378a290cb6bc16080a9 . . "VB.Ob.3736.GRSM125"^^ . . . "angiology" . . . "phenotype" . . . "enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products."^^ . . . "molecular microbiology" . "Susan J. Brown" . "eco" . . . . . "https://glytoucan.org/Structures/Glycans/$1"^^ . . . "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q="^^ . "annotation" . "phylogenetics" . . . . "rcb" . "M00002"^^ . "false"^^ . . . . "false"^^ . . "ontology" . . . . . . . . "The Dietary Restriction Gene Database" . . . . . "http://purl.obolibrary.org/obo/PR_"^^ . "1484"^^ . . "https://pharmacodb.ca/datasets/"^^ . "oryzabase.reference" . "culture" . . . "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^ . . . "KEGG Enzyme" . . . "^\\d{7}$"^^ . . . . "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier."^^ . . . . "structure" . . . "mieg@ncbi.nlm.nih.gov" . . . . . . . "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"^^ . . . . . . . . . "ViolinNet" . "A structured controlled vocabulary for the anatomy of fungi."^^ . . "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."^^ . . "ken.sd.hsu@gmail.com" . . . . . . . . "classification" . "8cf84adb-b4db-4807-ac98-0004247c35df"^^ . . "life science" . . . . . . . . . . "biomedical science" . "Gene Ontology Annotation Database" . . . "false"^^ . "KEGG Drug Group" . . . "https://ieeexplore.ieee.org/document/$1"^^ . "https://tools.ietf.org/rfc/rfc$1"^^ . "genomics" . "ontology" . "gard" . . . "Human Cell Atlas Ontology" . . . . . "SECONDARY_CAS_RN" . . . . . . . "false"^^ . . "RCSB_PDB" . "small molecule" . . "03307879"^^ . "Identifiers for subjects of experiments that investigate biological and health responses of terrestrial life to spaceflight"^^ . "^PA\\d+$"^^ . "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^ . . . . . . . "Cube db" . . "https://ssrn.com/abstract="^^ . "0000002"^^ . . . . "false"^^ . . . . . "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$"^^ . . . . . . . . . "http://xmlns.com/foaf/0.1/"^^ . . "Bambara groundnut ontology" . . . . . "Ax1"^^ . . . . . . . "IEEE Xplore document ID" . . . . . . "MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data.\n\nMetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)]. The majority of pathways occurring in it are from microorganisms and plants. MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number"^^ . "false"^^ . "http://cerevisiae.oridb.org/details.php?id="^^ . "http://xmlns.com/foaf/0.1/$1"^^ . . "laia.subirats@gmail.com" . _:N917cdb559cab4ff1a4f9851f7cd18070 . . . "c"^^ . "Histopathology Ontology" . . "The localization and quantitation atlas of the yeast proteome" . "A language for validating RDF graphs against a set of conditions"^^ . . . . . "Wikidata Property" . "human genetics" . "DisProt" . . "phenotype" . . "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/"^^ . . . . . "https://www.biosino.org/rdbsb/bioparts_detail/$1"^^ . _:N8a509524a9cb46e08282c1e5b3e5d629 "The World Health Organization" . . . . . "KEGG_RCLASS" . . . "0000001"^^ . . "classification" . . "0000449"^^ . . . "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1"^^ . "^\\w+$"^^ . "jaxmice" . . . "Confidence Information Ontology" . . . . "genome" . . . . . . . . . . "life science" . . _:N93f9dbd1f89b4471a84eceb8e53ab192 . . "Terence Murphy" . . "0001885"^^ . "Salmon Ontology" . . . "bfo" . . . . "https://www.re3data.org" . . . "0000-0003-4423-4370"^^ . . "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project."^^ . "http://www.hprd.org/protein/$1"^^ . . . "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats."^^ . . . . . "biology" . . "Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research."^^ . "https://biofactoid.org/document/"^^ . "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^ . . "go.chemicals" . "bibliography" . . . "person" . "^\\d+$"^^ . . "Agent"^^ . "^[A-Z]{1,2}\\d{5}$"^^ . "cdao" . "^\\d+$"^^ . . . . "60316"^^ . . . "http://www.gramene.org/db/protein/protein_search?protein_id=$1"^^ . . . . . . . . . "false"^^ . . "The Data Privacy Vocabulary provides an ontology (classes and properties) and taxonomies of concepts to represent information regarding how personal data is processed in the form of an ontology or a knowledge graph."^^ . . "inbred" . . "ehdaa" . "262393"^^ . "Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)"^^ . . . "protein" . . . . . . "0000001"^^ . "re3data" . . "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . . . . . . . . "false"^^ . . . . "Oryzabase Gene" . "taxonomy" . "mauno.vihinen@med.lu.se" . "Suggested Ontology for Pharmacogenomics" . . "37af84f2-bfd7-4653-b608-eaff44febba6"^^ . . . . "http://purl.org/spar/c4o/"^^ . _:N16f9ff7e027548918006462c9a16ba3a "helpdesk@cropontology-curationtool.org" . "life science" . . "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . "https://osf.io/"^^ . . . . "https://www.brenda-enzymes.de/ligand.php?brenda_group_id="^^ . . . . "90901"^^ . . . . . . . "false"^^ . . "polcaes@gmail.com" . . . . . . "chemistry" . "phebert@uoguelph.ca" . . "strain" . . "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . . . "272"^^ . . . . . . . . "Fly taxonomy" . . . . "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . . . . "fbol" . . . . "^\\d{7}$"^^ . . . . . "false"^^ . "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/"^^ . "Darwin Core is a vocabulary standard for transmitting information about biodiversity. This document lists all terms in namespaces currently used in the vocabulary."^^ . . "matthias.samwald@meduniwien.ac.at" . "https://bioregistry.io/pocketome:"^^ . . "dna" . . . . "false"^^ . "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1" . . . . . . . . "hoelzel" . . "false"^^ . . "138488"^^ . . . . . . . . . . "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " . "C. Robin Buell" . . "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . . "biomedical science" . . "dideo" . . "The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains."^^ . "BTO" . "PharmGKB Drug" . . "https://pharmacome.github.io/conso/"^^ . "false"^^ . . "true"^^ . "false"^^ . "^[-A-Za-z0-9\\_]*$"^^ . "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels."^^ . . . . "^A\\d+$"^^ . . "false"^^ . . "false"^^ . . . "plm" . . "https://rfam.org/family/$1"^^ . . "repository" . "ProtoNet Cluster" . "teddy" . . . "scpd" . "orphanet" . . "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1"^^ . "0000025"^^ . . "laylamichan@ciencias.unam.mx" . . . "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line="^^ . "^\\d{8}$"^^ . . "molecular entity" . . . . "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1"^^ . . "structural biology" . . . "philosophy" . . . . . . . . "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^ . "molecular interaction" . "http://purl.obolibrary.org/obo/AEON_"^^ . . . "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^ . . . . . . . . . . "https://dataguids.org/ga4gh/dos/v1/dataobjects/"^^ . . "^\\d{7}$"^^ . . "241"^^ . . "decipher" . . "ontology" . . . _:Nbe35d9abc7034bcf8e5cda681f62ccbf "helpdesk@cropontology-curationtool.org" . "obo" . "kegg.genes" . . . "Janna Hastings" . . . . "T30002"^^ . . . . . . "ontology" . . . . "registry" . . . "100"^^ . . "false"^^ . "LDCM0160"^^ . . . . . . . . "cido" . . "drug development" . "MAMpol005339"^^ . . . . . . . . "The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects."^^ . "AURKA"^^ . . . "false"^^ . . "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer."^^ . . . . . . . . . . "Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network"^^ . "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby."^^ . . "Asset Description Metadata Schema Vocabulary" . . "NFDI4Chem Collection" . . "false"^^ . "UBPROP" . "dbvar.studies" . . "pathway" . . . . "FuncBase Human" . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"^^ . . "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#"^^ . "earth science" . "https://www.metanetx.org/equa_info/"^^ . . . . . . . . . "https://biopragmatics.github.io/providers/schem/"^^ . . "Mouse Developmental Stages" . "DSSTox_CID" . . . . . . "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid="^^ . "ensembl.bacteria" . . "Gavin H. Thomas" . . "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^ . "http://purl.org/oban/$1"^^ . . . . "false"^^ . "http://purl.obolibrary.org/obo/OHPI_$1"^^ . "publication" . . "22RV1_12_2019"^^ . . . . . "ontology" . "United States Patent and Trademark Office" . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . . . . . "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"^^ . . . . . . . . "false"^^ . . "Pubchem" . "lotus" . . . "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . . "Homeodomain Research" . "anatomy" . . "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines."^^ . . . "ontology" . "SABIO-RK Reaction" . . . . . . . . . . . "CIÊNCIAVITAE ID" . . "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code="^^ . . "MGYA00002270"^^ . "https://www.eionet.europa.eu/gemet/en/concept/"^^ . . "Shoshana J. Wodak" . "https://www.vmh.life/#metabolite/$1"^^ . . "https://data.4dnucleome.org/biosources/"^^ . . . "qualityOfObservation"^^ . "false"^^ . "^\\d+$"^^ . "^\\S+$"^^ . . . . "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA."^^ . . "false"^^ . . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass="^^ . . . . . . "pseudogene" . . "biotools" . "joerg.waitelonis@fiz-karlsruhe.de" . . . . "fbdv" . "https://www.cellrepo.com/repositories/"^^ . . "Montana Smith" . . "^\\d+$"^^ . "false"^^ . . . . . . . "metabolite" . . . "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:"^^ . "gbif" . . "dialnet.article" . "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes."^^ . . . . . . "http://purl.obolibrary.org/obo/OBCS_$1"^^ . "AB" . "^\\d{7}$"^^ . "go.ref" . . "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"^^ . "obo" . . "sequence" . "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology."^^ . . "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available."^^ . . . . "^PED\\d{5}e\\d{3}$"^^ . "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome."^^ . "mir" . . . . . . . "051"^^ . . . . . "00000008"^^ . . . . . . "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . . . . . . . . . . . "protein" . . . . . . . "^oai\\:cwi\\.nl\\:\\d+$"^^ . . . . . "https://flybase.org/reports/FBrf"^^ . "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])?$"^^ . . "worldavatar.kin" . "https://cameochemicals.noaa.gov/chemical/$1"^^ . . "forest management" . . "ontology" . . "obo" . . "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^ . "nasaosdr.biospecimen" . "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^ . "http://research.bmh.manchester.ac.uk/informall/allergenic-food/?FoodId="^^ . . "GeneAnnot: Microarray Gene Annotation" . "organ" . "ValidatorDB" . "enzo" . . . . "^JCRB\\d+$"^^ . . . . . . . . "SEED Compound" . . . . . . . . "false"^^ . "data quality" . "nif_subcellular" . . _:N3912bb7c83314ce4bc4f6d0f364b7435 "rxnorminfo@nlm.nih.gov" . . "biomedical science" . . "10595"^^ . . . . . . . . "false"^^ . . "PhylomeDB" . . "false"^^ . "pharmacogenomics" . . . . . . "FuncBase Mouse" . "tchen@forsyth.org" . . "https://pmb-bordeaux.fr/dataexplorer/?ds="^^ . "gene" . . . "^\\w+$"^^ . "edeutsch@systemsbiology.org" . . "https://bioregistry.io/schema/#$1"^^ . . "^\\d+$"^^ . "^[-_0-9A-Za-z]{12}$"^^ . . "^\\d+$"^^ . . . . "https://www.phenxtoolkit.org/protocols/view/$1"^^ . "biology" . "ddc" . . . . . "salk" . . . . "pubchem.substance" . . . . "glycomapsdb" . . . . . . . . "false"^^ . "bhalla@ncbs.res.in" . . "^\\d+$"^^ . . . "karr@mssm.edu" . . . . . "gene" . . "AEO_RETIRED" . . "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. "^^ . . . . . . "https://www.novusbio.com/products/$1"^^ . "https://www.storedb.org/?"^^ . . . "http://www.proteinatlas.org/$1"^^ . . "GlycomeDB" . . . . . . . . . "https://metazoa.ensembl.org/id/$1"^^ . . "biodiversity" . "false"^^ . . "laevis" . "eNanoMapper ontology" . . . . . . . . . . . . "biochemistry" . . . "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . "tgd" . . . . . "life science" . . "CHEMBL465070"^^ . "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid="^^ . "organelle" . . . . . "anatomy" . . . . . . "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measures, and dimensions."^^ . . "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state."^^ . . . . . "SED-ML data format" . "cell" . . . . . "wikipedia" . . . "http://purl.obolibrary.org/obo/CHMO_"^^ . "https://www.ncbi.nlm.nih.gov/datasets/genome/"^^ . . . . "phenotype" . . . . "Document Components Ontology" . "pba" . "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an="^^ . . "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^ . . "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively."^^ . . . . "http://psb.kobic.re.kr/STAP/refinement1/result.php?search="^^ . . "https://search.clinicalgenome.org/CCID:"^^ . . . . "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^ . . . "false"^^ . . . . . . . "^PKDB[0-9]{5}$"^^ . . . . . . . "false"^^ . "false"^^ . . "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)"^^ . . . . . "DataCollection"^^ . . "rgap" . "0000000"^^ . . . "data management" . . . . "true"^^ . . "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form."^^ . . . "network model" . . . . _:N897fc53d0b0c403f9d8f803af679abd3 "vladimir.n.mironov@gmail.com" . . . . "Index Fungorum" . "CHEBI" . . . "holofood.sample" . . . "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia."^^ . "go.chebi" . . . "https://dialnet.unirioja.es/servlet/revista?codigo="^^ . . . "11478"^^ . "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid="^^ . . "https://bioregistry.io/vsdb:"^^ . . . "agronomy" . "false"^^ . "EcoPortal" . . . . . "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$"^^ . . . "people" . . "false"^^ . "biofactoid" . . . . . "https://www.linkedin.com/in/"^^ . . "RXCUI" . "life science" . . "This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from )" . "false"^^ . . . . . "SM0000020"^^ . "^[A-Za-z]+$"^^ . "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . . . "Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys."^^ . . "http://autism.mindspec.org/GeneDetail/$1"^^ . "SubstrateDB" . "MIPModDB" . . "vasilevs@ohsu.edu" . "^\\d+$"^^ . . "false"^^ . . . "https://entomology.ca.uky.edu/content/"^^ . "mediadive.solution" . . . "obo" . . . _:N4a972aca9ada49e2875dd165dcc104dc "Michael J. Adams" . . "^\\d+$"^^ . . . . "gsherloc@stanford.edu" . . . . _:Nff9cec83104c44d783fe68e5ff33f50a . "HPA000698"^^ . . . "https://pubchem.ncbi.nlm.nih.gov/classification/#hid="^^ . "ontologies" . . . "comparative genomics" . "https://pk-db.com/data/"^^ . "BE0000048"^^ . . . "ontology" . . . "C0017565"^^ . "^\\d{7}$"^^ . "MPATH" . "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."^^ . . "^GCA_[0-9]{9}(\\.[0-9]+)?$"^^ . "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains."^^ . "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . "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."^^ . . . . . . "ontology" . "false"^^ . "molecular structure" . . . "uc001rvw.5"^^ . . . . . . . . . "UMLS" . "AT1402"^^ . . . "false"^^ . . . "agriculture" . . "https://cropontology.org/rdf/CO_324:"^^ . "life science" . . . . . . "false"^^ . "chemont" . . . . "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database."^^ . . . . . "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^ . . . . _:N65ccae73c30e4c6baaff668b2af09913 . . "http://purl.obolibrary.org/obo/CLAO_$1"^^ . . "^\\d+$"^^ . . "false"^^ . . . "life science" . . . . . . "^\\d{7}$"^^ . . "EAWAG Biocatalysis/Biodegradation Database" . "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences."^^ . . "^\\d{7}$"^^ . "The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]"^^ . "WoRMS-ID for taxa" . "037727"^^ . "International repository of Adverse Outcome Pathways."^^ . . "^[1-9][0-9]*$"^^ . "interfil" . . "ontology" . "louis@imbb.forth.gr" . "medicine" . "false"^^ . "DeBiO" . . "https://scicrunch.org/resolver/RRID:NXR_"^^ . "SP_VAR" . "wwpdb" . . . "^\\d{7}$"^^ . . . "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$"^^ . "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"^^ . . "false"^^ . . . . . "A mid-level ontology for representing metadata related to NFDI resources, including individuals, organizations, projects, data portals, and more"^^ . . . "Jörg Waitelonis" . . "false"^^ . . . . . . "syoid" . . "2c6s"^^ . "http://purl.obolibrary.org/obo/AEO_$1"^^ . "https://gtdb.ecogenomic.org/tree?r="^^ . "^\\d{7}$"^^ . . . "microbiome" . "mim" . . . . . . "Identifiers for epitopes, which are the specific parts of antigens recognized by the immune system."^^ . "false"^^ . "biomedical science" . "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments."^^ . . "AJ Ireland" . . . . "ATCC(in host)" . "https://scicrunch.org/resolver/RRID:"^^ . . . . . . "false"^^ . "http://purl.obolibrary.org/obo/UPHENO_$1"^^ . "knowledge representation" . "hpm.peptide" . "http://ciliate.org/index.php/feature/details/$1"^^ . "centrally registered identifier" . . . "merriamwebster" . . . . . _:Nd2bf0f3b6406454fb160dae18729b3b0 . "^\\d{7}$"^^ . . . "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information."^^ . . "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry."^^ . "eVOC mouse development stage" . . . . "Alvis Brazma" . "^DRKS\\d+$"^^ . "protein" . . . . "ontology" . "protein" . . . "19803"^^ . "^[A-Za-z0-9]+$"^^ . . . . . . "Zazuko Prefix Server" . "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . . . "The Statistical Methods Ontology" . . . . "^\\d+$"^^ . . . . . . "ecogene" . . "human" . . . "http://purl.obolibrary.org/obo/CHEBI_$1"^^ . . . . . . . . . . "ontology" . . . . . "genome" . . "2-s2.0-0030770923"^^ . . . "AT1G01030.1"^^ . . "ontology" . . "https://gudmap.org/id/"^^ . . . . . "2"^^ . . "false"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_organ_"^^ . . . . "life science" . . "Darren A. Natale" . . "https://www.fao.org/fishery/en/species/"^^ . . "Sebastian Lobentanzer" . "MIPF0000002"^^ . . "ontology" . "https://mobidb.org/$1"^^ . . "life science" . . . . . "OntoBee" . . . "protein" . . "CHEBI" . "ardb" . . . . "dbmhc" . . "report" . . . . . . . . . . "IUPHARobj" . . . "maria.gould@ucop.edu" . "^[1-9]\\d*$"^^ . . . . "pancreatic islet function" . . "life science" . . . . "mipmod" . "anatomy" . . . . . "http://purl.obolibrary.org/obo/TTO_"^^ . . "bio.tools" . "ASKEM Epidemiology Prefixes" . . "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1"^^ . "proteomics" . . . . "http://purl.obolibrary.org/obo/NOMEN_$1"^^ . . . . "reaction data" . . "http://purl.obolibrary.org/obo/TAXRANK_"^^ . "biomaterial supply resource" . "dashr" . "david.sehnal@gmail.com" . "citation" . . . "^\\d{7}$"^^ . . . . . . . . . "classification" . "Michael Szcześniak" . . "https://www.alliancegenome.org/accession/$1"^^ . "false"^^ . . . . . "3305"^^ . . "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. "^^ . "^\\d{7}$"^^ . . "false"^^ . "http://purl.obolibrary.org/obo/ExO_$1"^^ . . "disease phenotype" . . "http://opendata.inra.fr/ATOL/ATOL_"^^ . "Meghan Balk" . . . "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"^^ . . . "https://bioregistry.io" . . . . "false"^^ . "false"^^ . "interaction" . "http://www.pharmgkb.org/disease/"^^ . "faseb list" . . "https://bioregistry.io/reo:"^^ . "NPC139585"^^ . . "^\\d{7}$"^^ . . . "methods" . . . . . . . "^\\d{3}$"^^ . "^M[0-9]{4,}$"^^ . . "vann" . "assay" . "true"^^ . . "chemical entity" . "http://www.gramene.org/db/literature/pub_search?ref_id="^^ . . . "obo" . . "http://purl.obolibrary.org/obo/VTO_"^^ . . "false"^^ . "ncbiortholog" . "Donna R. Maglott" . . . . . . . "drug interaction" . "protocol" . "PMCID" . "chemidplus" . . _:N64d84a756b6444efbcb16a76493a14df "kpetersen@who.int" . . . . "http://eugenes.org:7072/.bin/fbidq.html?$1"^^ . "huang@southalabama.edu" . . "nextdb" . "ElementNumber"^^ . . . . . . . . . . "http://metnetonline.org/browse_pathway2.php?pthID=$1"^^ . . . "food" . "PMC3084216"^^ . . "VirGen" . . "marilyn.safran@weizmann.ac.il" . "0000001"^^ . . . . . . . "dna" . . . "vep1@cdc.gov" . "pombase" . "zea" . . "biomedical science" . "expressed sequence tag" . "health" . . "RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale. "^^ . "false"^^ . "false"^^ . "^\\d+$"^^ . . "davidos@ebi.ac.uk" . . . . . "false"^^ . . . . . "data model" . . . . "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^ . "false"^^ . . "report" . . "false"^^ . . . . "false"^^ . . . . "ark" . . . . . "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."^^ . . . "adult" . . . . "0000106"^^ . "0000001"^^ . . . "BacMap Map" . "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^ . . . . . "BCRTi001-A"^^ . . . . . . "lipid" . . . . "100E"^^ . . . "false"^^ . . . . . . "http://www.w3.org/ns/activitystreams#"^^ . . . "^GLDS-\\d+$"^^ . "false"^^ . . "CTD Disease" . . "^\\d+$"^^ . . . "Global Biodiversity Information Facility" . "person" . "false"^^ . . . . . . . . . "https://biodolphin.chemistry.gatech.edu/detail/$1"^^ . . . . "http://purl.obolibrary.org/obo/SYMP_$1"^^ . . . . "obo" . "ornaseq" . "phylogenetics" . . "life science" . "metadata" . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . "PTN000000026"^^ . . . . . "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view."^^ . . . . . "Health Canada Clinical Trials Database" . . "The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes."^^ . . . . "validatordb" . . "https://discover.pennsieve.io/package/$1"^^ . "metabolomics" . . . "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)"^^ . . . "adult" . "hgnc.symbol" . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"^^ . "000017"^^ . . . . "https://bioregistry.io/abcam:"^^ . . "ontology" . . . "otl" . "interaction" . . "^[a-zA-Z0-9_\\.]+$"^^ . "The upper level ontology upon which OBO Foundry ontologies are built."^^ . . "PomBase" . . . . . "01.01.005"^^ . . . . . . . "bioinformatics" . . . . . . "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^ . "https://mycobrowser.epfl.ch/genes/"^^ . . "^\\d{7}$"^^ . "Sensors in DEIMS SDR"^^ . . "http://www.bind.ca/Action?identifier=bindid&idsearch="^^ . . "deustp01@med.nyu.edu" . . "https://pb.apf.edu.au/phenbank/strain.html?id=$1"^^ . "https://molbic.idrblab.net/data/cellline/details/$1"^^ . . "Office of Scientific and Technical Information (OSTI)" . "HIT000195363"^^ . . "subject agnostic" . . . "dhba" . . . "subject agnostic" . "https://humap3.proteincomplexes.org/displayComplexes?complex_key=$1"^^ . "Suzi Aleksander" . . . . . . . . . . . . . "gene" . "SCancerRNA provides identifiers for non-coding RNA biomarkers, including long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA, with data on their differential expression at the cellular level in cancer."^^ . . . . "Chicken Gene Nomenclature Consortium" . . . . . "National Center for Biotechnology Information Registry" . . . . . . . "https://hl7.org/fhir/us/"^^ . . . "^\\d+$"^^ . "ACHN"^^ . . . "http://w3id.org/nkos/$1"^^ . "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$"^^ . . "ontology" . . "ontology" . "^\\d{7}$"^^ . . . . . . "AGR" . . "https://bioregistry.io/collection/$1"^^ . . "todd@wormbase.org" . . "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field."^^ . . . . . . . . . . . "biologics" . . "ZDB-GENE-041118-11"^^ . . . "identifier for an author in IEEE Xplore"^^ . . . "false"^^ . . . "Marilyn Safran" . . . "plant breeding" . "false"^^ . "identifier for a source/publication venue (journal, conference, etc) in Scopus"^^ . . "false"^^ . . . "https://reporter.nih.gov/project-details/"^^ . . . "http://purl.obolibrary.org/obo/PROPREO_"^^ . . . . . . "^\\d+$"^^ . . . "http://uri.neuinfo.org/nif/nifstd/nlx_anat_"^^ . . . . "UP000005640"^^ . "measurement" . . . . "false"^^ . . . "00030692-0FE1-4A1B-955E-A2E55D659267"^^ . "http://purl.obolibrary.org/obo/EMAPA_"^^ . . . "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp"^^ . . "https://hdl.handle.net/hdl:20.500.12582/$1"^^ . "omics data analysis" . . . . . "alfred" . "false"^^ . . "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . "^\\d+$"^^ . . . . . . . "9001411"^^ . . . . "http://purl.obolibrary.org/obo/FAO_$1"^^ . . "Yiming Bao" . . "false"^^ . "DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary."^^ . "The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . . "http://rs.tdwg.org/dwc/terms/$1"^^ . . . . "C0020004/4992"^^ . "plant" . . . . "182"^^ . . "synbip.epitope" . . "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . . "ontology" . . . . . "ontology" . . . . . . "https://tree.opentreeoflife.org/taxonomy/browse?id="^^ . . "hpm.protein" . . . "multicellds" . "false"^^ . . . "Imke Tammen" . . . "semantic web" . . "ClassyFire" . . . "ontology" . . . . "false"^^ . . . "Transcriptional Regulatory Element Database" . . "http://oid-info.com/get/$1" . . . "9606"^^ . "life science" . "Dendritic cell" . . "false"^^ . "Workspace (Git repository) for modeling projects managed by the Physiome Model Repository"^^ . . . . . . . "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:"^^ . "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data."^^ . "http://purl.obolibrary.org/obo/CLO_$1"^^ . . "https://bartoc.org/en/node/$1"^^ . "false"^^ . "marie-paule.lefranc@umontpellier.fr" . "life science" . "dc" . "9"^^ . . . "botany" . . "https://cropontology.org/rdf/CO_357:$1"^^ . "^\\d+$"^^ . . . . "^\\d{7}$"^^ . . "http://ratmap.org/Showgene.php?gene_stable_id=$1"^^ . "habronattus" . . "Semantic Web Context" . . . . . . . . . "https://dblp.org/pid/"^^ . . . "40592-R001-100"^^ . . . "lei" . "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . "genomic sequence" . . . . "^(ENSFM|ENSGTV:)\\d+$"^^ . "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes)."^^ . "880798137"^^ . . "46"^^ . . . . "ClinVar Submission" . "The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories.\n\nThe Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).\n\nThere are few notable resources providing access to the Enzyme Nomenclature:\n\n
WebsiteHomepageNotes
ExplorEnzhttps://www.enzyme-database.orgThis is the resources officially recommended by IUBMB
IUBMB (via by Queen Mary)https://iubmb.qmul.ac.uk/enzymeThis is a web-based version of the 1992 publication.
IntEnzhttps://www.ebi.ac.uk/intenz
ExPaSyhttps://enzyme.expasy.org
"^^ . . "Zebrafish Phenotype Ontology" . . "Gary Bader" . . . "metaproteomics" . . . . . . "false"^^ . . . . "Environmental Molecular Sciences Laboratory Project" . . . "aeo" . . "false"^^ . . "NeuronDB" . "6200"^^ . . . . . "pephub" . . "http://zfin.org/$1"^^ . . "hl7.v2codesystem" . . . . . . "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/"^^ . "wos" . "http://purl.obolibrary.org/obo/RoleO_$1"^^ . . . "false"^^ . "https://cropontology.org/rdf/CO_336:$1"^^ . . . "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"^^ . . . "https://guolab.wchscu.cn/AnimalTFDB4//?#/family_summary/TF/"^^ . . . "^\\d{7}$"^^ . . "dermatology" . "protein" . "protocol" . . . . . . . . . . . . "ontology" . . . "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies."^^ . . _:Ne5298e406cb248968c01d8dd5959749c "Pierre Sprumont" . . . "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id="^^ . . . . . . . . "Agilent Probe" . "paul.fabry@usherbrooke.ca" . . . "metascience" . . _:N76406a461040473b99a2a1988bf44ce9 "gregg@greggkellogg.net" . . . . "http://purl.obolibrary.org/obo/ZFA_"^^ . . "false"^^ . . "0002959"^^ . "http://purl.obolibrary.org/obo/COB_$1"^^ . "https://www.nextprot.org/db/entry/"^^ . . . "https://osdr.nasa.gov/bio/repo/data/missions/$1"^^ . . . . . "^[a-z]+/[0-9]+$"^^ . . . . "mco" . "The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library's holdings in LocatorPlus, NLM's online public access catalog, are also provided. [from homepage]"^^ . . . . "annika.jahnke-bornemann@uni-hamburg.de" . . . "obo" . . "obo_rel" . "ICD" . . . "UniProt Archive" . "false"^^ . "Karel Berka" . . . . . . . "^[1-9][0-9]{2,6}$"^^ . . "Cell line collections (Providers)"^^ . . "https://www.disprot.org/"^^ . . . . "gramene.taxonomy" . . . "^\\w{2,4}\\d{5}$"^^ . . "ND50028"^^ . . . "hsapdv" . "GeoNames Feature Code" . . . "false"^^ . . "sequence" . . _:N49e50e7a4f0f4690bd2d5d7ba9790d2a . . "Event Venue Registry" . . . . . "https://www.kegg.jp/entry/$1"^^ . "Cell line collections (Providers)"^^ . "kenan@ucsd.edu" . . "harkemaj@msu.edu" . "https://www.ebi.ac.uk/chembl/target/inspect/"^^ . . . . "msigdb" . . . "population genetics" . . . "https://www.cbioportal.org/study/summary?id="^^ . . . "Patricia Siguier" . . . . "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"^^ . . . "http://www.pharmgkb.org/gene/$1"^^ . . . . . "anatomy" . . . "familyName"^^ . . . . . . . "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"^^ . "0000006"^^ . . "Semantic Sensor Network Ontology" . . . "TreeBASE" . . . . . "Allotrope Merged Ontology Suite"^^ . . . . "^C?\\d+$"^^ . . "mastodon" . . . "false"^^ . "^WBRNAi\\d{8}$"^^ . . . . "drug" . "genome" . . . . . . . . . "TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)" . "false"^^ . . . . . "kegg.module" . . . . . . "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications."^^ . "ontology" . "AKR-270"^^ . . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id="^^ . . . "tetrahymena thermophila" . . "https://bioregistry.io/cst.ab:"^^ . . "true"^^ . "true"^^ . . "hoganwr@gmail.com" . "http://www.allergome.org/script/dettaglio.php?id_molecule="^^ . . . . "^MMP\\d+.\\d+$"^^ . . . "false"^^ . "^\\d+$"^^ . "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/"^^ . "BIOZIL" . . . . . . . "false"^^ . "classification" . "https://bioregistry.io/abs:"^^ . . "Guangshun Wang" . . . "TDR" . . . . "clinvar.submission" . "https://www.alliancegenome.org/accession/"^^ . . . . "informall" . . . . . "http://purl.obolibrary.org/obo/TADS_"^^ . . "http://aps.unmc.edu/AP/database/query_output.php?ID="^^ . "^\\d+$"^^ . . "molecules" . "http://purl.obolibrary.org/obo/ZP_"^^ . . . . . . . . "animal organ development" . "Maude Pupin" . . . "HDAA2" . . . . "chemistry" . "ontology" . . "glycomics" . . "obo" . . "taxonomy" . "chembl" . . "classification" . "biomodels.db" . "false"^^ . . "International Molecular Exchange" . "CAE46076"^^ . "neuroscience" . . "biomedical science" . . "false"^^ . . . "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."^^ . . . "neurovault.collection" . . . "Langua aLimentaria Thesaurus" . . . . . . . . . . . . . "cheminformatics" . "ontology" . . "https://www.gwascentral.org/marker/$1"^^ . "Thomas Keane" . . . . . . "gobpid" . "https://packagist.org/packages/$1"^^ . "MF_01400"^^ . "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id="^^ . . "has local unique identifier example" . . . "PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets."^^ . . . . . . . . . . . . . "homd.taxon" . . "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration."^^ . . . . "obo" . . . . . . . . . . "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:"^^ . . . . . . "Expression"^^ . "preclinical studies" . . . . "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"^^ . . . . "https://mibig.secondarymetabolites.org/go/$1"^^ . "co_321" . . . . "omiabis" . "jcrb" . . . . . . . . . . . . . . . "false"^^ . "0000022"^^ . . . "https://drugs.ncats.io/drug/"^^ . . . . . . . "biology" . "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."^^ . "classification" . . . . . . "https://creativecommons.org/ns#$1"^^ . . "microbial" . . "rrrc" . "atfdb.family" . "basic research" . . . . . . . . "OMIMPS" . . "AOPWiki" . . . . . " A 7-character sid consists of \"d\" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('_' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1."^^ . . . . . . . . "decimal"^^ . "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"^^ . . "Lentil ontology" . . . "SMID-DB" . . . . "bioactivities" . "structure" . . . . . . . . . . . "researcher" . . "0745-4570"^^ . . . . "J55.713G"^^ . . "rscheuermann@jcvi.org" . "false"^^ . "Cluster of orthologous genes" . "pdro" . "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections)."^^ . . "life science" . "genetics" . . "Clement Jonquet" . . . . "https://rpcec.sld.cu/en/trials/$1"^^ . . . . . "MHC Restriction Ontology" . "literalForm"^^ . "^[A-Za-z]+\\/[0-9]+$"^^ . "identifier for a person, on the LinkedIn website"^^ . . . . "ontology" . . . "seed.role" . . . . . "imke.tammen@sydney.edu.au" . "MNXR101574"^^ . . . . . "false"^^ . . . "false"^^ . "3G6A5W338E"^^ . . . . . "false"^^ . . "disease" . "http://www.innatedb.ca/getGeneCard.do?id="^^ . . . . . "eagle-i resource ontology" . _:N58e9d840541e41ea876d0159112d39e0 . . . "http://physics.nist.gov/cgi-bin/cuu/Value?"^^ . . . . "https://bioregistry.io/dragondb.protein:"^^ . . . . "Analyses of microbiome data within MGnify"^^ . "false"^^ . . . "^\\d+$"^^ . . . . . "Peter Karp" . "dctypes" . . . . . "PF3D7_1328700"^^ . . "false"^^ . . "86"^^ . . . . . . "https://ensaiosclinicos.gov.br/rg/$1"^^ . . "SL-0002"^^ . "inhibitors" . "image" . "protein" . . "AADB12"^^ . . . . . . . . . _:Naceb801cb270407194aa4a0ac4c3af42 . . "Feng Zhu" . . . "RHEA" . "elisa-kits" . "Scopus Researcher" . . . . . . . "obo" . "0000001"^^ . . "ENSG00000026508"^^ . . "51"^^ . . . . . . . "https://osdr.nasa.gov/bio/repo/data/experiments/"^^ . . "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage)\nNote that the website uses a different identifier then the one reported in this semantic space."^^ . . . . "false"^^ . "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . "ARBA00000001"^^ . . . "MIMAT0046872"^^ . . . "true"^^ . . . "ndfrt" . "omics" . . . . . . "^\\d+$"^^ . "Oral Health and Disease Ontology" . . . . . "interaction" . "A-GEOD-50"^^ . . . "Cellular Phenotypes" . "http://lisanwanglab.org/DASHR/entry/"^^ . . . "false"^^ . . "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001)."^^ . "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS."^^ . . . . . "false"^^ . "data retrieval" . "false"^^ . . . . . . . "^PTM-\\d{4}$"^^ . "Kenan Azam" . . "1"^^ . "Integrated Canine Data Commons" . . "rnamods" . . . . . "https://ligandbook.org/package/$1"^^ . . "false"^^ . "dwishart@ualberta.ca" . . . "ontology" . . "py.vandenbussche@gmail.com" . . . "protein" . . "Common Core Ontologies" . . "perriere@biomserv.univ-lyon1.fr" . . . "peteremidford@yahoo.com" . "SPCC13B11.01"^^ . "life science" . "false"^^ . "chebi" . . "The ICD-11 Foundation is the comprehensive base layer of the International Classification of Diseases, encompassing all diagnostic concepts, definitions, and semantic relationships, designed for flexibility and adaptability across various use cases, including research, ontology development, and detailed health data analysis."^^ . "Minimal Information About Anatomy ontology" . "roberts@neb.com" . . . "psdo" . . . "0000046"^^ . . . "helpdesk@cropontology-curationtool.org" . "Polytraits Trait Definitions" . . . . . _:Ne5298e406cb248968c01d8dd5959749c "pierre.sprumont@unifr.ch" . . "Cell line databases/resources"^^ . . . . . . "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons."^^ . "biology" . . . . . "MMSL_CODE" . . "Dynamic Ecological Information Management System - Site and Dataset Registry - Dataset" . . . "noaa" . . . . . . . . . "false"^^ . . . . _:Ncf4fc7fd2d3c4f3ca6776004a143688b . . "Docker repository hosted on Docker Hub"^^ . "http://purl.obolibrary.org/obo/CRO_$1"^^ . . "enzyme" . "false"^^ . . . . . . . "mt002305"^^ . . . . . . . "software engineering" . "Measurement method ontology" . . . . "http://purl.obolibrary.org/obo/DIDEO_$1"^^ . "molecular biology" . _:N08af7157802e4fe1a36022ee8ba15c2f . "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam="^^ . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolites."^^ . "comparative genomics" . . "https://bioregistry.io/vipr:"^^ . . "life cycle" . "ontology" . . . "virology" . . . . _:Neb194957c4f949aabc4fdf80b0b22646 "Intellectual.PropertyServices@ama-assn.org" . "bfo11span" . "UM-BBD_enzymeID" . "false"^^ . . . . . "infection" . . "preprints" . . . . "false"^^ . . . "adverse reaction" . . "subject agnostic" . "inxight-drugs" . . . "bibliography" . . "The DevTox Project harmonizes the nomenclature used to describe developmental anomalies in laboratory animals, assists in the visual recognition of developmental anomalies with the aid of photographs, and provides a historical control database of developmental effects in laboratory animals."^^ . . . . . . "RiceNetDB Gene" . "^\\d+$"^^ . . "dna" . "vriend@cmbi.ru.nl" . "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information."^^ . . . . . . "GeneFarm" . "http://www.w3.org/ns/rdfa#$1"^^ . "^\\d+$"^^ . "unipathway" . . . . . . . "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$"^^ . . . . "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . . "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^ . "knowledge and information systems" . "small molecule" . . . "true"^^ . . "Identifiers for relationships between proteins and complexes, along with their type and provenance"^^ . . "false"^^ . . . . . . . "Jeremy Zucker" . . . . . . . . . . . . "https://doulix.com/constructs/$1"^^ . . . . . "^.+$"^^ . . "AnVIL DRS" . . "emap" . "http://purl.bioontology.org/ontology/CSP/$1"^^ . . . "protein" . . . . "false"^^ . . "biocompute" . "biomedical science" . "ontology" . . "Chris Mungall" . . . . . "false"^^ . . "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms."^^ . . "https://www.drugbank.ca/categories/"^^ . "true"^^ . "VEuPathDB ontology" . "pierre-alain.binz@chuv.ch" . "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1"^^ . . . "false"^^ . . . "NanoParticle Ontology" . "unimod" . . . . . "https://proteinensemble.org/$1"^^ . . . . . . "^C\\d+$"^^ . "FBgn0011293"^^ . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . . . . . "Categories in the AFTOL database"^^ . . . . "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump"^^ . . "Getty Thesaurus of Geographic Names" . . . "genome" . . . . . "drug-drug interactions" . . . . "http://purl.unep.org/sdg/SDGIO_$1"^^ . . "dna" . . "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"^^ . . . "bliemsl@xs4all.nl" . . "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies."^^ . "mirgenedb" . "Cellular Microscopy Phenotype Ontology" . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID="^^ . . . "An anatomical and developmental ontology for cephalopods"^^ . "http://dicom.nema.org/resources/ontology/DCM/"^^ . . "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . . . . . "false"^^ . "false"^^ . . . . . . "Neil D Rawlings" . . . . . . . "life science" . "dpvocab" . "dsmz" . . "phylogenomics" . "UniProt provides proteome sets of proteins whose genomes have been completely sequenced."^^ . "James Alastair McLaughlin" . . . "cog" . "epidemiology" . . . "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"^^ . . . . . . . . "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM="^^ . . . "FuncBase Fly" . . . . "ontology" . . . . . "pmap.cutdb" . . . "A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids."^^ . . . . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode="^^ . "k.dumschott@fz-juelich.de" . "Conrad L Schoch" . "data model" . . . . . "Biofactoid" . . . "phipo" . . "methods" . . "jp@senescence.info" . . . "orthologous" . "http://purl.obolibrary.org/obo/AGRO_"^^ . . . "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^ . "4DN"^^ . . . "interaction" . . . "reaction data" . "IP" . "Satya S. Sahoo" . . . . . . "taxonomic classification" . . "ontology" . . . . . . "false"^^ . "merops.entry" . . . . "Probes and Drugs" . . . "false"^^ . . . "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results."^^ . "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^ . . . . . . . "mutation" . . . "Variable"^^ . "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."^^ . . "https://www.uniprot.org/tissues/$1"^^ . . . . "statistics" . "NIST" . "ACYPI000159"^^ . . . . . "http://purl.obolibrary.org/obo/CMF_$1"^^ . . . _:Nd83d06f2d21b434d8cd5ee83981cdcff "Crop Ontology Helpdesk" . . "It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]"^^ . . "infectious disease medicine" . . . "http://www.pharmgkb.org/drug/$1"^^ . . "^ACTRN\\d+$"^^ . "arachnoserver" . . "enzyme" . . "^D\\d{4}$"^^ . "http://purl.obolibrary.org/obo/ONE_"^^ . "ccrid" . . . . "http://degradome.uniovi.es/cgi-bin/protease/$1"^^ . "http://purl.obolibrary.org/obo/OVAE_"^^ . "OriDB Schizosaccharomyces" . "https://bioregistry.io/hivreagentprogram:"^^ . "epidemiology" . "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$"^^ . . . . . . . . "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."^^ . . "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily."^^ . . . . . "siqian.he@nih.gov" . . "false"^^ . "^\\d{6}$"^^ . "false"^^ . . "pathway" . "ogg" . . . . . "^\\d{7}$"^^ . . "https://bbp.epfl.ch/nexus/web/studios/public/"^^ . . . . "false"^^ . . "Performance Summary Display Ontology" . . . "chemical biology" . "phenotype" . "zfa" . "upper-level ontology" . . . . . "rna secondary structure" . . "ontology" . "dg.6vts" . . . . "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . . . . "true"^^ . . . "pdb.ligand" . "Animal Genome QTL" . "genome-wide association study" . . . "disease" . . . . . . . . . . . . . . . "Curated Drug-Drug Interactions Database - Drug" . . . . "ico" . "^M\\d{4}$"^^ . . "taxonomic classification" . "data model" . . "iceberg.element" . "1018"^^ . . "abm" . "false"^^ . . . "false"^^ . . "ontology" . "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . . "^\\d+-\\d+(-[A-Z])?$"^^ . "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians."^^ . . . "anatomy" . . . . "268"^^ . . "true"^^ . . . "false"^^ . . . . "cpc" . "gene" . . . . . "^\\d{7}$"^^ . . . . . "https://w3id.org/linkml/"^^ . . . . . . . . . "https://protists.ensembl.org/id/$1"^^ . "ligandbox" . "Omar Harb" . . "A controlled vocabulary to support the study of transcription in the mouse brain"^^ . . . . . . "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . . "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it."^^ . . . "0000001"^^ . "33607"^^ . . . "animal" . . . "omics" . . "http://purl.org/gc/"^^ . "HoloFood animal" . . . "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$"^^ . "National Academic Research and Collaborations Information System" . . "https://umgear.org/p?id=$1"^^ . "false"^^ . "protein" . . "SNOMEDCT_US_2021_07_31" . . . "^[0-9]{8}$"^^ . . "http://purl.obolibrary.org/obo/ICO_$1"^^ . . . . . "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . . . . . "Selventa legacy protein family namespace used with the Biological Expression Language"^^ . . "http://www.imgt.org/ligmdb/view?id="^^ . "molecular medicine" . . "publication" . "ontology" . . . . . . . "ontology" . . . . . "preclinical studies" . . "http://www.cathdb.info/domain/"^^ . "^\\d+$"^^ . . . . . "https://bioregistry.io/go.rule:"^^ . . . "true"^^ . . . "food" . . . . . "enzyme" . . "An ontology to support comparative effectiveness researchers studying claims data."^^ . . "obo" . . . . "https://pubchem.ncbi.nlm.nih.gov/substance/"^^ . "false"^^ . . . "http://w3id.org/owlstar/$1"^^ . . "^\\d+$"^^ . "false"^^ . . . "subject agnostic" . . "The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data."^^ . "NCBI_taxid" . . "TB2:S1000"^^ . . "microbial ecology" . . . . . "GSTA1"^^ . . "false"^^ . . "^\\d+$"^^ . . "ontology" . . . . . . "rvita@liai.org" . "pathway" . . . . "http://www.ontologyrepository.com/CommonCoreOntologies/$1"^^ . . . "ontology" . . . "antibodyregistry" . "life science" . . . . "Metabolic Atlas Metabolite" . . . "http://hdl.handle.net/$1"^^ . "^\\d*$"^^ . "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes."^^ . "A structured controlled vocabulary for the phenotypes of Ascomycete fungi."^^ . . . . "ASPL0000349247"^^ . "false"^^ . "SNOMEDCT_US_2020_09_01" . . "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"^^ . "0000319"^^ . . "life cycle" . . . "SCancerRNA" . . . . . . . "B00162"^^ . "natural history" . . "agriculture" . . . "https://deims.org/taxonomy/term/"^^ . . . "Alayne Cuzick" . . . . . . . "VegBank" . . . . . . . . . . . . "has canonical prefix" . . "HemOnc Terminology" . "https://www.ncbi.nlm.nih.gov/homologene/"^^ . "http://sabiork.h-its.org/newSearch?q=ecnumber:"^^ . . "Linguist" . "rna" . "structure" . "^ISRCTN\\d+$"^^ . . "https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code=$1"^^ . . . "Mondo Disease Ontology" . . . "protein" . . . "0000002"^^ . . . . . . . . "gemet" . "https://icd.codes/icd10cm/$1"^^ . "The LifeWatch Metadata Catalogues plays a crucial role in managing metadata for digital objects, including Datasets, Services, Workflows and Virtual Research Environments. This catalogue serves as the central repository, ensuring that resources are accessible and reusable by stakeholders."^^ . . "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$"^^ . . "Ardan Patwardhan" . "Internet Engineering Task Force Language Tag" . "curated information" . "http://purl.obolibrary.org/obo/OHMI_"^^ . . . . . . . "biology" . . "0001417"^^ . . "gsso" . "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^ . "NCI" . "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank."^^ . "corum" . . "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases."^^ . . "graingenes.reference" . . "http://biohackathon.org/resource/hco#$1"^^ . . . . . "http://purl.obolibrary.org/obo/ECO_"^^ . . "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName="^^ . . . . "CDC2"^^ . . . "^\\d+$"^^ . . . . . . "^ILMN_\\d+$"^^ . . . . . . . . "cardiovascular disease" . "174"^^ . "http://purl.obolibrary.org/obo/TAHE_$1"^^ . . "j.detras@cgiar.org" . . . . "palayoor.n@northeastern.edu" . . . "drug" . "CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazards—such as explosions or toxic fumes."^^ . "Web Elements" . . . "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"^^ . . "1668761"^^ . "phenotype" . . . "microbial" . "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales."^^ . . "false"^^ . . . . . "agriculture" . . . "false"^^ . "https://string-db.org/cgi/network?identifier="^^ . . . "environment" . . . . . "proteomics" . "false"^^ . . "health science" . "agilent.probe" . _:Na6c73f5131054edfbc4300b3809f2683 "coi@bot.uc.pt" . . "^\\d+$"^^ . "Adam Godzik" . . "data model" . . . . . . . "pharmacogenomics" . . . . "WBbt" . "casspc" . . . . . . . . "true"^^ . . . . . . . . "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles."^^ . . "electronic health record" . . . . . . . . . . . . . "translational medicine" . . . "https://lincs.hms.harvard.edu/db/sm/"^^ . "obo" . . "enhancer" . . . "WormBase RNAi" . "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed."^^ . . "^\\d+$"^^ . "ontology" . "biomedical science" . . . _:N8cab39a79ae541dfae77361e5cd99995 "slarson@ncmir.ucsd.edu" . "iedb.epitope" . . . . . "John-Marc Chandonia" . . . "biomedical science" . "https://www.ebi.ac.uk/thornton-srv/m-csa/search/?s="^^ . "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context."^^ . . . . "http://www.peptideatlas.org/PASS/$1"^^ . . "Influenza Ontology" . . "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . "swiss-model" . . . . . . "false"^^ . . . . . . "^\\d+$"^^ . . . "https://hl7.org/fhir/us/$1"^^ . . "genome" . "false"^^ . "^\\d+$"^^ . . . "genome" . . . "https://rarediseases.org/?p=$1"^^ . . . . . . "genetic" . "statistics" . _:N49e50e7a4f0f4690bd2d5d7ba9790d2a "usha@molecularconnections.com" . . "life science" . . . . . . "dictybase" . "http://www.ebi.ac.uk/astd/geneview.html?acc=$1"^^ . . . . . . "Anita Bandrowski" . . "Cell line collections (Providers)"^^ . "danbri@w3.org" . "false"^^ . . "Pesticide Properties DataBase" . "^\\d+$"^^ . . . . . "disease" . . . . . "CATH superfamily" . "true"^^ . . . "S000002493"^^ . "genome" . . . . "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team."^^ . . . "anatomy" . . "false"^^ . . . . . . . "wikidata" . "charprot" . . "modeling and simulation" . "An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO."^^ . . . . . "CNP0171505"^^ . . . . . "johannes.wittmann@dsmz.de" . . . "0001655"^^ . . "https://lambdamusic.github.io/ontospy-examples/gold-2010owl/class-gold$1.html"^^ . . . . "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."^^ . . . . "false"^^ . "microbiology" . . . . . . "human disease model" . . . "true"^^ . "vivo" . "http://purl.obolibrary.org/obo/EUPATH_$1"^^ . "cellbank.australia" . "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id="^^ . . "phenotype" . . . "Oryzabase Stage" . . . "^[0-9a-zA-Z]{8}$"^^ . . . "http://purl.obolibrary.org/obo/OHPI_"^^ . . . . "vmhmetabolite" . . . "https://phagedive.dsmz.de/strain/$1"^^ . . "antibody" . "http://www.crop2ml.org/cropmdb/"^^ . . "false"^^ . . . . "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1"^^ . . . . "Christophe Dunand" . "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns."^^ . . . "false"^^ . "EUCTR" . . . "plasmodb" . . . . . "mpjensen@buffalo.edu" . . "life cycle stage" . . "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no="^^ . . . . . "protein" . . "molbic.protein" . "false"^^ . "^ENSGT\\d+$"^^ . . . . . . . "openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item."^^ . "^\\d{3}\\.\\d{2}$"^^ . "Registry and database of bioparts for synthetic biology" . "biolink" . . . . "HMS Library of Integrated Network-based Cellular Signatures Antibodies" . . "false"^^ . . . "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . . "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . . "A type for entries in the Bioregistry's collections" . . "classification" . "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." . "^\\d{7}$"^^ . . "obo" . . "^\\S+$"^^ . "Karen R. Christie" . . "diagnosis" . "false"^^ . . "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#"^^ . "phismith@buffalo.edu" . "Kelly T. Hughes" . "Geonamaes" . . . "^ARBA\\d+$"^^ . "false"^^ . . . "false"^^ . "genetic polymorphism" . "Ctibor Škuta" . . . . "BioProject" . . . . "FAIRsharing User" . . "protein" . . "false"^^ . . . . . . "aellenhicks@gmail.com" . . "Gene"^^ . . "http://terminology.hl7.org/CodeSystem/v2-$1"^^ . "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^ . . "fungorum" . . . . "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" . "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources."^^ . . . . . . "Structural Classification of Proteins - Unique Identifier" . . . . . "ontology" . "^\\d{7}$"^^ . "VFG2154"^^ . . . "ddinter.interaction" . "obo" . . . "deims.sensor" . "^PA\\d+$"^^ . . . . "https://www.ebi.ac.uk/arrayexpress/experiments/$1"^^ . . . "Plant Environment Ontology" . "https://www.ebi.ac.uk/intact/search?query=$1"^^ . . . . "obo" . . "1199"^^ . . . "^\\d{7}$"^^ . "^DP\\d{5}r\\d{3}$"^^ . . . "ncbiprotein" . "taxonomic classification" . . "obo" . . . "ratmap" . . . "uniprot.mnemonic" . . "biro" . "URGI Contact" . "regulation of gene expression" . . . "linguist" . . _:Ncd6f05b87b9d4df3ba70120207179446 "Kate Rose" . "http://purl.obolibrary.org/obo/MPATH_"^^ . . . . . . . "https://www.ebi.ac.uk/chembl/cell_line_report_card/"^^ . . . "OUYCCCASQSFEME-MRVPVSSYSA-N"^^ . "HIX0004394"^^ . . . "Sofia Robb" . "citation" . "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^ . "https://ngdc.cncb.ac.cn/genbase/search/gb/$1"^^ . . "false"^^ . "NIF Dysfunction" . . . "http://purl.obolibrary.org/obo/SPD_$1"^^ . "SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as \"sssom:mapping_justification\" are defined in the sssom namespace."^^ . . . . "population genetics" . . . "cell lines" . "rfam" . "Allergome" . . . . . "gabi" . . . . "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . . . . "obo" . "Henriette Harmse" . . . "^\\d{7}$"^^ . "false"^^ . . . "http://www.gramene.org/db/ontology/search?id=GRO:"^^ . "A formal represention for drug-drug interactions knowledge."^^ . "false"^^ . . "life science" . . "nutritional science" . . . . "Edison Ong" . . . "PELNAW"^^ . . . . "National Swine Resource and Research Center" . . . . . . "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#"^^ . . . . "NIF Standard Ontology: Cognitive Function" . . . "Minimum PDDI Information Ontology" . "life science" . "life science" . . "http://www.w3.org/ns/shex#"^^ . "Beta Cell Genomics Ontology" . "^\\d{7}$"^^ . "brain regions" . . . . . . . . . "scopus.work" . . . . "false"^^ . "obo" . "topfind" . . . . . . . . "chemistry" . . . . . . . . . "TAX" . . . . "mesh" . . . . "expression data" . "uo" . "leen.vandepitte@vliz.be" . . "https://www.genenames.org/data/gene-symbol-report/#!/symbol/"^^ . . . . "biomedical science" . . . . "fdb8a927-45c3-48b7-9743-cbb5e16837fa"^^ . . "^.{2,}$"^^ . . . . . . "f665230-5267"^^ . . "https://biopragmatics.github.io/providers/bs/$1"^^ . . . . . . . "ontology" . "^\\d+$"^^ . "https://cthoyt.com/evr/$1"^^ . . . "62"^^ . . . . "John G Tate" . . "https://lincs.hms.harvard.edu/db/datasets/"^^ . "false"^^ . . . "^TC\\d+$"^^ . "life cycle stage" . "https://www.ebi.ac.uk/interpro/entry/InterPro/$1"^^ . "^\\w+:[\\w\\d\\.-]*$"^^ . . . . . . "bcp47" . . "uniprot.core" . "Daniel Kahn" . . . . "Japan Collection of Microorganisms" . "transcription factor binding site prediction" . . . . . "false"^^ . "edam" . . . "http://purl.obolibrary.org/obo/CL_"^^ . "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."^^ . . "1150"^^ . . "UniProt Subcellular Locations" . . "^\\d+$"^^ . . . . . "Jaime Huerta-Cepas" . "false"^^ . "database management" . . "http://purl.obolibrary.org/obo/VSMO_$1"^^ . . . . "10004892"^^ . "medicine" . . "centrally registered identifier" . "frim1"^^ . . . . . . . . . "http://metlin.scripps.edu/metabo_info.php?molid=$1"^^ . "false"^^ . . . "^MMP\\d+.\\d+$"^^ . "Maria Gould" . "w3c rec" . . . . "small molecule" . "5fde96bdc5f1aa9ff0cce18a"^^ . "morpheus.lab/morpheus"^^ . "zdoucmm@gmail.com" . . . . . "Medical Data Models" . . . . "^SD\\d+$"^^ . . "zebrafish line" . . . "http://purl.obolibrary.org/obo/EPO_$1"^^ . . . . . . . "false"^^ . . "enviPath" . "nathan.baker@pnnl.gov" . . . "scop.sccs" . . . . "Paula Duek Roggli" . "Carnegie Stage" . . "ecso" . "ontology" . "structure" . "^[0-9]{1,7}$"^^ . . . "00005254"^^ . "r@iannel.la" . . . . . . "https://progenetix.org/services/ids/$1"^^ . . "odc.sci" . "Chickpea ontology" . "DrugBank Salts" . . . . . . "T06648"^^ . . "https://bcrj.org.br/pesquisa/?search="^^ . "begdb" . . . "DBCAT000600"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"^^ . . "http://purl.obolibrary.org/obo/ARO_"^^ . . . "1537"^^ . . "https://swissmodel.expasy.org/repository/uniprot/"^^ . . "nif.grossanatomy" . . "bioRxiv" . . . . . . . "Birgit Kersten" . "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID="^^ . "^\\d{7}$"^^ . "Academic Event Ontology" . "https://www.arraymap.org/pgx:$1"^^ . . . "0003003"^^ . "1398574"^^ . . . "MIRT000002"^^ . "http://www.pantherdb.org/panther/family.do?clsAccession="^^ . . "Tiago Lubiana" . "rexo" . . . . . "environmental science" . . "genome" . . . . . . . . "^CHEMBL\\d+$"^^ . "false"^^ . . "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"^^ . . "HGNC Gene Group" . . . "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-"^^ . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/MICRO_$1"^^ . . . "grassbase" . "false"^^ . "civic.eid" . "http://tolweb.org/$1"^^ . . . "pesticides" . . . "0000001"^^ . . . "Scholarly Contributions and Roles Ontology" . . . . "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated."^^ . . . . "^\\d+$"^^ . . "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC="^^ . . . . "1"^^ . "seo" . . . . . "5.A.1.1.1"^^ . . "genedb" . . . "gene" . "true"^^ . . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . . . . . . . . . . "tao" . "obo" . . "hydrogeology" . . . . "0000890"^^ . . . "false"^^ . "https://glyconavi.org/hub/?id=$1"^^ . . . . "https://www.ncbi.nlm.nih.gov/sra/$1"^^ . "false"^^ . . . . "NLXFUNC covers terms for cognitive function."^^ . . . "false"^^ . "dawood@helix.nih.gov" . "http://purl.obolibrary.org/obo/FLU_$1"^^ . . . . "social science" . . . . "PRIDE Project" . . . "^[\\d.]+$"^^ . _:N64d84a756b6444efbcb16a76493a14df "Kim Petersen" . "ssbd.project" . "215"^^ . . . . . . . "icd10" . . . . . . "http://homosaurus.org/terms/$1"^^ . "Mark Jensen" . . "false"^^ . "google.patent" . . "An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains"^^ . "ExAC Variant" . "^\\d{3}-\\d{3}-\\d$"^^ . "metabolomics" . . "http://www.crop2ml.org/cropmdb/$1"^^ . "http://biohackathon.org/resource/hco#"^^ . "^\\d+$"^^ . "false"^^ . . "epidemiology" . "Database of Escherichia coli Sequence and Function" . "adcad" . "https://repo.napdi.org/study/$1"^^ . . . "noncodev3" . "Sylvain V Costes" . . "comparative genomics" . "^[A-Za-z_0-9]+$"^^ . . "ecolexicon" . "protocol" . . . . . . "obo" . . . "pazar" . "oga.t@northeastern.edu" . "^\\d{7}$"^^ . "MI0026471"^^ . "false"^^ . . "Immune Epitope Database Assays" . "carnegie.stage" . . "^[0-9]{4}$"^^ . . . "jiezhen@med.umich.edu" . . . . . . "false"^^ . . . . . "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^ . . . "http://purl.org/linked-data/cube#"^^ . "75"^^ . "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"^^ . "assay" . . . . . "00000101"^^ . . . "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$"^^ . "The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/)."^^ . "https://www.xenbase.org/entry/$1"^^ . "^\\d{7}$"^^ . "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1"^^ . "1001"^^ . "^[A-Z0-9]{4}$"^^ . . . . . "anatomy" . . "false"^^ . . . . . . . . . "http://www.scancerrna.com/toDetail?id="^^ . . . . . . . . "http://www.w3.org/ns/oa#"^^ . . . . . . . "Peroxibase" . . . "BARC-013845-01256"^^ . "These resources represent software repositories" . . . . . . . "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . . . . . . . "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1"^^ . . . . . "NIAID ChemDB ID" . . "http://www.nematodes.org/nembase4/cluster.php?cluster=$1"^^ . . "http://csbl.bmb.uga.edu/DOOR/operon.php?id="^^ . "false"^^ . "phylogenetics" . . . "IPR016380"^^ . . . "life science" . "protein" . . "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources."^^ . "oid" . . . . . . "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."^^ . . . "true"^^ . . . "false"^^ . "false"^^ . "http://www.w3.org/ns/ssn/$1"^^ . "false"^^ . . "go.model" . "true"^^ . "^\\d{7}$"^^ . "PolBase" . "SitEx" . "false"^^ . . . . . . "Flavor and Extract Manufacturers Association" . . . "Sue Bello" . "214100"^^ . . . . "http://streptomedb.vm.uni-freiburg.de:8000/streptomedb/get_drugcard/"^^ . . . . . . . "gallont" . "James McLaughlin" . . . "^.+$"^^ . "http://purl.obolibrary.org/obo/ZECO_$1"^^ . . . "https://www.nextprot.org/db/entry/$1"^^ . . . . "https://www.pharmvar.org/gene/"^^ . "SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies."^^ . . . . "regulation" . "Human Proteome Map Peptide" . "2.1.1"^^ . . "murine" . . "article" . "researcher" . . . "http://emmo.info/emmo#EMMO_"^^ . . . . . . . "omics" . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . . . "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^ . . . . . . . . . . "^\\d+$"^^ . . . . . . . . "life cycle" . "packagist" . . . "false"^^ . . "false"^^ . . . . . . "false"^^ . "protein" . . . . "Cell line collections (Providers)"^^ . "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . "https://www.ebi.ac.uk/arrayexpress/arrays/$1"^^ . . . . "https://www.ebi.ac.uk/interpro/entry/antifam/"^^ . . "brain" . . . . . "With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [Fellowship for Interpretation of Genomes (FIG)](http://thefig.info/) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.\nThis prefix provides identifiers for molecular roles that describe the function of one or more proteins in microbes and plants."^^ . . . . . . "Lorenz Reimer" . . . "gthayman@mcw.edu" . "https://goldbook.iupac.org/terms/view/"^^ . . "53504"^^ . "small molecule" . . "agricola" . "SCTID_2010_1_31" . . . . . . . "SIGNOR Relation" . "Gramene Growth Stage Ontology" . . . "Adverse Event Reporting Ontology" . . . "http://purl.org/oban/"^^ . "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI)."^^ . "The S/MAR transaction DataBase" . . . "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials."^^ . "MSH2010_2010_02_22" . "antimicrobial" . . "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR)."^^ . . "Zenodo" . "https://www.picb.ac.cn/limore/cellLines/single?para="^^ . "metacyc.compound" . "genome" . . . . "false"^^ . "Joshua Klein" . . . "false"^^ . "Regulation of Transcription"^^ . . . . "ontology" . "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways."^^ . . "https://models.physiomeproject.org/workspace/"^^ . . . . . . . "https://eds.gene.le.ac.uk/home.php?select_db="^^ . "sabiork.reaction" . "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.)."^^ . . . . . . . . "false"^^ . . . . "HEPRO is an ontology of informational entities and processes related to health procedures and health activities."^^ . . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information."^^ . _:N6fdc8663cceb4d76b9b87a30ec710449 "more.info@allotrope.org" . . "https://metazoa.ensembl.org/id/"^^ . . "http://purl.obolibrary.org/obo/OMRSE_"^^ . . . . "ontology" . . . . "dna" . "http://func.mshri.on.ca/human/genes/list_functional_scores/"^^ . . "neurobiology" . . "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^ . "ontology" . . . . "life science" . . . . . "false"^^ . "shoshana@sickkids.ca" . . "biopragmatics/bioregistry/424"^^ . . . . . . "https://purl.dataone.org/odo/SALMON_"^^ . "niaid.chemdb" . "eaglei" . "EHDAA2_RETIRED" . "sbml.level-3.version-2"^^ . . . . "Lipid Ontology" . . . . . . . "false"^^ . "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1"^^ . "odamexplorer" . "wiktionary" . _:N54cc659311824b238eac9306a6627e94 "helpdesk@eionet.europa.eu" . . "^\\d{8}$"^^ . . "false"^^ . . . . "Biolink Model" . . . "Heather Piwowar" . . "author" . . . "Simple Knowledge Organization System" . . . "dbgap" . "https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1"^^ . "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank."^^ . . "http://scicrunch.org/resolver/SCR_"^^ . . "taxonomic classification" . . . "c.orengo@ucl.ac.uk" . . "identifier for a chemical compound per EINECS or ELINCS"^^ . . "https://www.isrctn.com/$1"^^ . "3000887619"^^ . . "Prefixes mentioned on the _external_ list on the FHIR [Code Systems](https://hl7.org/fhir/terminologies-systems.html) page. This list is mostly complete. Notably, some entries that have not been curated:\n\n- HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460))\n- [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries\n- [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_\n- [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_\n- [MDC](https://www.iso.org/standard/37890.html) (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation" . "BN000065"^^ . "MetaNetX chemical" . "https://mirgenedb.org/browse?qtype=mgid&org=ALL&query=$1"^^ . . . "beiresources" . . . "uniprot.resource" . "false"^^ . . "^\\d{6}$"^^ . "Daniel Gautheret" . . . "^\\d+$"^^ . . . "civic.source" . . . "hsa-mir-200a"^^ . "https://www.storedb.org/?STOREDB:DATASET"^^ . "0000440"^^ . "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^ . "obo" . "PubMed ID" . . "matrixdb.association" . "obo" . . "dna" . "^[1-9]\\d*$"^^ . . . . . . . . . . . . "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee."^^ . . "false"^^ . "protein" . . "diapriid@gmail.com" . . . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information."^^ . . "pathway" . . "shacl" . . . . "richard.scheuermann@nih.gov" . . . "true"^^ . . . . . . "ocid" . "ensembl.metazoa" . "https://cropontology.org/rdf/CO_346:$1"^^ . "life science" . . "false"^^ . . "NLX" . . "Sample processing and separation techniques" . . . . . . "Ontologized MIABIS" . . . . . "VMH reaction" . "https://flybase.org/reports/FBtc$1"^^ . . "scopus.affiliation" . "https://www.nextprot.org/term/$1"^^ . "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"^^ . . "https://fairsharing.org/organisations/$1"^^ . "immunology" . . . . . . . . "https://www.ebi.ac.uk/metabolights/"^^ . . "academy" . . "http://purl.obolibrary.org/obo/PdumDv_"^^ . "^\\d{7}$"^^ . . . . . "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"^^ . . . . "isDocumentRelatedTo"^^ . . "gregory.landrum@phys.chem.ethz.ch" . . . . . . "life science" . "Genome assembly database - INSDC accessions" . . . "interlex" . . . . "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions."^^ . "^\\d+$"^^ . "https://cropontology.org/rdf/CO_325:$1"^^ . "131"^^ . "researchgate.profile" . . . . "disease process modeling" . . . . "community care" . "flicek@ebi.ac.uk" . "false"^^ . . "jeffvin.wong@utoronto.ca" . "false"^^ . . "Ecological terms"^^ . "http://purl.obolibrary.org/obo/AISM_$1"^^ . "icdo" . "http://bigg.ucsd.edu/models/universal/reactions/"^^ . . . . "crates" . "http://www.w3.org/2006/vcard/ns#$1"^^ . . "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network."^^ . "domain" . "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^ . . . "pharmacology" . . . "An issue in any public repository on GitHub."^^ . . "skos" . "life science" . . "diagnosis" . . . . "http://tolweb.org/"^^ . "iao" . . . . . "medical biotechnology" . "^\\d+$"^^ . . . . . . "https://togoid.dbcls.jp/#"^^ . "Nicolas Maillet" . . . . "G00054MO"^^ . . . . . . . . . . . . . . . . . . . "http://purl.obolibrary.org/obo/EHDAA2_$1"^^ . . . "preclinical studies" . "symp" . "false"^^ . "Loggerhead nesting" . . "https://w3id.org/biolink/vocab/$1"^^ . . "zhufeng@zju.edu.cn" . "degradome" . . "true"^^ . "genome" . "en-GB"^^ . "David Blackburn" . . "false"^^ . "false"^^ . "^[1-9]\\d*$"^^ . . . . "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."^^ . . . . . "http://www.kegg.jp/entry/$1"^^ . "ekaterina.chuprikova@eurac.edu" . . . . "ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for compounds that compete with probes for binding to target proteins."^^ . . "New Zealand Threat Classification System" . . "TDWG Taxon Rank LSID Ontology" . "gramene.gene" . "HMS Library of Integrated Network-based Cellular Signatures Datasets" . . _:N3ce42fd5f38d402ba7e8cb590f8198f4 . "amino acid sequence" . "^\\d{7}$"^^ . "px" . . . "56305849200"^^ . "false"^^ . "^\\d+$"^^ . . . "Catalytic Site Atlas" . "false"^^ . . . . . "Ivan Herman" . . "jakkbl@gmail.com" . . . . . . "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases"^^ . . . "ngl" . "Paul Fabry" . . . . . . . "Metadata4Ing" . "identifier for an academic research group issued by the CNRS"^^ . . . "biology" . . . "cst" . . . "false"^^ . . "ontology" . "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features."^^ . "physiology" . . . "311935300"^^ . "http://www.w3.org/2000/01/rdf-schema#"^^ . "^\\d{7}$"^^ . "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications)."^^ . "life science" . "Cell line collections (Providers)"^^ . "67"^^ . "DBPedia" . "genecards.geneannot" . "http://purl.obolibrary.org/obo/KISAO_$1"^^ . . . . "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web."^^ . . . . . . "KEGG_DRUG_GROUP" . . . . . _:Nbc1316da7fc24fecb8577dee5db3c6dc . "molmedb" . . . "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid="^^ . "The Comprehensive R Archive Network" . "species-environment interaction" . "0000010"^^ . . . _:N8cab39a79ae541dfae77361e5cd99995 "Stephen Larson" . "Uber-anatomy ontology" . . "genomics" . . "Handle" . . "^\\d{7}$"^^ . . . . . . . "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^ . "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."^^ . _:N02281f2d0f434cfa9c8474d10915f353 "heinrich.herre@imise.uni-leipzig.de" . . . . . . "true"^^ . "ontology" . "http://data.food.gov.uk/codes/foodtype/id/$1"^^ . "Time Ontology in OWL" . . . "000059"^^ . . . . . "AGRICOLA_ID" . . "ProGlycProt" . "co_327" . . . . . . "functional genomics" . "Packagist" . . . . "Plant Stress Ontology" . . "ontology" . "GlycoPOST" . . . "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^ . "^EDI_\\d+$"^^ . . "PDBsum; at-a-glance overview of macromolecular structures" . . "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"^^ . "false"^^ . "https://www.metanetx.org/comp_info/"^^ . . . "Charles Ettensohn" . . . . . . "http://www.pantree.org/node/annotationNode.jsp?id=$1"^^ . "^\\d{8}$"^^ . . . . "bandrow@gmail.com" . . "assays" . . "A subspace of Metabolic Atlas for compartment-specific records for metabolites."^^ . . . "scop.sun" . . . . . "78"^^ . "http://www.kegg.jp/entry/$1"^^ . . "LiceBase" . "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html"^^ . . . . "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"^^ . "The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts."^^ . . . . . . "https://www.ncbi.nlm.nih.gov/nucest/"^^ . "ihw" . . . "http://purl.obolibrary.org/obo/ExO_"^^ . . . . . "^EGAS\\d{11}$"^^ . . "true"^^ . "17:41223048"^^ . . . "diet" . "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information."^^ . . "sheriff@ebi.ac.uk" . "^\\d+$"^^ . . "ontology" . . "obo" . "http://zinc15.docking.org/substances/$1"^^ . "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1"^^ . . . "ctcae" . "wormpep" . . "yetfasco" . . "^\\d+$"^^ . . "seinet" . "^[a-z0-9]+$"^^ . . "1h68"^^ . "mirnest" . "A Database of Human Hemoglobin Variants and Thalassemias" . "funderregistry" . . . . "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"^^ . . . . . . . . "AB0"^^ . . . "GRIN URL" . . "https://bioregistry.io/medlineplus:"^^ . "961"^^ . . . "false"^^ . . . . "false"^^ . "Wyeth W. Wasserman" . . . "HOSAPI0399"^^ . "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"^^ . "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN="^^ . "qtl" . . . . . "https://bioregistry.io/imgt.hla:"^^ . . . . . "false"^^ . . "Habronattus courtship" . . "^\\w+$"^^ . "life science" . . . . . . . "0000512"^^ . "100810"^^ . . . . . . . . . . . . . "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115="^^ . "obo" . "Simon Jupp" . . . "curies"^^ . "https://registry.identifiers.org/registry/"^^ . . . "false"^^ . . . . . . . "0000095"^^ . "Ontology for the Anatomy of the Insect SkeletoMuscular system" . . "toby.gibson@embl.de" . . . . . "protein" . . . . "false"^^ . . "https://www.semion.io/Author/"^^ . "^Q[A-Z0-9]+$"^^ . "Curated Drug-Drug Interactions Database - Interaction" . "BBA0001"^^ . . . . . "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^ . "exposure" . "false"^^ . . . . "^\\d{7}$"^^ . . "linguistics" . . . "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . "snctp" . "batchelorc@rsc.org" . "phenotype" . . . . . "biomedical science" . "https://bioregistry.io/p3db.site:"^^ . . . "MEROPS Family" . . . "false"^^ . "eric.sid@nih.gov" . "protein" . "false"^^ . "https://data.oncomx.org/OMX_$1"^^ . . . . . . . "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"^^ . "OMA Group" . "http://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . . "rat" . "https://doulix.com/biomodules/$1"^^ . "The international standard for identifying health measurements, observations, and documents."^^ . "https://massbank.jp/RecordDisplay?id=$1"^^ . . . "An ontologization of Public Library of Science (PLOS) journal keywords and topics. It's not clear how the IDs correspond to the actual pages. Appears in ADCAD."^^ . . . "schema" . . . . . . . "gene functional annotation" . "breeding" . . . . . "false"^^ . . . "true"^^ . . "http://purl.obolibrary.org/obo/VO_$1"^^ . . . "https://cropontology.org/rdf/CO_339:"^^ . . "philippe.rocca-serra@oerc.ox.ac.uk" . . "biopixie" . "http://mods.rna.albany.edu/mods/modifications/view/$1"^^ . . "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."^^ . . "Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species."^^ . . . . "phenotype" . "https://www.sharkipedia.org/trends/$1"^^ . . . . . . . "bbkg" . "life science" . "https://www.encodeproject.org/"^^ . . . "go.rule" . . . "false"^^ . . "true"^^ . . . . . . . . . . . "microbiome" . . "live mouse" . "This resource provides identifiers for listed hazardous wastes which are substances explicitly identified due to their potential harm to human health and the environment. These are categorized into four groups (F, K, P, and U) based on specific criteria, such as their source or inherent properties."^^ . . . . . "^GE\\d+$"^^ . . "BRENDA Enzyme" . . "false"^^ . "https://ice.ntp.niehs.nih.gov/api/v1/search?chemid="^^ . "true"^^ . . "https://www.wormbase.org/species/c_elegans/rnai/"^^ . . "rlwalls2008@gmail.com" . . . "Illumina Probe Identifier" . . . "true"^^ . "Database of small human noncoding RNAs" . . . . "apd" . "Scientific Event Ontology" . . "food" . . . . . "http://purl.obolibrary.org/obo/TO_"^^ . "0221"^^ . "biomedical science" . . . . . . . "life science" . . "pathways" . "cheminformatics" . . . . . "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$"^^ . . "Cell line collections (Providers)"^^ . "population dynamics" . . "true"^^ . . "http://classyfire.wishartlab.com/tax_nodes/C"^^ . "PTHR12345"^^ . "Bob Thacker" . . . "chemistry" . . "https://mycobrowser.epfl.ch/genes/"^^ . . . . . . . "Amazon Standard Identification Number" . "life science" . . . . . "disease phenotype" . . . "^m\\w+$"^^ . "0061106995455595"^^ . . "A modeling paradigm-specific registry of prefixes and their URL expansions" . . "rdbsb" . . . "Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a"^^ . "brazma@ebi.ac.uk" . "3hB06"^^ . . . _:N58e9d840541e41ea876d0159112d39e0 "loinc@regenstrief.org" . . . . . "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide)."^^ . "life science" . . . . . . . . . . . "http://vegbank.org/cite/$1"^^ . . . . . . . . . "carlosm@ebi.ac.uk" . "^\\d+$"^^ . . . . . . . "http://purl.obolibrary.org/obo/APO_"^^ . . "ontology" . . . . . . "COG0001"^^ . . . . . . "CoVoc Coronavirus Vocabulary" . "^\\d+$"^^ . "systems biology" . . "omics" . "ogms" . . . "Ribocentre is designed to contain comprehensive information of all natural ribozymes."^^ . . . . "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop="^^ . "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#"^^ . . . . "BioGRID Interactions" . . "life science" . "Gramene QTL" . "https://jrct.niph.go.jp/en-latest-detail/"^^ . . . . . "http://purl.obolibrary.org/obo/OBCS_"^^ . . "mmsinc" . . . . "ICEberg family" . . . . "mihail.anton@chalmers.se" . . . "http://dbpedia.org/resource/"^^ . . "^\\d+$"^^ . . . . . . . . . "w3c rec" . . . "Mauno Vihinen" . "false"^^ . "AgroPortal" . "biochemistry" . . . . . "http://purl.obolibrary.org/obo/BCO_"^^ . . . . "^\\d+(-\\d+)?$"^^ . "EY223054.1"^^ . "demographics" . . "SP_DI" . . . . "gene" . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues."^^ . . . . . "http://www.unimod.org/modifications_view.php?editid1=$1"^^ . "false"^^ . "gecko" . "modeldb.concept" . . . "^\\d+$"^^ . . "biology" . . . . . . . . "0000001"^^ . . . "http://scop.berkeley.edu/sunid="^^ . . . "Drosophila development" . . . "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"^^ . . . . "anatomy" . . . . "eccode" . . "VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host."^^ . "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . . "kcoyle@kcoyle.net" . . "https://bioregistry.io/metaregistry/ncbi/"^^ . . "subject agnostic" . . . . "^[A-Za-z0-9-]+$"^^ . . "protocol" . . "SciProfiles ID" . . . . "drug repositioning" . . "https://www.merckmillipore.com/catalogue/item/$1"^^ . . . . "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"^^ . . . . . . "Clair Kronk" . "UPVAR" . "161671"^^ . "^\\w+$"^^ . . "^\\d{4}$"^^ . "https://purl.dataone.org/odo/MOSAIC_$1"^^ . "60025709"^^ . "helpdesk@cropontology-curationtool.org" . . . . . "Cell line databases/resources"^^ . "google.scholar" . "http://purl.obolibrary.org/obo/EMAP_$1"^^ . "anatomy" . "XUO" . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . . "false"^^ . "ProDom" . . . . "^\\d{7}$"^^ . . "^\\d+$"^^ . . "gene" . . . . "Antibiotic Resistance Ontology" . "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . "sciflection" . . . . "false"^^ . . . "https://biopragmatics.github.io/providers/uniprot.ptm/"^^ . . . . . "disease" . . "ontology" . . . . . . . "biology" . . "protozoan" . . . "MarFun is manually curated database for marine fungi which is a part of the MAR databases."^^ . . . . . . "false"^^ . . . . . . "GenBase" . "agriculture" . "Protein Ontology" . . . . . . . "dwudwary@lbl.gov" . "false"^^ . . "http://uri.neuinfo.org/nif/nifstd/sao"^^ . . . . . "metadata" . . . . "http://www.ontologyrepository.com/CommonCoreOntologies/"^^ . "tsc" . . . "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'."^^ . . . "biomedical science" . "false"^^ . . . "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing."^^ . . "false"^^ . . . . . . . . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"^^ . "^\\d+$"^^ . . . . . . "agriculture" . . . "https://aftol.umn.edu/glossary?category=$1"^^ . . . . "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . . . . . . "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"^^ . . "false"^^ . . "sigmaaldrich" . "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . . . . . . "Sri Lanka Clinical Trials Registry" . . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules."^^ . "PDB Structure" . "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure"^^ . "^\\d+$"^^ . . "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/n2t:"^^ . . . . "Barry Smith" . . . "11084"^^ . "^\\w+(\\-|\\.|\\w)*$"^^ . . "classification" . "Reece Hart" . . "Regulation of Gene Expression Ontology" . "https://biosimulators.org/simulators/$1"^^ . . . _:Na240e2f055ba4e10bb275bdf6f56b7b6 "michael.lincoln@med.va.gov" . . "An ontology to support disciplinary annotation of Arctic Data Center datasets."^^ . . . . . "http://www.yeastract.com/view.php?existing=locus&orfname="^^ . "ontology" . "true"^^ . . "0000032"^^ . . . . "ontology" . . "clinvar.variant" . . "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species."^^ . "dc.terms" . . . . "BioData Catalyst" . "ontology" . . "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . "xlmod" . "1038233"^^ . . . . . . "preclinical studies" . . "false"^^ . . . . . . "false"^^ . "^\\d{7}(_\\d)?$"^^ . . . "https://metacyc.org/compound?orgid=META&id="^^ . . . "ResearchGate profile ID" . "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch."^^ . "Tissue List" . "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location."^^ . . . "infectious disease medicine" . "https://ontology.iedb.org/ontology/ONTIE_$1"^^ . "maya.schuldiner@weizmann.ac.il" . . . . "0000171"^^ . "health science" . "ontology" . "signaling" . . "AffyProbeset" . . "Identifiers for Major Histocompatibility Complex (MHC) restrictions of immune cells, detailing genetic factors that influence immune recognition."^^ . "0000001"^^ . . . . . . . . _:N807cfa133ea245f4be77cad9493a72c4 "adw_geeks@umich.edu" . . . . . . . "obo" . . . . "bioinformatics" . . . . . . . "Software Package Repositories" . . "disease process modeling" . "drks" . "frbr" . "^\\d{7}$"^^ . "ricenetdb.reaction" . . . "ontology" . "http://bigg.ucsd.edu/compartments/"^^ . "ontology" . . "false"^^ . "AY109603"^^ . . . . . "https://www.cancerrxgene.org/translation/Drug/"^^ . "36010371"^^ . . . "zinc" . . . "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project."^^ . "http://purl.obolibrary.org/obo/INO_"^^ . . . "0000086"^^ . "https://hub.docker.com/r/"^^ . . . . . . "biocuration" . . "civic.tid" . "pathology" . "dunand@lrsv.ups-tlse.fr" . "Open Tree of Life" . "https://dialnet.unirioja.es/servlet/libro?codigo=$1"^^ . "resource metadata" . "23"^^ . . . . . . . . . . . . "ontology" . . . . . . "Toshiaki Katayama" . . . "X58356"^^ . "http://purl.obolibrary.org/obo/OPMI_"^^ . . . "http://purl.bioontology.org/ontology/IDODEN_$1"^^ . "gene" . "mediadive.ingredient" . "https://www.uniprot.org/unirule/"^^ . . . "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . . "^[1-9]\\d*$"^^ . . . "https://absd.pasteur.cloud/antibody/$1"^^ . "1.1.1.1"^^ . "policy" . "ENSGT00550000074763"^^ . . "false"^^ . "reactions" . "transcriptomics" . . . . "AURKA"^^ . "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID="^^ . . . . "Topology Data Bank of Transmembrane Proteins" . "^\\d{7}$"^^ . "TransportDB" . . . . "https://www.animalgenome.org/CorrDB/q/?id=CorrID:"^^ . "ChemPro Probe" . . . . . . "200-003-9"^^ . . . . . "ontology" . . . . "^8\\d{4}$"^^ . . . "epigenetics" . "UMLS_CUI" . "stock" . . . . "false"^^ . "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."^^ . . "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1"^^ . . "classification" . . "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"^^ . . . . . "false"^^ . . . . "http://www.orpha.net/ORDO/Orphanet_$1"^^ . . . "The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)"^^ . "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"^^ . "0000008"^^ . "true"^^ . . "PD10000"^^ . "structure" . . . . . . "QJ51RV02"^^ . . . . . "UMIN000049383"^^ . . . . . "false"^^ . . . "uniprot.kw" . . "0000339"^^ . . . "Human Protein Complex Map" . "http://www.signaling-gateway.org/molecule/query?afcsid=$1"^^ . . . "PA448710"^^ . . . "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . . "Network Data Exchange" . . . . . "Rat Genome Database strain" . "basic science" . "ecyano.rule" . . . "collagenmutdb" . "https://www.biosino.org/rdbsb/bioparts_detail/"^^ . "CORDIS Article" . "https://cropontology.org/rdf/CO_343:"^^ . . "A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)" . "obo" . "cazy" . . "false"^^ . "Porifera Ontology" . . . . "genomics" . . . "false"^^ . . . "numpy"^^ . . . "gene" . . . "bel" . _:Ndaadbfc8604f4c8ca0720f4b4f87780f . . . "dna" . . . . . . . . . "http://purl.obolibrary.org/obo/MmusDv_"^^ . . "http://data.europa.eu/89h/"^^ . . . "health monitoring" . . "SpliceNest" . "mathematics" . "^\\d+$"^^ . "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"^^ . . "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."^^ . . . . "emaps" . . "1"^^ . . . . . "matrixdb" . . . "systems biology" . . "false"^^ . "pathguide" . "0000047"^^ . . "Tanja Bekhuis" . "https://absd.pasteur.cloud/antibody/"^^ . "aism" . . "https://bioregistry.io/gard:"^^ . . . . . "life science" . . . "false"^^ . . . . . . . . . " 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)"^^ . . . "ChemIDplus" . . . . "nhcdr" . . "life cycle stage" . . . "subject agnostic" . . "MITE (Minimum Information about a Tailoring Enzyme) is a data repository and associated data standard designed to capture the reaction- and substrate-specificities of tailoring enzymes. Community-driven and fully expert-reviewed, it represents enzymatic reactions using reaction SMARTS and links to established resources such as UniProt, NCBI GenPept, Rhea, and MIBiG. MITE serves as a knowledgebase for enzyme and pathway annotation, in silico biosynthesis, and machine learning applications."^^ . "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NDFRT&code=$1"^^ . "Dawood B. Dudekula" . "http://purl.obolibrary.org/obo/RXNO_"^^ . . . . . . . . . "00000001"^^ . . "ontology" . . . . "https://pephub.databio.org/$1"^^ . "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^ . . . "^\\d{7}$"^^ . . . "civic.assertion" . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_mol_"^^ . "false"^^ . . "https://datacommons.org/browser/$1"^^ . "botany" . . . . . . "plant phenotypes and traits" . "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information."^^ . . . "0000071"^^ . . . . "cellosaurus.resource" . "false"^^ . . . . "REACT" . . . "European Nucleotide Archive" . "structure" . . . . . "https://ssrn.com/author=$1"^^ . "gro-cpga" . "vcell" . "false"^^ . . . . . . . . . . "metadata" . "Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business."^^ . "^\\d{7}$"^^ . . "ontology" . . . "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands."^^ . "https://www.datanator.info/metabolite/$1"^^ . . . . "https://civicdb.org/links/evidence/$1"^^ . . . "food" . "hrehm@mgh.harvard.edu" . . . "protein" . "http://multicellds.org/MultiCellDB/"^^ . . "http://multicellds.org/MultiCellDB/"^^ . . . "^\\d{7}$"^^ . "rxno" . . . . "research project" . "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$"^^ . . "false"^^ . . "https://lccn.loc.gov/$1"^^ . "https://knowledge.lonza.com/cell?id="^^ . . "false"^^ . . . "An ontology of phenotypes covering microbes"^^ . . "Pathguide contains information about 702 biological pathway related resources and molecular interaction related resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated. (from homepage)" . . . . . . . . . "^[0-9]+$"^^ . "ConfIDent Event Series" . . . . "ModelDB concept" . . . . . . . . "false"^^ . . . . "publication" . "researcher" . "life science" . "FuTRES Ontology of Vertebrate Traits" . . "The Drug-Drug Interactions Ontology" . "PTM-0450"^^ . . "false"^^ . "life science" . "protein" . . "Fahim Imam" . . . . . . . . "p3db.protein" . . "false"^^ . . "rat model" . "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"^^ . . "ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for a panel of experts performing variant pathogenecity evaluation."^^ . "Compositional Dietary Nutrition Ontology" . . "^\\d+$"^^ . . . "pathology" . "NCBITaxon" . . "https://panoramaweb.org/$1.url"^^ . "https://www.encodeproject.org/$1"^^ . "guiderdoni@cirad.fr" . "OMA Protein" . . "genomics" . "biologics" . . "interaction" . "cell biology" . "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID="^^ . "xenbase" . "SNOWMEDCT_US" . . . "^[0-9a-z]{24,24}$"^^ . "https://cropontology.org/rdf/CO_333:$1"^^ . . . . . . . "ontology and terminology" . . "dna" . . . . "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1"^^ . "life science" . . "Human Dephosphorylation Database" . "neXtProt family" . "anatomy" . . . . "false"^^ . "^\\d{7}$"^^ . . . "rbo" . . . "true"^^ . . . "ncbigi" . "PED00037"^^ . . "dsm-v" . . . . . . . "UMR7315"^^ . . . . . . . "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^ . "gocc" . "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"^^ . "Guy Cochrane" . . "tanja.bekhuis@tcbinfosci.com" . . "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier."^^ . . . "vendor" . . . . "https://pmb-bordeaux.fr/maggot/metadata/$1"^^ . "273"^^ . "1251"^^ . . . . . . "https://lattes.cnpq.br/"^^ . . . . "TGN is a structured vocabulary currently containing around 1,106,000 names and other information about places. Names for a place may include names in the vernacular language, English, other languages, historical names, names and in natural order and inverted order. Among these names, one is flagged as the preferred name. TGN is a thesaurus, compliant with ISO and NISO standards for thesaurus construction; it contains hierarchical, equivalence, and associative relationships. Note that TGN is not a GIS (Geographic Information System). While many records in TGN include coordinates, these coordinates are approximate and are intended for reference only. The focus of each TGN record is a place. There are around 912,000 places in the TGN. In the database, each place record (also called a subject) is identified by a unique numeric ID. Linked to the record for the place are names, the place's parent or position in the hierarchy, other relationships, geographic coordinates, notes, sources for the data, and place types, which are terms describing the role of the place (e.g., inhabited place and state capital). The temporal coverage of the TGN ranges from prehistory to the present and the scope is global. The TGN is a hierarchical database; its trees branch from a root called Top of the TGN hierarchies (Subject_ID: 1000000). Currently there are two TGN facets, World and Extraterrestrial Places. Under the facet World, places are arranged in hierarchies generally representing the current political and physical world, although some historical nations and empires are also included. There may be multiple broader contexts, making the TGN polyhierarchical. The primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public."^^ . . "deims.taxonomy" . . _:N16f9ff7e027548918006462c9a16ba3a . "61467"^^ . "0000504"^^ . . "https://bioregistry.io/combine.specifications:"^^ . . . . . "81d0ea69a9ab134f6ba68314e982171a367d3ab739c85c5ba49701dd02170ed3"^^ . . "^\\d+$"^^ . . "taxonomy" . "inhand" . . . "^\\d+$"^^ . . . . . "Pierre.Cosson@unige.ch" . . "perkinelmer" . . . "KEGG Glycan" . . "Simon Cox" . . "Datasets inside StoreDB"^^ . . "^[A-Z][a-z][0-9]+$"^^ . "physiology" . . . . "obo" . "UMLS Semantic Types Ontology" . "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols."^^ . "false"^^ . . . . . . . . "^\\w+_COVID19_[-\\w]+$"^^ . "nfdi4chem.ontocape" . . "false"^^ . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"^^ . . "Identifier for an entity in open tree of life"^^ . . . . "metabolites" . "genome" . . . . "pirsf" . . . . . . "kegg.rclass" . . "http://purl.org/spar/pro/"^^ . "ShiBASE" . "stap" . . . "PubChem_Compound_CID" . "Vocabulary used in the RDF representation of SBML models."^^ . . "bioregistry.collection" . . "http://phenol-explorer.eu/foods/$1"^^ . . "taxonomy" . . . . . . . . . "^\\d+$"^^ . "^\\d+$"^^ . . . "Occupation Ontology" . . . . . . . "http://getentry.ddbj.nig.ac.jp/getentry/dad/"^^ . . "obo" . "NCBI Gene Expression Omnibus" . . "morphology" . . "stem cell" . . "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^ . . . . . "^\\w+$"^^ . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . . . "systems biology" . "gsfa" . . "xpo" . . . "sequence" . . . . . . "CIViC Therapy" . "RETIRED_EHDAA2" . "false"^^ . . . "false"^^ . . "mbaudis@me.com" . "true"^^ . . "http://purl.obolibrary.org/obo/AMPHX_$1"^^ . "organism supplier" . "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession."^^ . . . "http://purl.obolibrary.org/obo/HTN_$1"^^ . "164750"^^ . "enrique.blanco@crg.eu" . . "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default"^^ . . . . . . . . "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra."^^ . "The 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."^^ . . . . . . . "orcid" . . "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"^^ . . "irefweb" . . . . "An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date."^^ . . "assay" . . . . . . . . . "^[0-9][A-Za-z0-9]{3}$"^^ . "inxight" . . "molecular biology" . . . . . . "anatomy" . "EDI_244000"^^ . . "image" . . "usageNote"^^ . . "0000685"^^ . "Metabolome Express" . . "sylvain.v.costes@nasa.gov" . . "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"^^ . . . . "peroxibase" . . . "Vincent Robert" . "https://www.arabidopsis.org/protein?key="^^ . . . . . . "false"^^ . "agriculture" . "property" . . . "life science" . "meddra" . "40000617"^^ . "false"^^ . "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"^^ . . . . "CHEBI" . "http://uri.neuinfo.org/nif/nifstd/$1"^^ . "Digital Object Identifier" . . . . . . . "https://www.inaturalist.org/users/$1"^^ . . "life science" . . . "clinical studies" . . "ontology" . . "^[1-9]\\d*$"^^ . . . . "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant."^^ . . "life science" . . . . . . "false"^^ . . . . . "parasitology" . . "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_"^^ . . . "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease."^^ . . . "https://www.pgscatalog.org/pgs/$1"^^ . "16333295"^^ . . "EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)"^^ . "https://catalog.integbio.jp/dbcatalog/en/record/$1" . . . . "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$"^^ . . . "false"^^ . "true"^^ . . "Pearl millet ontology" . "life science" . "1000001"^^ . "false"^^ . . "^\\d+$"^^ . . "gene" . . . . . . . . "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks."^^ . . "ToxoDB" . . "ahamosh@jhmi.edu" . . "P00266"^^ . "http://www.kegg.jp/entry/$1"^^ . . . . . "https://w3id.org/faircookbook/$1"^^ . "true"^^ . . . . "vac" . . . . "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^ . . . "rna" . . . . . . "https://fda.report/applications/"^^ . . "^[CN]*\\d{4,7}$"^^ . . . . "false"^^ . . . . . . . . "life science" . "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data."^^ . "biocuration" . . "br/1"^^ . "false"^^ . . . . . . . . . . . "zoology" . "http://purl.obolibrary.org/obo/OBCI_"^^ . . "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"^^ . . . "0000008"^^ . "Austrian Library Network" . "nztcs" . . . . . . . "Identifiers.org" . "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects."^^ . . . "Tick Cell Biobank" . "transcriptomics" . "GitLab" . . "154022"^^ . . . . . "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs."^^ . . . . "false"^^ . . . "title"^^ . "http://purl.obolibrary.org/obo/PD_ST_"^^ . "developmental biology" . . . . "Tom Gilbert" . "^\\d+$"^^ . . . . "genome" . . . "false"^^ . . . . "developmental biology" . . . . "false"^^ . . . . "http://www.cathdb.info/cathnode/$1"^^ . "https://www.uniprot.org/uniref/"^^ . "doi"^^ . "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^ . "Allan Peter Davis" . . "^CONSO\\d{5}$"^^ . . "FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors."^^ . . . "mmmp:biomaps" . . . . "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L"^^ . . . "obo" . . "life science" . . "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"^^ . . . "MetaCyc Reaction" . . . . . . . . . "Health Canada Drug Identification Number" . "Q-2958"^^ . "Andrea Gaedigk" . . "0000015"^^ . . . . . . "mirbase" . "Enzo Life Sciences" . _:N807cfa133ea245f4be77cad9493a72c4 "Animal Diversity Web technical staff" . . . . . . "sulo" . . . . "pride.project" . . "kegg.genome" . . "http://purl.uniprot.org/uniprot/"^^ . "biosimulations" . . "2023"^^ . . "^H\\d+$"^^ . . "false"^^ . . "environmental science" . "false"^^ . . "disease" . . "aphidbase.transcript" . "false"^^ . . "http://purl.obolibrary.org/obo/MIAPA_$1"^^ . . . "false"^^ . . . . "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^ . "Cell line collections (Providers)"^^ . . "Yeast Metabolome Database" . . "false"^^ . "^.*?--%3E.*?$"^^ . . . "k-12 teacher" . . . . . . . . . "Regulation of Transcription Ontology" . "false"^^ . . "Dialnet article ID" . . . . . . . "fish" . . . "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"^^ . . . . . "Cell line collections (Providers)"^^ . . . . "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$"^^ . . "https://www.gwascentral.org/phenotype/$1"^^ . . "MIRIAM Registry collection" . . "sao" . . . . . . . "Olivier Bodenreider" . "Chen Yang" . "ugis@ebi.ac.uk" . . "https://unicarb-db.expasy.org/msData/"^^ . "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)"^^ . . . "false"^^ . "The Prescription of Drugs Ontology" . . . "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data."^^ . "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution."^^ . "C0026339"^^ . . . "Mark Gerstein" . . _:N917cdb559cab4ff1a4f9851f7cd18070 "helpdesk@cropontology-curationtool.org" . "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"^^ . . . . . . . "alzgene" . "efo" . . . . "obo" . . . "One of the 23 stages of embryo development"^^ . "researcher" . . . "Patrice Buche" . . . . . . . . . . . . "false"^^ . "omics" . . "virsirna" . . "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1"^^ . . . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"^^ . "false"^^ . . . . "https://animaldiversity.org/accounts/"^^ . "CiteXplore" . . . . . "mpid" . "obo" . "genetic engineering" . . . "physics" . . . "ceph" . . "Evan E Bolton" . . "ontology" . "Juan Jose Medina Reyes" . "ModelDB" . . . . . "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . "metabolites" . "bioregistry" . . . . "false"^^ . . . "Represents chemical kinetic reaction mechanisms."^^ . . . . . . . "IC9CM" . "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France)."^^ . . . . . . . . _:Necd84e73a13140e7a380ffb479ea75a5 "Terue Takatsuki" . . . "^IRCT\\d+N\\d+$"^^ . "false"^^ . "blast" . . . "26"^^ . . . "provides for" . "^\\w+$"^^ . "https://europepmc.org/article/CBA/"^^ . . "rnaloops" . "false"^^ . . "Animal Genome Cattle QTL" . . . . . . "chris@sanderlab.org" . . "http://www.nematodes.org/nembase4/cluster.php?cluster="^^ . . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/NCBITaxon_$1"^^ . "neurondb" . . . . _:N20ef6feb9e1b47f89c0612370582861d "custserv@nlm.nih.gov" . "GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E."^^ . . . . . "Pharmacogene Variation Consortium" . . . "ubprop" . . . . . . "http://www.ncbi.nlm.nih.gov/clinvar?term="^^ . "scopus.eid" . . "false"^^ . . . . "http://www.bootstrep.eu/ontology/GRO#"^^ . "100291"^^ . . . . . "Arabidopsis Small RNA Project" . "false"^^ . . "biology" . . . "^P(X|R)D\\d{6}$"^^ . "true"^^ . "Genome Properties" . . . . "NLM Publisher Codes" . . . . . . . . . "vendor" . . "caps" . . . "bioinformatics" . . . "Quinoa Ontology" . "false"^^ . "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid="^^ . . . . . . "mcourtot@gmail.com" . . "true"^^ . "^[1-9][0-9]*$"^^ . . . . . "oryzabase.strain" . "pancreatic development" . "false"^^ . "genetics" . . . "hpscreg" . . . . "^\\d+\\-\\d+\\-\\d+$"^^ . . . . "0471491039"^^ . "Cancer Data Standards Registry and Repository" . "http://purl.obolibrary.org/obo/AGRO_$1"^^ . . . "false"^^ . . "International Fungal Working Group Fungal Barcoding." . . . . . "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank."^^ . "37"^^ . . . . . . . "KEGG Reaction" . . "false"^^ . "bactibase" . . . "https://bioregistry.io/cazy:"^^ . . "https://biopragmatics.github.io/providers/peff/"^^ . "PubMed" . "false"^^ . . . . . . . "protein" . "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23"^^ . "https://datacommons.org/browser/"^^ . "false"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"^^ . . "unite" . . "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$"^^ . . "obo" . . . . "http://www.humanproteomemap.org/protein.php?hpm_id=$1"^^ . . "Physico-chemical methods and properties" . . . . "life science" . . "http://www.wikidata.org/entity/"^^ . "afo" . . . . . "iNaturalist User" . . . . . . "research" . "false"^^ . "Phy000CLXM_RAT"^^ . "http://purl.obolibrary.org/obo/GO_$1"^^ . "0005452"^^ . . "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies."^^ . . "Leszek Vincent" . . . . "biomedical science" . . "PD000596"^^ . . . "sbo" . "false"^^ . "false"^^ . . . "mmp.db" . . . "rsk00410"^^ . "spradling@ciwemb.edu" . . "gnps.task" . . "Ligand-Gated Ion Channel database" . . "anatomy" . "Veterinary Substances DataBase" . . . . "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$"^^ . "molecular biology" . . . . "consulting" . . . . "wb.rnai" . . . "feolo@ncbi.nlm.nih.gov" . "Wes Schafer" . . . . "0000001"^^ . . . . . "https://pubseed.theseed.org/SubsysEditor.cgi?page=FunctionalRolePage&fr="^^ . . . "false"^^ . . . . . "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC."^^ . "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=$1"^^ . "Joao Pedro de Magalhaes" . . . "Prefix Commons" . . "https://molbic.idrblab.net/data/cellline/details/"^^ . "Cell line collections (Providers)"^^ . . . . . . . "infection" . "geographical location" . "ontology" . "https://www.merckmillipore.com/catalogue/item/"^^ . "Andrew C. McShan" . . . . . . "rnacentral" . . . . . "biomedical science" . . . "https://www.geonames.org/recent-changes/featurecode/$1/"^^ . . "life science" . . . "MolMeDB" . "arba" . . . "immunology" . "false"^^ . . "development" . . . . "zfs" . . . . "^[A-Za-z-0-9_]+(\\@)?$"^^ . . "Plant Transcription Factor Database" . "tcb" . . . . . . "PF00004"^^ . . . . . "https://purl.dataone.org/odo/SASAP_"^^ . . "obo" . . . . "sequence" . "software engineering" . "false"^^ . . "bel" . . . . . . . . . . . . . . . "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours."^^ . "Inge Jonassen" . . _:N0f7e99b8116b4e7bbec7f40bc95ea67c "AGROVOC Team" . . . . . "addexbio" . . "LIPID MAPS" . . . . "rgd" . . . . . "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation."^^ . "disease" . . "anatomy" . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1"^^ . . . . . . "mutant mouse repository" . "^\\d+$"^^ . . . . . . . . "false"^^ . "David Clunie" . "http://ecmdb.ca/compounds/$1"^^ . "http://purl.obolibrary.org/obo/ENVO_$1"^^ . . . "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . . "^\\w{5}\\.\\d{2}\\..*$"^^ . "metadata standardization" . . "genomics" . "genome" . "obo" . . . . . "Pathogen Transmission Ontology" . . "https://pk-db.com/data/$1"^^ . "roman@ebi.ac.uk" . "knowledge and information systems" . . . "001"^^ . . "Social Science Research Network Article" . . . "richard@cyganiak.de" . . "^ML\\w+$"^^ . . . . . . "HMS LINCS Cell" . . . "protein" . . "_3dmet" . "Mathias Uhlen" . "false"^^ . . "ICD10WHO" . "genomics" . . . . "GARD" . "interaction" . "ID of a researcher in Authenticus website"^^ . . "jfernand@um.es" . "cell biology" . "^ANF\\d{5}$"^^ . "ontology" . . "cell types" . "ADA"^^ . "00000674"^^ . . . "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id="^^ . "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid="^^ . "Open Data for Access and Mining" . . . . . . . . "https://disprot.org/$1"^^ . . . "Ligand Expo" . . "http://www.w3.org/ns/oa#$1"^^ . . . "fair" . "sequence" . "genomics" . . . . . . . . "An application ontology for use with miRNA databases."^^ . . . "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information."^^ . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/ORNASEQ_"^^ . . "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information."^^ . "https://bioregistry.io/collection/"^^ . "dpo" . . . "http://www.innatedb.ca/getGeneCard.do?id=$1"^^ . "An ontology to capture confidence information about annotations."^^ . . . . "life science" . . . "Human Developmental Stages" . . . . "cell replacement" . . "GPST000024"^^ . "^\\w+$"^^ . "^\\d+$"^^ . . . "Identifiers.org namespace" . "false"^^ . "false"^^ . . . . "false"^^ . . . . "http://dbpedia.org/property/$1"^^ . _:N3a99a6f176d64698a2bcce4519dcb0c7 "custserv@nlm.nih.gov" . "^\\d{7}$"^^ . . . . . . "Tarcisio Mendes de Farias" . . . . "63250"^^ . . "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." . . . . . "http://www.w3.org/ns/odrl/2/$1"^^ . . . . . "https://www.alzforum.org/mutations/"^^ . . . "true"^^ . "nrfc" . . . "life science" . . "7943"^^ . "Genatlas" . . "obo" . "http://aims.fao.org/aos/agrovoc/c_$1"^^ . . . . "false"^^ . " Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . "0000003"^^ . "Amos.Bairoch@sib.swiss" . . . . . . "SNOMED_CT_US_2018_03_01" . . "false"^^ . "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1"^^ . "false"^^ . "https://pmb-bordeaux.fr/maggot/metadata/"^^ . "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$"^^ . "Drivers of human diseases including environmental, maternal and social exposures."^^ . . . "health science" . . "National Drug Data File" . "report" . "Antoine Danchin" . . . "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . . "rna" . . . . . . "DRKS00031815"^^ . _:N3a99a6f176d64698a2bcce4519dcb0c7 "NLM Customer Service" . "false"^^ . . "obo" . . "researcher" . "Functional Requirements for Bibliographic Records Entity-Relationship Model" . . "false"^^ . . . . "0000004"^^ . . "https://metacyc.org/META/NEW-IMAGE?object=$1"^^ . "3D Metabolites" . "http://purl.obolibrary.org/obo/MC_"^^ . "leafsnap" . . . . . . . . . . "http://www.pharmgkb.org/pathway/$1"^^ . "genomics" . "protein" . "http://pepbank.mgh.harvard.edu/interactions/details/$1"^^ . . "OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies."^^ . "false"^^ . . . "false"^^ . . . "ohmi" . . "life science" . . "http://purl.obolibrary.org/obo/OMP_$1"^^ . . "Xenopus Phenotype Ontology" . . "fly lines" . . . "Michael Baudis" . . "database" . "56586"^^ . "covid-19" . "regulation" . . "datacommons" . . "DataCite Ontology" . . . . "HBG004341"^^ . . . . . . "oborel" . . . "fisheries science" . . . . . "bibliography" . "614"^^ . . . . "Q9UKQ2"^^ . "https://herv.img.cas.cz/s/"^^ . "kaggle" . . . . . "life science" . . . "Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog."^^ . . . . "MeSH 2013" . . . . . . . . . "anatomy" . "http://purl.org/spar/bido/"^^ . "biology" . "http://vita.mbc.nctu.edu.tw/search.php?acc=$1"^^ . "ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for human proteins that interact with chemoproteomic probes."^^ . "biomedical science" . "https://mediadive.dsmz.de/medium/$1"^^ . . "H-InvDb Protein" . "Cancer cell LInes GEne fusions portAl" . . . "Ge Gao" . "https://togoid.dbcls.jp/" . . "false"^^ . . . . "DOME Registry" . "https://cran.r-project.org/web/packages/"^^ . "Metabolic Atlas" . . . . . . "false"^^ . "Chris P. Ponting" . "10020.2"^^ . "maglott@ncbi.nlm.nih.gov" . . . "false"^^ . . . . "Ronald C. Beavis (Ron Beavis)" . "food" . "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR."^^ . "omics data analysis" . "^JCGG-STR\\d{6}$"^^ . . "fly" . . "environmental science" . . . "molecular entity" . "https://lincs.hms.harvard.edu/db/cells/"^^ . . . . "clingene" . "biobank" . . "Fab.Schreiber@gmail.com" . "biochemistry" . . "stweedie@ebi.ac.uk" . . "16793"^^ . . . . . . "mouse strain" . . . . "https://www.cytion.com/$1"^^ . "sep" . . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene."^^ . "bartoc" . . . . "PSEEN0001"^^ . . . . . . . . . "http://purl.dataone.org/odo/SENSO_$1"^^ . "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1"^^ . "obo" . "knockout" . "https://cropontology.org/rdf/CO_320:"^^ . "^\\d+$"^^ . . "0000127"^^ . . "icd9" . "https://www.rrrc.us/Strain/?x=$1"^^ . "David Brodbelt" . "google.book" . "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . . . . "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . . . "false"^^ . "National Repository of Fish Cell Lines" . . "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations."^^ . . . . . "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI)."^^ . "chemistry" . . . "The first number is the chapter then the remainder are subsections."^^ . "Karen Eilbeck" . . "drugbank.bioentity" . . "narcis" . . "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"^^ . "Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)" . . . "http://eol.org/schema/terms/$1"^^ . "ontology" . . . "Virus' miRNA target" . . . "241889"^^ . . . "CRISP Thesaurus" . . "false"^^ . . "http://purl.obolibrary.org/obo/ORNASEQ_$1"^^ . "false"^^ . . . "taxonomy" . "selventa" . . . . . "stacia@stanford.edu" . . "obo" . "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^ . . . . . "Rahuman Sheriff" . "cell" . . . . . "ChecklistBank" . . . . . "vario" . . "plant phenotypes and traits" . . . . . . . "mark@gersteinlab.org" . "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1"^^ . . . . "https://lincs.hms.harvard.edu/db/cells/$1"^^ . "pylebail@rennes.inra.fr" . . . "ydpm" . . "Hathi Trust Digital Library" . "https://bioregistry.io/resolve/github/issue/$1"^^ . "http://purl.obolibrary.org/obo/WBls_"^^ . "https://depmap.org/portal/cell_line/$1"^^ . . "eu89h" . "http://purl.org/phylo/treebase/phylows/study/$1?format=html"^^ . . . . "An ontology about scholarship"^^ . "life science" . "Environment Ontology for Livestock" . "biomedical science" . . "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis."^^ . "structure" . . . . . . "Influenza Virus Database" . "http://www.bioinfo.org/NONCODEv4/show_gene.php?id="^^ . . "SNOMEDCT_US_2021_09_01" . "Cell line collections"^^ . . . "ipi" . "tccd" . "Metabolites in drugbank"^^ . "https://glottolog.org/resource/languoid/id/"^^ . "life science" . "false"^^ . "The set of prefixes used in the Cellosaurus resource"^^ . . "ped.ensemble" . "^\\d{1,5}$"^^ . "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . . . "SBML RDF Vocabulary" . "https://sed-ml.org/urns.html#language:$1"^^ . . . "Cell Signaling Technology Antibody" . . "http://purl.obolibrary.org/obo/kestrelo_$1"^^ . "life cycle stage" . . . . . . "4667"^^ . . . . . . . "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^ . "regulation of gene expression" . . . . . . . . "ontology and terminology" . "Benjamin M. Gyori" . . "^[0-9]+$"^^ . . . "http://biocyc.org/getid?id="^^ . "NUI" . . . . . . . . . "data management" . "genome" . "natural language processing" . . . . . . "https://ssbd.riken.jp/database/dataset/$1"^^ . "PhosphoSite Protein" . "GrassBase" . . "0000460"^^ . . . . "^PWY\\w{2}\\-\\d{3}$"^^ . "PT00819"^^ . . "^\\d{7}$"^^ . . . "nuclear" . . . "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . . . . . . "kerafast" . "smoxon@lbl.gov" . . "forest management" . . . "https://w3id.org/sssom/"^^ . "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites."^^ . . "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]."^^ . . . "obo" . . . . . . . . "ASPL0000349247"^^ . "obo" . "false"^^ . "http://purl.obolibrary.org/obo/PR_$1"^^ . "http://scop.berkeley.edu/sccs="^^ . "false"^^ . . . . "^\\d+$"^^ . . . "false"^^ . . "^\\d{7}$"^^ . . "montana.smith@pnnl.gov" . "clinical studies" . . . . . . "genomics" . . . "A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods"^^ . "gene" . . . . . . "Homosaurus" . . "maizegdb.locus" . . . . . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/MI_"^^ . "bido" . . . . "structure" . . "Michael Riffle" . . . . "David S. Wishart" . . . "bibliography" . . "0000027"^^ . . . "isbn" . "Electron Microscopy Public Image Archive" . . . . "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . "uniprot.chain" . "BDGP insertion DB" . . "drug discovery" . . "miR-1"^^ . "BindingDB is the first public database of protein-small molecule affinity data."^^ . . . . . "ontology" . . . . "10531"^^ . . "VIRsiRNA" . . . . "https://www.wikidata.org/wiki/Property:$1"^^ . . . . "life science" . . . . "biomedical science" . . "pdbsum" . "https://www.thermofisher.com/antibody/product/"^^ . . "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models."^^ . . "true"^^ . "bioimaging" . . . "obo" . . . "http://www.ebi.ac.uk/efo/EFO_$1"^^ . . "computer science" . "^RCV\\d+(\\.\\d+)?$"^^ . . . "false"^^ . "rubygems" . _:N4c94689a87b548d6ae5f280e9e8e0183 . "false"^^ . "0000001"^^ . . "afpo" . . . "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id="^^ . . "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"^^ . . . . "http://purl.obolibrary.org/obo/MONDO_"^^ . . . . "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits."^^ . . . . . . . . . . "biology" . . "https://bioregistry.io/ppdb:"^^ . "http://purl.obolibrary.org/obo/$1_$2" . . "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/"^^ . . . . . "http://purl.obolibrary.org/obo/BSPO_"^^ . . . "^\\d{7}$"^^ . "nih initiative" . . . "http://purl.obolibrary.org/obo/XAO_$1"^^ . "https://aopwiki.org/events/$1"^^ . . . "small molecule" . . "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id="^^ . . . . . . "epawaste" . . . "Social Insect Behavior Ontology" . . . . . . "false"^^ . "epigenetics" . "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"^^ . . . . "https://www.storedb.org/store_v3/download.jsp?fileId="^^ . "skip" . . . "0000001"^^ . . "hgnc.family" . . "cio" . . . . "life sciences" . "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"^^ . . . . . . . "DSMZCellDive" . . . "drosophilidae" . "heart" . "SIDER Drug" . "https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema="^^ . "satyasahoo@ieee.org" . . . "exac.variant" . . . . "molecular biology" . "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"^^ . . . . . . . . . . . . . . . "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . . . . . . . . . . . "data analysis service" . . . . "ontology" . . "nmr" . . "mouse strain" . . "Viral Bioinformatics Resource Center" . "genome" . . . . . . . . . . . . "SNOMEDCT_US_2018_03_01" . . . "umls.sty" . "PepBank Peptide Database" . . . "false"^^ . "https://bioregistry.io/imgt.primerdb:"^^ . . . . . . "Grape Ontology including OIV and bioversity descriptors. INRA July 2017"^^ . . "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . "achcar11"^^ . . . "molecular chemistry" . "https://bioregistry.io/d1id:"^^ . . "false"^^ . "^[1-9]\\d{5}$"^^ . . . . "false"^^ . . "millipore" . . . "http://w3id.org/nfdi4ing/metadata4ing#$1"^^ . . "https://data.oncomx.org/OMX_"^^ . . . . . "person" . "false"^^ . . "sh" . "po" . . . "https://bioregistry.io/beiresources:"^^ . "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . . . . . "nif.std" . "jonrkarr@gmail.com" . . "SysBioCancer2022"^^ . . "ecoliwiki" . "transportdb" . "John Kunze" . "nsf.award" . . . . "metaregistry" . . "computational biology" . "https://easychair.org/cfp/"^^ . . . "CIViC Evidence" . "Subcellular Anatomy Ontology" . "protocol" . . . "subject agnostic" . . "sheepqtldb" . . . . "Orphanet" . "https://pharmacodb.ca/cell_lines/"^^ . . . . . "https://www.ebi.ac.uk/biomodels/"^^ . . . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1"^^ . . "http://purl.obolibrary.org/obo/SLSO_"^^ . . . . . "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"^^ . . . . . . . . . . . . "SNOMECT" . . . . . . . "http://purl.org/vocab/frbr/core#$1"^^ . . "https://www.aapc.com/codes/cpt-codes/$1"^^ . "functional genomics" . "authorea.author" . . "drug report" . . "sosa" . . . . . . "jorvis@gmail.com" . . "Peter Midford" . . . "https://www.cancerrxgene.org/translation/Drug/$1"^^ . "Oat ontology" . . "agriculture" . . . "145"^^ . . . . . "Mouse Developmental Anatomy Ontology with Theiler Stage" . . . . . . . "genomics" . "ontology" . . . . . . "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . . . . . "obo" . "genomics" . . "structure" . "PrefixOrTermMapping"^^ . . . . . . "metadata" . . . . "^NPA\\d{6}$"^^ . "true"^^ . "blast" . "biomedical science" . . . "image" . "http://purl.obolibrary.org/obo/MAO_$1"^^ . "^\\d{7}$"^^ . . . . "obo" . . . "genomics" . . . . . . . "Carbohydrate Active EnZYmes" . . . . . . "false"^^ . . . "lonza" . "obo" . . . . . . "Korean Clinical Research Information Service" . "0000101"^^ . "Ctenophore Ontology" . . "Korean Cell Line Bank" . . . . "ontology" . "false"^^ . . . "EDAM Topic" . "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis."^^ . . "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy."^^ . . "^\\d+$"^^ . "^\\d{7}$"^^ . . . . . "gene" . . . . "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi."^^ . . . . "^[A-Z]+$"^^ . . . . . "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information."^^ . "false"^^ . . "obo" . . . . . . . . . . "Sequence types and features ontology" . . . . . "medicine" . . "https://www.kazusa.or.jp/huge/gfpage/$1"^^ . "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"^^ . "MSBNK-IPB_Halle-PB000166"^^ . "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . . . . . . . . "data model" . . . . "Database of one-to-one ortholog information provided by the NCBI as a subset of their Gene resource. Used for users to access ortholog information for over 1000 species of vertebrates and arthropods."^^ . . "mhucka@caltech.edu" . . "https://registry.identifiers.org/registry/$1" . . "false"^^ . . . "^\\w+\\_\\w+$"^^ . "chris.ponting@ed.ac.uk" . . . . . "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . . "https://bioregistry.io/dashr.expression:"^^ . . "non-coding rna" . "AffyProbeset"^^ . . . "^\\d+$"^^ . . _:N6fdc8663cceb4d76b9b87a30ec710449 . . "http://purl.obolibrary.org/obo/ICEO_"^^ . . . "drug" . "dbpedia.property" . . . . . . . "0000011"^^ . "ikufareva@ucsd.edu" . . "false"^^ . "https://ror.org/"^^ . . "^\\d+$"^^ . . "Laboratory"^^ . . . . "SRX000007"^^ . . . "cognitive neuroscience" . . . . . "4776"^^ . . "ontology" . "model organism" . . . . . "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit."^^ . "https://foodb.ca/foods/"^^ . "Manufacturers of Vaccines" . . . . . . . . . "CIViC Variant Group" . . . . "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id="^^ . "gmd.profile" . "RID1"^^ . "false"^^ . "https://cropontology.org/rdf/CO_360:$1"^^ . "0e39569d-ff81-4b78-9c34-b07309504d80"^^ . . "http://pombe.oridb.org/details.php?id=$1"^^ . . "Nathan Sheffield" . . "A semi-automatically generated knowledgebase"^^ . . . . . . . . "https://trialsearch.who.int/Trial2.aspx?TrialID=$1"^^ . . "Hilmar Lapp" . "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE."^^ . . "^\\d{7}$"^^ . "0000088"^^ . . "ontology" . . . . . . . . . . . . "PNS12@cam.ac.uk" . . "http://wodaklab.org/iRefWeb/interaction/show/"^^ . "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata."^^ . . . . . . . . "http://vbrc.org/gene_detail.asp?gene_id="^^ . "Multum MediSource Lexicon" . . "Daniel N. Wilson" . "http://stitch.embl.de/interactions/"^^ . . . "false"^^ . . "peco" . "137"^^ . . "mouse" . . "genome" . "http://scop.berkeley.edu/sccs=$1"^^ . "A free dictionary"^^ . . . . . "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"^^ . . . "Cooperative Patent Classification" . . "false"^^ . "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\"."^^ . . . . . . "cell" . . "ICDCM_2005" . . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/PAO_$1"^^ . "GnpIS" . . . . . . . . . . . . . "network model" . . . . "ontology" . . "http://snomed.info/id/$1"^^ . "data model" . "26957"^^ . . . . . . . . "false"^^ . "CP0041613"^^ . "CO_325" . . . "rs17852708"^^ . . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$"^^ . . . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes."^^ . . . . . . "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id="^^ . . . . . . "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^ . "https://loinc.org/$1"^^ . "nddf" . . "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons."^^ . "mirbase.family" . . "^[0-9a-f\\-]+$"^^ . . . . . . . "life science" . "Katy Börner" . . . "life science" . . . . . . . . "false"^^ . "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"^^ . "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis."^^ . . . "https://ensaiosclinicos.gov.br/rg/"^^ . "ga4ghdos" . . "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00"^^ . "reaxys" . "WBPhenotype" . . . . "probonto" . . . "^UMIN\\d+$|^C\\d+$"^^ . "biomedical science" . "clinical decision support systems" . . "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . "http://purl.obolibrary.org/obo/LEPAO_"^^ . . . "Identifiers.org Terms" . . "^\\d{7}$"^^ . . . . . "omics" . "citation" . . "deims.network" . . "protcom" . . . "station.6051b2f8b9142a5b8c676342"^^ . . . "http://vivoweb.org/ontology/core#"^^ . . "obo" . . . . . "UM-BBD compound" . . . . "^[a-z]+(\\..*?)?$"^^ . . . . . . . "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies."^^ . . . "^\\d{7}$"^^ . "false"^^ . . "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS)."^^ . "David Sehnal" . "translational medicine" . . . . . . . "^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$"^^ . . . "Q5BJF6-3"^^ . . "eff796f3-6195-11e5-8ac5-06603eb7f303"^^ . . . . . . . . "academy" . "omid" . . . . . . . . . . . . "WikiPathways is a database of biological pathways maintained by and for the scientific community."^^ . "phenomics" . . . . . . "false"^^ . "^\\d+$"^^ . "zazuko" . "life science" . "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components."^^ . "false"^^ . . "http://www.genome.jp/dbget-bin/www_bget?aaindex:"^^ . . . "Chinese Biological Abstracts" . . "computational biology" . . . . "Cell line collections (Providers)"^^ . . "false"^^ . . "dna" . . . . "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . . . _:N51f8a03301c741d5b216ca7d5de38061 "mb4@sanger.ac.uk" . . . . . . . . "luiPattern"^^ . . . . . . . . . "https://bioregistry.io/registry/"^^ . . . . . . . "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies."^^ . . . "obo" . "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:"^^ . . . . . . "malaria" . "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER."^^ . "http://www.ebi.ac.uk/astd/geneview.html?acc="^^ . "false"^^ . "ideal" . . . . . . . . "ttd.target" . . . "cell biology" . . . . "fluticasone"^^ . . . "FMAID" . . "23159291"^^ . "biology" . . . "false"^^ . "apollosv" . . . . "https://bioregistry.io/csd:"^^ . . _:N1e12b17b8ed7446da447ace8539ffd7d "NCI Thesaurus Mailbox" . . . . . . "http://www.bindingdb.org/compact/"^^ . "http://purl.obolibrary.org/obo/BTO_"^^ . . "ssrn.author" . . . . "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities."^^ . "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id="^^ . "computational biology" . . . . "https://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf="^^ . "^(\\d\\d\\d|V\\d\\d|E[8-9]\\d\\d)(\\.\\d{1,2})?$"^^ . "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . . "life science" . "https://www.ebi.ac.uk/biosamples/sample/$1"^^ . . "classification" . . . . . "Miguel A. Fortuna" . . "brenda.ligand" . . "biosimulations" . "neuroscience" . . "00000021"^^ . "dr.sebastian.koehler@gmail.com" . . "genome" . "Orphanet Rare Disease Ontology" . . . "^\\d+$"^^ . . . . "linkml" . . . . . . . "botany" . "HGNC gene symbol" . . . . . "target" . . . "wosid" . "Protein Ensemble Database" . . "ncbitaxon" . . . . . _:N3b98a4a211264478917f1232ff435bb6 "davem@umn.edu" . . . "^[A-Za-z_0-9]+$"^^ . _:N0e2e1d6413374a399b3b9188d3ae66b0 "Ian Davis" . . . "protein" . "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI."^^ . "CAS_RN" . "glycomedb" . . . "https://ecocyc.org/gene?id="^^ . . "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank."^^ . . . "cell" . . . "SNOMEDCT_US_2022_09_01" . "false"^^ . . . . "plant cell biology" . "false"^^ . "An organization in FAIRsharing, including universities, labs, etc."^^ . "https://assets.nemoarchive.org/"^^ . . . . . . "mmp.cat" . . . . "SWISS-MODEL Repository" . . _:N6842dbf57b3c4a21a8744d80c34d0343 "Sean Roberts" . . . . . . "phenotype" . "agsd" . . . _:N9bc6191d1bcf433094fa654b9c56d349 . . . "metanetx.reaction" . . . . "https://prosite.expasy.org/$1"^^ . . "^[a-zA-Z0-9_\\.]+$"^^ . "identifier for an educational organization issued by the UK Register of Learning Providers"^^ . "biomodels.kisao" . . "^[A-Za-z_0-9]+$"^^ . . "http://go.drugbank.com/drugs/"^^ . . . "disprot.region" . . "disorder" . . . . . . . "TA_H3"^^ . . "false"^^ . . "global health" . "experimental measurement" . . "CAID" . . . "An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). "^^ . . "obo" . . . "^CE\\d{5}$"^^ . "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility."^^ . . "obo" . . . . "urmas.koljalg@ut.ee" . . . "https://mediadive.dsmz.de/medium/"^^ . . . . . . . . . . . . . "^RID\\d+$"^^ . . "meetings" . . . "van_slyke@zfin.org" . . . . "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law."^^ . "false"^^ . . "SIGNOR-252737"^^ . "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers."^^ . . . "true"^^ . . "false"^^ . . . "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. \"Inheritance\" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method × object of research."^^ . "ontology" . . "0000009"^^ . _:N59c39d99399a4ca48085273a0476dbd0 . . . . "true"^^ . "false"^^ . "^PDC\\d+$"^^ . . . . . . . . . "agriculture" . "https://dialnet.unirioja.es/servlet/revista?codigo=$1"^^ . "anatomy" . "6000122"^^ . "^C\\d{8}$"^^ . . "m.naguthana@hotmail.com" . "is deprecated" . . "Drosophila RNAi Screening Center" . . "https://cropontology.org/rdf/CO_321:"^^ . . "true"^^ . "12e8LH"^^ . . "gene" . "DEF"^^ . "TBK Reddy" . . . . . . "http://purl.bioontology.org/ontology/HOIP/HOIP_$1"^^ . "^[a-f0-9]{64}$"^^ . "https://biopragmatics.github.io/providers/diseaseclass/$1"^^ . . "gene" . . "imaging" . . . . . "https://w3id.org/mixs/$1"^^ . . . . "hidden markov model" . "^\\d{7}$"^^ . . . . "life science" . "vmhgene" . . "drugs" . . "Malachi Griffith" . . "nsheffield@virginia.edu" . "protein" . . "orthology" . "organic molecular chemistry" . "000204"^^ . . "false"^^ . . . . . . . . . . . . "false"^^ . . . . . . . . "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information."^^ . . "CranioMaxilloFacial ontology" . "5fce9b7300001250"^^ . "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID="^^ . . . . . . . . . "NeuroNames" . . "https://www.pirbright.ac.uk/node/"^^ . "DataNode"^^ . . . . . "Q47475003"^^ . . . "structural biology" . "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$"^^ . . . "NLXINV" . "Ismail Fliss" . "protein" . . "STOREDB at University of Cambridge" . "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . . "ssbd.dataset" . . . "^CH_\\d+$"^^ . . . "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/"^^ . . . . . . . . . "UniGene" . "false"^^ . . . "clyh" . . . . . . . . . . . "Rv1908c"^^ . "rna" . . "EC" . . . . . "life science" . . . . "mutant mouse strain" . "A comprehensive compendium of human long non-coding RNAs"^^ . . . . . "sensor data" . . . . . "false"^^ . "protein" . . . . . . "structure" . . . "Reaxys" . . . "Clinical Trials Information System" . "publons.publication" . "biology" . "datanator.reaction" . . . "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands."^^ . "https://smpdb.ca/view/"^^ . . . . "322"^^ . "^CAL\\d{7}$"^^ . . . . _:N2acde302dfca4afbac04bb5927b795b9 . "biology" . . . . "https://www.pharmvar.org/gene/$1"^^ . . "https://w3id.org/faircookbook/"^^ . "gramene.protein" . . . . "karel.berka@upol.cz" . "false"^^ . "protein" . "ExO" . . . . "imanis" . "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data."^^ . "240-17-488-3-4-12"^^ . "obo" . . "false"^^ . "SchemaDefinition"^^ . . . "icd10cm" . "false"^^ . "eugenes@iubio.bio.indiana.edu" . "wbphenotype" . "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . . "false"^^ . "^\\d+$"^^ . "false"^^ . . "http://purl.obolibrary.org/obo/VTO_$1"^^ . "https://bioregistry.io/phosphopoint.kinase:"^^ . "d.smedley@qmul.ac.uk" . . . "sumirp77@gmail.com" . . "ontology" . . . . . . . . . . "astrophysics and astronomy" . _:N6148f200d9cb438085c4c05608cd2555 . "BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it."^^ . . . "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval."^^ . . "false"^^ . . . "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^ . . . "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^ . "^[0-9][A-Za-z0-9]{3}$"^^ . "EUbOPEN is a project focusing on organizing chemogenic library collections, advancing chemical probe discovery, profiling bioactive compounds, and making project data more accessible."^^ . . . . "biochemistry" . . . . . . "ctibor.skuta@img.cas.cz" . "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . . "ontology and terminology" . . "EDAM Ontology" . . "false"^^ . . "rapdb.transcript" . . . . . . . . . . . . "7345"^^ . "cnrs" . . . . "ontology" . . . . . . . "0000024"^^ . "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression."^^ . "oncology" . "World Wildlife Fund Ecoregion" . "https://biopragmatics.github.io/debio/$1"^^ . "http://www.w3.org/ns/shex#$1"^^ . "90062901"^^ . "Asteraceae Genome Database" . "MEDRA" . "proglyc" . . . . . . . . "biology" . . . "ontology" . . . . "http://purl.obolibrary.org/obo/GO_"^^ . . "NIST Chemistry WebBook" . "http://arabidopsis.info/StockInfo?NASC_id="^^ . . . "0000140"^^ . "SM00015"^^ . . . . "datf" . . . "computational biology" . "false"^^ . . "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$"^^ . "life science" . . . . . . "omics" . . . "false"^^ . . . "Elementary Multiperspective Material Ontology" . . . . . "dentistry" . . . "false"^^ . . . . "fetal fibroblast" . . . "false"^^ . . . . . "Yossih@tauex.tau.ac.il" . "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."^^ . . . . . "disease model" . . _:N66f61cac451a4680a38a6bf866d20c5b "World Health Organization" . "ontology" . "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world."^^ . "glyconavi" . "pathway model" . . "false"^^ . . "Pascale Gaudet" . "^\\S+$"^^ . . "^\\d+$"^^ . . . . "h_aktPathway"^^ . . "Benchmark Energy & Geometry Database" . . . "https://www.addexbio.com/productdetail?pid="^^ . . . . . . "01625"^^ . . "img.taxon" . . . . . "true"^^ . "virmirdb" . "false"^^ . "kristian.axelsen@sib.swiss" . "http://vocab.getty.edu/page/tgn/$1"^^ . . "false"^^ . . . . . "hospital" . "biological regulation" . "false"^^ . . "data model" . . . . . . . "Pier Luigi Buttigieg" . . "publication" . . "oryzabase.stage" . . "bibliometrics" . "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules."^^ . . . . "false"^^ . "https://permalink.obvsg.at/"^^ . "GCF_000001405"^^ . . . . . "false"^^ . . "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^ . . . . . . . . . . . . . . . "Xenobiotics Metabolism Database" . "subject" . "oct 2016"^^ . "uniprot.var" . . . . . "mi" . . "preclinical studies" . "Higher order grouping of Pfam families"^^ . "pathway" . "ls-c35719-120"^^ . "genetics" . "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information."^^ . . . . "geology" . . "dna" . . . . . "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information."^^ . . "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . "cheminf" . . . . . "zenodo" . . . . . "humap" . "http://purl.obolibrary.org/obo/ZEA_$1"^^ . "obo" . "http://www.cathdb.info/cathnode/"^^ . "gene" . . . . . . . "LINCS Protein" . . . "genewiki" . . "molecular biology" . . "https://lincs.hms.harvard.edu/db/proteins/"^^ . . . . . "protocol" . . "https://www.ebi.ac.uk/interpro/set/pfam/$1"^^ . . . "http://uri.neuinfo.org/nif/nifstd/nlx_res_"^^ . . "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol="^^ . "developmental biology" . "PubMed Central" . "https://reactome.org/content/detail/"^^ . "biomedical science" . . "biology" . . . "life science" . . . . . . "Abcam" . . "aaeA"^^ . . . . . "^(\\d{8}|(\\w+\\d+\\w+))$"^^ . . . "humanities" . "Alan Bridge" . . . . "publication" . . . "http://purl.obolibrary.org/obo/SOPHARM_"^^ . "true"^^ . . . . . "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality."^^ . . . . . . . "https://cropontology.org/rdf/CO_337:"^^ . "fly" . . . . "false"^^ . "trait" . "https://www.isrctn.com/"^^ . "^(R)?PXD\\d{6}$"^^ . "social and behavioural science" . "agriculture" . "span" . . . . "The Natural Products Atlas" . . "https://hamap.expasy.org/unirule/"^^ . . . "dbvar.variants" . "classification" . . . "Rhiannon Cameron" . "ncit" . . . "false"^^ . "00000001"^^ . . "false"^^ . _:N4a972aca9ada49e2875dd165dcc104dc . . . "protein" . . . "^[A-Z-_0-9]+$"^^ . "https://bionumbers.hms.harvard.edu/bionumber.aspx?id="^^ . . . . . . "^[1-9]\\d{0,11}$"^^ . . "rnao" . "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. "^^ . . . . . "Chemical Methods Ontology" . "geography" . "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . . "awalker@apa.org" . "noncodev4.gene" . . "false"^^ . . "568815597"^^ . . . . "stefan.kuhn@dmu.ac.uk" . "R-BTA-418592"^^ . . . "co_343" . "dan5@georgetown.edu" . . "mental health" . "^[1-9]\\d{0,6}$"^^ . "49"^^ . "^\\d+$"^^ . "12345"^^ . . "https://coicatalogue.uc.pt/index.php?t=specimen&COINumber="^^ . . . . "protocol" . . . . . . . "knowledge and information systems" . . . "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc="^^ . . "loggerhead" . . . . . . . . . . . . "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."^^ . . "catalog" . . . . . . . . "AB1925000"^^ . "ega.study" . . "true"^^ . "India Clinical Trials Registry" . . "radlex" . . . . "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"^^ . "false"^^ . . . . "ontology" . "grid.225360.0"^^ . . "cosmic" . . "http://purl.obolibrary.org/obo/MPIO_$1"^^ . . . . . "fibroblast" . . "^10.\\w{4}/\\w{10}$"^^ . . . . "UK Higher Education Statistics Agency" . . . "CIViC variant" . . "^\\d+$"^^ . "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \n\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things."^^ . "ontology" . "CHEBI" . . "false"^^ . . "BAMSC981"^^ . . . . "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species."^^ . . "ontology" . . . . "pass2" . . . . . . "http://genomics.senescence.info/diet/details.php?id=$1"^^ . . . . . "1a05"^^ . . . . . . . "https://www.npatlas.org/explore/compounds/$1"^^ . . . . . . . . . . . . . . "A Semantic Web Rule Language Combining OWL and RuleML" . . . "^FB\\w{2}\\d{7}$"^^ . "rna" . . "false"^^ . . "Gazetteer" . "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM="^^ . "transcriptomics" . . "metadata" . "DIP-743N"^^ . . "pharmgkb.drug" . "developmental biology" . . . . "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId="^^ . "false"^^ . . . "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . . "bootstrep" . . . . . . . "UM-BBD_reactionID" . "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1"^^ . "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy."^^ . . . . . . . . . "classification" . . "http://purl.obolibrary.org/obo/MP_"^^ . "2d-page" . "Cowpea Trait Dictionary in template v5 - IITA - August 2015"^^ . "^[A-Za-z0-9]+$"^^ . "BQJCRHHNABKAKU"^^ . . . . . . . . "0000001"^^ . . "European Medicines Evaluation Agency" . . . "development" . "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession="^^ . "https://scicrunch.org/resolver/RRID:$1_$2" . . "The bioRxiv is a preprint server for biology"^^ . . "false"^^ . . . "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms."^^ . . "https://rfam.org/family/"^^ . "Gene Ontology Causal Activity Model" . . . "http://www.geneontology.org/formats/oboInOwl#"^^ . . . . . . . . . . "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI."^^ . "http://purl.obolibrary.org/obo/OHD_$1"^^ . . . "rpillich@ucsd.edu" . "idocovid19" . . "gene" . "materials informatics" . "DDB0016567"^^ . . . "pharmacogenomics" . "1174"^^ . . "A type for entries in the Bioregistry's metaregistry." . "cell biology" . "http://champ-project.org/images/ontology/cao.owl#CAO_$1"^^ . "false"^^ . . "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . . "biopragmatics/bioregistry/416"^^ . . . . . "165a"^^ . . . "nutritional science" . . "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^ . . . . . "genbank" . . . . . . . . "0000052"^^ . "false"^^ . . "false"^^ . . . . "rnavdb" . . "functional genomics" . . . "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language."^^ . . . "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster="^^ . "^\\d{7}$"^^ . . "plant development stage" . "identifier of scientific author in www.cienciavitae.pt"^^ . . . "chemical entity" . . "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . "j.huerta@csic.es" . "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . "iNaturalist Observation" . . . . . . . "Theiler Stage" . . . . "life science" . "botany" . "genecards" . "https://www.langual.org/langual_thesaurus.asp?termid=$1"^^ . "Richard H. Scheuermann" . "Maciej.Antczak@cs.put.poznan.pl" . . "true"^^ . "false"^^ . "publication" . . . . . . . . . "21552"^^ . . . . "agrkb" . . . "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA)."^^ . "vitro" . . . . "https://stemcells.nindsgenetics.org?line=$1"^^ . . . "https://www.ebi.ac.uk/gxa/experiments/"^^ . "disease" . "131392"^^ . . . . . . . . . "food" . . . . "reecehart@gmail.com" . "false"^^ . . . . . . "false"^^ . "false"^^ . "Database of Quantitative Cellular Signaling: Pathway" . . . "false"^^ . "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^ . . "^\\d+$"^^ . . "apaonto" . "Cell line databases/resources"^^ . "Homologous Organ Groups" . . "ppo" . . . "humap3" . . . . . "false"^^ . . "LinkedIn personal profile ID" . . . "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^ . "https://www.nextprot.org/term/"^^ . "https://fungi.ensembl.org/id/$1"^^ . "2244"^^ . "0001"^^ . . "6978836"^^ . "0000001"^^ . "false"^^ . . "fsnp" . "A manually curated resource for the representation and annotation of metabolic pathways"^^ . "345201101230312003"^^ . . "report" . . . . "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^ . "BD1a05-A-A-IPM1"^^ . . "^\\d+$"^^ . . . . . "https://purl.org/nfdi4plants/ontology/dpbo/DPBO_$1"^^ . . . . . . "NCT00222573"^^ . . "https://lincs.hms.harvard.edu/db/antibodies/"^^ . . . . . "http://purl.obolibrary.org/obo/MICRO_"^^ . . . "model organism" . "http://www.cellsignal.com/reference/pathway/$1.html"^^ . . "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains."^^ . "https://bioregistry.io/loop:"^^ . "^F\\d{4}$"^^ . . . . "dietary restriction" . . . "metabolomics" . . "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails."^^ . . . "0000564"^^ . . . . . "http://planttfdb.cbi.pku.edu.cn/tf.php?uid="^^ . . . . . . . . "neuroscience" . . . . "171"^^ . "glycomics" . . . "work" . "http://www.ymdb.ca/compounds/$1"^^ . "proteomics" . . . "Human Protein Reference Database" . "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1="^^ . . . . "Alzforum Mutations" . "false"^^ . . _:N6148f200d9cb438085c4c05608cd2555 "Anita Ghebeles" . "http://purl.obolibrary.org/obo/STATO_$1"^^ . . "mutant strain" . . . . . . . "^\\d{7}$"^^ . . . . . . "salamander" . "antibody" . . . . "conferences" . . . "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^ . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id="^^ . . "^\\d{7}$"^^ . . "Willy Wong" . . "Glyma0021s00410"^^ . . "Japan Consortium for Glycobiology and Glycotechnology Database" . . . . "https://glytoucan.org/Structures/Glycans/"^^ . "false"^^ . "4544"^^ . "environmental material" . "0000190"^^ . . "https://lccn.loc.gov/"^^ . "491187"^^ . "https://tetrahymena.vet.cornell.edu/display.php?stockid="^^ . . . . . . . . . . . "000000021"^^ . "Healthcare Organizations and Services Ontology" . . . "computational neuroscience" . "fossilworks.journal" . . "omics" . . "loinc" . . . "https://civicdb.org/links/drugs/$1"^^ . . . . "false"^^ . . "Andreas Ledl" . "co_367" . _:N5ed93a11628a4d9ab1825cec2f063b06 "kasschau@cgrb.oregonstate.edu" . "false"^^ . . "Uniprot Core Ontology" . "MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for proteins that serve as molecular targets in cell-based bioactivity measurements."^^ . . . "neurolex" . "^\\d{7}$"^^ . . . "chemistry" . . "false"^^ . . . . . . . . "data management" . . "Universal Natural Products Database" . . . "DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects."^^ . . "Sorghum TDv5 - Oct 2019"^^ . . . . . "^\\d+$"^^ . . "nlx.qual" . . "wd" . . . . . . . . . . . . . . "RNAloops" . . "^\\d+$"^^ . . . "http://www.jstor.org/stable/$1"^^ . "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . . "life science" . . . "BiGG Compartment" . . . . "Leszek@missouri.edu" . "obo" . . "mental health" . . . "^[AEP]-\\w{4}-\\d+$"^^ . "https://go.drugbank.com/salts/$1"^^ . "ecyano.experiment" . "ontology" . "^\\w+_?\\d+(.\\d+)?$"^^ . . "Martin Ramirez" . . . . . "natural science" . "Andreas Ruepp" . "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer"^^ . . . . . . "http://purl.obolibrary.org/obo/PPO_"^^ . . "mmsl" . "https://biopragmatics.github.io/providers/goche/$1"^^ . . . "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt="^^ . "protein complexes" . . . . "false"^^ . . . "false"^^ . . . . . "National Center for Advancing Translation Sciences BioPlanet" . "http://bioportal.bioontology.org/ontologies/"^^ . . . . . . "https://morpheus.gitlab.io/models/$1"^^ . . "MicrobeamManipulation"^^ . . . . "http://purl.obolibrary.org/obo/ICEO_$1"^^ . . . . . "life science" . "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege."^^ . "doqcs.model" . . . . . "immunology" . "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^ . . "http://edamontology.org/topic_"^^ . "ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides and maintains identifiers for alleles."^^ . "false"^^ . . . "false"^^ . . "data set" . "A user of FAIRsharing"^^ . . "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^ . "false"^^ . . . "biomedical science" . . "pathway" . . . . "ktk@netlabs.org" . "model" . . . . "ChiCTR2300070727"^^ . . . "genomics" . "cog.pathway" . . . . . . . . . . . . . . "^\\d+$"^^ . "pscdb" . "gdc" . . "false"^^ . . "MIRIAM Legacy Registry Identifier" . "http://ascl.net/"^^ . . "Andrea Jacobs" . . . . "HGVST1828"^^ . . "ebisc" . . "Cuban Registry of Clinical Trials" . "SNOMEDCT_US_2023_02_28" . . "ENST00000407236"^^ . "false"^^ . "urdbms.syndromefinder" . . "ncbiTaxUID" . "MobiDB is a database of protein disorder and mobility annotations."^^ . . . . "0000156"^^ . . . "http://purl.obolibrary.org/obo/FBdv_$1"^^ . "agriculture" . . . . . . . "cath.superfamily" . . . . . "GPM32310002988"^^ . . "oryzabase.gene" . "false"^^ . . . . "ontology" . . "jgraybeal@stanford.edu" . "Software ontology" . . "0000183"^^ . . "false"^^ . "^[a-z0-9]{10}$"^^ . "SUPERFAMILY" . . . . . "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id="^^ . . . "^\\d+$"^^ . "hsa-let-7a-2-3p"^^ . "phenotype strain survey data" . . . . . "Chemical Entity Materials and Reactions Ontological Framework" . . "Selventa legacy disease namespace used with the Biological Expression Language"^^ . . . . . . . . . "https://www.kazusa.or.jp/rouge/gfpage/$1"^^ . . "System capabilities, operating ranges, and survival ranges ontology" . . "19-T4"^^ . . "trans" . . "labo" . "AutDB" . . . "^\\d+$"^^ . . . "https://bioregistry.io/ccdc:"^^ . . . "horticulture" . "DepMap Cell Lines" . . . . "BG11523"^^ . "http://purl.org/spar/cito/$1"^^ . "^[EL]D[SG]-\\d+$"^^ . . "has reviewer" . . . . . "cgd7_230"^^ . "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" . "false"^^ . . . . "M58335"^^ . . . "^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$"^^ . . "false"^^ . . . . . "International repository of Adverse Outcome Pathways."^^ . "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1"^^ . . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . "SNOMEDCT" . . "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations."^^ . . . . . "msaier@ucsd.edu" . . "true"^^ . "https://osdr.nasa.gov/bio/repo/data/experiments/$1"^^ . "nci.drug" . . . . "4DNSR73BT2A2"^^ . . . . . . "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1"^^ . . . . . "Cell line collections (Providers)"^^ . "Sanger Cell Model Passports" . "Giorgio Ascoli" . . "bioinformatics" . "gro" . . . "^\\d+$"^^ . . "ontology" . "false"^^ . . . . . "interaction" . . . . "fd8d0743-344a-4758-bb97-f8ad84a37357"^^ . . "false"^^ . . . . . "37271072100"^^ . "31623"^^ . . . "MESHD" . . "false"^^ . . "biomedical science" . . . "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"^^ . "cas" . _:N54ddddf5000c4fd2a7b74bbe1329da40 . . . . . . . . . "obo" . . "health science" . . . . "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent."^^ . "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . "expression data" . . "false"^^ . "FamPlex" . . . "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo="^^ . . . . . "genes" . "^\\w.+$"^^ . "false"^^ . . . . . . . . . . . "Alice Allen" . . . . . . "Identifiers for space-related data from experiments that investigate biological and health responses of terrestrial life to spaceflight"^^ . . . "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id="^^ . . "kuiper@bio.ntnu.no" . . . "htn" . . . "^\\d{6}$"^^ . "false"^^ . "rbeavis@thegpm.org" . . . "75"^^ . . . "buccal_gland"^^ . . . "https://bioregistry.io/lrg:"^^ . . "viaf" . . "ontology" . . . "ChEMBL-Cells" . . . . "catalogs" . . . . "false"^^ . . . . "^A\\d{4}$"^^ . "Unique Ingredient Identifier" . . "Plasmodium Life Cycle" . . "Citation Counting and Context Characterisation Ontology" . . "^\\d{7}$"^^ . . . . . "biology" . . . . "false"^^ . "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific."^^ . "SAMEA10104908"^^ . _:Nf89cb9e92fd74e19980b1425b32a783c . . . "disease" . "lcnafid" . . . "epidemiology" . "repository" . "^\\d+$"^^ . . "An ontology of commonly encountered and/or high level Drosophila phenotypes."^^ . "unipathway.compound" . "exac.transcript" . . . "minid.test" . "CropMRespository is a database of soil and crop biophysical process models."^^ . "Harshad Hegde" . "HMS LINCS Compound" . . . . "^\\d{7}$"^^ . . . . . . . "Golm Metabolome Database Reference Substance" . "ontology" . . "https://scicrunch.org/scicrunch/interlex/view/ilx_$1"^^ . "A*01:01:01:01"^^ . . "https://bioregistry.io/ecoliwiki:"^^ . . "yuki.yamagata@riken.jp" . . . "https://www.npatlas.org/explore/compounds/"^^ . "Vernon Putz-Anderson" . . . "Golm Metabolome Database GC-MS spectra" . "21157"^^ . "ontology" . "Conference Ontology" . "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication."^^ . "TC" . . . . "^\\d{5}$"^^ . "https://semanticscience.org/resource/CHEMINF_$1" . . "https://www.ebi.ac.uk/ega/datasets/"^^ . . . "obo" . . . . "https://cryptodb.org/cryptodb/app/record/gene/$1"^^ . . . . . . "false"^^ . "http://biomodels.net/rdf/vocabulary.rdf#"^^ . . "^[A-Z_]{3}[0-9]{4,}$"^^ . . "ligandexpo" . "https://odc-tbi.org/data/$1"^^ . . . "0000984"^^ . . "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary."^^ . . . "^[A-Za-z0-9]+$"^^ . . . . "t3db" . "Identifiers for payloads associated with experiments that investigate biological and health responses of terrestrial life to spaceflight"^^ . "One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]"^^ . . "dragondb.allele" . . "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region."^^ . . "medicine" . "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . . . "JMChandonia@lbl.gov" . "vandf" . "^\\d+$"^^ . . . . . . . . . . . . "compulyeast" . . . "CLPUB00496"^^ . . "datanator.gene" . "Integbio" . "taxonomic classification" . . . "http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php?specie=$1"^^ . . "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue="^^ . . . "Evan Patterson" . "E-MEXP-1712"^^ . . "hpath" . . . "http://www.w3.org/2003/01/geo/wgs84_pos#$1"^^ . "Pan African Clinical Trials Registry" . "subject agnostic" . . . . "https://cropontology.org/rdf/CO_336:"^^ . _:Na27634e4bd594b8fa9866144dd316fcb "julie@igbmc.u-strasbg.fr" . "interaction" . . . . "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/"^^ . . "mcro" . . "Stefan Schulz" . . "false"^^ . "PUBCHEM_CID" . . . . . "International Standard Book Number" . "drugbankv4.target" . . "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID="^^ . . "AOPWiki (Key Event Relationship)" . . . "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease."^^ . . . "protein" . "SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes.\n\nIt assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed."^^ . "human" . "Name-to-Thing" . . . . "^\\d+$"^^ . . . "http://purl.obolibrary.org/obo/PO_"^^ . "The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources."^^ . . . "http://www.w3.org/ns/shacl#"^^ . . . . "false"^^ . . . "true"^^ . . "https://www.iedb.org/epitope/"^^ . "sequence" . . . . . . . . . . . "https://www.ncbi.nlm.nih.gov/protein/"^^ . . . "nasaosdr.experiment" . . . . . . "GWAS Central Marker" . . "Units of measurement ontology" . . "protein" . . . . "lipidbank" . "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^ . . . "anatomy" . . . . . "false"^^ . . "ontology" . "life science" . . "^TA\\d+$"^^ . . . . . . . . . . . . "^\\d{7}$"^^ . "cmecs" . "drsc" . "Biotin_biosynthesis"^^ . . "http://www.candidagenome.org/cgi-bin/locus.pl?dbid="^^ . . "The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collection refers to the genomic data of Asteraceae species."^^ . "http://purl.obolibrary.org/obo/LPT_$1"^^ . . . "drug name" . "false"^^ . "^\\d+$"^^ . . . . . "biosimulators" . "https://bioregistry.io/bpdb:"^^ . . "Allergy"^^ . "https://registry.dome-ml.org/review/"^^ . "Maxwell L. Neal" . . . "oral surgery" . . . . . . "sewilson@lbl.gov" . . . . . "agriculture" . "false"^^ . "agriculture" . . . "mKIAA4200"^^ . . . . . "protein" . . . . . "obo" . . . . "comparative genomics" . "rna" . "false"^^ . "Insertion sequence elements database" . "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1"^^ . . "Liver Cancer Model Repository" . "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"^^ . . . "true"^^ . "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . . . "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . "ISRCTN10175490"^^ . . . . . . . "iuphar.family" . . . . . . "pepbank" . "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. "^^ . . . . . "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books."^^ . . . "false"^^ . . "RGD" . "Silvio Peroni" . "Imanis Life Sciences cell line products" . . "sgn" . . "Ontology describing a controlled vocabulary for taxon ranks."^^ . . . "disease" . . . "physical geography" . "M3G stands for “Metadata Management and distribution system for Multiple GNSS Networks”. M3G allows to upload, validate, and distribute GNSS station metadata such as IGS-style site logs, information about local networks, DOIs, nominal data provision, data licenses attached to the daily RINEX data, etc..."^^ . _:Nfbab19d7fc574378a290cb6bc16080a9 "faldo@googlegroups.com" . . . "data identity and mapping" . "https://www.ebi.ac.uk/gwas/studies/$1"^^ . "MMP3888430"^^ . . . "dmba" . "obo" . "true"^^ . "The International Harmonization of Nomenclature and Diagnostic criteria" . . . . . . "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus."^^ . "dbsnp" . . . "00023232"^^ . "https://proteinensemble.org/"^^ . . "https://www.fishbase.ca/summary/$1"^^ . "bibliometrics" . "transcriptomics" . . "false"^^ . "false"^^ . "protein" . "ontology" . "life science" . . "These are the terms that are improted for FOVT to describe vertebrate traits."^^ . . "0000106"^^ . . . "false"^^ . . . "disease" . . . "subject agnostic" . "natural product" . . . . "false"^^ . "https://civicdb.org/links/diseases/"^^ . "phenotype" . . . "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^ . "http://purl.obolibrary.org/obo/CL_$1"^^ . . . "cameo" . "co_325" . "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web."^^ . "false"^^ . "metagenomics" . . . . "neurobiology" . . "Integrated Genomic Resources of human Cell Lines for Identification" . "Plant Phenology Ontology" . . . "https://togoid.dbcls.jp/#$1" . . . . . . "https://istransbase.scbdd.com/database/trans/"^^ . "Cell line collections (Providers)"^^ . "ukprns" . . "tissue" . "http://geneontology.org/docs/gene-product-information-gpi-format/#"^^ . . . . . . . . . . "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."^^ . . . . . . "sebastien.moretti@sib.swiss" . "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . . . "https://registry.identifiers.org/registry?query=MIR:"^^ . "Apollo Structured Vocabulary" . "biomedical science" . . . "obo" . "beetlebase" . . "ALX-210-175"^^ . . . . . . "Helen Berman" . . . "^\\d{7}$"^^ . . "Tick Anatomy Ontology" . "https://biopragmatics.github.io/providers/sfam/$1"^^ . "miw023@ucsd.edu" . "Stages 1-28 of mouse embryo development"^^ . "civic.therapy" . "life cycle stage" . . "Human Intermediate Filament Database" . . "domain" . . . . _:N666c4a679d674cfab27ee5b6c85aa4cc "WikiData Support" . "Tree of Life Web Project" . . "false"^^ . . . . "^[1-9]\\d*$"^^ . "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id="^^ . "N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a"^^ . "The China National Center for Bioinformation's (CNCB) Genome Warehouse (GWH) is a public repository holding genetic information for a wide range of species including humans, plants, animals, and microorganisms. Identifiers in this resource correspond to genomes of various species. The goal of the resource is to make genomic data accessible to researchers in areas like precision medicine and biotechnology."^^ . . . "data science" . "unichem" . . "ensembl.protist" . "biomedical science" . . . . . "gene" . . . . "PharmacoDB Cells" . "^[a-zA-Z0-9][A-Za-z0-9_]+$"^^ . . . . . "ontology" . "Database of Macromolecular Interactions" . . . "This database provides identifiers for catalytic bioparts which are fundamental to the design, construction, and optimization of biological systems for specific metabolic pathways. It provides basic information, function information (including catalytic functions, qualitative and quantitative parameters, and biopart expression), and sequence information (nucleotide sequence and amino acid sequence)"^^ . "nbrc" . _:N0b5ff4c94c7444bdbeeac143810f9087 "klimke@ncbi.nlm.nih.gov" . . . . . . "wormbase" . . . . . . . "Selventa legacy chemical namespace used with the Biological Expression Language"^^ . . . "hello@vivekkrish.com" . "Assists in resolving data across cloud resources."^^ . . "topics" . . . . "false"^^ . "0001017"^^ . . "mex" . . . "https://github.com/$1"^^ . "chebi" . . . "ontology" . . . . . . "https://bioregistry.io/ligandexpo:"^^ . "https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1"^^ . "life cycle stage" . . . "phenotype" . . . . "^\\w+$"^^ . . "http://www.w3.org/ns/ssn/"^^ . "silvio.tosatto@unipd.it" . "sickle cell disease" . "CIViC Source" . "Current Procedural Terminology" . "vaccination" . . "rrid" . . . . . "obo" . . "obo" . "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"^^ . "Five Stars of Online Research Articles Ontology" . . . . . "A database-specific registry supporting curation in the Gene Ontology" . "oboformat" . . "LG Chemical Entity Detection Dataset (LGCEDe)" . "taxonomy" . . "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . "ajacobs@cas.org" . . "false"^^ . . "https://meshb.nlm.nih.gov/record/ui?ui="^^ . . . "tngb" . . "^(?:\\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\\d+)?)$"^^ . . . . . . "http://purl.org/linked-data/cube#$1"^^ . . . "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features."^^ . "Datanator Gene" . . . . . . "E-MTAB-2037"^^ . . . . . "Activity"^^ . . "3SBPLMKKVEVR"^^ . "Encyclopedia of Life" . "disease" . "publications" . "ICD9CM" . "dsm5" . "metabolomics" . "academy" . . . . "phenotype" . . . "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . . "CID" . . . . . "VCell Published Models" . "LTS0004651"^^ . . "https://loinc.org/"^^ . "^PPR\\d+$"^^ . "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . "erv" . . . . "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins."^^ . . . . . . . "toxoplasma" . . _:N4c94689a87b548d6ae5f280e9e8e0183 "helpdesk@cropontology-curationtool.org" . . "obo" . "ontology" . "regulation" . . . . . . . . . "https://www.pgscatalog.org/pgs/"^^ . . "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082"^^ . . "fix" . . . . . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1"^^ . "health_care_quality_assessment"^^ . "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples."^^ . . . . . . "https://www.abmgood.com/search?query="^^ . . . "metatlas" . . . . . . "^\\d+$"^^ . . . "https://ligandbook.org/package/"^^ . . "00620027"^^ . "cgrove@caltech.edu" . "ps048"^^ . "silva.taxon" . . "protein" . . "MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a data repository and associated data standard designed to describe biosynthetic gene clusters involved in the production of specialized metabolites. It also stores data on measured biological activities and links to other resources such as NCBI, NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and training dataset for machine learning."^^ . "^\\d+$"^^ . "TAIR Gene" . "d4e2515"^^ . "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1"^^ . . "BGC0000001"^^ . "false"^^ . . . . "metacyc.reaction" . . "6"^^ . "functional genomics" . . . "gene" . . "https://bioregistry.io/metaregistry/biocontext/$1" . . "ICD9" . "wos.researcher" . . . "http://purl.obolibrary.org/obo/PHIPO_$1"^^ . "235" . . "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts."^^ . "DrugBank" . . . . . . . "GenPept" . . "https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_$1"^^ . "false"^^ . "O80725"^^ . . . . . . . "https://bioregistry.io/geonames.feature:"^^ . . . . . . "https://biomedit.ch/rdf/sphn-ontology/sphn#"^^ . "229233"^^ . "ricenetdb.gene" . . "LifeWatch Metadata Catalogue" . . . . "https://knowledge.lonza.com/cell?id=$1"^^ . . "^\\d+$"^^ . . "evolution" . . . "true"^^ . "Alexey M. Eroshkin" . "physiology" . "life science" . "The Ontology of Genes and Genomes" . . . . . "LigandBox" . "0000008"^^ . . "false"^^ . "^\\d+$"^^ . "false"^^ . . . "miriam"^^ . . . "obo" . . "biochemistry" . "NASA GeneLab" . . . . . . "false"^^ . . . . . . "http://www.oid-info.com/get/2.16.840.1.113883.6" . . . . . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid="^^ . . . "false"^^ . . "small molecule" . . "false"^^ . . . . . "life science" . . . . . . . "translation_language"^^ . "cran" . "ms" . . . "chemical entity" . . "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)"^^ . "SoyBase" . . "102l"^^ . . . . . "MEROPS Entry" . "634515043"^^ . . . "interaction" . "Bastian Fromm" . . . . "OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX."^^ . "Lycalopex_vetulus"^^ . . . . . . . . "^\\d+$"^^ . . . . . . "http://www.w3.org/ns/sosa/$1"^^ . . . . "InterLex" . . "metadata" . . "structure" . "https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry?primaryAC="^^ . . . "https://bioregistry.io/metaregistry/go/$1"^^ . . . "http://www.cellsignal.com/products/$1.html"^^ . . . . . "identifier for a person, used by ResearchGate profiles"^^ . "^1\\d{4}-\\d{3}$"^^ . . "vrandecic@gmail.com" . . . "classification" . . . . . "false"^^ . "kyinno" . . . "PTM" . . . . "dashr.expression" . . . "merriam_webster" . "Predicates in the Encyclopedia of Life data schema for describing animals, plants, and other organisms"^^ . . . "anatomy" . . . . . . "https://hub.docker.com/u/"^^ . "Cambridge Structural Database" . . . " Philip Strömert" . . "has local unique identifier pattern" . . . "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources."^^ . . . "vendor" . "life science" . "NIF Standard Ontology: Organisms" . "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$"^^ . "Alzheimer's Disease Ontology" . . . . "http://purl.obolibrary.org/obo/FOODON_"^^ . . . . . . "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:"^^ . "scdo" . "unique academic work identifier assigned in Scopus bibliographic database"^^ . . . "https://flowrepository.org/id/"^^ . . . . "ontology" . . "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^ . "https://cropontology.org/rdf/CO_365:"^^ . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . "Colleen Xu" . "scopus.publication" . "deims.site" . "^\\d+$"^^ . . . . . "Charles Tapley Hoyt" . "gemma.l.holliday@gmail.com" . . . "Amphibian gross anatomy" . "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid="^^ . "msio" . . "NM_006262"^^ . "protein" . . "José Victorino Ruiz Lavida" . . . . "functional genomics" . . . . "Jeremy D. Glasner" . . . "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . "Medical Subject Headings" . . "false"^^ . . . "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor."^^ . . . . . . "https://cbcb.cdutcm.edu.cn/AGD/genome/details/?id="^^ . . . "protein" . . . "https://www.ncbi.nlm.nih.gov/bioproject/?term="^^ . . . . "http://ddinter.scbdd.com/ddinter/interact/$1"^^ . "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n"^^ . "http://www.signaling-gateway.org/molecule/query?afcsid="^^ . . "https://cropontology.org/rdf/CO_345:$1"^^ . "phenology" . . "plant phenotypes and traits" . "Food Type identifiers, supporting codes and vocabularies based on the EFSA FoodEx2 (https://www.efsa.europa.eu/en/data/data-standardisation) that are being tested in the development of the FSA's code and data standards repository. These codes may be used within FSA data."^^ . "Kai Blin" . . . "meetings" . "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al."^^ . . . . . "An open, community-driven registry of conference and event venues.\n\nEVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research organizations.\n\nThis benefits researchers assembling information about in-person conferences and events by enabling them to refer in an unambiguous way to the venue where it takes place.\n\nThis repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w), meaning that the data and code are all in one repository that anyone can contribute to."^^ . . . . "phylogenetics" . "false"^^ . "ontology" . . "^\\d+$"^^ . _:N3ce42fd5f38d402ba7e8cb590f8198f4 "bgee@isb-sib.ch" . . . . . "stefan.guenther@pharmazie.uni-freiburg.de" . . . . "certain"^^ . . "small molecule" . . . . "16S rRNA gene database" . . . "^\\d+$"^^ . . "^\\d{7}$"^^ . "obo" . . . "intact.molecule" . . . "^(STUDY|FILE|DATASET)\\d+$"^^ . "https://bioregistry.io/phosphopoint.protein:"^^ . "BioStudies database" . . "^\\d+/.+$"^^ . . . "https://mips.helmholtz-muenchen.de/corum/?complex_id="^^ . "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch="^^ . "microscope" . . . . . "0001009"^^ . . . "Bacterial Tyrosine Kinase Database" . . . . "true"^^ . "ENSFM00500000270089"^^ . . . . . . "cryopreservation" . "false"^^ . "enzyme" . "https://www.ebi.ac.uk/intact/interaction/"^^ . . . "^WP\\d{1,5}(\\_r\\d+)?$"^^ . . . . "7499841"^^ . . . . "^PTHR\\d{5}(\\:SF\\d{1,3})?$"^^ . . "InTextReferencePointer"^^ . "social science" . . . . . . "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . "PANTHER Node" . "^\\d+$"^^ . . "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$"^^ . . "true"^^ . "ontology" . . "false"^^ . . "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^ . . . . . "life science" . . "false"^^ . . "UCSC Genome Browser" . "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information."^^ . "3"^^ . "Dataset"^^ . . "EOL Secretariat" . . . "protein" . "A nomenclatural ontology for biological names" . . . . . . . . . . . "https://hpscreg.eu/cell-line/"^^ . "1"^^ . "http://purl.obolibrary.org/obo/XAO_"^^ . . . . . . . . "Role Ontology" . . "false"^^ . "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"^^ . "false"^^ . "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"^^ . . "srao" . . "http://purl.obolibrary.org/obo/GNO_$1"^^ . "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."^^ . "expression" . . . "classification-model"^^ . . . . "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id="^^ . "http://purl.obolibrary.org/obo/MAO_"^^ . "FAIRSharing" . . "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."^^ . . "disease process modeling" . . . . . "http://bigg.ucsd.edu/models/$1"^^ . . "disease" . . . "Chlamydia"^^ . "https://molmedb.upol.cz/mol/$1"^^ . . "food" . "ecology" . . . "relationships" . . "archdb" . . . "53d583d8-40c6-40e1-9296-23f821cd77a5"^^ . . "protein" . . . . . "cto" . . . . "protein" . "YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes."^^ . . . "OpenAlex" . "10153"^^ . . "false"^^ . . . . . "false"^^ . . "^\\d+$"^^ . . . . . "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences."^^ . . . . . "metabolomics" . . . . . . "LNCipedia" . . "WormBase" . . . . "207LH0002X"^^ . "skosxl" . . . "false"^^ . "Jesper Friis" . . . . "gianni.cesareni@torvergata.it" . "https://mycobrowser.epfl.ch/genes/$1"^^ . . . . "https://www.webofscience.com/wos/woscc/full-record/WOS:"^^ . "rex" . . . . . . "FlowRepository" . "false"^^ . . . . . . "false"^^ . . . . "false"^^ . . . . . "biology" . "Richard Boyce" . . "https://mmp.sfb.uit.no/databases/marfun/#/records/"^^ . . "FB" . . "genome" . "ProtoNet ProteinCard" . . . . . . . . . "^\\d{7}$"^^ . . . . . . . . . "glycosylation" . "transcription factor" . . . "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends)."^^ . "Ensembl" . . . "DBPedia Property" . . . . . "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems."^^ . . "Term"^^ . . . . . . "report" . . "ontology" . "https://icd.who.int/browse10/2019/en#/$1"^^ . . "Database of Genotypes and Phenotypes" . "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF."^^ . . . "ccds" . "data model" . . . . . . "life science" . . . . "Dominik Martinat" . "metabolomics" . . "false"^^ . . "mathematics" . . . . "ctd.disease" . "biology" . . . . . "https://omim.org/MIM:"^^ . "0002233"^^ . . . . "taxonomy" . "protein" . "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code="^^ . "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it."^^ . "false"^^ . "Doug Howe" . . . . . . . "dev.ga4ghdos" . . . "Will Simpson" . . "National Microbiome Data Collaborative" . "https://publons.com/publon/$1"^^ . . . "go.chemical" . . . . . "mwitt@purdue.edu" . . "ecology" . "ontology" . . . "genomics" . "^\\d+$"^^ . . . . . . . . . "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments."^^ . . . . . . "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^ . . . . "http://purl.obolibrary.org/obo/DC_CL_"^^ . "https://civicdb.org/links/assertions/"^^ . . . . "^\\d+$"^^ . . . . . "omia.variant" . . . . . . "anatomy" . . . . . . "GOLD genome" . "sustainability" . . . _:Ndb0972dc29f34ae4850340e2ec03eacd "helpdesk@cropontology-curationtool.org" . . . "false"^^ . "^DBCAT\\d+$"^^ . . . . "^\\d+$"^^ . . . "Bio-Pesticides DataBase" . . . "http://www.proglycprot.org/detail.aspx?ProId=$1"^^ . "Philippine Health Research Registry" . . . . . . . "https://w3id.org/sulo/"^^ . . . . . . . . . . . "fbql" . . "false"^^ . . . "0000040"^^ . . . "A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies)."^^ . . . . . "genome" . . . . . . . "Bioregistry Collections" . . . . . _:N400c4b1a400c48adac7f4fd308153dbb . . . . . . "classification" . "Michael Y Galperin" . "^[A-Za-z]+$"^^ . "hsa-let-7a"^^ . . . . . "neurology" . . "Livestock Breed Ontology" . "Molbase" . "https://flybase.org/reports/FBtc"^^ . . . . "19"^^ . . . . "biomedical science" . . "https://www.enzolifesciences.com/"^^ . "genetics" . . . . "civic.disease" . "ERM00000044"^^ . . . . "http://www.w3.org/2008/05/skos-xl#"^^ . . . . . "ML0224"^^ . . . . . . . "AC119"^^ . . . . . "false"^^ . "https://sed-ml.org/urns.html#format:"^^ . . "^\\d+\\.\\d+$"^^ . "StreptomeDB" . . . "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon."^^ . . . . . . "glycosciences.db" . "https://cropontology.org/rdf/CO_335:"^^ . . . . . . . "https://istransbase.scbdd.com/database/trans/$1"^^ . "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . . "structure" . . "mro" . . . . . . . . . "Prefix Commons" . . . . . . "small molecule" . "genomics" . . "PeptideAtlas" . . . . . "A user in DockerHub"^^ . . . "http://www.ifomis.org/bfo/1.1/snap#"^^ . "eropmoscow" . . . "Uniprot ID" . "0000012b-5661-2f63-2f73-b43980000000"^^ . "0000400"^^ . "http://edamontology.org/data_"^^ . . . . "donovan.parks@gmail.com" . . "http://vegbank.org/cite/"^^ . "Cell line collections (Providers)"^^ . . . "Surjeet Kumar Arya" . . "ito" . "evidence" . . . "apetrov@ebi.ac.uk" . "structure" . . . . . . . "Interlab Cell Line Collection" . . . . "false"^^ . "^[1-9]\\d*$"^^ . "ettensohn@cmu.edu" . . . "^\\d{7}$"^^ . . . "nlm" . . . "Probability Distribution Ontology" . . . . . "E13035"^^ . . . . "http://purl.obolibrary.org/obo/FLOPO_"^^ . . "data governance" . . . "false"^^ . . . "0002999"^^ . "mutant mouse strain" . "fanta" . . . . "emmo.cif" . "^HIT\\d{9}(\\.\\d+)?$"^^ . . . . . . "idoden" . . . . . "An ontology for description of concepts in the nutritional studies domain."^^ . "taxonomy" . . . "Common Access to Biological Resources and Information Project" . . "false"^^ . . . . . "rateRule"^^ . . . . . "Maryann Elizabeth Martone" . . . . . . "life science" . "^\\d{8}$"^^ . "^\\d+$"^^ . . . "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/"^^ . . . . . "co_340" . . . "ontology" . "false"^^ . . . . "https://www.rebuildingakidney.org/id/"^^ . . "https://deims.org/dataset/"^^ . "miriam.collection" . "adrien.coulet@loria.fr" . "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species."^^ . "MO000027"^^ . "Southwestern Environmental Information Network" . . . . "Ramona Walls" . . "study design" . "https://gnomad.broadinstitute.org/variant/"^^ . . . "IPR" . . "obo" . "http://www.kegg.jp/entry/"^^ . . . "pathogen" . . . . . . . . . . "FDA Application" . "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . "0000198"^^ . . "false"^^ . . . . . . . "panther.node" . "m4i" . . . "phenomics" . . "false"^^ . . . . . . . "ontology" . "http://purl.obolibrary.org/obo/SWO_$1"^^ . "clustering" . "Cell line collections (Providers)"^^ . "http://biobanknetwork.telethon.it/Sample/View?sampleId="^^ . "false"^^ . . "fr" . . "genome" . . . . . . . . "life science" . . . "^\\w{1,2}\\d+$"^^ . . . . "false"^^ . . . . "plant phenotypes and traits" . "biomedical science" . "0019030"^^ . . . . . "^([hm]\\_)?\\w+Pathway$"^^ . . "hypercldb" . "http://uri.neuinfo.org/nif/nifstd/"^^ . "FxnI151FMs"^^ . . . "adenovirus" . . "Sol Genomics Network" . "https://mmp.sfb.uit.no/databases/marref/#/records/$1"^^ . . . "pspub" . "https://catalog.integbio.jp/dbcatalog/en/record/$1"^^ . . . . "omit" . . . "ECOCYC" . . "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . . "^\\d+$"^^ . . "osti.article" . . "chembl.cell" . "https://www.ebi.ac.uk/interpro/entry/antifam/$1"^^ . . . "KIAA0001"^^ . "Informed Consent Ontology" . . "http://www.phosphosite.org/siteAction.do?id="^^ . "Vir-Mir db" . . "traumatology" . "http://purl.obolibrary.org/obo/EHDAA2_"^^ . . "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^ . "tgilbert@sund.ku.dk" . . . . "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec="^^ . . . "uspto" . "BioSystems" . . . "d.e.starns@liv.ac.uk" . "Gene Regulation Ontology" . "aspgd.protein" . . "linguistics" . . "natural science" . "ontology" . . . . . . . . . "http://purl.uniprot.org/core/"^^ . . "duplication" . . . . . . . "gene name" . "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record."^^ . . . . . . . . . "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available."^^ . "20003"^^ . "S7000002168151102"^^ . . . . . . "https://chemkg.github.io/chemrof/$1"^^ . "bioinformatics" . . "78073"^^ . . . "false"^^ . . "false"^^ . . "computer science" . . . _:Nc67eaa5da835457d851cd6b2d8c36cbd "Patricia Brooks" . "https://thebiogrid.org/interaction/$1"^^ . . "^\\w+$"^^ . . "SNOMEDCT_US" . "sequence" . "ontology" . "http://www.ncbi.nlm.nih.gov/clinvar/$1"^^ . . . . "tarbase" . . . "roleo" . . . . "^ChiCTR(-[A-Z]+-)?\\d+$"^^ . . . "Funding, Research Administration and Projects Ontology" . . . . "experimental measurement" . . "viralzone" . . . "false"^^ . . . . . "SEQF10030.1"^^ . "funding agencies" . . "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."^^ . "https://bioregistry.io/cellbank.australia:"^^ . . . . "http://purl.obolibrary.org/obo/TGMA_"^^ . . . "https://cropontology.org/rdf/CO_366:"^^ . . "immds"^^ . . "ontology" . "https://www.datanator.info/gene/$1"^^ . . . "https://bioregistry.io/registry/$1" . . . . . "nfdi4chem.osmo" . "false"^^ . "http://purl.obolibrary.org/obo/FLU_"^^ . "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . "reo" . . . . . "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule="^^ . . . . "Jakob Voß" . . . "Anna L. Kaysheva" . . . "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId="^^ . . . "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No="^^ . . . . "https://cropontology.org/rdf/CO_350:"^^ . "https://bioregistry.io/resolve/github/pull/"^^ . . . "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_"^^ . "Creative Biolabs Protein provides identifiers for protein-related entities, including therapeutic proteins, proteolytic enzymes, antibody-like scaffold proteins, soluble T cell receptors, and tetramers."^^ . "Registry of Toxic Effects of Chemical Substances" . . . . . . . "Ramasubbu Sankararamakrishnan" . . . . . . . . . . "data management" . . . "smtifahim@gmail.com" . . . . . . . "^\\d{7}$"^^ . . . "UTRdb" . . "time" . . "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID="^^ . . . "Justin Whorton" . "^DDB_G\\d+$"^^ . . "false"^^ . . . . . . . "dgrc" . . . "A registry of commonly used prefixes in the life sciences and linked data. The source data for this registry is a spreadsheet on Google called the Life Science Registry. This registry was previously known as Prefix Commons and was available at https://prefixcommons.org." . . . "stem cell" . "Christine Pourcel" . . "https://bioregistry.io/p3db.protein:"^^ . . . . "chemical" . . . . . . . . . . . . . . . . . . . . "^MMAR\\_\\d+$"^^ . "ai10e-kctd13b"^^ . . "protein" . . . "IMGT/HLA human major histocompatibility complex sequence database" . . "http://purl.obolibrary.org/obo/GAZ_$1"^^ . . "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^ . . . "0001707"^^ . . . . "http://id.nlm.nih.gov/mesh/vocab#"^^ . "A collection of resources added during Biocuration 2025 in Kansas City, MO, USA." . . "false"^^ . "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^ . "Foundational Model of Anatomy" . "Histidinol dehydrogenase (EC 1.1.1.23)"^^ . "^\\w+$"^^ . "disease" . . . . "SoyBase is a repository for curated genetics, genomics and related data resources for soybean."^^ . "small molecule" . "experimental animal" . . . . "PicTar" . "Identifiers for missions associated with experiments that investigate biological and health responses of terrestrial life to spaceflight"^^ . . . "philip.stroemert@tib.eu" . . "Philippe Le Mercier" . "https://w3id.org/mixs/"^^ . . "biomedical science" . _:Nb9ff211bb43b4bc4bd882e7f759848d4 . . . "false"^^ . . "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . . "proteomics" . . . "ontology" . . . . . "hagr.genage" . . "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id="^^ . . "An ontology covering the taxonomy of teleosts (bony fish)"^^ . "^\\d+$"^^ . . . . . "http://www.w3.org/ns/dcat#$1"^^ . . . . "obo" . . "https://w3id.org/biolink/vocab/"^^ . "obo" . "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F"^^ . "false"^^ . . . . "SFB_COVID19_MW286762"^^ . . . "Stephen Fisher" . . . "industry" . . . . . . "Obstetric and Neonatal Ontology" . "Span" . "ontology" . "VIAF ID" . "0000547"^^ . "cdd" . . . . . . . . . . "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR."^^ . . . . . "gene" . . . . . . . . "false"^^ . . "68513255-fc44-4041-bc4b-4fd2fae7541d"^^ . "00000"^^ . . . "^RBR-\\w+$"^^ . . . . . "Mutant Mouse Resource and Research Centers" . . . . . . "anatomy" . "phenotype" . . . . . . . . "false"^^ . . . . . "ontology" . . "true"^^ . "http://purl.obolibrary.org/obo/EPIO_$1"^^ . . "MIMIC III Database" . . . "roundworm" . "false"^^ . "true"^^ . . . . . . "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID="^^ . . . "^[A-Z0-9]+$"^^ . . . . . . . . . . . . . . . . . "http://opm.phar.umich.edu/protein.php?pdbid="^^ . . . . "false"^^ . "An ontology for non-coding RNA, both of biological origin, and engineered."^^ . . "molecule" . . "3618"^^ . . . . . . . "0000983"^^ . "false"^^ . . "Human ancestry ontology for the NHGRI GWAS Catalog"^^ . "pdbe" . . "307"^^ . "mutation" . "http://edamontology.org/format_"^^ . "^\\d+$"^^ . "1351341"^^ . . . "histology" . "Ontology for Biomarkers of Clinical Interest" . . . "Kim Durante" . . "IUPAC Gold Book Compendium of Chemical Terminology" . "genome" . . . . . . . . . "https://commonchemistry.cas.org/detail?cas_rn="^^ . . . "Biocuration Conference 2025 Collection" . . . "4D Nucleome Data Portal Biosource" . "bcbc" . "preclinical studies" . "false"^^ . . . "food" . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . . . . . . . . . . . . . . . "pathway" . "http://exac.broadinstitute.org/transcript/$1"^^ . "false"^^ . . . . "false"^^ . . . . "biostudies" . . "false"^^ . "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination."^^ . . . "Christian Hauschke" . "pgx" . . . "liz.allen@f1000.com" . "1a24"^^ . . . . . . . . . "^Os\\S+g\\d{7}$"^^ . "prov" . . . . . . "homologous" . . . . . . . "^PR\\d{5}$"^^ . . . . "The Virus Infectious Disease Ontology" . "https://horizondiscovery.com/en/search?searchterm="^^ . _:N66f61cac451a4680a38a6bf866d20c5b "info@who.int" . "^[a-f0-9]+$"^^ . . . . . . . . . . . "Lebanon Clinical Trials Registry" . . . . . "http://www.case.edu/EpilepsyOntology.owl#"^^ . "ClinGen Clinical Genome Expert Panel" . . . "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . . "gene expression" . "false"^^ . "ontology" . "DBG2 Introns" . "Johannes Wittmann" . . . . . . . "true"^^ . . "Alex Bateman" . "ontology" . . "002804"^^ . . . "Genetic Testing Registry" . . "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"^^ . "immunology" . . . "false"^^ . . . . "https://www.kaggle.com/"^^ . . . . "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals."^^ . . "false"^^ . "metabolomics" . . . "zhu@iastate.edu" . . "^\\d+$"^^ . . . "0000196"^^ . "phenotyping" . . . . "knowledge and information systems" . . . . "ST000900"^^ . "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains."^^ . . . . "ChEMBL target" . "archaeology" . "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays."^^ . "PSI Extended File Format" . _:N5ed93a11628a4d9ab1825cec2f063b06 . . . . . . . . "811"^^ . "https://modeldb.science/"^^ . "medicine" . . "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1"^^ . "elements" . . . "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid="^^ . . "dggr" . "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . "ontology" . . . "Unified Medical Language System Atomic Unique Identifier" . "^M\\d{5}$"^^ . "0001"^^ . . "to" . . "classification" . . "98034"^^ . . . . . "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^ . "plant" . "Virus Pathogen Resource" . . . "http://www.w3.org/2003/11/swrl#"^^ . "0000139"^^ . . "K"^^ . "icd9cm" . . . "https://www.kegg.jp/entry/"^^ . "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN."^^ . . . . . "https://civicdb.org/links/variant_group/$1"^^ . . "bigg.model" . . . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/DERMO_"^^ . . . . . . . . "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1"^^ . . "493771"^^ . . . . "BRAF"^^ . . "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#"^^ . "IA"^^ . . "genetic interaction" . "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. "^^ . . . "The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included."^^ . "life science" . . . . "false"^^ . "Rafael Richards" . "European Mouse Mutant Archive" . . "human genetics" . . . . . . . . "Stewart Thomas Cole" . . . "Plant Ontology" . "deoxyribonucleic acid" . . "https://www.hipsci.org/lines/#/lines/$1"^^ . . . . "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI."^^ . . . . . . . . . . "Vilma Hualla Mamani" . "https://purl.brain-bican.org/ontology/mbao/MBA_"^^ . "foodon" . "lang"^^ . . . . "http://addgene.org/"^^ . . "unique identifiers" . . . . "http://dictybase.org/gene/$1"^^ . . "https://fanta.bio/cre/$1"^^ . . . . . . . . . "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene."^^ . . . "false"^^ . "MolBiC Compound" . . "life science" . . . . . . . "comparative genomics" . . . . "genomics" . "metadata standardization" . . . . . . . . . . . . . . "protein" . "false"^^ . "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups."^^ . . . . "The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO."^^ . . . . . . . "Creative Biolabs Antigen provides identifiers for antibody-based entities such as recombinant, functional, engineered, and format-specific antibodies as well as antibody processing tools, which are essential for applications in diagnostics, therapeutics, and immunology."^^ . . . "emsl.project" . . . "mirEX" . . . "S0960-9822(11)01319-4"^^ . . . "genomics" . . . . . "false"^^ . . _:N66f61cac451a4680a38a6bf866d20c5b . . . . . "Wormpep" . . . "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^ . . "Medical Dictionary for Regulatory Activities" . . . . _:N6842dbf57b3c4a21a8744d80c34d0343 . . . . . . . . . "https://hub.docker.com/r/$1"^^ . . "10007835"^^ . . "genomics" . . "http://multicellds.org/MultiCellDB/"^^ . "bioinformatics" . . . "GXA Expt" . "dna" . . . . "genomics" . . . . "^[a-zA-Z0-9 +#'*]+$"^^ . "false"^^ . . . "^[a-z_A-Z0-9]+$"^^ . . . . "Identifiers for synthetic binding proteins, providing detailed information on their sequences, structures, targets, and functional properties for research, diagnostic, and therapeutic applications."^^ . "An experimental run, served thrugh the ENA"^^ . "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies."^^ . . . "obo" . "dal.alghamdi92@gmail.com" . . "tumor" . . . . "genes" . . . "http://standards.iso.org/iso/15926/part14/"^^ . . . . . . . "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"^^ . . "phenotype" . . . "geo"^^ . "zhangzhang@big.ac.cn" . "Dublin Core Elements (1.1)" . . "^[0-9a-f\\-]+$"^^ . . . . . "FooDB Food" . . "ZFA_RETIRED" . . "http://purl.obolibrary.org/obo/FBSP_"^^ . . "atmospheric science" . . . . . . "^\\w+$"^^ . . "fig|306254.1.peg.183"^^ . . . "ontology" . . "biomedical science" . "http://www.chemspider.com/Chemical-Structure.$1.html"^^ . . . . . "http://www.wikidata.org/entity/$1"^^ . "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/"^^ . . . . . . . "nkos" . . . "http://purl.obolibrary.org/obo/ERO_$1"^^ . . . "gene ontology enrichment" . "Documentation of the Phenoscape Curation Workflow"^^ . . "https://civicdb.org/links/assertions/$1"^^ . . . "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^ . . "systemic neuroscience" . . . . "http://purl.obolibrary.org/obo/UO_$1"^^ . . . . "16129"^^ . . "Human Genome Variation Society Nomenclature" . . . . . "project management" . "pharmacodb.cell" . . . "28"^^ . "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." . . . . . . . . . . "metadata" . . . "The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science."^^ . . . . "false"^^ . "false"^^ . . "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes."^^ . "nlx.chem" . "MESH_DESCRIPTOR_UI" . . . "1122888"^^ . . . . "jws" . . "igrhcellid" . "KEGG LIGAND" . . "gene" . "ABL1"^^ . "Asteraceae Genome Database" . "ontology" . . . . "reaction data" . . "false"^^ . "false"^^ . . "nucleotide" . "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist="^^ . "^IPR\\d{6}$"^^ . . . . "13"^^ . . "http://ctdbase.org/detail.go?type=disease&db=MESH&acc="^^ . "neurophysiology" . "david@mbi.ucla.edu" . . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid="^^ . . . . . "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^ . . "animal" . . . "02069237"^^ . "408"^^ . . . . "1"^^ . "pmr.workspace" . "FAIRsharing Subject Ontology" . "C. elegans ORFeome cloning project" . "^\\d+$"^^ . "phylogenetics" . . . "pfam" . "A terminology for the skills necessary to make data FAIR and to keep it FAIR."^^ . "pathology" . "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"^^ . . . . "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus."^^ . . . . . . . . . "https://www.novusbio.com/products/"^^ . . . . . . "mapping_justification"^^ . "physical samples" . . "^\\d{7}$"^^ . "senso" . . "UniProt Keywords" . "^\\d{7}$"^^ . . . . "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^ . . "http://purl.obolibrary.org/obo/OGG_$1"^^ . "false"^^ . . . . . "uniprot" . "transcriptomics" . . . . . . . . . . . "false"^^ . . . _:N0a7be7ab7ef34589ac0a212ca0b90c7b "hq@HL7.org" . . "life science" . "^(\\d+)|(\\w+)$"^^ . "Jose P. Faria" . . . . . . "molecular entity" . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . "false"^^ . . . . . . . . "^\\d+$"^^ . "evan@epatters.org" . "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."^^ . . . . . . "Liz Allen" . . "splash" . "biomedical science" . . . . . . . "false"^^ . "resource metadata" . "descriptor" . . . . . . . . . . "https://cbcb.cdutcm.edu.cn/AGD/plant/details/?id="^^ . . . . "https://aopwiki.org/aops/$1"^^ . . "4201PAT-CCTCC00348"^^ . . "^[0-9]+$"^^ . "312.33"^^ . . . . . . . . "protein" . . "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . . "https://covid19.sfb.uit.no/api/records/$1"^^ . . "^PT\\d+$"^^ . "^\\d+$"^^ . "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . . "GeneDB" . "false"^^ . "^\\d+$"^^ . "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line"^^ . "GND ID" . "NMR-instrument specific component of metabolomics investigations" . "insdc.gcf" . . "http://purl.obolibrary.org/obo/PSO_"^^ . . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . . . "life science" . "http://edamontology.org/format_$1"^^ . "EC number" . . . "do" . . "http://www.jcvi.org/charprotdb/index.cgi/view/"^^ . "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"^^ . . . . . . . . "0000210"^^ . . "PTPN1"^^ . . . "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community."^^ . . . "Ontology of Host-Microbiome Interactions" . . . "true"^^ . "environmental science" . . "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies."^^ . "life science" . . . . . . . . "whimar@ohsu.edu" . . . . . . . . "TarBase" . "983"^^ . "false"^^ . "^PA\\d+$"^^ . "http://purl.org/spar/c4o/$1"^^ . . "cell culture" . . . . "pdc.study" . . "spar" . . . . . "reaction" . "false"^^ . . "unists" . . . . "^\\d+$"^^ . . . . "https://thebiogrid.org/interaction/"^^ . "Selventa Complexes" . "ontology" . . . . "botany" . "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . . . . "false"^^ . "person" . . . "http://ctdbase.org/detail.go?type=gene&acc="^^ . . "https://www.ncbi.nlm.nih.gov/clinvar/submitters/"^^ . "erik.vannimwegen@unibas.ch" . . . "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q="^^ . "http://autism.mindspec.org/GeneDetail/"^^ . . "John Beverly" . . . . "7dfd3f10-d410-45a4-983d-8fbd6dfbc374"^^ . . . . . "sopharm" . . "^[0-9]+$"^^ . "identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)"^^ . . "ontology" . "cell" . . . . . . . . . . . . . "time" . . . "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information."^^ . . . "civic.variantgroup" . "funding bodies" . . "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"^^ . . "trichdb" . "mutant" . . "Sickle Cell Disease Ontology" . . . "mutant" . "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance."^^ . . . "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . "https://bidd.group/NPASS/compound.php?compoundID=$1"^^ . . . "false"^^ . . . . . . . "false"^^ . "gene" . "false"^^ . . "false"^^ . . . "IUPHARfam" . "http://www.treefam.org/family/"^^ . . . . . "Python"^^ . . . "059486"^^ . "false"^^ . . "false"^^ . . . . "computational chemistry" . . . "^\\d{5}$"^^ . . "disease" . "http://www.pocketome.org/files/$1.html"^^ . . "Identifiers for microbially derived natural products that contains compound structures, producing organism taxonomy, biosynthetic and chemical properties."^^ . "taxonomy" . . . . . "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession)." . . . . . "genome" . "Bernd Müller" . . . "http://scop.berkeley.edu/sid="^^ . "SPAR Ontologies" . "^[AEP]-\\w{4}-\\d+$"^^ . . "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)."^^ . . "developmental biology" . . . . . . . . . . . . . "Sweet Potato ontology" . . . . . . . . "pathway" . "Hector Escriva" . . . . "https://www.scopus.com/sourceid/"^^ . . . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/T4FS_"^^ . . . . "Encyclopedia of Life Schema" . . . "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]."^^ . . "keilbeck@genetics.utah.edu" . . "nbdc01071" . . . "0002902"^^ . "PR000001"^^ . . "subject agnostic" . . "biochemistry" . . "false"^^ . _:Ne852999e3f544bc9a8d299321e8ffa10 . "https://cn.dataone.org/cn/v2/resolve/{$1}"^^ . . . . "bork@embl.de" . . . . . "Rutger Vos" . "qb" . . "false"^^ . "structure" . . . "https://www.uniprot.org/database/" . . "http://purl.obolibrary.org/obo/MOP_"^^ . . . . . "Integrated Microbial Genomes Gene" . "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1"^^ . . . . . . . . . . . . . "dockerhub.user" . "http://hawaii.eagle-i.net/i/"^^ . . . . . . "nlx.br" . "Drug Target Ontology" . . "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines"^^ . "genome" . "Vocabulary of Interlinked Datasets" . . . . "VFDB Gene" . . . "life science" . "http://purl.obolibrary.org/obo/DDANAT_$1"^^ . . . "https://rarediseases.info.nih.gov/diseases/$1/index"^^ . "^[1-9][0-9]{14}$"^^ . . . . . . . . . "http://purl.obolibrary.org/obo/VariO_$1"^^ . . . . . . . . . . "neuronames" . . . . . . "kegg.disease" . "https://biopragmatics.github.io/providers/sfam/"^^ . . . "77"^^ . "Ontology of Biological Attributes" . . . . "obo" . . . . "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"^^ . . . . . . . . "^EB\\d+$"^^ . . "https://www.disprot.org/idpo/IDPO:"^^ . "classification" . "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."^^ . . "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^ . . . . "chemical" . . . . "^CL\\d+$"^^ . . . . . . . "sugarbind" . . "rna" . "http://purl.obolibrary.org/obo/OHMI_$1"^^ . . "obo" . . . . . . . . . . . . . "AC00963334"^^ . "false"^^ . . "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1"^^ . . . . . . . . "unipathway.pathway" . "false"^^ . . . "CH_001923"^^ . "phenotype" . "CropMRepository" . . . . . . . . . . "https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn"^^ . . "bioinformatics" . "18466622"^^ . "dna" . "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1"^^ . . . "expression" . . "Bio-MINDER Tissue Database" . "fideo" . "false"^^ . "Dictyostelium discoideum phenotype ontology" . "false"^^ . . . . "https://bioregistry.io/cabri:"^^ . . . . "NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. \n(Developed by the SIB Swiss Institute of Bioinformatics)"^^ . "structure" . . . . . . "false"^^ . "morbidity" . "ontology" . "congenic rat" . . "0000121"^^ . . . "false"^^ . . . . _:N162037c0c5e841c8ad3e24ff5b417396 "William Bug" . "false"^^ . . . "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"^^ . "National Uniform Claim Committee Taxonomy" . . "^\\d+$"^^ . . . "http://qudt.org/schema/qudt#$1"^^ . "1100107"^^ . . . . . . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line="^^ . . "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/"^^ . . "http://purl.obolibrary.org/obo/BCGO_$1"^^ . _:N3c4b513e02ff428db6a004195c0275ba . "Sharkipedia Species" . "00000105"^^ . . . . _:N3257f323b5f24eeab5090d84680d8d04 "J.Bard@ed.ac.uk" . . . "^HIP\\d{9}(\\.\\d+)?$"^^ . "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]"^^ . "false"^^ . . "Alan Wood's Pesticides" . "upheno" . . . . . "mcmelek@msn.com" . "https://www.abmgood.com/search?query=$1"^^ . "classification" . "phenotype" . . . "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . "genome" . . . . _:N9bc6191d1bcf433094fa654b9c56d349 "davem@umn.edu" . "2011"^^ . . "International Nonproprietary Names" . . . "false"^^ . "homd.seq" . "hmsl_id" . . . . . . "^\\d+$"^^ . "rna" . "false"^^ . . . "false"^^ . . "https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/"^^ . . . . "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1"^^ . "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID="^^ . . . . . . "unirule" . . . "CCLE_867"^^ . . "http://bigg.ucsd.edu/models/universal/reactions/$1"^^ . . . . . "Protein Model Database" . . . . . "false"^^ . "Authenticus ID" . . . "Job.Dekker@umassmed.edu" . "bsg-000052"^^ . . . "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"^^ . . "life science" . "http://synbip.idrblab.net/data/bts/details/$1"^^ . . . "biomedical science" . "http://www.hgmd.cf.ac.uk/ac/gene.php?gene="^^ . "structure" . . . . . . . . . . "tcdb" . . . "PF11_0344"^^ . "myco.marinum" . . . "^[A-Za-z_0-9]+$"^^ . "http://homosaurus.org/terms/"^^ . . . _:N65ccae73c30e4c6baaff668b2af09913 "Qiong Gu" . . . "IntAct Molecule" . . . . . . . "https://eds.gene.le.ac.uk/home.php?select_db=$1"^^ . . "http://purl.obolibrary.org/obo/PORO_$1"^^ . "protein families" . "image collection" . . . . . . . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/ERO_"^^ . . "life science" . . "jonathanmtclark@gmail.com" . . . "Anvil" . . "ICEberg integrative and conjugative element" . "Sean May" . . . . . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments."^^ . "false"^^ . . "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1"^^ . "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^ . . . . . . . . . "gene" . . "The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage)"^^ . . . "https://w3id.org/BCI-ontology#"^^ . . . . . . "http://purl.obolibrary.org/obo/ZECO_"^^ . . . "MycoBrowser" . . . . . "rbca.jackson@gmail.com" . "^\\d{7}$"^^ . . . . . "An ontology to describe entities related to prescription of drugs"^^ . "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."^^ . . . "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid="^^ . "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^ . "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1"^^ . . . . "obo" . "http://www.kegg.jp/entry/"^^ . . "nasaosdr.mission" . . "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature."^^ . "imgt.ligm" . "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . "http://exac.broadinstitute.org/transcript/"^^ . . . . "64ba"^^ . . "https://easychair.org/cfp/topic.cgi?tid=$1"^^ . "USA National Service Center Number" . "true"^^ . . . . . "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization."^^ . . . "preclinical studies" . . . . "National Microbial Pathogen Data Resource" . . "ma" . . . . . . . . . . . "ctd.chemical" . "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"^^ . . "omon" . "m4i" . "Evgeny M Zdobnov" . . "Leif Oxburgh" . . . . "http://purl.obolibrary.org/obo/GALLONT_"^^ . . . . . . . . "http://purl.obolibrary.org/obo/LEPAO_$1"^^ . . . . . . "ontology" . . "false"^^ . "ESi007-A"^^ . "Prefixes useful in annotating documentation provenance." . . . . "false"^^ . . "^\\w+$"^^ . . . "IRCT20080904001199N7"^^ . . . . "^\\d+$"^^ . "false"^^ . "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$"^^ . . . "systems biology" . "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links."^^ . . . "https://www.kazusa.or.jp/rouge/gfpage/"^^ . . . "false"^^ . . . "1000160"^^ . "^\\d{7}$"^^ . . "genomics" . . . . . "https://coconut.naturalproducts.net/compound/coconut_id/"^^ . "pathogen" . . "true"^^ . . . "http://purl.obolibrary.org/obo/PHIPO_"^^ . . . . "^\\d+$"^^ . . "17165"^^ . . . "Tetrahymena Genome Database" . . . "Bibliometric Data Ontology" . . . . "ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons."^^ . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . "https://www.metabolome-express.org/datasetview.php?datasetid="^^ . "has resource example" . . . . . "amphx" . "analytical chemistry" . . . . . . . . "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells."^^ . . . "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."^^ . . . "metascience" . . "chemistry" . . "transcript" . . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id="^^ . . . . "ENSG00000169174"^^ . "false"^^ . "3517823"^^ . . . "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1"^^ . . . "discoverx" . "eolife" . "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . . "meshUID" . "bioregistry"^^ . "https://bioregistry.io/polbase:"^^ . . . . . "BioModels Database" . "http://www.w3.org/ns/adms#"^^ . . "vrobert@unistra.fr" . . "Andrew G. McArthur" . "food" . . "y3ax-8bq3-60"^^ . "^\\d+$"^^ . "false"^^ . . "Telethon Network of Genetic Biobanks" . "mouse" . . "Jianmin Wu" . "true"^^ . . . . . . "false"^^ . "nucleotide" . "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr="^^ . "protein" . "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events"^^ . . "https://bioregistry.io/$1:$2" . . . "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology."^^ . "LDS-1110"^^ . . . "http://purl.obolibrary.org/obo/RBO_"^^ . . . . "2"^^ . . . . . . . "biocatalogue.service" . . . "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . . "protein" . "false"^^ . . . . "false"^^ . "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"^^ . "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded."^^ . "This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files."^^ . "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1"^^ . "unit" . . . . . "Image Data Resource" . "hcpcs" . . . . "Earth Metabolome Ontology" . . "Transport Systems Tracker" . "chemistry" . . "1731"^^ . . "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana."^^ . . "false"^^ . "NCITt" . "Dynamic Ecological Information Management System - Site and Dataset Registry - Locations" . . . . . "^\\d+$"^^ . "pathway" . "ICEberg integrative and mobilizable element" . . "false"^^ . . . "proteomics" . . "imsr_tac" . "000064"^^ . . . . . . . . "phenotype" . . "false"^^ . . . "https://www.pesticideinfo.org/chemical/"^^ . . . . . . "HD+118-001"^^ . "http://www.genomesize.com/result_species.php?id=$1"^^ . . "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters."^^ . "0154"^^ . . . "https://www.biozol.de/en/product/"^^ . "protein" . . . . "^RPCEC\\d+$"^^ . . . "poro" . "http://purl.obolibrary.org/obo/RXNO_$1"^^ . "0000003"^^ . . . . . . . "false"^^ . . . . "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"^^ . "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"^^ . . "http://ddinter.scbdd.com/ddinter/drug-detail/"^^ . . . . "fcb" . . . . . "http://purl.uniprot.org/uniprot/$1"^^ . "NeuroLex Anatomy" . . . "^\\d{7}$"^^ . . . . . "http://purl.obolibrary.org/obo/GECKO_$1"^^ . "kegg.glycan" . . . . . . . "ECCODE" . "obo" . . . . . . "drug interaction" . . . "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/"^^ . . . . . . . "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data."^^ . . "obo" . "https://prefix.zazuko.com/" . . "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id="^^ . "life science" . "abcam" . . "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"^^ . "model organism database" . "biology" . . . . . "MGnify Analysis" . "ontology" . "taxonomy" . "false"^^ . . . . . "knowledge and information systems" . "Werner Müller" . "A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number."^^ . . "C. elegans phenotype" . . . . . "http://thebiogrid.org/$1"^^ . "ontology" . . . . "theiler" . . "^\\d+$"^^ . . "^\\w+$"^^ . "qtldb" . . "Clinical measurement ontology" . . . "false"^^ . . . . . "https://terminology.hl7.org/CodeSystem-v3-$1"^^ . "false"^^ . . "http://purl.obolibrary.org/obo/MAT_"^^ . . . . . . . "^AT\\d+$"^^ . . "http://foodb.ca/compounds/"^^ . . "jmg11@cam.ac.uk" . "vega" . "^B\\d{5}$"^^ . "genome" . "gaog@mail.cbi.pku.edu.cn" . "^\\d{5}$"^^ . . . . . . "HL7 V2 Code Systems" . "http://www-snorna.biotoul.fr/plus.php?id=$1"^^ . . . "https://mycobrowser.epfl.ch/genes/$1"^^ . . . . . . . . . "Rat Strain Ontology" . . "antibodies" . "http://www.phosphosite.org/siteAction.do?id=$1"^^ . "genomics" . "zp" . . "https://www.confident-conference.org/index.php/Event_Series:$1"^^ . . . "http://foodb.ca/compounds/$1"^^ . "https://bbp.epfl.ch/nexus/web/studios/public/$1"^^ . "ontology" . "https://models.physiomeproject.org/exposure/$1"^^ . "illumina.probe" . "false"^^ . . "https://www.re3data.org/repository/$1" . "sjbrown@ksu.edu" . . _:Nd83d06f2d21b434d8cd5ee83981cdcff "helpdesk@cropontology-curationtool.org" . . "UniProt Chain" . . . "Giacomo Lanza" . . . . "depends on" . . . . "The DOME registry is a curated set of papers related to machine learning methods in biology, each with its own unique DOME identifier."^^ . . . "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception."^^ . . . . "false"^^ . "false"^^ . "https://www.nsf.gov/awardsearch/showAward?AWD_ID="^^ . . . . . "^\\d+$"^^ . "Yeast Genome Order Browser" . . "Networks in DEIMS SDR"^^ . . . "http://www.w3.org/ns/adms#$1"^^ . . . . . . "dcat" . "obo" . "ppdb@gifu-u.ac.jp" . . . . . . "depod" . . "^\\S+$"^^ . . "http://www.w3.org/2004/02/skos/core#"^^ . "^\\d{7}$"^^ . . . "dbvar.study" . "^\\d+$"^^ . "^\\w+$"^^ . . "^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$"^^ . . "John Cottrell" . . "model" . "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . . "interaction" . "https://tools.ietf.org/rfc/rfc"^^ . "https://www.sigmaaldrich.com/US/en/product/sigma/"^^ . "https://aopwiki.org/stressors/"^^ . . . "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases."^^ . . "ChEMBL_ID" . "http://purl.obolibrary.org/obo/CHEBI_"^^ . . . . . . . . "classification" . "false"^^ . . _:N76406a461040473b99a2a1988bf44ce9 . . "rna" . "Ioannis.Xenarios@unil.ch" . "true"^^ . . . "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"^^ . "Person" . "lw" . "^HGVM\\d+$"^^ . . . "life science" . . "NMRShiftDB structure" . . . "false"^^ . "http://purl.obolibrary.org/obo/MOP_$1"^^ . "false"^^ . . . . . . "tmjlowe@ucsc.edu" . . "chemistry" . . "AOPWiki (Stressor)" . . "chemical" . . . "602"^^ . "false"^^ . "false"^^ . "life science" . "cath" . "CIViC Molecular Profile" . . . . "3000045"^^ . "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"^^ . . . . "sabiork.kineticrecord" . "patent" . "http://wheat.pw.usda.gov/report?class=gene;name="^^ . . "mdl" . "terms" . . . . "dna" . . . . "The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation."^^ . . "genotype" . . . . "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^ . . "selventa" . "genomics" . "animal husbandry" . . "^[a-z_A-Z0-9]+$"^^ . . . . . . "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra."^^ . "https://www.sharkipedia.org/traits/$1"^^ . "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data."^^ . . . . . . . . "Etsuko Yasugi" . . . . "Guide to Pharmacology Ligand" . "imaging" . "small molecule" . . "protein" . . . "true"^^ . . . . . . "jgrethe@ucsd.edu" . "A vocabulary for the catalysis disciplines" . . . . . . . . . . . . . "gene expression" . . "^\\d{8}$"^^ . . . . "4238"^^ . . "http://purl.obolibrary.org/obo/MMO_$1"^^ . "http://gmd.mpimp-golm.mpg.de/Analytes/$1"^^ . . . . . . "^mt\\d+$"^^ . . . "MycoBrowser marinum" . . . "gno" . . . . "Natural Product Activity and Species Source Database" . "http://modelseed.org/biochem/compounds/$1"^^ . . "26753"^^ . "85dc6019-9654-4ba0-8338-08c4ffe8fe47"^^ . . "vendor" . . . . "https://biopragmatics.github.io/providers/hog/"^^ . . . "bioinformatics" . "https://github.com/biolink/biolink-model" . . "ontology" . . "genomics" . . . . "ygyingli@ncsu.edu" . "http://func.mshri.on.ca/fly/genes/list_functional_scores/"^^ . . . . "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^ . . "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"^^ . "http://www.kegg.jp/entry/"^^ . . . . . . . "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . . . "Lars Eisen" . "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^ . . "duret@biomserv.univ-lyon1.fr" . "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . "https://www.swisslipids.org/#/entity/SLM:$1"^^ . "chemistry" . . "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1"^^ . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID="^^ . "microarray" . . "Unipathway" . "microbiology" . . . . "false"^^ . . . . "^\\d{7}$"^^ . . . . . . "4000027"^^ . . . "Human Endogenous Retrovirus Database" . . . "Kinetic Simulation Algorithm Ontology" . . . . . . . "proteomics" . . . "0002066"^^ . . "Integrative and Conjugative Element Ontology" . . "^G\\d+$"^^ . . "runbiosimulations" . . . "obo" . . "false"^^ . . "classification" . . . . . . . "identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829"^^ . . . "proteomics" . . . . . . "fhir.implementation" . . "modularmassactionprimer"^^ . . . . . "11"^^ . . . . "life science" . . "http://bioinfo.lifl.fr/norine/result.jsp?ID="^^ . . . "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . "^[A-Za-z0-9_\\-]+(/[A-Za-z0-9_\\-]+)?$"^^ . . . . "BSU29180"^^ . "AB_262044"^^ . . . . . . "http://zinc15.docking.org/substances/"^^ . . . . . "Development Data Object Service" . "Capability"^^ . . . "bpeters@lji.org" . "20560"^^ . "https://publons.com/publon/"^^ . "false"^^ . . . "oharb@pcbi.upenn.edu" . . . "BUNA790102"^^ . "Vendor for assays, cells, and antibodies"^^ . . . . . . . "reproduceme" . . "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . "Zhiliang Hu" . . . . . . "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession="^^ . . "^\\d+$"^^ . "https://bioregistry.io/zazuko:"^^ . . "^[a-z][a-z]/[0-9]+$"^^ . . . . "^P\\d{5}$"^^ . "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession="^^ . "Food Interactions with Drugs Evidence Ontology" . . "JCRB1355"^^ . . . "A download link for the given resource" . "false"^^ . "^[0-9][A-Za-z0-9]{3}$"^^ . "00001"^^ . "0101963"^^ . "00000098"^^ . _:Ne852999e3f544bc9a8d299321e8ffa10 "helpdesk@cropontology-curationtool.org" . "true"^^ . . . "http://standards.iso.org/iso/15926/part14/$1"^^ . . "http://purl.obolibrary.org/obo/ECTO_$1"^^ . "plant phenotypes and traits" . . "biorxiv" . "false"^^ . . . "codelink" . . . "w3c rec" . . . . . "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified."^^ . . "0000005"^^ . . "sider.effect" . . . . . . . . "^\\d{7}$"^^ . . "Panorama Public" . "Frederic Bastian" . . "gold.genome" . "http://purl.org/ontology/bibo/$1"^^ . . . . . "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^ . "Lattes Platform number" . . . . "drosophila" . . . "Wikipedia" . "xuo" . . . . . . "^G(PL|SM|SE|DS)\\d+$"^^ . . . "https://string-db.org/cgi/network?identifier=$1"^^ . "^\\d+$"^^ . . . "Product number for the European Medicines Agency"^^ . "srodriguez142857@gmail.com" . . . "^[A-Z\\-]+$"^^ . . . . "protein" . "Small Angle Scattering Biological Data Bank" . . . . "TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them."^^ . . "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . . . _:N4fea6f4caf8d4e8983848b4539eb6da8 "Julian Seidenberg" . . "High-quality Automated and Manual Annotation of microbial Proteomes" . "g__Prochlorococcus_A"^^ . "oa" . . "false"^^ . . "ubio.namebank" . "chemistry" . . . "life science" . "true"^^ . "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database."^^ . "^[a-z0-9\\-_]+$"^^ . "life science" . "proteomics" . . . "MITE0000001"^^ . . "^\\d{7}$"^^ . . . "phenomics" . . "ftp://hgdownload.cse.ucsc.edu/goldenPath/"^^ . . . . . . "Bgee stage" . "proteins" . . . . . . "smc.bgc" . . . . "true"^^ . "Brendan MacLean" . . . . . . . . "ontology" . "atmospheric science" . "https://bacdive.dsmz.de/strain/$1"^^ . "obo" . . . "ERP004492"^^ . . . . "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."^^ . . . . . "depod@embl.de" . "life science" . . . "project management" . . . "careerPrizeMoney"^^ . . . . . "447860"^^ . . "ISO Object Identifier" . "tgn" . . "http://genomics.senescence.info/genes/details.php?id=$1"^^ . . . . . . "pkarp@ai.sri.com" . . . . . . . . "cba" . "eVOC (Expressed Sequence Annotation for Humans)" . . . . . . "Iranian Registry of Clinical Trials" . "https://www.gwascentral.org/phenotype/"^^ . "false"^^ . . . . "giardiadb" . "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments."^^ . "true"^^ . "biology" . . . . . . "1"^^ . "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^ . . . . "genpept" . . "allergome" . "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i="^^ . . "obo" . "http://id.nlm.nih.gov/mesh/vocab#$1"^^ . "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . . . "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="^^ . "PubChem Substance ID (SID)" . . "229"^^ . . . "ontology" . "repeatsdb.protein" . . . . . "EDAM Ontology" . . . . . "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . . . . . . . . "false"^^ . . . . "Evidence and Conclusion Ontology" . "false"^^ . "https://lobid.org/gnd/"^^ . . . . . . . . . . "National Xenopus Resource" . . . . "David.Linke@catalysis.de" . . . "metadata standardization" . . "ScerTF" . "Wojciech M. Karlowski" . "^SIGNOR-\\d+$"^^ . . . "Cowpea ontology" . "https://www.ebi.ac.uk/pdbe/entry/emdb/"^^ . "life science" . . "natural science" . "https://omabrowser.org/oma/hog/HOG:"^^ . "Birgit Meldal" . "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools."^^ . . . . . . . "http://bioportal.bioontology.org/ontologies/$1"^^ . "sequence feature" . . "molecular interaction" . . "Maize gross anatomy" . . "http://purl.obolibrary.org/obo/TXPO_"^^ . . . . "false"^^ . "Food Classification and Description System (from FSA Food Type identifiers)" . "Human developmental anatomy, timed version" . . . . "Protein Alignment organised as Structural Superfamily" . "Polymorphism and mutation databases"^^ . . . "A set of guides on implementing various processes within hospitals or healthcare systems."^^ . . "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates."^^ . . . "zfin" . . . . "false"^^ . "https://eol.org/pages/$1"^^ . . "C12345"^^ . . . . "lschriml@som.umaryland.edu" . . _:N54ddddf5000c4fd2a7b74bbe1329da40 "data@food.gov.uk" . . . . "false"^^ . . "RepeatsDB Structure" . . . . . . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME"^^ . . "^SLCTR/\\d{4}/\\d+$"^^ . "ontology" . "genomics" . . . . . . . "Genomic Data Commons Data Portal" . "false"^^ . . "^\\d+$"^^ . . . . . "http://purl.obolibrary.org/obo/BFO_"^^ . "obo" . . . "BRENDA Ligand" . "LINCS Cell" . . . "preclinical studies" . . . "phylogenetics" . . . . . "bioportal" . "false"^^ . . . "bold.taxonomy" . "edam.format" . . . . . "Plant Gall Ontology" . . . "brain" . "pmp" . . "expression data" . . "biomaterial manufacture" . . . "Omar S. Harb" . "MSH" . "disorder" . . . "ontology" . "https://scholar.google.com/citations?user=$1"^^ . . _:Nd2bf0f3b6406454fb160dae18729b3b0 "Stephan Schurer" . . . "Cell Lines in PubChem"^^ . "https://civicdb.org/links/variant/"^^ . "0187632"^^ . . "false"^^ . "h.doerpholz@fz-juelich.de" . . "lreha@ualberta.ca" . . . "obo" . . "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1"^^ . . . . . "The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library"^^ . "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways."^^ . . _:N7735554169874ebcad108460d8ad0f99 . "true"^^ . "Dictybase Gene" . "http://purl.obolibrary.org/obo/FBcv_$1"^^ . . "life science" . . . . . "nmr" . . . . "https://openalex.org/$1"^^ . "obo" . "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"^^ . "mice" . . "ontology" . . . . . "https://progenetix.org/services/ids/"^^ . "French National Center for Scientific Research - Research Group Identifier" . . . . . . . . "H-InvDb Locus" . . . . . . . "false"^^ . "mondo" . . . . "pgs" . "ssrn.article" . "http://www.jcvi.org/charprotdb/index.cgi/view/$1"^^ . "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."^^ . "https://www.metanetx.org/chem_info/"^^ . . "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_"^^ . . . "ferroliganddb" . "TF101014"^^ . . . . "ontology" . "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NDFRT&code="^^ . "false"^^ . . "false"^^ . . "iceberg.ice" . . . . "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas."^^ . . . . "https://bmrb.io/data_library/summary/index.php?bmrbId="^^ . . . . . "chiro" . . . . . . "SciCrunch Registry" . "4"^^ . . "ontology" . "protein" . "C. elegans Small Molecule Identifier Database" . . . "obo" . "Biocompute Object" . . "contributor"^^ . . "rna" . . . . "protein" . . . "ksdrew@uic.edu" . . "RCV000033555.3"^^ . . . "false"^^ . "health science" . "Reproductive and behavioural traits of both adult and larval stages, as well as information on environmental preferences and a few morphological traits."^^ . "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available."^^ . . . . "omics" . . . . . . "subtilist" . "http://www.imgt.org/ligmdb/view?id=$1"^^ . . "https://bartoc.org/en/node/$1" . "metascience" . . . . . "NITE Biological Resource Center" . "pathway" . "proteomics" . . . . . . . . "Collection of European paediatric cardiac coding files"^^ . "PubChem CID" . . "umls.st" . . . "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . . "Contains information about cells and data sheets related to transfection."^^ . "https://smc.jgi.doe.gov/bgc/$1"^^ . "TRQ"^^ . . . . . . . . . . "epidemiology" . . . . . "Eric W. Sayers" . . . "organism supplier" . . . "1"^^ . . "environmental science" . "http://purl.obolibrary.org/obo/ONS_"^^ . . "cherry@genome.stanford.edu" . . . . . . . . "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^ . . . . . . "SNHG3"^^ . "http://purl.obolibrary.org/obo/FBbt_"^^ . . "false"^^ . "transcriptomics" . "^\\d+$"^^ . "genome" . . . "structure" . "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use." . "obo" . . . . "life cycle stage" . . "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1"^^ . . . "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1"^^ . . "mtbd" . "FaBiO, the FRBR-aligned Bibliographic Ontology" . . . . . "239287"^^ . . . "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."^^ . . . . "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1"^^ . "Erik Segerdell" . "CSP2005" . . . . . "Chemspider" . . "https://pubchem.ncbi.nlm.nih.gov/element/"^^ . . . "00000011-a"^^ . "hemonc" . "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."^^ . "clao" . . . . . "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://gpcrdb.org/protein/$1"^^ . . "knowledge representation" . "^\\d+$"^^ . . "peptideatlas" . "life science" . . . . . . "http://purl.obolibrary.org/obo/DINTO_$1"^^ . . "pharmacodb.dataset" . "life science" . . . "Melanie Courtot" . . "nicolas.terrapon@univ-amu.fr" . . "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment."^^ . . "1257009"^^ . . . . . . . . . . "false"^^ . . "chemistry" . . "co_365" . "https://www.linkedin.com/in/$1"^^ . "obo" . _:N1e6e5dec4199411f836fb44038b9f4a1 . "MedDRA" . . "InChI" . . . . . . . . . "mota@i.nagoya-u.ac.jp" . . . . . "gmd.gcms" . . . . . . . . "independent variable" . "^\\d{8}$"^^ . . "false"^^ . . . . "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines." . "Jens Klump" . . "The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes."^^ . "protein" . . . "database management" . "physics" . "nmrshiftdb2" . . . . "literature curation" . "Genome assembly database - RefSeq accessions" . "idot" . . "ybradford@zfin.org" . . . "sharesAuthorInstitutionWith"^^ . "Tanya Barrett" . . "genetic strain" . . . . . . "true"^^ . . . . "baseDimensionEnumeration"^^ . "Vertebrate Taxonomy Ontology" . . "protein" . "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . "Ambystoma Genetic Stock Center" . . . "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."^^ . . . . "true"^^ . . "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . . "TTD Target" . . "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families."^^ . . . . "researcher data" . . . "false"^^ . "exo" . . "medgen.gtr" . . _:Nabe22b48689941088d1d9afa5a934350 . "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1"^^ . "metabolite" . "false"^^ . . . "true"^^ . "https://w3id.org/seo#"^^ . . "true"^^ . "false"^^ . . . . . "spike.map" . . . . . . . "UniProt Variants" . "^HIX\\d{7}(\\.\\d+)?$"^^ . "obo" . . . . "false"^^ . . . "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors."^^ . . . . . . . . . . . . . . "^\\d{7}$"^^ . "^\\d+$"^^ . "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/"^^ . "^\\w+$"^^ . "Don Gilbert" . . . . . . "data management" . . "ecosystem" . . . . "post-translational modification" . . . "FungiDB" . . . . . "chemistry" . . . "http://www.fairsharing.org/ontology/subject/SRAO_$1"^^ . "wujm@bjmu.edu.cn" . "dorloff@ncmir.ucsd.edu" . . "authoredBy"^^ . . . . . . "database" . "nutritional science" . . . "false"^^ . "http://mirbase.org/cgi-bin/mature.pl?mature_acc="^^ . . . . "false"^^ . . . . _:Nbc1316da7fc24fecb8577dee5db3c6dc "Alain J. Cozzone" . . "false"^^ . . "ProteomicsDB Peptide" . "SWEETRealm" . "small molecule" . . "^\\S+$"^^ . . . "report" . . . . "true"^^ . "false"^^ . "U49845"^^ . . "semantic web" . "topics" . . . "false"^^ . . "life science" . . "http://purl.obolibrary.org/obo/ZEA_"^^ . "^[a-z0-9\\-]+$"^^ . . "obo" . . "^\\d{7}$"^^ . . . . . "^CPX-[0-9]+$"^^ . . . "biological sample" . . "genome" . . "A combination of an ISBN and local unique identifier for articles and other published works. Please see the [Wikipedia page](https://en.wikipedia.org/wiki/Publisher_Item_Identifier) for a detailed explanation. Some PIIs are used as the local identifiers in DOIs, such as https://doi.org/10.1136/S0003-4967(24)38620-0."^^ . "^[A-Za-z0-9_]+$"^^ . . . "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"^^ . . "^[0-9]+$"^^ . "helpdesk@cropontology-curationtool.org" . . . "Cell line databases/resources"^^ . . . "PharmGKB Disease" . . . "false"^^ . . "ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG)."^^ . "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . "topics" . . . . . . . "false"^^ . . . . "false"^^ . . . . "sperm" . "Milton H. Saier, Jr." . . . "alan.rubin@wehi.edu.au" . . . "^.*/.*$"^^ . . "false"^^ . . "nif.cell" . "genomics" . . . . "disease" . "http://www.bootstrep.eu/ontology/GRO#$1"^^ . . . . . . . . "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"^^ . "life cycle" . . "Dublin Core Types" . . "Nonribosomal Peptides Database" . . "insdc.run" . . . "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."^^ . "pubchem.aid" . . "https://ngdc.cncb.ac.cn/genbase/search/gb/"^^ . "http://n2t.net/ark:"^^ . . "umls" . "https://www.re3data.org/repository/"^^ . "chemistry" . "bgee.organ" . . "https://purl.brain-bican.org/ontology/mbao/MBA_$1"^^ . . . "10142"^^ . . . . "https://viperdb.org/Info_Page.php?VDB=$1"^^ . . . . "video resource" . . "^\\d{7}$"^^ . . . . . "data management" . . . . "http://www.w3.org/2006/time#$1"^^ . . . . "http://purl.obolibrary.org/obo/GOREL_$1"^^ . . "false"^^ . . . . . "mw.project" . . . . . . . . . . . . "structure" . . "ontology" . . . . "https://www.scopus.com/sourceid/$1"^^ . . "mass spectrum" . "IUPHAR_LIGAND" . "0000091"^^ . . . . . . . . "MIMPS" . . "xenopus" . . . . "https://www.dbgi.org/earth_metabolome_ontology/#"^^ . . "hco" . . . . . . "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources."^^ . _:N0a7be7ab7ef34589ac0a212ca0b90c7b "HL7 Support" . . "Inge.Jonassen@uib.no" . . . . . "obib" . "identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/)"^^ . . . . "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland."^^ . "annotation" . "FBcv" . . . . "Tobias Schulze" . "clb" . "medicine" . "spar" . "mesh.2012" . . . "Hugh P Shanahan" . "https://mobidb.org/"^^ . "^\\d+$"^^ . . . . . "itis" . "gpcrnava" . "false"^^ . . "http://purl.obolibrary.org/obo/MFO_$1"^^ . "chemistry" . . . . . "https://dblp.org/pid/$1"^^ . . . . . . _:Nc67eaa5da835457d851cd6b2d8c36cbd "pbrooks@hcfa.gov" . "https://clinicalgenome.org/affiliation/$1/"^^ . . . . . . "https://biopragmatics.github.io/providers/icepo/$1"^^ . . . "Layla Michán Aguirre" . "Paul Flicek" . . _:Nf5506d4f4bbc4a948d01fceca090af87 "brennan.thomas@epa.gov" . "transcriptomics" . "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management."^^ . "life science" . "CutDB" . . "ontology" . "clinvar.variation" . . . . "SwissLipid" . . "false"^^ . . . "classification" . . "false"^^ . . . . . . "^[\\w\\-:,]{3,64}$"^^ . "Animal Genome Chicken QTL" . . . "false"^^ . "^IID\\d+$"^^ . . "0000000"^^ . . . "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/"^^ . "biochemistry" . . . . . . . "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . "genotype" . "Zebrafish developmental stages ontology" . . "^[CRPA]\\d+$"^^ . . . . "false"^^ . . "PR" . "omics data analysis" . . . . "biodiversity" . . . . . "This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports."^^ . . "structure" . . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . . . "eukaryotic" . "http://edamontology.org/operation_"^^ . . "Legacy site for IETF RFC proposals"^^ . . . . . . . . . . . . . . . . "0005"^^ . "immunology" . . . . "mat" . . . . "false"^^ . . . . . . "Ontological Interpretations for Web Property Graphs" . "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community."^^ . . "BioAssay Ontology" . . . . . . . . "false"^^ . . . . . . . "nlx.oen" . . . . "000000001"^^ . . "https://smc.jgi.doe.gov/bgc/"^^ . . "2679240"^^ . . "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^ . "fao" . . "https://biopragmatics.github.io/providers/sdis/$1"^^ . . "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals."^^ . . "true"^^ . . "nbn" . "https://data.terra.bio/ga4gh/drs/v1/objects/$1"^^ . "NCI Drug Dictionary ID" . . "fly" . "protein" . "Jennifer C. Giron" . "obo" . . . . "Job Dekker" . "slctr" . "98346"^^ . . "false"^^ . "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs)."^^ . . . . . . . . "http://purl.uniprot.org/isoforms/$1"^^ . . . "kaken" . "false"^^ . . "true"^^ . . . . . . . "https://bioregistry.io/cst:"^^ . . . . "publication" . . "https://cropontology.org/rdf/CO_345:"^^ . . "^\\w{4}\\d{8}$"^^ . "cell" . . . "Berkeley Drosophila Genome Project EST database" . "protein analysis" . . . "2004-2820"^^ . . . . . . "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . . . . . . . . . . "cell biology" . . . "marker" . "EAWAG Biocatalysis/Biodegradation Database" . "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes."^^ . "^\\d{7}$"^^ . . . . "true"^^ . . . . . "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications."^^ . "^\\w+$"^^ . . . . . . . . . "ecology" . . . . "omia" . "01N50ZZ"^^ . . . . . . "false"^^ . . . "fplx" . "0000295"^^ . . . "ontology" . "toni.gabaldon@crg.eu" . . . "false"^^ . . "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^ . . . . . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid="^^ . . "oclc" . "http://purl.obolibrary.org/obo/MF_$1"^^ . "http://www.ubio.org/browser/details.php?namebankID="^^ . . "protein" . "EcoCyc" . . . "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . "^\\d+$"^^ . . "F11903"^^ . "false"^^ . . . "activityBoundOf"^^ . . "false"^^ . "https://gpcrdb.org/protein/"^^ . . . . . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_inv_"^^ . . . "http://purl.obolibrary.org/obo/OGSF_$1"^^ . "SCOP(e) concise classification string" . "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^ . "disease" . "https://deims.org/locations/$1"^^ . . "http://purl.obolibrary.org/obo/ECAO_$1"^^ . "^\\d{7}$"^^ . . . . . "Lindsey Anderson" . . . . . . . . . . . "proteomics" . . "integbio" . "chemistry" . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid="^^ . "false"^^ . "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"^^ . . "James C. Hu" . . . . "Healthcare Common Procedure Coding System" . "food" . "chemical biology" . . "lewis.geer@nih.gov" . "An additional Japanese clinical trial registry"^^ . "https://phagedive.dsmz.de/strain/"^^ . . . . . . _:N4c939bb599ca423bb976492fa09c22ae . . . . . . . . "cell" . . . . "https://europepmc.org/article/AGR/"^^ . "ismail.fliss@fsaa.ulaval.ca" . "neurodegeneration" . . "false"^^ . . _:N4f2dacaced1b47daa7675d633ebdf89a "helpdesk@cropontology-curationtool.org" . . . "gene" . . . . . "true"^^ . "000000341"^^ . "00007294"^^ . . "^OSR\\d{4}$"^^ . "^\\d+$"^^ . "quality" . . . . . "cmo" . . "pathway" . "^ST[0-9]{6}$"^^ . "structure" . . "ontology" . . . . "Mouse Genome Informatics" . "wgs84" . "Information for ligands in the BRENDA database."^^ . . "Vertebrate trait ontology" . . . . "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"^^ . . . . . . . _:N6ca1bb0cc3fd4af98bcb641d1e142a7b . . . . . . "version 2019 - pvs"^^ . . . . "Wikidata" . "sov:WRfXPg8dantKVubE3HX8pw"^^ . . "http://purl.obolibrary.org/obo/NCRO_"^^ . "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^ . "NodeShape"^^ . "LOC_Os02g13300"^^ . . "genomics" . "http://purl.bioontology.org/ontology/HOIP/HOIP_"^^ . . . . . . "genomics" . . . . "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . "greatchen@cdutcm.edu.cn" . "TopFind" . "dsm-iv" . . "ontology" . . "A repository of software packages written in Rust."^^ . . . . "Q-2958"^^ . . "Stemcell Knowledge and Information Portal" . "https://www.storedb.org/store_v3/study.jsp?studyId=$1"^^ . "AcknowledgementCondition"^^ . . . " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries."^^ . . "interoperability" . "https://neurovault.org/collections/$1"^^ . . "cell lines" . . "pd_st" . "applied microbiology" . "gene prediction" . "JCOIN" . "AmoebaDB" . "false"^^ . "UniProt Isoform" . . . . . . "miRNEST" . . "false"^^ . "mbrochhausen@uams.edu" . "obo" . . . . . "Hazardous Substances Data Bank" . . "NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4 includes robust protein predictions (NemPep4), and protein families for 63 nematode species, over 600,000 ESTs and over 250,000 proteins."^^ . "http://purl.obolibrary.org/obo/MCO_$1"^^ . . "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)."^^ . . . . _:N0062499e39e142ee87957c7f094e9cf7 "Allen Institute for Brain Science" . . . "uniprot.tissue" . . . . . "db-object-id"^^ . "false"^^ . . . . . "structure" . . "https://bioregistry.io/kyinno:"^^ . "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^ . . "software"^^ . "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^ . . "Jason E. Stajich" . "351"^^ . "proteomics" . . "http://purl.obolibrary.org/obo/CTO_"^^ . . . . . . . "^\\d{7}$"^^ . "MFCD00011659"^^ . "https://proteinensemble.org/$1"^^ . . . "https://www.authorea.com/users/"^^ . . . . "expression data" . . "3532759"^^ . "disease" . . "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary."^^ . . _:Ndaadbfc8604f4c8ca0720f4b4f87780f "J.Bard@ed.ac.uk" . "noaa.cameo" . . . . . . "comparative genomics" . "http://purl.obolibrary.org/obo/ECTO_"^^ . "http://www.w3.org/ns/odrl/2/"^^ . . "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO)."^^ . "Metabolic Atlas Reaction" . "^[0-9]+$"^^ . . "false"^^ . . . . . "map" . . . . "kestrelo" . . . . . "duo" . . "lindsey.anderson@pnnl.gov" . "life science" . . . . "http://biohackathon.org/resource/faldo#"^^ . "expression data" . "AAA35559"^^ . "Bill Hogan" . "https://www.facebase.org/data/record/#1/isa:dataset/accession="^^ . "virology" . "biochemistry" . "NCit" . . . "taxrank" . "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012"^^ . "^CL\\d+$"^^ . . . "genome" . . "life science" . . "^[0-9a-f\\-]+$"^^ . . "1"^^ . "FBbi" . "https://www.uniprot.org/uniparc/"^^ . . "small molecule" . . . . . "biopragmatics/bioregistry"^^ . . "endocrinology" . . "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$"^^ . "20000614040"^^ . "2A"^^ . . "http://purl.jp/bio/4/id/$1"^^ . . "false"^^ . . "Database of structurally defined protein interfaces" . . "Erik van Nimwegen" . . . _:Nb688cf72c2554cf28a7a96c359a92fb7 . "https://bioregistry.io/cnrs:"^^ . . . . "gene expression" . "health science" . . . "http://www.conoserver.org/?page=card&table=protein&id="^^ . . "Yeast Intron Database v4.3" . . . "2000191"^^ . "false"^^ . . . "false"^^ . . . . . . . "http://www.vbase2.org/vgene.php?id=$1"^^ . "structure" . "anatomy" . . "^SMP\\d+$"^^ . . . . . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances."^^ . "ontology" . . "genome" . . . "vsao" . "^\\d{7}$"^^ . "http://www.w3.org/ns/prov#"^^ . . "true"^^ . . "^\\w+$"^^ . . . . . "https://giardiadb.org/giardiadb/app/record/gene/$1"^^ . . . "0000509"^^ . "MJoachimiak@lbl.gov" . "http://localhost/plosthes.2017-1#$1"^^ . "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^ . . . "signor" . . "https://www.vmh.life/#gene/$1"^^ . . . . "Richard John Roberts" . . . "spbase" . . . "GrainGenes" . . . . "https://spdx.org/licenses/$1"^^ . . . "kopka@mpimp-golm.mpg.de" . . . . "neuroname" . . . "PubChem Element" . "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"^^ . "false"^^ . "false"^^ . "Dataset"^^ . . . . "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId="^^ . . . . . "https://cordis.europa.eu/project/id/"^^ . "09200010"^^ . . . . "^[1-9]\\d*$"^^ . . . "^R\\d+$"^^ . . . "https://w3id.org/seo#$1"^^ . . . "LBCTR2023015204"^^ . . . "The hu.MAP integrates several large scale protein interaction datasets to obtain a comprehensive view of protein complexes."^^ . . . "prefLabel"^^ . . . "vw253@cam.ac.uk" . . . . "https://www.inaturalist.org/taxa/$1"^^ . "statistics" . "Dan Berrios" . "Jacqueline Campbell" . . . "phenotype" . . . . "https://cropontology.org/rdf/CO_330:$1"^^ . . . . . "anatomy" . "http://hogenom.univ-lyon1.fr/query_sequence?Go=Submit+Query&seq=$1"^^ . . . . "DB-0174" . . "pcl" . . "SNOMED" . "https://bioregistry.io/treebase:"^^ . . "biochemistry" . . "supfam" . . . . . "ontology" . . "^\\d+$"^^ . "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information."^^ . "^\\d{7}$"^^ . "COI Catalogue is a herbarium with c. 800.000 specimens, organised in separate collections due to the research priorities over the years."^^ . . . . "Ontology about C. elegans and other nematode phenotypes"^^ . "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1"^^ . . . "numerical identifier for an author in SciProfiles by MDPI"^^ . . . "knowledge and information systems" . . . . . . . . . "obo" . . "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"^^ . . . . "storedb.file" . . . . . . "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . . . "food" . . . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^ . . . . "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid="^^ . "The Ageing Gene Database" . "TripleExpression"^^ . . . "napdi" . "false"^^ . . "^\\d{7}$"^^ . . "Jennifer R Smith" . . . . "vaccines" . "https://dcmi.github.io/openwemi/ns#"^^ . . "Progenetix" . "^\\d+$"^^ . . "sonami@riken.jp" . "Human Disease Ontology" . "MEROPS Clan" . . "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . . . . "storedb.study" . . "false"^^ . . . . "lifengcheng@zju.edu.cn" . . . . "computational chemistry" . . . "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . "https://www.addexbio.com/productdetail?pid=$1"^^ . . . . . . . "geno" . "COMBINE specifications" . . "Echinobase" . . . "Metadata Management and distribution system for Multiple GNSS Networks" . . . . "https://www.uniprot.org/arba/$1"^^ . "6038"^^ . "http://metlin.scripps.edu/metabo_info.php?molid="^^ . . . . . . . "omim.ps" . "^\\d{8}$"^^ . "Vertebrate Genome Annotation Database" . . . . "brain imaging" . . . "https://www.webelements.com/$1"^^ . . "Description of a Project" . . "Vitis ontology" . . . . . "ontology" . . . . . . . "gainesville.core" . . . . . "https://www.proteomicsdb.org/#human/proteinDetails/"^^ . "https://www.nwo.nl/en/projects/$1"^^ . . "MSV000082131"^^ . . "PyPI" . . . "false"^^ . "https://nbn-resolving.org/"^^ . . "http://www.kegg.jp/entry/$1"^^ . . . "ebf69ca24298b28b2361e7d43eb52d6c"^^ . . . "http://www.w3.org/2006/vcard/ns#"^^ . "eukaryota" . "bams" . . . . . . "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO)."^^ . . . . . . . . . . . "ontology" . . . . . . . "false"^^ . . . "https://pathbank.org/view/"^^ . . . "https://www.authorea.com/users/$1"^^ . . . . "International Histocompatibility Workshop cell lines" . . . . . "CAMEO Chemicals ID" . . . . . . . "https://odc-tbi.org/data/"^^ . . "gene" . . "biozil" . . . "https://rnaloops.cs.put.poznan.pl/search/details/"^^ . . "disease phenotype" . . . "organ" . . "obo" . . . . . "CALM1"^^ . . . . . "person" . . "identifier for researchers in Japan used in goverment-based research funding (from 1980s)"^^ . . "iceo" . "anatomical therapeutic chemical code" . "opmi" . . . . "false"^^ . . . . "pathway" . . "informatics" . . . . . "36"^^ . "http://protege.stanford.edu/plugins/owl/protege#"^^ . . "^\\d+$"^^ . . "^[0-9]*$"^^ . . "false"^^ . . "diagnosis" . "Creative Biolabs" . . . . . . . "2gc4"^^ . . "https://pubchem.ncbi.nlm.nih.gov/cell/$1"^^ . "http://www.radiomics.org/RO/"^^ . "D053716"^^ . . . . . "http://www-snorna.biotoul.fr/plus.php?id="^^ . . . . . "SNOMEDCTCT" . "false"^^ . . "false"^^ . . . "InChIKey" . . . "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones."^^ . "life science" . . . . "https://www.uniprot.org/uniprotkb/$1"^^ . . "hilmar.lapp@duke.edu" . "ontology" . "disease" . . . . . . . . . . . "ISBN-10" . "^\\d+$"^^ . "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms."^^ . . "developmental biology" . . . . . . . . . "identifier of an entry in the NCI Drug Dictionary"^^ . . . . . . "Terence D. Murphy" . "cellular component" . . . . . "biomedical science" . "false"^^ . . "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank."^^ . . . "ontology" . . . _:Nbd51a28cea234a7bba1dd4d7394dfcbe "mssohelp@meddra.org" . "^[0-9a-f\\-]+$"^^ . . . . . . . "http://www.pathoplant.de/detail.php?accNo="^^ . "Database of Spatially Interacting Motifs in Proteins" . . "IntAct provides a freely available, open source database system and analysis tools for protein interaction data."^^ . . . . . . . "http://www.ontobee.org/" . . "https://www.holofooddata.org/sample/"^^ . . . "^MIMAT\\d{7}$"^^ . "insertion"^^ . "obo" . "486"^^ . . . . . . "^\\d{7}$"^^ . . . . "g.gkoutos@bham.ac.uk" . . . . . "life science" . "functional genomics" . "structure" . . . "proccaserra@gmail.com" . . "Jeffrey A. Detras" . . . . . "false"^^ . "http://ecoliwiki.net/colipedia/index.php/$1:Gene"^^ . "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)" . . "false"^^ . . . . . "systems biology" . "false"^^ . "https://fairsharing.org/users/$1"^^ . . . "Next Generation Biobanking Ontology" . "anatomy" . . "1"^^ . . . . . . . . . "45539"^^ . "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein."^^ . "57"^^ . . . . . . "^\\d+$"^^ . . "false"^^ . "pubmed"^^ . . . . . . . . . "ptm site prediction" . "UniRef90_P00750"^^ . . . . . . . "identifier for an organisation in author affiliations per Scopus"^^ . "scholia.resource" . . . "ontology" . . "lrg" . . . . . "^\\w+$"^^ . . . . "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records."^^ . . . "biology" . . . "mutation" . "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id="^^ . . . "National Drug Code" . "https://bioschemas.org/profiles/"^^ . . . "false"^^ . . . . . . . . "abandrowski@ncmir.ucsd.edu" . . "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . . "medicinal chemistry" . "http://purl.org/obo/owlEOL_"^^ . . "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon."^^ . . . . "false"^^ . "Information for ligand groups (chemical classes)."^^ . . . "false"^^ . . "Lindsay Cowell" . . . "HGVM15354"^^ . "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard."^^ . . . . . "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . . . "^KW-\\d{4}$"^^ . . . "false"^^ . "https://hdl.handle.net/hdl:20.500.12582/"^^ . . . . . . "http://purl.obolibrary.org/obo/TAHH_"^^ . "co_335" . "Encyclopedia of DNA Elements" . . "A hierarchical classification of congenital heart disease "^^ . "http://plugins.biogps.org/cgi-bin/wp.cgi?id="^^ . "0000001"^^ . . . "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . "P683" . . . . . "Integrated Taxonomic Information System" . "disease" . "false"^^ . . "miRBase mature miRNA" . . "false"^^ . "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances."^^ . "biomedical science" . "FDA Submission Tracking Number" . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions."^^ . . . . "pubchem.classification" . . . "rna" . "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."^^ . . "http://purl.obolibrary.org/obo/AfPO_$1"^^ . . "0010034"^^ . . . "lipro" . "berman@rcsb.rutgers.edu" . "http://www.ontobee.org/ontology/$1" . "Mammalia Polymorphism Database" . "ChemPro Target" . . . . "4QHKG"^^ . "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name="^^ . . . . . . "Primate Brain Atlas" . "allergen" . "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . . "ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for chemoproteomic probes used to label human proteins in living cells."^^ . "DTXSID7032004"^^ . . . . . "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp="^^ . "Genotype Ontology" . . "Zach Landis-Lewis" . . . . "vz" . . . . . . . "3639"^^ . . "https://cropontology.org/rdf/CO_367:$1"^^ . . "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic."^^ . . . . . . . . . "obo" . "109082"^^ . "false"^^ . . . . "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported."^^ . . "0100010"^^ . . . "false"^^ . "Golm Metabolome Database Profile" . . . . "http://purl.obolibrary.org/obo/NCBITaxon_"^^ . "Erik.Segerdell@cchmc.org" . . . "https://civicdb.org/links/molecular_profile/$1"^^ . "https://sparontologies.github.io/fabio/current/fabio.html#"^^ . "ontology" . . . "rliningt@sfu.ca" . . . . "cl3603"^^ . "false"^^ . . . . "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^ . . . "https://bitbucket.org/$1"^^ . "Val Wood" . . . . "birnlex" . . . . . . "biomedical science" . "mirbase.mature" . "gene expression" . . . "http://www.ebi.ac.uk/efo/EFO_"^^ . "http://purl.obolibrary.org/obo/OVAE_$1"^^ . "dc_cl" . _:N162037c0c5e841c8ad3e24ff5b417396 "wbug@ncmir.ucsd.edu" . . . . . . "sequence" . "Observational Medical Outcomes Partnership" . "https://bioregistry.io/dragondb.allele:"^^ . . . "life science" . "https://w3id.org/semapv/vocab/$1"^^ . . . . . "^\\d{5}$"^^ . "Lindsey.Anderson@pnnl.gov" . . . "false"^^ . "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures."^^ . . "^TTDS\\d+$"^^ . . "Jeff Beck" . . "false"^^ . . . . "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found."^^ . . "preclinical studies" . . "CATH domain" . . "NIF Standard Ontology: Qualities" . "https://www.confident-conference.org/index.php/Event_Series:"^^ . . . . . . . "Protein Affinity Reagents" . "^UDB\\d{6}$"^^ . "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"^^ . . . "communication science" . "iobc" . . "dct" . "The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)"^^ . "https://www.sharkipedia.org/trends/"^^ . "http://purl.obolibrary.org/obo/TAO_$1"^^ . . . "sequence" . . "protein" . . "Beta Cell Biology Consortium" . . "panther.pathway" . "http://purl.obolibrary.org/obo/FYPO_$1"^^ . . . . "pathobiochemistry" . . . "false"^^ . "biology" . . . . . . . . "http://purl.uniprot.org/annotation/"^^ . "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . . . . "eo" . "0000187"^^ . . . "grid" . . "dragondb.protein" . . "hj@uestc.edu.cn" . "biology" . "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^ . "ISA1083-2"^^ . . . . "ontology" . "taxonomic classification" . "myco.tuber" . _:N400c4b1a400c48adac7f4fd308153dbb "helpdesk@cropontology-curationtool.org" . . _:N2e4f5c23f0764470a04c3cfb1e6c4e0a . "dna" . . "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . . "reactions" . . "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1"^^ . . . "A0TMC"^^ . "https://www.kegg.jp/entry/$1"^^ . . "obo" . . "faseb list" . "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^ . . . . . . . . "eukaryotic Subcellular Localization database" . . . . . . . "D.Schomburg@tu-braunschweig.de" . . . "identifier for a fungus taxon in Index Fungorum"^^ . "false"^^ . . . . "BT20_BREAST"^^ . . "http://www-bionet.sscc.ru/sitex/index.php?siteid="^^ . "https://medical-data-models.org/forms/$1"^^ . "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-"^^ . . . . . "structure" . "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1"^^ . . . . "mouse" . . . "^\\d+$"^^ . . "Yeast Deletion and the Mitochondrial Proteomics Project" . . . . . . . . "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."^^ . "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^ . . "MESHCS" . . . "tobias.schulze@ufz.de" . . . . "P3DB Protein" . . "tto" . . . . . "false"^^ . "TVAG_386080"^^ . . . . . "^\\w+(\\.)?(\\d+)?$"^^ . . "40565"^^ . "false"^^ . . . "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information."^^ . . "bibliography" . . "pseudomonas" . "false"^^ . . . . . "Signaling Network Open Resource" . . . . . . "false"^^ . "^\\d+$"^^ . "disease" . "biomedical science" . . "false"^^ . "http://purl.obolibrary.org/obo/ECOCORE_"^^ . . "http://ddinter.scbdd.com/ddinter/drug-detail/$1"^^ . "population genetics" . "botany" . . "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections."^^ . "pencehe@oneonta.edu" . . . "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"^^ . . "false"^^ . . "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^ . . . . "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"^^ . . "nanotechnology" . . . . . . . . . "false"^^ . . "UniProt Diseases" . . . "12300"^^ . . . . . . _:N3257f323b5f24eeab5090d84680d8d04 "Jonathan Bard" . . . . "SNOMEDCT_US_2024_03_01" . . . . . . . "https://world-2dpage.expasy.org/repository/"^^ . "algorithm" . . . "false"^^ . . "annotation" . . . "https://www.osti.gov/biblio/$1"^^ . . . "http://purl.obolibrary.org/obo/ADO_"^^ . "IID00001"^^ . . "https://bioregistry.io/dbd:"^^ . . "biology" . "Carl F. Schaefer" . . . "https://www.fishbase.ca/summary/"^^ . . . . "https://viperdb.org/Info_Page.php?VDB="^^ . . . . . . "prints" . . . "25512"^^ . "0010039"^^ . . "false"^^ . . . . "false"^^ . . . "https://guolab.wchscu.cn/AnimalTFDB4//?#/family_summary/TF/$1"^^ . . . "ZFIN" . . . . . . . . . . . . . "https://morpheus.gitlab.io/models/"^^ . "agriculture" . "data management" . . "false"^^ . . . . . . . "http://www.genome.jp/dbget-bin/www_bget?ec:"^^ . . . "biomedical science" . . "0000029"^^ . "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . . "fypo" . . . . . "false"^^ . "^\\d+$"^^ . . _:N6a6323aa9606436298cdc45138bb0a17 "INOH curators" . "false"^^ . . . . . "146421"^^ . . . "NLXMOL" . . . . . . "https://deims.org/sensors/$1"^^ . . . "Christoph Wohner" . "ChemicalStructure"^^ . . "John Garavelli" . . . "medicine" . "artificial intelligence" . . . "^\\d+$"^^ . "https://biopragmatics.github.io/providers/peff/$1"^^ . . . . "https://bioregistry.io/chemspider:"^^ . . . . "1"^^ . "Paleobiology Database" . . . . . "^\\d+$"^^ . . . . "UniProt Post-Translational Modification" . . . . "/53355/cl010066723"^^ . "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage."^^ . "https://mged.sourceforge.net/ontologies/MGEDontology.php#"^^ . "http://sabiork.h-its.org/newSearch?q="^^ . "^\\d+$"^^ . "CellBank Australia" . "false"^^ . . . . "bioproject" . "^\\d+$"^^ . "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id="^^ . . . "PLOS Thesaurus" . "general & upper" . . "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology."^^ . . . . . . . "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions."^^ . . . . . . . . "Cross-linker reagents ontology" . . . . . . . "ontology" . . . "2011488555"^^ . "invertebrate" . "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world."^^ . "data model" . "Cell Signaling Technology Pathways" . "https://www.glycoepitope.jp/epitopes/"^^ . . . . "https://icd.who.int/browse10/2019/en#/"^^ . . . . . . . "false"^^ . . "Nucleic Acids Phylogenetic Profiling" . . . . "subject agnostic" . . . "159787"^^ . "iuphar.receptor" . "kegg_genomes" . . . "Motonori Ota" . . "joerg.overmann@dsmz.de" . . . . . "http://bio2rdf.org/affymetrix:$1"^^ . "civic.variant" . . "http://www.geneontology.org/formats/oboInOwl#$1"^^ . . . . "^\\d{7}$"^^ . . "Harry E. Pence" . . . "norine" . . "false"^^ . . . "The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/)."^^ . "reaction" . "^[cdfgops]__\\w+\\S+$"^^ . "embryo" . "0000487"^^ . . "feature"^^ . "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1"^^ . . "false"^^ . "FR-FCM-ZYGW"^^ . . "^001\\d{5}$"^^ . . . . . . . . "protein" . . "MicrosporidiaDB" . . "false"^^ . . "false"^^ . . "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . . . . . "genomics" . . . "http://purl.obolibrary.org/obo/RS_$1"^^ . "cultured cell line" . "ASRP1423"^^ . . . "tahh" . "https://en.wiktionary.org/wiki/"^^ . "proteomicsdb.peptide" . . "false"^^ . "tol.webproj" . . . "tiago.lubiana.alves@usp.br" . . _:N666c4a679d674cfab27ee5b6c85aa4cc "info@wikidata.org" . "Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project." . . "biology" . . "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"^^ . . . . "G-Rich Sequences Database" . . . . "health science" . "clustering" . "false"^^ . "YMDB00001"^^ . . "1"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_"^^ . "REPRODUCE-ME Ontology" . . . . . . "depmap" . . . . . "https://rrid.site" . . "obo" . "co_322" . . "false"^^ . . . . "http://purl.obolibrary.org/obo/WBbt_"^^ . "JGI Phytozome" . "https://www.ebi.ac.uk/chembl/compound/inspect/$1"^^ . . . . "https://pubchem.ncbi.nlm.nih.gov/element/$1"^^ . "2029"^^ . "data identity and mapping" . "UniProtKB-SubCell" . . . . . . "false"^^ . . "propreo" . . . . . . . "ribonucleic acid" . . . "obo" . "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^ . . . "sty" . . . "http://tables.pseudogene.org/[?species_name]/$1"^^ . "edda" . _:N3a99a6f176d64698a2bcce4519dcb0c7 . "false"^^ . . "022586"^^ . . . . "false"^^ . . "^\\d+$"^^ . "ontology and terminology" . "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view."^^ . . . . "GDS1234"^^ . . . . . "MMAR_2462"^^ . . "molecular biology" . "mass spectrometry" . . . . . . . . "0058"^^ . . "false"^^ . . "ecocore" . . . . "kinetics" . . . . . . . "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information."^^ . "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs."^^ . . . . . . "http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_$1"^^ . . "true"^^ . . "dna" . . "The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)"^^ . "^\\d{7}$"^^ . . "^PGS[0-9]{6}$"^^ . . . . "GLIDA Ligand" . "http://www.w3.org/2006/time#"^^ . . . . . "Epilepsy Ontology" . . "Ion Channel Electrophysiology Ontology" . . . . "https://www.langual.org/langual_thesaurus.asp?termid="^^ . . . . "false"^^ . "obo" . "UR000124451"^^ . "nomen" . . . . "model organism" . . . "https://plants.ensembl.org/id/"^^ . "1693"^^ . "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . . . "obo" . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . . "50-00-0"^^ . . "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . "AS000060"^^ . "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^ . . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id="^^ . . . "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."^^ . . . "emotion" . . . . . . . . . "interaction" . "^\\d{7}$"^^ . . . "classification" . "false"^^ . . "1"^^ . "MassIVE" . . "muamith@utmb.edu" . "reaction" . . . . . "beta cell" . "gary.bader@utoronto.ca" . . "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups"^^ . . "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR)."^^ . . . . . . . "omics" . . "^[m,M]{2}[0-9]{5}[0-9]*$"^^ . . "http://purl.obolibrary.org/obo/CMO_"^^ . "Vertebrate Skeletal Anatomy Ontology" . "false"^^ . . . . . . "Simplified molecular-input line-entry system" . "Joe Flack" . . . . . "^[1-9]\\d{0,5}$"^^ . . . "ontology" . . . . "ontology" . . . "chemistry" . . "resource metadata" . . "has URI pattern" . . "^\\d{16}$"^^ . . "349124"^^ . "coexistence" . . . . . . "approved drug" . . . . "20"^^ . . . "https://www.ebi.ac.uk/complexportal/complex/$1"^^ . . "false"^^ . . . "preprints" . . "false"^^ . . . . "false"^^ . . . . . "adriano.rutz@ik.me" . . . "A frontend to Wikidata"^^ . "YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references."^^ . "life cycle" . "biology" . . . . . . . "PF11779"^^ . . . . "A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc."^^ . . "http://purl.obolibrary.org/obo/SEP_$1"^^ . . "co_324" . "https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/$1"^^ . . . "EGID" . . "688"^^ . "https://cropontology.org/rdf/CO_338:"^^ . "true"^^ . "Space Life Sciences Ontology" . . . . "101"^^ . "^[A-Z0-9]+$"^^ . . . . . . . . . "arthit@gmail.com" . . . . . . . . "true"^^ . . "gobp" . "Software Heritage is the universal archive of software source code."^^ . "4214"^^ . . . "foodex2" . . . . "https://www.metanetx.org/comp_info/$1"^^ . . "https://www.clinicaltrialsregister.eu/ctr-search/search?query="^^ . . "4685"^^ . . "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"^^ . . "https://glyconavi.org/hub/?id="^^ . "https://www.ncbi.nlm.nih.gov/sra/"^^ . . "Toxic Process Ontology" . . . . "scopus" . . . . . . "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^ . . "Virtual Contact File" . "chemistry" . . . . "^\\d+$"^^ . . "aisling.doyle9@gmail.com" . . "co_366" . "false"^^ . . . . . "^OS-\\d+$"^^ . "CVCL" . . "https://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=$1"^^ . _:Nabe22b48689941088d1d9afa5a934350 "psidev-gps-dev@lists.sourceforge.net" . "Molecular Interactions Controlled Vocabulary" . . . . "nlm.publisher" . . "http://purl.obolibrary.org/obo/SLSO_$1"^^ . "rna" . . . . . . . . "life science" . . "vgnc" . . . . . . . . "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . "false"^^ . . . . . "life science" . . "botany" . . "gene" . "true"^^ . . . . "assetConcepts"^^ . . . . _:N59c39d99399a4ca48085273a0476dbd0 "Crop Ontology Helpdesk" . . . . "KCT0008394"^^ . . "^\\d+$"^^ . "^M\\d+$"^^ . . . _:Nc7ff09a926f849c5b587faf344121bb6 "BioModels.net team" . . . "false"^^ . . . . . . . . "^\\d+$"^^ . . "Alpha Tom Kodamullil" . . "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources."^^ . . . . "The 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."^^ . . "https://www.mlcommons.org/mlc-id/$1"^^ . "VIPERdb" . . "The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]"^^ . . . "druzinsk@uic.edu" . . "ssn.system" . . . "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression."^^ . . . . . . . . . . . "false"^^ . "tair.protein" . . . "ontology and terminology" . "^C\\d{4}$"^^ . . "false"^^ . . . "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."^^ . "Schema.org" . "biomedical science" . "protein" . . "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid="^^ . "has provider formatter" . "report" . . . "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . . . . "false"^^ . "help@emdatabank.org" . "^N[0-9]{10}$"^^ . . "https://cellmodelpassports.sanger.ac.uk/passports/"^^ . . "protein" . . . . . "https://www.ebi.ac.uk/intact/interaction/$1"^^ . . "Reactome" . . "survey" . . "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC="^^ . "Database of human Major Histocompatibility Complex" . "ontology" . . . "false"^^ . . . "phenomics" . . "go" . . . . _:N000e2f2c430b437ca9757e0c7abe8844 . "experimental condition" . "http://purl.obolibrary.org/obo/TAXRANK_$1"^^ . . . . "lucas.leclere@obs-vlfr.fr" . . . . "virology" . . . "http://erop.inbi.ras.ru/result2.php?PepName=$1"^^ . . . . . . "The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample."^^ . "gene expression" . . "NCI_Thesaurus" . . . "omics" . . "^\\w\\d{4}\\w\\d{2}(\\-[35])?$"^^ . . "ambystoma" . . . . "iresite" . "Robert Druzinsky" . "flu" . "https://bioregistry.io/pubmed:"^^ . . . . "Gene Normal Tissue Expression" . . . "life science" . . "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"^^ . . . . . . . . "false"^^ . . . "https://fedirect.toolforge.org/?id=$1"^^ . "biology" . . "ontology" . . . . . . . . . "obo" . . . "MediaDive Solution" . "^\\d{7}$"^^ . . "ontology" . "Causal_Graphical_Model"^^ . "small molecule" . "https://biomedit.ch/rdf/sphn-ontology/sphn#$1"^^ . . "https://biopragmatics.github.io/providers/bs/"^^ . "http://lisanwanglab.org/DASHR/entry/$1"^^ . . . . . _:N4c939bb599ca423bb976492fa09c22ae "PLOS Taxonomy Team" . "person" . . "^GPST[0-9]{6}$"^^ . . . . . "ontology" . . . "biomedical science" . . . . . . "qualities" . "concentration" . . "Mihail Anton" . "Wikidata Property" . . "1000100"^^ . "false"^^ . . . "p3db.site" . . . . . "false"^^ . . . "http://api.hymao.org/api/ref/$1"^^ . . "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE)."^^ . "^C\\d+$"^^ . . "GitHub username" . . . . . . "https://web.expasy.org/cellosaurus/cellopub/$1"^^ . "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^ . . . . . . "jmwhorton@uams.edu" . . "VSAO_RETIRED" . "http://purl.obolibrary.org/obo/AMPHX_"^^ . . . . . . "^\\d{7}$"^^ . "false"^^ . . "http://pax-db.org/#!species/"^^ . . . . . . . . . "Ontology of Genetic Susceptibility Factor" . "HOMD Sequence Metainformation" . "maria.taboada@usc.es" . . "false"^^ . "http://purl.obolibrary.org/obo/MFOEM_"^^ . . . . "pocketome" . . "RCB0002"^^ . "reagent" . "^\\d+$"^^ . . . . . "https://www.ebi.ac.uk/interpro/entry/pfam/"^^ . "pharmacology" . "BitterDB Receptor" . "1.1.1.1"^^ . . . . . . "dna" . . "Gene Ontology Database references" . . . "http://purl.obolibrary.org/obo/STATO_"^^ . . "https://www.cytion.com/"^^ . "metadata" . "https://www.e-cyanobacterium.org/bcs/entity/$1"^^ . . . _:Ne852999e3f544bc9a8d299321e8ffa10 "Crop Ontology Helpdesk" . . "electrocardiography" . "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/"^^ . . "Alzheimer Gene Database" . "200282"^^ . "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID="^^ . . . . "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"^^ . . . . . "icd11.foundation" . . . _:N000e2f2c430b437ca9757e0c7abe8844 "yingqin@rti.org" . "false"^^ . "false"^^ . . . . . . . "^\\d{7}$"^^ . "ontology" . "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation."^^ . . . . "https://bdsc.indiana.edu/stocks/"^^ . . . "https://orcid.org/$1"^^ . "http://purl.obolibrary.org/obo/SIBO_$1"^^ . . "computer science" . "53367"^^ . "^[A-Z0-9]{6,7}$"^^ . . "kelly.hughes@utah.edu" . "2200934"^^ . . "georgeta.bordea@u-bordeaux.fr" . . . _:Nfd0101ddf2334c2a8efd7de6e4562d34 "Michelle Futornick" . . . . "AgentIdentifierScheme"^^ . . "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information."^^ . . "Roman Baum" . . . "^\\d+\\w?$"^^ . "https://www.ncbi.nlm.nih.gov/gene/$1"^^ . . "^[\\w-]+$"^^ . "^PTN\\d{9}$"^^ . . _:N9c235fb11e19416398c9a272c05b8505 "Crop Ontology Helpdesk" . "Variants in dbVar."^^ . "ecology" . "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases."^^ . . "dna" . "cabri" . . . "008893080"^^ . "^\\d+$"^^ . . . . "false"^^ . "https://purl.brain-bican.org/ontology/hbao/HBA_$1"^^ . . "hipsci" . . . "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln="^^ . "hancestro" . "The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format."^^ . "life science" . . "Potato ontology" . . . . . . "salmon" . "https://bioregistry.io/odam:"^^ . . . "structure" . . . . "^ITMCTR\\d+$"^^ . "Statistical Torsional Angles Potentials" . . "http://purl.obolibrary.org/obo/VBO_"^^ . . "https://bioregistry.io/metaregistry/"^^ . "Nikkaji number" . . . . . "PIR Superfamily Classification System" . . "celia.michotey@inrae.fr" . . _:Nbd51a28cea234a7bba1dd4d7394dfcbe . "molecular chemistry" . "Schema for the export of the Bioregistry as RDF"^^ . . . . . "Irina Medvedeva" . . "The International Standard Book Number (ISBN) is for identifying printed books."^^ . "Luis González-Montaña" . . . . . . "Colin Batchelor" . "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. "^^ . . . . "smart" . . "Terminology of Anatomy of Human Embryology" . . . "^\\d{7}$"^^ . "ontology" . . . "ForwardStrandPosition"^^ . . . " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB."^^ . . . "^\\d+(\\w+)?$"^^ . . . "Harry Caufield" . "^\\d{7}$"^^ . . . "Citlalli Mejía-Almonte" . "knowledge and information systems" . . . . "Contains entries for various database identifiers" . "International Traditional Medicine Clinical Trial Registry" . "https://bioregistry.io/dragondb.dna:"^^ . "AMDEFA"^^ . . "David Craik" . "false"^^ . "ClinVar Record" . . . . "^\\d+$"^^ . . . . . . . "false"^^ . . . . . . "ensemblglossary" . . "Daniel W Udwary" . . . . . . "true"^^ . . "Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present."^^ . . . . . "René Ranzinger" . . . . . . _:Nea10c93db2cc4773a2f1c43109510bc3 . "mirte" . . . . . "Physical Medicine and Rehabilitation" . "reaction" . "protein" . . . "12"^^ . "niclas.karlsson@medkem.gu.se" . . . . "https://biopragmatics.github.io/providers/hog/$1"^^ . . "false"^^ . "protein" . . "UniProtKB_VAR" . . "^\\d{6}$"^^ . . "daniel.wilson@uni-hamburg.de" . . . . . . . "ontology" . . . . "protein" . . "http://purl.obolibrary.org/obo/ECO_$1"^^ . . . . . . "chemistry" . . "allyson.lister@oerc.ox.ac.uk" . . . "^XB\\-\\w+\\-\\d+$"^^ . . . . . "nanoparticle" . "NASA Open Science Data Repository Study" . "Allen Institute Ontologies" . "wyeth@cmmt.ubc.ca" . "dna" . "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^ . . . . "eukaryotic" . . "did" . . . . "false"^^ . "benjamin_gyori@hms.harvard.edu" . "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id="^^ . . . . . . "https://gateway.eubopen.org/compound/$1"^^ . . "^\\w+$"^^ . "false"^^ . "^(E|D|S)RR[0-9]{6,}$"^^ . . "extraction_set"^^ . "^\\d+$"^^ . . . . "HWUPKR0MPOU8FGXBT394"^^ . . "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^ . "https://bioregistry.io/resolve/github/pull/$1"^^ . . "PACTR202304525632216"^^ . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . . . . "Matúš Kalaš" . "disease" . . "OSR0818"^^ . "omics data analysis" . "ontology" . . "life science" . "2639"^^ . . . "^LDCM\\d+$"^^ . . . "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1"^^ . . . _:Nbfb950c0fbdf4b68a9b1844647f8b090 "naritomi@med.u-ryukyu.ac.jp" . . . . . . . . . . . . . . "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"^^ . "obo" . "BiGG Metabolite" . . . "pseudogene.org" . . "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . "MycoBrowser smegmatis" . "seaver@anl.gov" . . . "igsn" . "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries"^^ . . . "disease" . . "lipidomics" . . "^rs[0-9]+$"^^ . "David N. Orloff" . . "false"^^ . "http://degradome.uniovi.es/cgi-bin/protease/"^^ . . . "^NONHSAT\\d{6}$"^^ . . . "false"^^ . . . "1"^^ . "^[a-zA-Z]+.+$"^^ . . "false"^^ . . "https://www.uniprot.org/proteomes/$1"^^ . "ontology" . "http://purl.obolibrary.org/obo/VO_"^^ . "false"^^ . . "MMP02954345.1"^^ . "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id="^^ . . . . . . . . "^\\w+$"^^ . "plant anatomy" . . . . . . "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease."^^ . . "false"^^ . . "single nucleotide polymorphism" . . . . . "ontology" . . "Genetic Code" . . "Higher-level classifications of COG Pathways"^^ . "Ontology about the development and life stages of the C. elegans"^^ . . "chemistry" . . . . . . "gold standard" . "http://rs.tdwg.org/dwc/terms/"^^ . . . . "G8944"^^ . . . . "BioLegend" . . "health science" . "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^ . . . . . "http://eol.org/schema/terms/"^^ . . . . "ons" . . "Reactions in drugbank"^^ . . . . . . . . . . . . . . . . . . . "^MITE\\d{7}$"^^ . "frim1"^^ . . . . . . . . . "expression data" . . . . "genotyping" . . . . . . . "sdap" . . . . . . . . . . . . . . . . . . "metascience" . "https://www.ebi.ac.uk/ipd/imgt/hla/alleles/?query=eq(name,%22$1%22)"^^ . "https://www.ncbi.nlm.nih.gov/books/"^^ . "imgt.hla" . . . . . "A collaborative project intended to create an encyclopedia documenting all living species known to science"^^ . . . "http://purl.uniprot.org/annotation/VAR_"^^ . . "BioTools" . . . . . "enzyme" . . . "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp="^^ . . . . . . . . . "^GN_[A-Za-z0-9_:]+$"^^ . . . . "Carole Goble" . . "https://easychair.org/cfp/topic.cgi?tid="^^ . . . . "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma."^^ . . . "https://go.drugbank.com/metabolites/"^^ . "metascience" . . "data model" . "pathway" . "civic.gid" . . . . "5112"^^ . . . . . . "comparative genomics" . . . . "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . . . "^\\d{7}$"^^ . . . "^\\d+$"^^ . . . . . "molecular biology" . . "false"^^ . . . . . . "1784"^^ . . . "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . . "MCDS_L_0000000001"^^ . . "https://go.drugbank.com/salts/"^^ . "https://cropontology.org/rdf/CO_320:$1"^^ . "life science" . . "98"^^ . "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1"^^ . . . "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors."^^ . . . "gene" . . . "goccid" . "elm" . . "protein" . . . "genetics" . "00000443"^^ . . . . "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . "pubchem.bioassay" . "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)"^^ . . . . . "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences."^^ . . "anne.morgat@sib.swiss" . "genomics" . . . . "owl" . "obo" . "false"^^ . . . . "Dengue Fever Ontology" . "InterPro" . . "nlx.func" . . "ctis" . "clinical LABoratory Ontology" . . . . "OMIT" . . . . . "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . . "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way."^^ . . . . . "edgar.wingender@edgar-wingender.de" . . . . "false"^^ . . "giacomo.lanza@ptb.de" . "disease" . . . . . . . "scomp" . . . . . . . . "false"^^ . "http://purl.obolibrary.org/obo/CDAO_$1"^^ . . "pharmacodb.tissue" . . . . . "longevity" . . "model" . . . . . "coconut" . . "Jianjiong Gao" . . . . . "molecular function" . . . "https://glycopost.glycosmos.org/entry/$1"^^ . "https://genelab-data.ndc.nasa.gov/genelab/accession/"^^ . "phylogeny" . "gfrishkoff@gsu.edu" . . "dialnet.journal" . . . "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."^^ . . . "mental health" . "MNXM1723"^^ . "computational biological predictions" . "Adrian Gschwend" . . . . "47419"^^ . . . "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain."^^ . "ALA"^^ . "RNA SSTRAND" . . . . "st00576"^^ . . "anatomy" . "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs."^^ . . . . "http://purl.obolibrary.org/obo/BFO_$1"^^ . . . . "International repository of Adverse Outcome Pathways."^^ . "https://www.uniprot.org/keywords/$1"^^ . . . "seed.reaction" . "Genetic and Rare Diseases Information Center" . . "Yeast Searching for Transcriptional Regulators and Consensus Tracking" . "G77500AY"^^ . . . . "ANOVA"^^ . . "https://www.wwpdb.org/pdb?id=$1"^^ . "knowledge and information systems" . . "biocuration" . "Simple Modular Architecture Research Tool" . "^spike\\d{5}$"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_$1"^^ . . "sequence" . . "protein" . . . . . . "biology" . . . . . . . . . "^[A-Z]-[0-9A-Z]{3}-[0-9A-Z]{3}$"^^ . . "ascl" . . "SpBase" . . . . "KEGG Compound" . "^TIGR\\d+$"^^ . . . . . "oban" . . . "false"^^ . "OpenCitations Corpus" . . . . . . . . "^BD\\d[a-zA-Z0-9]+-[A-Za-z]-[A-Za-z]-[A-Za-z0-9]+$"^^ . "life sciences" . . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code="^^ . "tbreddy@lbl.gov" . "classification" . . "UBREL" . "http://edamontology.org/topic_$1"^^ . "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$"^^ . "1050"^^ . . "http://purl.obolibrary.org/obo/LABO_"^^ . "environmental science" . . . . "joshua.adam.klein@gmail.com" . . "^\\d+$"^^ . . . . . "^[A-Za-z0-9_-]+$"^^ . "Odor Molecules DataBase" . . "Epidemiology Ontology" . "microbiology" . "http://synbip.idrblab.net/data/bts/details/"^^ . . _:N1b21c85bc1024f35a6e8554763c3ebbe "helpdesk@cropontology-curationtool.org" . "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^ . . . "agriculture" . "^SAMEA\\d{9}$"^^ . . . . . "true"^^ . . . . . "0000066"^^ . . "life science" . . "obo" . . "Eric W. Deutsch" . "http://purl.obolibrary.org/obo/MOD_"^^ . . . "http://w3id.org/nkos/"^^ . "https://signor.uniroma2.it/relation_result.php?id=$1"^^ . . . . . . . "http://www.cs.tau.ac.il/~spike/maps/$1.html"^^ . . . "phenotype" . "mmmp.biomaps" . . "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^ . "https://portal.issn.org/resource/ISSN/$1"^^ . . "https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/"^^ . . . . . "chemistry" . . . . "biology" . "false"^^ . "Identifiers for lipid-protein interactions, including details about protein functions, protein families, lipid classifications, lipid-protein binding affinities, membrane association type, and atomic structures."^^ . . "Michal Linial" . . "http://purl.enanomapper.org/onto/ENM_"^^ . . . "epio" . . . . . "ontology" . . . . . "ontology" . "Diagnostic and Statistical Manual of Mental Disorders (5th Edition)" . . . "zebrafish" . . . . "false"^^ . "https://comptox.epa.gov/dashboard/"^^ . "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:"^^ . . "^\\d+$"^^ . . . . . "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . . . . . "false"^^ . . . . . "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^ . . . . . . . . . . "approved drug" . . . . . "cst.ab" . . . . . . "hms.lincs.cell" . . "https://go.drugbank.com/reactions/"^^ . "environmental science" . . . . . . . "Hannele Laivuori" . "^\\d{4,6}$"^^ . "queerNewspapers"^^ . "researcher" . "R. Burke Squires" . "Candida Genome Database" . . . . . . "false"^^ . . . . "http://uri.neuinfo.org/nif/nifstd/birnlex_"^^ . "Database of Genomic Structural Variation - Study" . . "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1"^^ . "https://fungi.ensembl.org/id/"^^ . . . . "BIND accession number" . "https://nanocommons.github.io/identifiers/registry#"^^ . . . "life science" . . . "^MNEST\\d+$"^^ . . . . . "false"^^ . . "http://www.whocc.no/atc_ddd_index/?code="^^ . "http://purl.obolibrary.org/obo/CIO_"^^ . "protein" . "biology" . . . "commoncoreontology" . . "spp" . . "CCDC Number" . . . . . . "JECFA provides identifiers for flavors, food additives, contaminants, toxicants, and veterinary drugs. Each entry includes chemical details, acceptable or tolerable intake limits, and links to related reports and monographs."^^ . "http://lincsportal.ccs.miami.edu/cells/#/view/$1"^^ . "classification" . "identifier of a compound in the UniChem database"^^ . . "Exposure ontology" . "https://europepmc.org/article/ppr/"^^ . "false"^^ . . "protein" . "https://bioportal.bioontology.org/" . . . . "ontology" . "false"^^ . . "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO="^^ . . "^[0-9]+$"^^ . "phenotype" . . . . . "proteomics" . "PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them."^^ . . "ribonucleic acid" . "0002927"^^ . "true"^^ . . "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins."^^ . "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . . . "obo" . "https://www.swisslipids.org/#/entity/SLM:"^^ . . "The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data."^^ . "lpt" . "ontology" . . . "http://purl.org/net/orth#$1"^^ . "chembl.target" . "MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats."^^ . . . "ctgov" . . . . . . . . "vhog" . "molecules" . . . "^ps\\d+$"^^ . "MultiCellDS Digital snapshot" . . . . . "CA981206459"^^ . "dc11" . "MAM01234c"^^ . . "life science" . . . . "http://purl.obolibrary.org/obo/VSAO_$1"^^ . "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene."^^ . . . . . "Homology Ontology" . "00100005"^^ . . . . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1"^^ . "http://purl.obolibrary.org/obo/SPD_"^^ . . . "Kidney and Urinary Pathway Ontology" . . . . . . "^(LCL|LDC|ES|LSC|LPC)-\\d+$"^^ . . . . "jimhu@tamu.edu" . "false"^^ . . . . "expression" . . "researcher" . "TA14985"^^ . . "false"^^ . "yperez@ebi.ac.uk" . "genetic disorder" . "EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823"^^ . . "PS00001"^^ . . "gdsc" . . . . . . . . . . . "bgee.stage" . . . "0000728"^^ . "genome" . . . . . . "0000773"^^ . . "interaction" . . . "CRISP" . . . . . . "^([A-Z]+)?\\d+(\\.\\d+)?$"^^ . "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . "datanator.metabolite" . . . "190000021540"^^ . "ontology and terminology" . . . . . . . "isfinder" . "false"^^ . "life cycle" . "http://ratmap.org/Showgene.php?gene_stable_id="^^ . . . "disease" . . "https://cropontology.org/rdf/CO_350:$1"^^ . . . "The BioDeep database is a comprehensive database of metabolite information in living organisms: by aggregating metabolite information from multiple public databases and large-scale natural language text mining work, we have built a large scale knowledge network for biological knowledge interpretation. By using the BioDeep database, it is possible to query such large scale metabolic knowledge network."^^ . . "annotation" . . "4779"^^ . . . . . . . . . "uniprot.taxonomy" . "^M\\d+$"^^ . "jrsmith@mcw.edu" . "ontology" . . . . "Luis A. Gonzalez-Montana" . . "^EG\\d+$"^^ . . "false"^^ . "obo" . "https://bdsc.indiana.edu/stocks/$1"^^ . . . "biomedical science" . . . . "Vertebrate Gene Nomenclature Committee" . . . . "^\\d+$"^^ . "clement.jonquet@inrae.fr" . . "repeatsdb.structure" . . . . . "Unified Medical Language System Concept Unique Identifier" . "https://bartoc.org/" . . . . . "^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}$"^^ . . "vmhreaction" . . "https://pubchem.ncbi.nlm.nih.gov/bioassay/"^^ . . "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database."^^ . . . . . . . "03212fd7_abfd_4828_9c8e_62c293052d4b"^^ . "false"^^ . "true"^^ . "NA06985"^^ . . . . . . . "An ontology to describe entities related to cardiovascular diseases"^^ . . . "KEGG.COMPOUND" . . . . . . . . . "lepao" . . . "This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]"^^ . "life science" . . "100000000000001"^^ . "^\\d+$"^^ . . . . . . . . "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . . . . . "ontology" . . . . . . "https://www.ncbi.nlm.nih.gov/nucest/"^^ . . "http://purl.obolibrary.org/obo/FOVT_$1"^^ . "vocabularies" . . . "The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations."^^ . . "cell biology" . "^\\d{7}$"^^ . . _:N4fea6f4caf8d4e8983848b4539eb6da8 "j@deltaflow.com" . "false"^^ . "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"^^ . . . . . . . . . "ligea" . . . "obo" . "obo" . . . . . . . "Orthology Ontology" . . . . . . . "phenotype" . . . "http://purl.obolibrary.org/obo/GEO_$1"^^ . . . . . . "https://www.fisheries.noaa.gov/species/"^^ . . "cheminformatics" . . . "0000000"^^ . . "easychair.topic" . . . "diseaseclass" . "http://dbpedia.org/resource/$1"^^ . . "life science" . "http://purl.obolibrary.org/obo/NGBO_$1"^^ . . "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . "ontology" . . . . . "^\\d{7}$"^^ . . . . . . "false"^^ . "DailyMed" . "2008-005144-16"^^ . . . "ontology" . "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"^^ . "aallen@ascl.net" . . . . . . "EntrezGene" . "CALIPHO Group Ontology of Human Anatomy" . . . . . "^\\d{7}$"^^ . "primary health care" . "natural language processing" . "http://purl.obolibrary.org/obo/GALLONT_$1"^^ . . "0000255"^^ . . . "Fungal Nomenclature and Species Bank" . . . . "false"^^ . . . . . "true"^^ . . . "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments."^^ . . . . "http://www.genome.jp/dbget-bin/www_bget?cpd:"^^ . "plant" . "^2\\d{4}$"^^ . . "Rosemary Shrestha" . . "MaizeGDB Locus" . . "kushida@biosciencedbc.jp" . . . "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^ . . . "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1"^^ . . . . . . "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$"^^ . "^\\d+$"^^ . . . . . "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment."^^ . . . "drugs" . . . . . . "^DBCOND\\d+$"^^ . "03yrm5c26"^^ . . . "funcbase.human" . . . "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"^^ . . . . . . "L000001"^^ . . . "Ontology of Precision Medicine and Investigation" . . . . . "spider" . . . . . . . . . . . . . . . "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_"^^ . . . . . "false"^^ . "OSC1416"^^ . "population genetics" . . . . . . . . . "eroshkin@burnham.org" . . . . . "^\\d+$"^^ . "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."^^ . "false"^^ . "Kathryn Dumschott" . . . . . "human" . "miaa" . . . . "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id="^^ . "https://www.iedb.org/receptor/"^^ . "tRNA Gene Database" . . "3546"^^ . . . . "true"^^ . . "HS000015122"^^ . . . . "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"^^ . . . "Raja Mazumder" . "false"^^ . "https://www.kegg.jp/entry/$1"^^ . . . . "3355"^^ . "biomedical science" . . . . "cell" . . "false"^^ . . . "false"^^ . . . "embryonic stem cell" . "gene expression" . . "pancreatic islet development" . . . "Taxonomy in DEIMS SDR"^^ . "http://oid-info.com/get/$1"^^ . . . "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"^^ . "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. This entry represents UniProt mnemonics which combine an alphanumeric representation the protein name and a species identification code representing the biological source of the protein."^^ . . . "obo" . . "obo" . . . "https://sed-ml.org/urns.html#language:"^^ . "true"^^ . . "1023371"^^ . . "^\\d+$"^^ . . . . "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."^^ . . "biomedical science" . "false"^^ . . . "true"^^ . . . "Digital archive of scholarly articles" . . "Disease Drivers Ontology" . "brettolivier@gmail.com" . . . "http://purl.obolibrary.org/obo/SWO_"^^ . "scr" . "Human Medical Genetics" . . . . "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/"^^ . . . "false"^^ . . "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value="^^ . "nicole@tislab.org" . "bibliography" . "The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page)."^^ . "DragonDB Protein" . "Frederique Lisacek" . . "Banana ontology" . "life science" . . . "immunology" . "strain" . "Pathway ontology" . . . . . "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . "http://dictybase.org/gene/"^^ . . . "ontology" . "http://purl.obolibrary.org/obo/RO_$1"^^ . . "rnamod" . . . . "Genomic Distribution of structural Superfamilies" . . "^\\d{7}$"^^ . . . . "https://bacteria.ensembl.org/id/$1"^^ . . . . . "^\\w+$"^^ . . . "agaedigk@cmh.edu" . . . . "mobidb" . . . . . "false"^^ . . "ontology" . "http://purl.obolibrary.org/obo/MFOMD_"^^ . . "http://mods.rna.albany.edu/mods/modifications/view/"^^ . . . . "PhosphoSite Residue" . "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes."^^ . "false"^^ . "ID in osf.io"^^ . . "false"^^ . "gene" . . . . "^URS[0-9A-F]{10}(\\_\\d+)?$"^^ . . "alignedWith"^^ . "Mental Disease Ontology" . . . . "ncbi.gc" . "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number."^^ . . . . "http://www.cazy.org/$1.html"^^ . . "molecular interaction" . . . . . . . . "sphn" . "bioinformatics" . . "cell" . . . "March 2017 version "^^ . . . . . . "^SKIP\\d+$"^^ . . . "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."^^ . "false"^^ . . . "https://www.cellrepo.com/repositories/$1"^^ . . . "false"^^ . . . "jrct" . "taxonomy" . . "Amanda Hicks" . . "gmelin" . . "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1"^^ . . . . "structure" . . . "false"^^ . "https://www.ebi.ac.uk/ols4/ontologies/fma/terms?obo_id=FMA:$1"^^ . . . . . "true"^^ . "rdo" . "mf" . "HL7 External Code Systems are stored within the greater OID system" . . "mutant" . "RiceNetDB Protein" . . "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences."^^ . . . . "environmental science" . "hsa00190"^^ . . "rgd.qtl" . . . . "false"^^ . . . "liumeng94@sjtu.edu.cn" . "person" . . . . . "hospital" . "phylogenomics" . . "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"^^ . . "false"^^ . . "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . "Jean-Luc Jannink" . . . "0001157"^^ . . "galen" . "BibliographicRecord"^^ . "true"^^ . . . "nucleotide" . . . . . "Comprehensive Resource of Mammalian protein complexes" . . "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors."^^ . "Method"^^ . . "^\\d{1,7}\\-\\d{2}\\-\\d$"^^ . . . . "http://purl.obolibrary.org/obo/MS_"^^ . . "entrez gene/locuslink" . "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]."^^ . "p.buttigieg@gmail.com" . "false"^^ . . . . . "sedml.language" . . . . . . . "fbbt" . "^\\d+$"^^ . "https://www.inaturalist.org/taxa/"^^ . . . "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."^^ . "^T3D\\d+$"^^ . "98127"^^ . . . . . "ClinGen Allele Registry" . . . . "http://purl.bioontology.org/ontology/IDODEN_"^^ . "https://osdr.nasa.gov/bio/repo/data/missions/"^^ . "163"^^ . . "yid" . . "life science" . . . "false"^^ . . . . "NASA Open Science Data Repository Experiment" . "false"^^ . . "FishBase" . "GlyTouCan" . "Aclame" . "https://www.worldcat.org/oclc/"^^ . . "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^ . . "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . "ontology" . "https://bioregistry.io/pmap.substratedb:"^^ . . "TS-0001"^^ . . "https://ieeexplore.ieee.org/author/"^^ . . "SNR17A"^^ . . . . . . "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1"^^ . "https://zenodo.org/record/$1"^^ . . . . "false"^^ . "^BAMSC\\d+$"^^ . "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database."^^ . . . "http://purl.obolibrary.org/obo/IDO_$1"^^ . "nckyrpides@lbl.gov" . "domain" . . . "Supplier of mice for research purposes. [from RRID]"^^ . . . . . "http://synbip.idrblab.net/data/sbp-target-complex/details/"^^ . . . . . . . . "Lipid"^^ . . "viperdb" . . "FAIRsharing.62qk8w" . . . . "Computer Retrieval of Information on Science Projects Thesaurus" . "soil science" . . . . "https://www.kew.org/data/grasses-db/www/"^^ . . . . . "0459895"^^ . . "https://www.imanislife.com/?s="^^ . "MLCommons Association" . . "NCI2004_11_17" . "false"^^ . "ontology" . . "Global Biodata Coalition - Global Core Biodata Resources" . "Lukas A. Mueller" . . . "74"^^ . "Flora Phenotype Ontology" . "http://purl.obolibrary.org/obo/PO_$1"^^ . . . . "Medical Dictionary for Regulatory Activities Terminology" . . "true"^^ . . . "obo" . . . "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . . . "5277619"^^ . "OBO Metadata Ontology" . "https://www.ebi.ac.uk/gxa/genes/"^^ . "http://purl.obolibrary.org/obo/MIAPA_"^^ . "rdfs" . . . . . . "https://sumlineknowledgebase.com/?page_id=$1"^^ . . "geography" . . "https://bioportal.bioontology.org/ontologies/$1" . . . . . "genefarm" . "Nematode & Neglected Genomics" . . . . "https://mycobrowser.epfl.ch/genes/$1"^^ . . . "https://cropontology.org/rdf/CO_348:"^^ . "2649230"^^ . . . "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system."^^ . . . . "Addgene Plasmid Repository" . "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . "^\\d+$"^^ . . . "genomics" . . "^(SMP|PW)\\d+$"^^ . "https://omabrowser.org/oma/vps/$1"^^ . "Rhea, the Annotated Reactions Database" . . . . . . "https://bioregistry.io/chemicalbook:"^^ . . . . . . . . . "biochemistry" . "DateTimeDescription"^^ . "false"^^ . . "false"^^ . . . "domain" . . . "false"^^ . "life science" . "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-"^^ . "botany" . . "https://gtdb.ecogenomic.org/tree?r=$1"^^ . "UM-BBD_ruleID" . . "mutation" . "rna_sstrand" . . . . "github" . "false"^^ . . "Database of Arabidopsis Transcription Factors" . . . . . "foodb" . "Dalia Alghamdi" . . . . . "botany" . . "life science" . . . . . . "GeneID" . . "true"^^ . . "http://purl.obolibrary.org/obo/PPO_$1"^^ . "chemspider" . "obo" . "https://cropontology.org/term/$1:$2" . . . "ApiDB_PlasmoDB" . . . . . "false"^^ . . . . . "Protein modification" . . . "UK Provider Reference Number" . . "A0014"^^ . "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards."^^ . . . . . . "interoperability" . . . "^\\d+$"^^ . . . "PhageDive is a database for bacteriophages and archaeal viruses. It provides information regarding taxonomy, host strain, phage morphology, life cycle, origin and genomic data."^^ . "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . . "taxon" . "ontology" . "phenotype" . "doid" . . . "ontology" . "https://biopragmatics.github.io/providers/cvx/"^^ . . "false"^^ . . . . . . . . . "0000609"^^ . . . . "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs."^^ . "ordo" . . "chemdb" . . "ecyano.model" . . "life science" . "anzctr" . . "botany" . "https://nanbyodata.jp/disease/NANDO:$1"^^ . "phylomedb" . "disease" . . . " The Creative Commons Rights Expression Language (ccREL) lets you describe copyright licenses in RDF. For more information on describing licenses in RDF and attaching those descriptions to digital works, see [ccREL](https://wiki.creativecommons.org/CC_REL) in the [Creative Commons wiki](https://wiki.creativecommons.org/)."^^ . "https://www.vmh.life/#reaction/$1"^^ . . . . . . . . "expression data" . "Gwen Frishkoff" . . . "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations."^^ . . "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"^^ . "BLL"^^ . . . "unipathway.reaction" . . . "false"^^ . . "life science" . "signaling" . . "0000070"^^ . . . . . . . "scicrunch" . . "http://purl.obolibrary.org/obo/AAO_$1"^^ . "false"^^ . "structure" . . . "Wiktionary" . . . . "Niclas Karlsson" . "enzymatic reaction" . . . . "KESTREL Ontology" . "^\\d+$"^^ . _:N1801bde68c8d481ebfecc1136b76f50c "custserv@nlm.nih.gov" . . . . . "nif.dysfunction" . . . "sharkipedia.trait" . "47"^^ . . "tgv139393198"^^ . . . . . "The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners."^^ . "^[a-z]{3}-[a-km-z0-9]{7}$"^^ . "false"^^ . . "HIP000030660"^^ . "DRSC05221"^^ . . . . "0000010"^^ . "https://repeatsdb.org/structure/$1"^^ . "drugcentral" . "gene" . "phenotype" . . . "false"^^ . . . . . "ontology" . . "^\\d+$"^^ . "Agricultural Online Access" . "DDB_G0267522"^^ . "http://www.w3.org/ns/rdfa#"^^ . . . . . "UniProt Proteomes" . . "gene" . . "^c\\d+$"^^ . . . . "false"^^ . . . "S6"^^ . . . "DB-0174"^^ . . . . . . . . "http://purl.obolibrary.org/obo/OGMS_$1"^^ . "subject agnostic" . . "^5\\d{4}$"^^ . . . "aBq"^^ . . . . . "bibliography" . "SNOMEDCT_US_2020_03_01" . . . . . . . "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name="^^ . . . . . . . . . "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . . . . "Lindsey N. Anderson" . "^\\w{4}$"^^ . . . . . . "functional genomics" . "http://purl.obolibrary.org/obo/OMIABIS_$1"^^ . "false"^^ . "rare disease" . "http://purl.bioontology.org/ontology/CSP/"^^ . . . . "Microbial Protein Interaction Database" . "http://purl.org/dc/terms/"^^ . "doqcs.pathway" . . "Terminology for Description of Dynamics" . . "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . . "34"^^ . . . "MetaNetX reaction" . "life science" . . "chemistry" . . "subject agnostic" . . "ontology" . . . . "isacorreia@tecnico.ulisboa.pt" . . "Signaling Gateway" . . . "ontology" . . "regulation" . "https://euclinicaltrials.eu/app/#/view/"^^ . . . "botany" . . . . "protein" . "chmo" . . "plasmid" . . . . "false"^^ . . "^ENST\\d{11}$"^^ . "Monique Zahn" . "neurophysiology" . . . . "RBR-6qvdftm"^^ . "http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?winid=1&recid="^^ . "https://omabrowser.org/oma/vps/"^^ . "false"^^ . . . . . "0100011"^^ . . . . "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_"^^ . . . . "C2584994"^^ . "^\\d{7}$"^^ . "^\\d{7}$"^^ . . . "false"^^ . . "https://drks.de/search/en/trial/"^^ . . . "smc.source" . "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology."^^ . . "WiCell Research Institute Cell Collection" . . . "https://www.alzforum.org/mutations/$1"^^ . . . "SNOMEDCT_US_2019_03_01" . . . "^IND\\d+$"^^ . . "clinvar.record" . "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier."^^ . . . . . . . . . . "false"^^ . "obo" . . . . "umbbd.reaction" . . "https://cropontology.org/rdf/CO_322:"^^ . . "https://deims.org/networks/"^^ . "ncbigene" . . . . . . . . . . . "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . "false"^^ . . "developmental biology" . . . "595"^^ . . "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research."^^ . "Anton I Petrov" . . "https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/"^^ . . "stian@soiland-reyes.com" . "NP_012345"^^ . _:Ndb0972dc29f34ae4850340e2ec03eacd "Crop Ontology Helpdesk" . . . . . . . "gene" . . . . . . "hamap" . . . "SNOMEDCT_US_2015_03_01" . _:N2acde302dfca4afbac04bb5927b795b9 "Rafael Gonçalves" . . "12"^^ . "^\\d{7}$"^^ . . . "https://sed-ml.org/urns.html#format:$1"^^ . . . . . . . "false"^^ . . "https://arxiv.org/abs/$1"^^ . . . "diseases" . . . . . . "http://www.chemspider.com/"^^ . _:Ndb0972dc29f34ae4850340e2ec03eacd . "http://edamontology.org/operation_$1"^^ . . . . . . "ontology" . . . . . . . . . "PROV Namespace" . . . . "https://www.biorxiv.org/content/10.1101/$1"^^ . . . "SwissProt" . . "http://sideeffects.embl.de/drugs/$1"^^ . . "https://www.thaiclinicaltrials.org/show/$1"^^ . . . . . _:Nff9cec83104c44d783fe68e5ff33f50a "WHO Collaborating Centre for Drug Statistics Methodology" . "genetics" . "david.gloriam@sund.ku.dk" . "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating."^^ . . "false"^^ . . "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value="^^ . "EAWAG Biocatalysis/Biodegradation Database" . . "mp" . . . "WWF" . . . "^\\d+$"^^ . "Ensembl Protists" . . . . . "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process."^^ . "molecular interaction" . . "soybase" . "https://health-products.canada.ca/dpd-bdpp/info?lang=eng&code="^^ . "^\\d{7}$"^^ . . "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^ . . "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1"^^ . "genomic" . "false"^^ . . "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/"^^ . . . "https://www.mlcommons.org/mlc-id/"^^ . . . "Tanay Shah" . "Immune Epitope Database Receptors" . "http://purl.obolibrary.org/obo/MA_$1"^^ . "conoserver" . "false"^^ . . "^[0-9]+$"^^ . "http://purl.obolibrary.org/obo/CDAO_"^^ . "wbbt" . "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"^^ . "phenotype" . . "chromosome" . . "https://www.kaggle.com/$1"^^ . . . "antibodies" . . "^([a-zA-Z]+-)?\\d+(\\.\\d)?$"^^ . "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . . "https://deims.org/sensors/"^^ . . "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1"^^ . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information."^^ . . . "Peer Bork" . . . "false"^^ . . . . . "Selventa Diseases" . . . "false"^^ . "epidemiology" . "agriculture" . "molecular function" . . . . "https://sdbs.db.aist.go.jp/CompoundView.aspx?sdbsno="^^ . "clo" . . . . "xmetdb" . . . . "false"^^ . . "George Gkoutos" . "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId="^^ . . . "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . . . "subject agnostic" . . "ontology" . . "https://bioregistry.io/metaregistry/prefixcommons/"^^ . . . . . . . . . "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . . . . . . "Identifier for a species on the noaa fisheries website"^^ . "http://purl.obolibrary.org/obo/MC_$1"^^ . "owl" . . . _:Nbfb950c0fbdf4b68a9b1844647f8b090 . . . . . "0000001"^^ . . . . . "SNOMEDCT_2005_07_31" . "Global Research Identifier Database" . "^\\d+$"^^ . . . "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps."^^ . "mouse" . . "cryopreserved" . . . . "^AA\\d{4}$"^^ . "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data."^^ . "Gemma L. Holliday" . . . . . . "21877"^^ . "false"^^ . "https://bioregistry.io/cadsr:"^^ . . . . "icd10pcs" . "false"^^ . . . . . . "phenomics" . . . . "false"^^ . . . "false"^^ . . . "biosamples" . . "https://pb.apf.edu.au/phenbank/strain.html?id="^^ . . . "https://deims.org/$1"^^ . . . . . . "false"^^ . "Uber Anatomy Ontology" . . "^(\\w){3}$"^^ . "Clytia hemisphaerica Development and Anatomy Ontology" . . . . . . "projects_to"^^ . "Bibliographic Reference Ontology" . . "Cell Biolabs cell line products" . . . . "ontology" . . "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object="^^ . . . . "https://omabrowser.org/oma/hog/HOG:$1"^^ . "biomedical science" . . "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf"^^ . . . . . . "DrugBank Reaction" . "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1"^^ . . "bioinformatics" . . "frapo" . "echinobase" . . . "2381/12775"^^ . "identifier for a scientific journal, in the UniProt database"^^ . "false"^^ . . . . . "pubmed" . . . . "ontology" . . "hhe@ebi.ac.uk" . "phosphosite.sitegroup" . . "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1"^^ . "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum"^^ . . . . . . "SED-ML model format" . . "^\\d+$"^^ . . . . "structure" . "phenotype" . "phenotype" . . . "Reference"^^ . . "swisslipid" . "true"^^ . . "090924"^^ . "tropicalis" . "ARCBedrest"^^ . . . . . "MESHPP" . "ontology" . . . . "phenotype" . . . . . . "OriDB Saccharomyces" . . . . . . . "Immune Epitope Database References" . . . . . "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae."^^ . "http://cellimagelibrary.org/images/"^^ . "http://www.w3.org/2002/07/owl#"^^ . "life cycle stage" . "https://gitlab.com/$1"^^ . . "1981638"^^ . . "genome" . "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^ . . . . . . . . "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . . "shah.tanay2@northeastern.edu" . . . . "http://swissregulon.unibas.ch/query/"^^ . . "ontology" . . "miriam" . "obo" . "ontology" . . "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^ . "false"^^ . . . . "mbrochhausen@gmail.com" . . . . "Cell Line Ontology [derivative]" . . . "https://mycobrowser.epfl.ch/genes/$1"^^ . . "citation" . "n2t" . . "E12768"^^ . "Gmelins Handbuch der anorganischen Chemie" . . . . . . "gold standard" . . "Uberon" . "gene prediction" . . "Alexander Diehl" . . . "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^ . . "false"^^ . . . . . "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . . . "^\\d{7}$"^^ . . . . "cellimage" . . "GenAtlas is a database containing information on human genes, markers and phenotypes."^^ . "Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank."^^ . . "NBR016799"^^ . . . "Identifier (name code) for a taxon in the catalogue of life in taiwan"^^ . . . . "0007807"^^ . "^[0-9A-Za-z\\-.]+$"^^ . . . . . "pathway" . . "conso" . "^PR[0-9]{6}$"^^ . "http://viroligo.okstate.edu/main.php?vid="^^ . . . . . . "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId="^^ . "OMA HOGs" . . . . "http://purl.obolibrary.org/obo/OBCI_$1"^^ . "^(Q|P|E|L)\\d+$"^^ . "false"^^ . . "bcrc" . . . . "nlx.sub" . "data visualization" . . . . . . . "Vertebrate skeletal anatomy ontology."^^ . . "https://catalog.hathitrust.org/Record/"^^ . . "LCL-2085"^^ . "remote sensing" . "https://www.probes-drugs.org/compound/$1"^^ . "novus" . . . . . . . "Quantities, Units, Dimensions, and Types Ontology" . . . . "Damian Smedley" . "Sugar Kelp trait ontology"^^ . . . . . . . . . "KG09531"^^ . "ENSG00000139618"^^ . "4005"^^ . "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^ . . "mod" . . . "PharmGKB Variant" . . "rbrinkman@bccrc.ca" . . . "^VB\\.[A-Za-z][A-Za-z]\\..*$"^^ . . "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^ . . . "geochemistry" . "false"^^ . . . . . "https://rapdb.dna.affrc.go.jp/locus/?name=$1"^^ . "biology" . . . . "transcriptomics" . . "^[0-9][A-Za-z0-9]{3}$"^^ . . "false"^^ . . . . . . "true"^^ . "http://www.ontology-of-units-of-measure.org/resource/om-2/"^^ . "https://www.mycobank.org/page/Name%20details%20page/"^^ . "structure" . . . "protein" . . "http://purl.obolibrary.org/obo/WBbt_$1"^^ . . "miRNA Target Prediction at EMBL" . . . "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset."^^ . . "phenomics" . . . "Proteomic Data Commons" . . "IUPAC Compendium of Analytical Nomenclature (Orange Book)" . . . . . . . "FlyBase Controlled Vocabulary" . . . "Matthias Samwald" . . . . "^\\d+$"^^ . . . "Daniel C. Berrios" . "data retrieval" . "http://purl.obolibrary.org/obo/DINTO_"^^ . "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms."^^ . . "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"^^ . . "goche" . "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . . . . . "chemical entity" . "sdgio" . . . . . "chemical" . . . . . . "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more."^^ . "Mouse Tumor Biology Database" . . . . . . . "foster@uchicago.edu" . . . "PhosphoSite Site Group" . "Veterinary Nomenclature" . . "RPCEC00000423"^^ . . "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . . . "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs."^^ . . . "Paragraph"^^ . . . . "http://www.w3.org/ns/prov#$1"^^ . . . "https://www.storedb.org/store_v3/study.jsp?studyId="^^ . . "Anita Caron" . . . "Open Biomedical Annotations" . "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory."^^ . . "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa."^^ . . . "PhenX Toolkit" . . "PED00017e001"^^ . . . . "Leen Vandepitte" . . . "repec" . . . . . . . . "GCST000035"^^ . . . . . "https://deims.org/taxonomy/term/$1"^^ . "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions."^^ . . "homologene" . "SNOMEDCT_US_2022_12_31" . . "Pathguide" . "false"^^ . "life science" . . "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries."^^ . . . "ontology" . . . "A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces."^^ . . . "ML0224"^^ . . "disease" . . . "obo" . . . "cellular component" . "^[a-z]+(\\-[a-z]+)*$"^^ . _:N86e26dc551344b7eb215b4a1720001f4 "Radiological Society of North America" . "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products."^^ . "https://www.rebuildingakidney.org/id/$1"^^ . "^[WAICV]\\d{2,}$"^^ . . "Non-Coding RNA Ontology" . "hescriva@obs-banyuls.fr" . "WikiGenes" . . "fairsharing" . . "data science" . . . "deepak.unni3@lbl.gov" . . . "^KIAA\\d{4}$"^^ . "OMIA variants" . . . "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^ . . "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1"^^ . "false"^^ . "^\\d+$"^^ . . "false"^^ . . . "90000018"^^ . "http://dictybase.org/gene/$1"^^ . "ontology" . . . "^[0-9]+$"^^ . . . "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^ . . "^\\d+$"^^ . . . . "xml" . . . . "false"^^ . . . . . "UPa" . "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^ . . . "false"^^ . "proteins" . "false"^^ . . "ChEMBL-Targets" . . "^\\d{7}$"^^ . "Loop ID" . "ChEMBL database of bioactive drug-like small molecules - Cell lines section" . "0000004"^^ . . . . "functional genomics" . . . "false"^^ . . . . . . . . . . . . . "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms."^^ . "false"^^ . "Salk Institute for Biological Studies" . . . "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^ . "nlx" . . "TogoID Ontology" . "ukprn" . . "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning."^^ . "health sciences" . "https://www.ncbi.nlm.nih.gov/gene/"^^ . . . . . "http://purl.obolibrary.org/obo/MIRO_$1"^^ . . . "false"^^ . "ena.embl" . . . "obo" . . "cattleqtldb" . . . . . "https://w3id.org/oc/meta/"^^ . . . . . "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid="^^ . . "^\\w+$"^^ . . . . . . . . . . . "Andrew I Su" . "http://purl.obolibrary.org/obo/MAT_$1"^^ . "00573"^^ . . . "gudmap" . . . . "debio" . "ontology" . . . "epidemiology" . . _:N51890f3833da42e6897ff51393426bab "michael.lincoln@va.gov" . . . . . . . "amalik@ebi.ac.uk" . "false"^^ . . "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker."^^ . "^RCB\\d+$"^^ . . "013681"^^ . . . . . . . . "http://purl.obolibrary.org/obo/ATO_$1"^^ . . "false"^^ . . "ontology" . . "12DICHLORETHDEG-PWY"^^ . "DICOM Controlled Terminology"^^ . . . . "0002350"^^ . "food" . . . "false"^^ . . . "Anatomical Therapeutic Chemical Classification System" . "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42)."^^ . . . . . . . "ontology" . "biology" . "5621"^^ . "The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the samples semantic space represent samples derived from animals in HoloFood trials."^^ . . "Yi Zhao" . . . "doi" . . . . "Hugh.Shanahan@rhul.ac.uk" . "biomedical science" . "Stefan Günther" . . . . . "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id="^^ . "Selventa Chemicals" . "Cell line databases/resources"^^ . . "RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project"^^ . "Hong-Yu Ou" . . "number for the Lattes Platform entry on the person or group. Relationship between entry and subject must be supported by a source"^^ . . "http://www.treefam.org/family/$1"^^ . "Rebuilding a Kidney" . "anatomy" . . "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . . . "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1"^^ . "http://edamontology.org/data_$1" . . . . "aop.relationships" . . "NCBI Taxonomy" . "citation" . . . "^\\d+$"^^ . . "strain" . "life science" . . "Global Natural Products Social Molecular Networking Task" . . . . "http://jaxmice.jax.org/strain/$1.html"^^ . . . . . . . "pdb" . . "http://purl.uniprot.org/annotation/VAR_$1"^^ . "anatomy" . "ontology" . "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . "general & upper" . "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g="^^ . "bmeldal@ebi.ac.uk" . . "false"^^ . . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene."^^ . "2116"^^ . . . "Cellosaurus identifeirs for publications, like Pubmed"^^ . "https://www.pombase.org/gene/"^^ . "IEEE Xplore author ID" . . . "https://github.com/prefixcommons/biocontext" . . . . "Carlos Moreno" . . "ncats.drug" . . "Represent chemical entities having particular CHEBI roles"^^ . . . "genetics" . . . "false"^^ . . . . "false"^^ . "https://proteinensemble.org/"^^ . . "https://cropontology.org/rdf/CO_326:"^^ . . . "study design" . . "http://purl.obolibrary.org/obo/CHEMINF_"^^ . . "quality" . "Medaka Developmental Stages" . "Cellosaurus Publication" . "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1"^^ . "^\\d+$"^^ . "^\\d+$"^^ . . . "https://www.cameo3d.org/sp/targets/target/$1"^^ . . . "Keahi Kaʻiwalani Adolpho" . . "false"^^ . "phylogenetics" . . . . . . . "false"^^ . "interaction" . "citation" . "jak@ucop.edu" . . . "biosystems" . . . . . . . . "^\\w+\\d+$"^^ . . "somatic" . . . . "ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea."^^ . . . "brenda" . . "Data Privacy Vocabulary" . . . . . . "vfb" . "ddpheno" . . "false"^^ . . . . "ontology" . . . "Cell line databases/resources"^^ . "GlycoEpitope" . "planttfdb" . "false"^^ . . "clinical studies" . . "http://oncotree.mskcc.org/api/tumorTypes/search/code/"^^ . "obo" . . . . . . "^\\d{7}$"^^ . . . . . . "https://bcrj.org.br/pesquisa/?search=$1"^^ . . . . . . "false"^^ . . . "single cell" . "AllSomeInterpretation"^^ . "SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops."^^ . . . "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"^^ . "https://www.yeastgenome.org/locus/"^^ . . . "deborahlehr"^^ . "intenz" . . . . . . "EDAM Data" . . . "https://bioregistry.io/panorama:"^^ . "genomics" . "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones."^^ . "ontology" . . . "https://publons.com/researcher/"^^ . . "Literature references in Gramene"^^ . . . "surjeet.arya@uky.edu" . . "glycosciencesdb" . "^\\d{7}$"^^ . . . . "NCIT" . . . "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."^^ . "bindingdb" . . . . . . "MIRBASE_FAMILY" . "lincs.protein" . . . . "longevity" . "http://purl.obolibrary.org/obo/NIF_CELL_$1"^^ . "^\\d{7}$"^^ . . . . . "r3d100014165" . "false"^^ . "victorinolavida@ciencias.unam.mx" . "Life cycle stages for Human"^^ . . . . . . . . . . "Association-Rule-Based Annotator" . "false"^^ . . . . . "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^ . "Gene Product Information Schema" . "HoloFood sample" . "D00001"^^ . "https://ssbd.riken.jp/database/project/"^^ . "Laboratory of Systems Pharmacology Compound" . "cell" . "wikigenes" . . . . . . . "ontology and terminology" . . . "http://purl.obolibrary.org/obo/HABRONATTUS_"^^ . . "rna" . "Common Terminology Criteria for Adverse Events" . . . . "gnome" . "^(\\d|\\w)+-\\d$"^^ . . "http://purl.obolibrary.org/obo/DOID_"^^ . "small molecule" . "Sharkipedia Trait" . . . . . . "SIDER Side Effect" . "https://www.abcam.com/$1.html"^^ . . . "life science" . . . . "publishing" . "Neuro Behavior Ontology" . "protein" . . "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . . . . . "life science" . . . . . "https://query.biodeep.cn/metabolite/$1"^^ . "genomics" . . "https://abrc.osu.edu/stocks/number/SALK_$1"^^ . . "https://www.inaturalist.org/observations/"^^ . . "genetics" . . "false"^^ . . . . . . . . . "biology" . "NIHhESC-10-0083"^^ . . . . . . "2u4tf"^^ . "alzheimer's disease" . . "http://sideeffects.embl.de/drugs/"^^ . . . . . "Thai Clinical Trials Registry" . "pathway" . "protein" . . "phenotype" . "engelsta@ohsu.edu" . . . "true"^^ . "false"^^ . . "Immune Epitope Database MHC Restrictions" . . "^\\w+$"^^ . . . "gwascentral.phenotype" . . . "false"^^ . . . . "ontology" . "phosphosite.curation" . . "gmd" . "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1"^^ . . "^\\w+$"^^ . . . "expression" . . "19757"^^ . "false"^^ . . "disorders" . "0000031"^^ . . "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_"^^ . "C00000001"^^ . "Sierra Moxon" . . . "A controlled vocabulary to support the study of transcription in the primate brain"^^ . . "botany" . . . . _:Ncd6f05b87b9d4df3ba70120207179446 "kate.rose@noaa.gov" . . "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes."^^ . . . . . . "phenotype" . . _:Neb194957c4f949aabc4fdf80b0b22646 "American Medical Association" . . "National Organization for Rare Disorders" . "false"^^ . . "^[0-9]+\\.[0-9]+$"^^ . . . . "life science" . . . . "https://www.biorxiv.org/content/10.1101/"^^ . "genetics" . . . "http://purl.obolibrary.org/obo/PRIDE_$1"^^ . "structural bioinformatcs" . "http://purl.obolibrary.org/obo/SIBO_"^^ . "NBK331"^^ . . . . "Nathan Baker" . . "subject agnostic" . . "Sebastian Koehler" . "ontology" . . "Intrinsically Disordered proteins with Extensive Annotations and Literature" . . . "erm" . "neuroscience" . "AntWeb" . "ev:E00032"^^ . "265"^^ . . . . . "Molecular Interaction Database" . . . . "^[0-9a-zA-Z\\.\\-\\_]+$"^^ . "221058"^^ . "NRFC051"^^ . . . . "1kfv"^^ . . . . . "Terry Hayamizu" . . "gtr" . . . "false"^^ . "^[1-9]\\d{0,6}$"^^ . "bcio" . . . . . "phylogeny" . . . "eugenes" . "false"^^ . . . "csp" . . . . "RXN-14904"^^ . . "fda.application" . . . "http://purl.obolibrary.org/obo/FBdv_"^^ . . . . "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . . . "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links."^^ . "utrdb" . . "anatomy" . . "Kids First" . "P01116"^^ . . . . . . . "ontology" . . "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components."^^ . . "br/0601"^^ . "false"^^ . . "peptideatlas.dataset" . "pactr" . "1667659"^^ . "http://www.whocc.no/atcvet/atcvet_index/?code=$1"^^ . . "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task="^^ . . "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"^^ . . . . . . . "cellular components" . . . . . . . "http://www.wikigenes.org/e/gene/e/$1.html"^^ . . . . "ato" . . . "false"^^ . "life science" . . "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . . "PR00001"^^ . . "genome" . . . . . . "PS" . . . . . . . "false"^^ . . "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^ . "International Classification of Diseases, 11th Revision (Foundation Component)" . "npass" . "https://nrid.nii.ac.jp/ja/nrid/10000"^^ . . . . "The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR."^^ . . "Malaria Ontology" . "http://www.alzgene.org/geneoverview.asp?geneid="^^ . "The World-2DPAGE database" . . . "ontology" . "oryzabase.mutant" . . . "https://drugs.ncats.io/drug/$1"^^ . "resource metadata" . . "https://e-cyanobacterium.org/bcs/rule/$1"^^ . "cancer" . "support@bel.bio" . . . "pruitt@ncbi.nlm.nih.gov" . "AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms."^^ . "Scopus Publication" . . . "cghdb" . . "300165/p13898_2106T"^^ . "false"^^ . . . "oriental-cds@163.com" . "^SEQF\\d+(.\\d+)?$"^^ . "biomagresbank" . . . . . . . "ontology" . . "pathway" . . . "authenticus" . "20021"^^ . "^(C|D|M)\\d{6,9}$"^^ . "Tudor Oprea" . "life science" . . . "https://packagist.org/packages/"^^ . "VIVO Ontology" . "^\\d+$"^^ . "Cell line databases/resources"^^ . "RIKEN Bioresource Center Cell Bank" . "marine environment" . . "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. "^^ . . "qudt" . "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^ . "metagenomics" . . "glytoucan" . . . "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB."^^ . "Database of biopesticides maintained by the University of Hertfordshire "^^ . . "DBSALT001211"^^ . . "aclum@lbl.gov" . . "molecular biology" . "false"^^ . . "Brachiaria ontology" . . . . . . . . "metabolites" . "67035"^^ . . "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum="^^ . . . "homologous" . . . "^[A-Z-a-z0-9]+$"^^ . . . "The Mammalia Polymorphism Database is a secondary database designed to provide a collection of all the existing polymorphic sequences in the MammaliaOnline query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches)."^^ . "ivan@w3.org" . . "German Clinical Trials Register" . "^\\d+$"^^ . "plant phenotypes and traits" . . . . . "2022.07.08.499378"^^ . "biopesticides" . "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" . . . . . "false"^^ . "false"^^ . . . "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^ . . . . . . . "model" . . . . . "false"^^ . "false"^^ . . "centrally registered identifier" . "^\\d+$"^^ . "ChemSpider" . "Genetics Home Reference" . . "090801"^^ . . . _:Nba7554ca26554c07b2d86a5cfbf6b404 "Crop Ontology Helpdesk" . "http://purl.org/dc/terms/$1"^^ . . . "false"^^ . "https://biopragmatics.github.io/providers/uniprot.ptm/$1"^^ . . . "Minimum Anformation About a Phylogenetic Analysis Ontology" . . "chembank" . "ontology" . . . . . . "phenotype" . . . "cognition" . _:N624f0a74bb6a428e94c2706fa793e914 "helpdesk@cropontology-curationtool.org" . . "dna" . . "e0333"^^ . . . . "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^ . . "Nicolas Terrapon" . "false"^^ . . "31253.11.sciencedb.j00001.00123"^^ . . . . . . . . . . "https://datanator.info/reaction/$1"^^ . . . . "jstor" . . . "gene" . . "http://purl.obolibrary.org/obo/FBcv_$1"^^ . "ChemicalBookNo" . . . . "experiment" . . "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata."^^ . "gene" . . . . . "imaging" . . "true"^^ . "300108/p3934_A-172"^^ . . "^FC(HS|MM)_\\d+$"^^ . . _:Nc67eaa5da835457d851cd6b2d8c36cbd . "https://www.holofooddata.org/sample/$1"^^ . "http://purl.obolibrary.org/obo/PSO_$1"^^ . "^\\d+$"^^ . "https://orcid.org/"^^ . "protein" . "ontology" . . . . "http://reg.clinicalgenome.org/allele?hgvs="^^ . "phenotype" . . . . . . . "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . . "ovae" . . "phenomics" . "anatomy" . "https://sciprofiles.com/profile/"^^ . "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot="^^ . . . . . . "Zoë May Pendlington" . . "C. elegans development ontology" . "^[0-9]+$"^^ . . . "genome" . "life cycle" . . "false"^^ . "proteomics" . . "gene" . . . . . . "virology" . "genotyping" . "Meng LIU" . "BiGG Model" . "bioinformatics" . . . "Carlos Oscar S. Sorzano" . "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1"^^ . . "Thermo Fisher Scientific" . . "false"^^ . . . . . . "8000221"^^ . . "knockout" . . . . . . . "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."^^ . "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term="^^ . . "false"^^ . . "obo" . . . "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList"^^ . . . "nsrrc" . "false"^^ . . "drug discovery" . . . . . "^\\d+$"^^ . . . . . . "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^ . . . . . "genome" . . . "gene" . . "^\\d+$"^^ . "developmental biology" . . "PRINTS compendium of protein fingerprints" . . . . . "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"^^ . "UniProt" . . "An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io)."^^ . . . . "obo" . . . . "physiology" . "BP100000"^^ . . . . "COL3A1"^^ . "https://sorgerlab.github.io/famplex/"^^ . "https://bioregistry.io/mirex:"^^ . . . . "biomedical science" . . . . "qafeQTWIWmcC"^^ . . "E5.11.2.0.0.0.4"^^ . . "false"^^ . . _:Nff9cec83104c44d783fe68e5ff33f50a "whocc@fhi.no" . . "Joel Richardson" . . "chebi"^^ . . . "true"^^ . . "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information."^^ . . . "Annotated Regulatory Binding Sites" . . . . . . "obo" . . "false"^^ . . . . "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . "gomfid" . "Ontology of Vaccine Adverse Events" . . . . . . "15"^^ . "UMLSSG" . . . "http://www.pharmgkb.org/gene/"^^ . "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$"^^ . . . . . "medicine" . "BioDolphin" . "anatomy" . "https://www.ebi.ac.uk/gxa/experiments/$1"^^ . . . "Indications and other conditions in drugbank"^^ . "^\\d+$"^^ . . "http://purl.obolibrary.org/obo/CEPH_"^^ . "CNCB Genome Warehouse" . . _:N920933e26da64a52ba1a715b160061bc "Albert Goldfain" . . . "^[0-9\\-_]+$"^^ . . . . . . . . . "Cell Image Library" . . . "supply" . . . . . "interaction" . . "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1"^^ . . . . . . . . . . . "small molecule" . . . . . . . "false"^^ . . "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^ . . "protein" . . . "EPA Hazardous Wastes" . . "tm.shah@cgiar.org" . . . "behavior" . "ontology" . . "false"^^ . . "true"^^ . . "http://open-services.net/ns/core#$1"^^ . . . . . . "sequence" . "false"^^ . . . "E-cyanobacterium entity" . . . . . . . . . . "human health" . . "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e="^^ . "protein" . "PANTHER Pathway" . . . "fbbi" . "sharkipedia.species" . "frbr"^^ . . "biolegend" . . . "SKIP001214"^^ . "5"^^ . "Adriano Rutz" . "Fernanda Dorea" . . . . . . "genecards.genenote" . "992"^^ . "obo" . . . . . . "KEGG COMPOUND" . . . "n.queralt_rosinach@lumc.nl" . . "^\\d{6}(-\\d+)?$"^^ . "^[a-zA-Z0-9-_]+$"^^ . . "http://purl.obolibrary.org/obo/CHMO_$1"^^ . . . . . "genome" . . . _:N70395268008041129aa070422efd733c "Jim Amsden" . . "https://pubseed.theseed.org/SubsysEditor.cgi?page=FunctionalRolePage&fr=$1"^^ . "false"^^ . . "chemical" . "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id="^^ . . "^Os\\S+t\\d{7}-\\d{2}$"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_qual_"^^ . . . "^\\d{7}$"^^ . . . . "Yuki Yamagata" . "subject agnostic" . . "PMC" . "sepio" . . . . "radiology" . . . "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs)."^^ . "0016"^^ . . "tol" . "^\\d{4}-\\d{3}[\\dX]$"^^ . . "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . . . . "iceberg.family" . "https://flybase.org/reports/"^^ . "dna" . "^H\\d\\.\\d{2}\\.\\d{2}\\.\\d\\.\\d{5}$"^^ . "botany" . . . . . "false"^^ . "protein" . . "tdwg.taxonrank" . . . . . . "obo" . . . . "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data."^^ . . . . . "molecular structure" . "http://purl.obolibrary.org/obo/LOGGERHEAD_"^^ . . "creativebiolabs.protein" . . "Groundnut ontology" . . "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions."^^ . . "true"^^ . "Model Card Report Ontology" . "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia.variant' prefix is used for genetic variants associated with phenes listed in OMIA"^^ . . . "david.c.blackburn@gmail.com" . . "Sumir Pandit" . "The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members."^^ . . . . . . . "http://purl.obolibrary.org/obo/RoleO_"^^ . "livestock" . . . "Compluyeast-2D-DB" . . . "false"^^ . "https://bioregistry.io/skm:"^^ . . . . "NONCODE v4 Gene" . "http://purl.obolibrary.org/obo/HsapDv_"^^ . . . "PF" . . . "http://purl.obolibrary.org/obo/DISDRIV_"^^ . "anatomy" . . "false"^^ . . . . . . . . . . . "^FR\\-FCM\\-\\w{4}$"^^ . . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . "phylogenetics" . "4"^^ . "Infectious Disease Ontology" . . "true"^^ . . "robert.thacker@stonybrook.edu" . . . . . "Phenol-Explorer" . . "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#"^^ . . . . "WikiPathways" . . . "false"^^ . . . . "125768"^^ . "^jRCT\\w?\\d+$"^^ . "UPC04349"^^ . . . . "workflow" . . "http://purl.obolibrary.org/obo/PGDSO_"^^ . . . . "FAIRsharing Organization" . . . . "https://www.ebi.ac.uk/ena/browser/view/"^^ . . "shex" . "B-5720-2018"^^ . . "http://purl.obolibrary.org/obo/FBbi_$1"^^ . "epso" . "bel" . "http://cgsc.biology.yale.edu/Site.php?ID=$1"^^ . . . . . . "Denny Vrandečić" . "MGnify Project" . . . "101"^^ . . . . "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^ . . . . . . "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible."^^ . . "A0118748"^^ . . . . . "Neuroscience Multi-Omic BRAIN Initiative Data" . . _:N920933e26da64a52ba1a715b160061bc "albertgoldfain@gmail.com" . . . "false"^^ . . . . . . . . . . "life science" . "Vitro Application Ontology" . . . "^\\d{8}$"^^ . "botany" . . "ab275461"^^ . "earth science" . . . . . . . . "one" . . "articles" . . "false"^^ . "https://biopragmatics.github.io/providers/scomp/"^^ . . "peff" . . . "glottolog" . . "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref="^^ . . . "^bt\\d+$"^^ . . "systems biology" . "http://purl.obolibrary.org/obo/OBI_$1"^^ . "biodiversity" . . . . "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"^^ . . . "genome" . . . "https://bioschemas.org/profiles/$1"^^ . "https://www.kegg.jp/entry/"^^ . . "immunology" . . . . "quality" . . . . "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^ . . . "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013."^^ . . . . "6b1"^^ . . . . . "matt@tislab.org" . . . . . . . "P3DB Site" . "obo" . . "http://purl.obolibrary.org/obo/RNAO_$1"^^ . . "dna" . . "http://www.narcis.nl/publication/RecordID/$1"^^ . . . . . "FBdv" . . . "algorithm" . "https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md"^^ . "knapsack" . . "Proteoform Atlas" . "NHMRC Australian PhenomeBank" . . . . . "^\\d+$"^^ . "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId="^^ . . "life sciences" . "Medaka fish anatomy and development" . "biomedical science" . . "drug" . "false"^^ . . "LNC" . . "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . "^D\\d+$"^^ . "https://www.fisheries.noaa.gov/species/$1"^^ . "vfdb.genus" . . "co_330" . . . "food" . . "COMe" . . . "http://viaf.org/viaf/"^^ . . . "term"^^ . . . . . . . "Support Email" . "false"^^ . . . _:Nba7554ca26554c07b2d86a5cfbf6b404 . "registry" . . . . . . "IPI"^^ . . "life sciences" . "chris.overall@ubc.ca" . . "Database portal containing replicate experiments of different assays and samples"^^ . "0007133"^^ . "ordb" . . . . . "A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources."^^ . "The Python Package Index (PyPI) is a repository for Python packages."^^ . . "nsc" . "^[A-Za-z0-9]+$"^^ . "ontology" . "odam" . . "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . . "http://purl.obolibrary.org/obo/HAO_"^^ . . "Silvio C.E. Tosatto" . . "Yam ontology" . "^PA\\w+$"^^ . . "researcher" . . . "obo" . . . . . . "graph" . . . . . . "https://gateway.eubopen.org/compound/"^^ . . "ontology" . . . . . . "true"^^ . . "http://dicom.nema.org/resources/ontology/DCM/$1"^^ . . "ontology" . . "^\\d{7}$"^^ . "DrugBank" . . "InfragenericTaxon"^^ . "ontology" . . "0000001"^^ . . "http://purl.obolibrary.org/obo/ARO_$1"^^ . . "LMPR0102010012"^^ . . . . . . . . "ontology" . "false"^^ . . "animal husbandry" . . . . . "structure" . . . . "omim" . . . . . . . . "^\\d+$"^^ . . . . . . "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"^^ . "semapv" . "0000000"^^ . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$"^^ . . . "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . . . "http://purl.obolibrary.org/obo/FYPO_"^^ . "false"^^ . . . "Zebrafish Information Network Gene" . "https://www.pirbright.ac.uk/node/$1"^^ . . "false"^^ . . "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^ . . "ontology" . "https://bioregistry.io/metaregistry/$1"^^ . . . "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1"^^ . . "medical informatics" . . . "seed" . . . . . "interaction" . . "simon.harding@ed.ac.uk" . . "chemical in the database supplied by Pesticide Action Network North America"^^ . . . "false"^^ . . . . . . "000410"^^ . "swisslipids@isb-sib.ch" . "plant phenotypes and traits" . . . . . . . . . "vjenkins@morgan.harvard.edu" . "metagenomics" . . "YRC PDR" . "00042"^^ . "https://cropontology.org/rdf/CO_359:"^^ . . "nasaosdr.study" . . "AKR"^^ . "VEGA" . . . . . . "https://horizondiscovery.com/en/search?searchterm=$1"^^ . . . "J. Michael Cherry" . . . "agriculture" . . "S-EPMC6266652"^^ . . "ecology" . "miriam.resource" . "Fernanda Farinelli" . . . "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"^^ . . "brenda.ligandgroup" . "Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases."^^ . _:N1e6e5dec4199411f836fb44038b9f4a1 "pbrooks@hcfa.gov" . . . . "9530"^^ . "LinJ.20.0070"^^ . "larvae" . . . "seed.compound" . . "1cukA01"^^ . "social and behavioural science" . "^\\w+(\\-)?\\w+(\\-)?\\w+$"^^ . . . . "BioSchemas" . . . . "Selventa Families" . . . "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"^^ . . . . . "paleodb" . "interaction" . "Eschmeyer's Catalog of Fishes" . . . . "false"^^ . . "http://purl.org/gc/$1"^^ . "434"^^ . "false"^^ . "genome" . . "obo" . "128796-39-4"^^ . "WB" . "false"^^ . . . . "Geographical Entity Ontology" . . . . "https://www.npmjs.com/package/$1"^^ . . . "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts."^^ . . . . . "fionamcc@arizona.edu" . "https://www.researchgate.net/profile/"^^ . . "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia' prefix is used for phenes, either across species (omia:001000) or in a specific species (omia:001000-9615)"^^ . "https://dandiarchive.org/dandiset/"^^ . . "RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project."^^ . "The data sources used in xrefs in the ChEBI ontology. More information in the \"Data Sources\" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx)." . "^\\w{14}$"^^ . "^\\d{7}$"^^ . "report" . . . . "life science" . "^GPM\\d+$"^^ . . "http://purl.org/obo/owlEOL_$1"^^ . "Workflow"^^ . . . . . . . "Isabel Sá-Correia" . . "Process Chemistry Ontology" . "cultured cell" . "nando" . . . "ILMN_129894"^^ . "csd" . "4DN" . . "single-cell multimodal omics" . . . . "APID Interactomes" . . "^\\d+$"^^ . "molecular structure" . . . . . "false"^^ . . . "patrice.buche@inrae.fr" . . . . "covid19" . "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . "BridgeDb Vocabulary" . "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp="^^ . . . . "ecology" . "http://purl.obolibrary.org/obo/TGMA_$1"^^ . "research" . "caripark@iastate.edu" . "https://rubygems.org/gems/"^^ . "^[0-9]+$"^^ . . . . "CL000025"^^ . . . . . . "^[a-zA-Z_][a-zA-Z0-9\\-_]+$"^^ . . . . "http://ascl.net/$1"^^ . . . "^\\w+$"^^ . . . . . . _:N45a654d99b614bda80dfa8f601ce799f "Tim Vandermeersch" . "life science" . . "odc.tbi" . . . . "Pfam" . . "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^ . "kupo" . . "ontology" . . "COI Catalogue" . . . . "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi."^^ . . "prodom" . . "https://model.geneontology.org/"^^ . . . . . . . "false"^^ . . "Christine Orengo" . "false"^^ . "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1"^^ . "^(cl|tum)\\d+$"^^ . "anatomy" . . "metascience" . . . . . "false"^^ . "http://purl.obolibrary.org/obo/UO_"^^ . "biomedical science" . "interaction" . "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1"^^ . . "false"^^ . . . . . . . . . . "ontology" . . . . . "life science" . . . . . . "life science" . . . . . . "PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected."^^ . "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome."^^ . . "DDB0191090"^^ . "nbo" . . . "MTBLS1"^^ . . . "false"^^ . "PRO" . "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id="^^ . . . "MEDIGUE Claudine" . . "^A\\d+$"^^ . "phenotype" . "openalex" . . . . . . . "431472"^^ . "nxr" . . . "Anatomical Entity Ontology" . . . . . "nfdi.core" . . . . . . . . . "ontology" . . . "^\\w+$"^^ . . "taxon" . . "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^ . . . . "http://purl.obolibrary.org/obo/TTO_$1"^^ . . "https://w3id.org/nfdi4cat/voc4cat_"^^ . . . . "false"^^ . . . . . . "fetus" . . . "dg.anv0" . . . . . "https://www.wormbase.org/db/seq/protein?name="^^ . . . . "https://www.genedb.org/gene/$1"^^ . "https://www.arraymap.org/pgx:"^^ . "nmpdr" . "metabolomics" . "https://www.webofscience.com/wos/woscc/full-record/WOS:$1"^^ . . . . . . . "zenodo.record" . . "reactome" . "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"^^ . "^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$"^^ . . . "Store DB" . . . . . "drugbank.condition" . . . . . . "046"^^ . . "https://schema.org/$1"^^ . . "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands."^^ . . . . . . . . . . . . . "food" . "food" . "structure" . . . "Kyoto Stock Center" . "Sharkipedia Trend" . . . . "http://www.w3.org/ns/dcat#"^^ . "1433C_TOBAC_1_252"^^ . . "NIST/CODATA ID" . . . "0000598"^^ . . "000000159"^^ . . "OntoRXN" . . . . . . . "Platynereis Developmental Stages" . . "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT="^^ . . . "false"^^ . "^PMC\\d+(\\.\\d+)?$"^^ . . . . . . . "beta-carotene"^^ . . "^\\d+$"^^ . . . "subject agnostic" . "SwissRegulon" . . . "ontology" . "Open Citation Identifier" . "food chemistry" . . . . . . . . . . _:N58db97b10310498eaf818badfeb1bc7a "Frédérick Giasson" . "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme."^^ . . "food" . "https://goldbook.iupac.org/terms/view/$1"^^ . "^[A-Za-z0-9\\-\\/]+$"^^ . . . . "http://purl.obolibrary.org/obo/SYMP_"^^ . "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies."^^ . "hao" . "recombinant host" . "dailymed" . "health science" . . . . . . . . . "Li-San Wang" . . . . "microbiology" . "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."^^ . "faseb list" . "https://glottolog.org/resource/languoid/id/$1"^^ . . "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population."^^ . . "^\\d{8}$"^^ . "https://browser.planteome.org/amigo/term/PECO:$1"^^ . . "environmental science" . . . . . "true"^^ . . "https://www.confident-conference.org/index.php/Event:"^^ . . "Guoqing Zhang" . . "false"^^ . "false"^^ . . . . . . . . . . "apid.interactions" . "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."^^ . "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1"^^ . . . . . . . . . . "^\\d{7}$"^^ . _:N41d2d4542c2841fe918d2f7b4dec472c "helpdesk@cropontology-curationtool.org" . "Lepidoptera Anatomy Ontology" . . . "Astrophysics Source Code Library" . "data management" . . . "has alternative prefix" . . . . . . . "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies."^^ . . "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms" . . . "false"^^ . "^TTHERM\\_\\d+$"^^ . . . . "publons.researcher" . "https://github.com/"^^ . "drug metabolism" . . . . "https://cropontology.org/rdf/CO_356:"^^ . . . "RDF Schema" . . . . "ontology" . . . . "^CCDS\\d+(\\.\\d+)?$"^^ . . . . . . . . "cell biology" . . . . "^\\d+$"^^ . . . "conferences" . . "200906038218908385"^^ . "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1"^^ . . . "https://bioregistry.io/pscdb:"^^ . . . . "kegg.enzyme" . "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . . "Snapshot" . "https://www.ncbi.nlm.nih.gov/gtr/conditions/"^^ . "EMAPA_RETIRED" . "ontology" . . . . . . . . "ontology" . "phenotype" . "ADH1"^^ . . . . . "Coronavirus Infectious Disease Ontology" . "3771992"^^ . "genome" . . "omp" . . . . . "owl" . . "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0="^^ . . "https://envipath.org/package/$1"^^ . . . . . "https://pubseed.theseed.org/SubsysEditor.cgi?page=ShowSubsystem&subsystem=$1"^^ . . "true"^^ . "Ontology for Chemical Kinetic Reaction Mechanisms" . "ontology" . "Open Data Commons for Spinal Cord Injury" . "^\\d(\\d|\\w)$"^^ . "ontology" . . . "https://crates.io/crates/"^^ . "false"^^ . . "ontology" . . "genetic disorder" . . "Dylan McGagh" . "https://www.ebi.ac.uk/pride/archive/projects/$1"^^ . "Hypertension Ontology" . "sasbdb" . "chebi" . _:Na59068c51e694496ab883410d5241e56 "maria.herrero@kcl.ac.uk" . . . . . "ontology" . . . . . "false"^^ . "BRENDA Tissue Ontology" . . . . . . . . "false"^^ . "MolBiC Cell Line" . "j.harry.caufield@gmail.com" . . . . . "11061"^^ . "^\\d{7}$"^^ . . "FCB005"^^ . . . . . "https://pharmacodb.ca/cell_lines/$1"^^ . . . "^\\w+$"^^ . . "Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant."^^ . "false"^^ . "Torsten Schwede" . . . . "ontology" . "secretariat@eol.org" . . . . "https://e-cyanobacterium.org/models/model/"^^ . . "false"^^ . . . . . "http://purl.obolibrary.org/obo/IDOMAL_$1"^^ . . "obo" . . "http://pathguide.org" . "phenotype" . _:N734d9cfa9fd84fc6b5c1595bb8b23cda "helpdesk@cropontology-curationtool.org" . "^\\d{7}$"^^ . . . "chembl.compound" . . "pato" . . . "bt0001"^^ . . . . . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code="^^ . . "dna" . "Elizabeth Arnaud" . "false"^^ . "This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group."^^ . . . . . "obo" . "opl" . "^[0-9a-fA-F]{32}$"^^ . "IPP900099"^^ . . "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:"^^ . . . . . . . . . "Complex Portal" . . "life science" . "0000000"^^ . . . . . . . . "1242"^^ . . . "diagnosis" . . "LINCS_LDP" . "false"^^ . "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers."^^ . . . . "Yang Chai" . "^GenProp\\d+$"^^ . . . . . . . "false"^^ . . "Molecular Design Limited Hash" . "uniprot.location" . . . . . . . . . "https://mmp.sfb.uit.no/databases/marcat/#/records/"^^ . . . . . . . . . . . . . "cohd" . . . . . . "resource metadata" . . "schober@imbi.uni-freiburg.de" . "false"^^ . "myco.lepra" . "FHIR United States Implementation Guides" . . . "^\\d{7}$"^^ . "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)."^^ . . . "Gene Expression Ontology"^^ . . . . . "false"^^ . "oarcs" . . . "identifier of an article in Dialnet"^^ . . "https://cropontology.org/rdf/CO_360:"^^ . "metagenomics" . . "000177759000002"^^ . . "http://bigg.ucsd.edu/models/"^^ . "https://mged.sourceforge.net/ontologies/MGEDontology.php#$1"^^ . "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." . "FBgn0000015"^^ . . . . "http://senselab.med.yale.edu/ORDB/Data/$1"^^ . . . . "18030"^^ . "civic.mpid" . "agriculture" . . . . . . . . "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements."^^ . . "http://research.bmh.manchester.ac.uk/informall/allergenic-food/?FoodId=$1"^^ . . . "International Protein Index" . "structure" . "vcard" . . "4195"^^ . "false"^^ . . "^PAp[0-9]{8}$"^^ . . . "OSR00185W"^^ . . . . _:N49e50e7a4f0f4690bd2d5d7ba9790d2a "Usha Mahadevan" . . . . "eggNOG" . . . "https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema=$1"^^ . . . . . . . "https://cropontology.org/rdf/CO_365:$1"^^ . "swissregulon" . "^\\d+$"^^ . . . . . "botany" . . . . "false"^^ . . . "false"^^ . "^\\d{7}$"^^ . . . . "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^ . . "systems biology" . "FBbt_root" . "PjrpzUIAAAAJ"^^ . "Hs635"^^ . . . . "http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1"^^ . . "0000061"^^ . "odrl" . . . . . . . "5.1"^^ . "systems biology" . "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#"^^ . . "ontology" . "famplex" . . . . "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas="^^ . . "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br"^^ . . . "subject agnostic" . "ontology" . . "bacdive" . "insdc" . . . . "Glenn King" . . "http://data.food.gov.uk/codes/foodtype/id/"^^ . "Information about the C57BL/6J. Includes genetic background and disease data."^^ . "https://biopragmatics.github.io/providers/cvx/$1"^^ . . . "glycomics" . . . . . . "^[1-9]\\d*$"^^ . "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."^^ . . . . . . "http://www.pharmgkb.org/pathway/"^^ . . . . . "http://www.ifomis.org/bfo/1.1/snap#$1"^^ . "Andy Deans" . "co_356" . . . . . . "Kalpana Panneerselvam" . "ACH-000001"^^ . "pathogen" . "http://iflastandards.info/ns/fr/frbr/frbrer/$1"^^ . "frbr" . . . "http://purl.obolibrary.org/obo/COVOC_$1"^^ . . . "false"^^ . "http://purl.obolibrary.org/obo/TRANS_$1"^^ . . . . . . . . . "http://purl.obolibrary.org/obo/MFMO_"^^ . "centrally registered identifier" . "LOC_Os01g49190"^^ . . "http://rebase.neb.com/rebase/enz/$1.html"^^ . . . "botany" . . "_4dn.replicate" . "O08709"^^ . . . "plant phenotypes and traits" . "https://www.cabi.org/cabebooks/ebook/"^^ . "c0000005"^^ . "come" . "wikidata.property" . . "Vaccine Adjuvant Compendium" . "^osa-miR\\d{3,5}[a-z]{0,1}$"^^ . . "hms.lincs.antibody" . . . . "wmk@amu.edu.pl" . . "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . "ClinicalTrials.gov" . . "ali.syed@kaust.edu.sa" . . "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."^^ . . . "Gary L Andersen" . "clingen.allele" . "subject agnostic" . . . . "GWAS Catalog" . . "miro" . . "false"^^ . "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name="^^ . "false"^^ . . . . . "goldbook" . . "nmdc" . "- 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 centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes."^^ . . . . "obo" . . "chemical" . . "false"^^ . . "Bactibase" . . "false"^^ . . "variant" . . . . "bioinformatics" . . "genetree" . . . "ontology" . . . . . . "idomal" . . . . . "gene" . "affy.probeset" . . "umbbd.pathway" . . . . . . . "life science" . . . "https://pharmacome.github.io/conso/$1"^^ . "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations."^^ . . . "dorothea.iglezakis@ub.uni-stuttgart.de" . . . . "PGS000018"^^ . "Marc_Ciriello@hms.harvard.edu" . . . "The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan."^^ . . . . "https://www.ebi.ac.uk/biosamples/sample/"^^ . . . . "oncotree" . . . "a.kranz@fz-juelich.de" . "^\\d{5,}$"^^ . "diagnosis" . . . "^\\d+$"^^ . . . "^[a-zA-Z0-9\\-:#\\.]+$"^^ . "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^ . . . . "drugs" . . "synbip.bts" . "DBrodbelt@RVC.AC.UK" . "genomics" . "9861/3"^^ . "https://fairsharing.org/users/"^^ . "BastianFromm@gmail.com" . . "Neuronal cell types"^^ . . "^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$"^^ . "^\\d+$"^^ . "https://jjj.bio.vu.nl/models/$1"^^ . . . . "^\\d+$"^^ . "http://www.informatics.jax.org/accession/MGI:"^^ . "TIGR00010"^^ . "interaction" . . "chemistry" . . . . "Samuel Friedman" . . . "exac.gene" . . . "descriptionAnnot"^^ . "life science" . . "botany" . "http://purl.obolibrary.org/obo/OlatDv_"^^ . "MEDLINE" . . . . . "Brassica ontology" . . "zebrafish" . . . . . . . . . . . . . "development" . . "false"^^ . "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^ . . . . "pictar-vert" . "NIF Standard Ontology: OEN Terms in Neurolex" . . . . . "25782"^^ . . . "Nicholas Furnham" . . . "biomedical science" . _:N5ed93a11628a4d9ab1825cec2f063b06 "Kristin D. Kasschau" . . _:Na240e2f055ba4e10bb275bdf6f56b7b6 . . "^\\d{7}$"^^ . . "cellosaurus" . . "PaxDb Protein" . "https://units-of-measurement.org/"^^ . "SNOMED CT (International Edition)" . . . "gxa.gene" . . . "http://vocabularies.bridgedb.org/ops#$1"^^ . "https://www.cellosaurus.org/CVCL_"^^ . . "^[1-9][0-9]*$"^^ . . . . . "100101"^^ . "Luana Licata" . . "life science" . . . . "https://ocid.ontochem.com/prefname?ocid="^^ . . . . . . . . . "eubopen" . "1580791"^^ . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1="^^ . . . . "Jawahar Swaminathan" . "protein" . . . _:N86e26dc551344b7eb215b4a1720001f4 "radlex-feedback@lists.rsna.org" . "ricenetdb.protein" . "biology" . . "rna" . . . "biocuration" . . . . . . . . . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes."^^ . "Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses."^^ . "biochemistry" . . "ontology" . . . . . . . . . "centrally registered identifier" . "ortholog" . . . "^(conceptualization|data-curation|formal-analysis|funding-acquisition|investigation|methodology|project-administration|resources|software|supervision|validation|visualization|writing-original-draft|writing-review-editing)$"^^ . . . . . "life science" . . . . . . . . "ExAC Transcript" . . "earth science" . "5046"^^ . . "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]"^^ . . "https://flybase.org/reports/FBrf$1"^^ . . "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1"^^ . . . "hcvdb" . "imotdb" . . "Yasset Perez-Riverol" . . . . . . . . . . . "doap" . "people/11035"^^ . . "false"^^ . . "WP732"^^ . "^\\d+$"^^ . . . "marine biology" . . . . . "BioCyc collection of metabolic pathway databases" . . "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments."^^ . . "^\\w{2,3}(-\\w+)?$"^^ . . "Dewey Decimal Classification" . "d4akea1"^^ . . "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . . "life cycle stage" . . . "pid.pathway" . "life science" . . "https://swissmodel.expasy.org/repository/uniprot/$1"^^ . . "obo" . . "regulation" . . . . "development" . "transgenic" . . "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym="^^ . "^GCF_[0-9]{9}(\\.[0-9]+)?$"^^ . . "food" . . . "https://scicrunch.org/resolver/RRID:$1"^^ . "biology" . . . . . . . . . . . . . . "Blue Brain Project Knowledge Graph" . . . . . "^LTS\\d{7}$"^^ . . . . "Oryzabase Mutant" . . . "9008500"^^ . . "false"^^ . . "SNOWMEDCT" . . . "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."^^ . . . . "http://genomics.senescence.info/diet/details.php?id="^^ . . . "http://purl.obolibrary.org/obo/BTO_$1"^^ . . . . "false"^^ . . "Gerhard Mayer" . . . "^\\d+$"^^ . "MTHICD9_2006" . . . . . . . "Ulrike Wittig" . . . "enzymology" . . . "http://www.bindingdb.org/compact/$1"^^ . "^SCV\\d+(\\.\\d+)?$"^^ . . "https://datanator.info/reaction/"^^ . . . . . . "https://purl.brain-bican.org/ontology/dhbao/DHBA_"^^ . . "life science" . . . . . "sequence feature" . . . "Scholia Registry" . "anatomy" . . "European Searchable Tumour Line Database" . . "GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC."^^ . "https://www.chemspider.com/search?params=$1"^^ . . "0001"^^ . . . "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)"^^ . "cdt" . "metanetx.compartment" . . . . "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id="^^ . . . . "false"^^ . . "An ontology to represent genomics cohort attributes."^^ . . . . "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN)."^^ . . "Life cycle stages for Platynereis dumerilii"^^ . . "^\\d{7}$"^^ . "false"^^ . . . . . . "https://go.drugbank.com/bio_entities/$1"^^ . . . "botany" . . . . . . "https://coicatalogue.uc.pt/index.php?t=specimen&COINumber=$1"^^ . . . "nje5@georgetown.edu" . "Matt Yoder" . . . "pathway" . . "w3c rec" . . "drug" . . . . . "^\\d{1,9}$"^^ . . "experiment" . . "hso" . . . "Database of Macromolecular Movements" . . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"^^ . "image" . . "http://www.kegg.jp/entry/"^^ . . . "http://www.ecogene.org/gene/"^^ . . "Sensitive Data Ontology" . . . "8639.1"^^ . . . "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . . "small molecule" . . "TP53"^^ . "gene" . "International Classification of Diseases, 10th Revision, Clinical Modification" . "false"^^ . "KEGG" . . . . . . . . . "subject agnostic" . "Identifiers for synthetic binding protein-target complexes, detailing their components, 3D structures and docking statistics"^^ . . . "^\\d+$"^^ . "https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/$1"^^ . "^DRSC\\d+$"^^ . . "chempro.target" . "INN_ID" . "false"^^ . "^\\d+$"^^ . "XB-GENE-922462"^^ . . "http://darcsite.genzentrum.lmu.de/darc/view.php?id="^^ . . . . "PSI-MOD" . . "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."^^ . . . . . . . "dockerhub.repo" . "http://purl.obolibrary.org/obo/PCL_$1"^^ . "metabolite" . . "spdx" . . "srvoss@uky.edu" . . "dna" . . "http://pax-db.org/#!protein/$1"^^ . . "obo" . "asrp" . "glycomics" . "app-d678n-tottori"^^ . . . "ClinVar Variation" . . "https://cropontology.org/rdf/CO_337:$1"^^ . . . . . . . . "Scopus affiliation ID" . "virology" . . . . . "ontology and terminology" . . . . . "http://purl.obolibrary.org/obo/ZFS_$1"^^ . . . . . . . "false"^^ . "bel" . . . . "https://bioregistry.io/iceberg.ime:"^^ . . "MM00040"^^ . . . . "5ede4273-b26c-4ea4-adb7-3ce294ab3397"^^ . . "The Artificial Intelligence Ontology" . "multicellds.snapshot" . . . "Mosquito gross anatomy ontology" . . . "Minimal set of terms for anatomy"^^ . . "has identifier space owner" . . . . "protein" . "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^ . . . . . . . "ogms/OMRE" . . . "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1"^^ . "https://resolver.api.identifiers.org/resolveMirId/"^^ . . . "maggot" . . . . "http://purl.obolibrary.org/obo/CDNO_"^^ . "IRD Segment Sequence" . . . . "structrual bioinformatics" . . . "obo" . "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine."^^ . "The Ecosystem Ontology" . "MT"^^ . . . "551115"^^ . . . "https://cropontology.org/rdf/CO_324:$1"^^ . "0000389"^^ . . . . . . . "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"^^ . "iso.3166" . . . . . . . . . "^\\d+$"^^ . "false"^^ . . . . . . . "https://redoxibase.toulouse.inrae.fr/display_perox/view_perox/$1"^^ . "life science" . "umbbd.compound" . "botany" . . . . . "ribocenter" . "PDB_CHEM_ID" . . . "molecular entity" . "reagent" . . . "cienciavitae" . "http://www.interfil.org/details.php?id=$1"^^ . "AT4G01080"^^ . . . "false"^^ . . "https://bioregistry.io/odor:"^^ . "structural biology" . "false"^^ . "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download."^^ . . . . . . . "jens.klump@csiro.au" . . . . "false"^^ . "https://chem.nlm.nih.gov/chemidplus/rn/$1"^^ . "life science" . . "true"^^ . . "https://chemprosquare.idrblab.net/data/probe/details/$1"^^ . "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases"^^ . "opm" . "Marijane White" . . . . . . . . . . "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s."^^ . "Properties in DBPedia."^^ . "LIPID_MAPS_instance" . . . . . . . "fish" . . . . "umbbd.rule" . . . . . "438782"^^ . "^\\d+$"^^ . "false"^^ . . . . . . "http://wodaklab.org/iRefWeb/interaction/show/$1"^^ . . "0000123"^^ . "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1"^^ . . . . . . . . . . "http://antibodyregistry.org/AB_"^^ . "pharmacology" . . . "^\\d{7}$"^^ . "^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\\.[0-9]+(-[0-9]{3}\\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$"^^ . . . "false"^^ . "false"^^ . . "false"^^ . . "ftt" . "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . . . "1868"^^ . "bhsung@kribb.re.kr" . . . . . "disease process modeling" . "ontology" . "Library of Congress Control Number" . "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . "ontology" . "Publishing Workflow Ontology" . . "dna" . . . "0000062"^^ . . "The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. [from homepage]"^^ . . . "Robert Hoehndorf" . "false"^^ . . . "Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)"^^ . . "false"^^ . "https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn$1"^^ . "measurement" . "TogoID" . "false"^^ . _:N1e6e5dec4199411f836fb44038b9f4a1 "Patricia Brooks" . . . "^(VT)?\\d{7}$"^^ . . "http://purl.obolibrary.org/obo/PLANP_"^^ . . "https://idr.openmicroscopy.org/search/?query=Name:idr$1"^^ . . . . . . "^\\d+$"^^ . . . "http://europepmc.org/articles/$1"^^ . "d.craik@imb.uq.edu.au" . . . "^A[A-Z]+\\d+$"^^ . . . . . . "https://www.iedb.org/mhc/$1"^^ . . "ecology" . "preclinical studies" . . "1426686"^^ . . . . "^PIRSF\\d{6}$"^^ . . "PA131"^^ . . . "cstr" . . . . . "modeling and simulation" . "false"^^ . . . . "geoinformatics" . . . . . . "true"^^ . "false"^^ . . . . . . "https://rnaloops.cs.put.poznan.pl/search/details/$1"^^ . . . . . . . "The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny."^^ . "https://www.uniprot.org/diseases/$1"^^ . "obo" . "tk2@ebi.ac.uk" . . . . . "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . . . "^(CE[0-9]{5}|WB[A-Z][a-z]+\\d+)$"^^ . . . . "ECU03_0820i"^^ . "structure" . . . . "10194"^^ . . . "nicolas.matentzoglu@gmail.com" . . . . . "https://go.drugbank.com/indications/"^^ . . . . . . "^MMP\\d+.\\d+$"^^ . . . . . . "Rice Genome Annotation Project" . "0045310"^^ . . . . . . "hpa" . _:N897fc53d0b0c403f9d8f803af679abd3 . . . . . "true"^^ . "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . . . . . . "ontology" . "false"^^ . . "bioinformatics" . . . . . . "5601141"^^ . . "traits" . . . "^[a-z0-9-]+$"^^ . . . . . . . . . "false"^^ . . . . . "topics" . "disease" . . "https://gold.jgi.doe.gov/resolver?id=$1"^^ . . "GLAndersen@lbl.gov" . . . "database" . "Protein Interaction Network Analysis" . . . "^\\d{7}$"^^ . "false"^^ . "omics data analysis" . . "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . "https://molbic.idrblab.net/data/protein/details/"^^ . . "sequence" . . . . . . . "rdf" . . "https://senselab.med.yale.edu/ModelDB/ModelList?id="^^ . . . . . . "^\\d+$"^^ . "frim1"^^ . "obo" . . . "ricecyc" . "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^ . . "BlastRule" . . "http://www.co-ode.org/ontologies/galen#$1"^^ . "gene" . "Transporter Classification Database" . . . "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession="^^ . . . . "bila" . "annotation" . "false"^^ . . "pharmacology" . . "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^ . . . . "hivreagentprogram" . "Núria Queralt Rosinach" . . "evgeny.zdobnov@unige.ch" . "EGAD00000000001"^^ . "^ERM[0-9]{8}$"^^ . . . . "false"^^ . "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"^^ . . "http://purl.obolibrary.org/obo/BCO_$1"^^ . . "biomedical science" . . . "microRNA Ontology" . . . "wikidata" . "10046"^^ . . "https://massbank.jp/RecordDisplay?id="^^ . "false"^^ . "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web"^^ . . "pathogen" . "Biological Spatial Ontology" . . . "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^ . . . "https://amoebadb.org/amoeba/app/record/gene/"^^ . "https://www.dsmz.de/collection/catalogue/details/culture/"^^ . "omics data analysis" . . . "ontology" . . "structure" . . . . . . . . . "http://purl.obolibrary.org/obo/T4FS_$1"^^ . "https://transyt.bio.di.uminho.pt/reactions/"^^ . . . . . "^rx[0-9]{5}$"^^ . . . "false"^^ . "bioinformatics" . "mesh.vocab" . . "^\\d{2,7}-\\d{2}-\\d|DTXSID\\d{7,9}|[A-Z]{14}-[A-Z]{8}[SN][A-Z]-[A-Z]$"^^ . . "gold.meta" . . . "false"^^ . . . . "environmental science" . . "NIF Standard Ontology: Investigations" . "CTX" . . . "nstd102"^^ . "http://purl.bioontology.org/ontology/npo#NPO_$1"^^ . . . "structure" . "http://purl.obolibrary.org/obo/SCDO_"^^ . . . . "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . . . "http://purl.obolibrary.org/obo/REX_"^^ . . . . . . . "false"^^ . . "gcst" . . "ontology" . "proteomics" . . . . "Polygenic Score Catalog" . . . "https://uts.nlm.nih.gov/uts/umls/semantic-network/$1"^^ . . . . . . "119514"^^ . "fyler" . . "false"^^ . . . . . . . . "https://portal.issn.org/resource/ISSN/"^^ . "^\\d{7}$"^^ . . "biomedical science" . . . . . . "http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php?specie="^^ . . "0001191"^^ . "Life cycle stages for Medaka"^^ . . "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database."^^ . "0001410"^^ . "Daniel Sonenshine" . "1000"^^ . . . . . . . . . "Mouse adult gross anatomy" . "This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes."^^ . "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . . "drugbank.reaction" . . "0000253"^^ . "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities."^^ . . . "AY321118"^^ . . . "idr" . . "citation" . "false"^^ . . "rna" . "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions."^^ . . . . . . . "Yeast Phenotype Ontology" . "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access."^^ . . "iceberg.cime" . "https://bioregistry.io/wicell:"^^ . . "http://www.fao.org/gsfaonline/additives/details.html?id=$1"^^ . . "chemistry" . "Minimal Anatomical Terminology" . . "false"^^ . "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . . . . . . . . . . . . "An ontology of metadata from protege"^^ . . "http://purl.obolibrary.org/obo/DRON_"^^ . "bioinformatics" . "Ontology of Organizational Structures of Trauma centers and Trauma systems" . . "http://pax-db.org/#!protein/"^^ . . . . . . "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . . "^\\d+$"^^ . "frbr" . . . . . . . "pennsieve" . "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."^^ . "Gi07796"^^ . . . . . . . "ontology" . "obo" . . "Nicolas Le Novere" . . "http://purl.obolibrary.org/obo/OBA_"^^ . . "ontology" . . . . . . . . . . . "epidemiology" . . . . "true"^^ . . "false"^^ . . . "napp" . "reagent" . "1178"^^ . . "MOL000160"^^ . . "^(Gi|Gc)\\d+$"^^ . . . . "74"^^ . "BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format."^^ . . . . . . . . . "http://cutdb.burnham.org/relation/show/"^^ . . . "Locations in DEIMS SDR"^^ . . "false"^^ . . . . . . "false"^^ . . . . . "uniprot/swiss-prot" . . . . "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation."^^ . "events" . . . . "0002005"^^ . . . . . . . . . . "EDAM Format" . . . "BioTop" . . "Molecular Signatures Database" . "HMDB00001"^^ . . . "SIGNOR-C41"^^ . . "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families."^^ . . . "evm" . . . "http://purl.obolibrary.org/obo/LIPRO_$1"^^ . . . "foodb.food" . "oba" . "https://rism.online/"^^ . . . . "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"^^ . . . "^D\\d+$"^^ . . "FOOD00020"^^ . . "http://www.orpha.net/ORDO/Orphanet_"^^ . . "ontology" . "false"^^ . "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view."^^ . . . . . . "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions."^^ . . "electronic health record" . . "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"^^ . . . "http://purl.obolibrary.org/obo/FBSP_$1"^^ . . . . . "Publishing Roles Ontology" . . . "olivier@nlm.nih.gov" . . . . . . "gene" . . "geography" . . . "0000550"^^ . . . . "1755"^^ . . "^\\d+$"^^ . . . "cd00400"^^ . _:Nbfb950c0fbdf4b68a9b1844647f8b090 "Kenji Naritomi" . "00000268"^^ . . . "^[0-9X\\-]+$"^^ . "Yohann Paris" . "Minerva María Romero Pérez" . . . . "false"^^ . . . "IPI00000001"^^ . "https://doulix.com/constructs/"^^ . "http://genomics.senescence.info/genes/details.php?id="^^ . . . "false"^^ . "1001"^^ . . "21692"^^ . . "lincs.cell" . . . . "false"^^ . . "030719"^^ . . "biomedical science" . . . "obo" . . . . . . "https://aopwiki.org/relationships/$1"^^ . "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code="^^ . . . . . "International Classification of Diseases, 10th Revision" . "Ontology for genetic interval" . . "geography" . "http://purl.obolibrary.org/obo/DOID_$1"^^ . . . . . . "http://purl.obolibrary.org/obo/BOOTSTREP_"^^ . "true"^^ . "https://bioregistry.io/kerafast:"^^ . "0000546"^^ . . . "false"^^ . . . "^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . . "false"^^ . . . "https://bioregistry.io/metaregistry/scholia/"^^ . "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^ . . . "Database of Genomic Structural Variation - Variant" . . . . "Silvio Tosatto" . . . . . "https://e-cyanobacterium.org/models/model/$1"^^ . "http://purl.obolibrary.org/obo/FIX_$1"^^ . . . . . . "false"^^ . . "Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)"^^ . . . . . . "Hölzel Diagnostika" . "https://www.worldwildlife.org/ecoregions/"^^ . . . . . . . "paolo.romano@hsanmartino.it" . . . . . "obo" . . . . . . . "https://omia.org/variant/omia.variant:$1"^^ . "data model" . . . "gene expression" . "autdb" . "http://www.gramene.org/db/genes/search_gene?acc="^^ . . "health science" . . . "pw" . . "protein" . . . . "^MMP\\d+.\\d+$"^^ . . "Comparative Data Analysis Ontology" . . "^[0-9]+$"^^ . . . . "model organism database" . . "Nikos C. Kyrpides" . . "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid="^^ . . . . "false"^^ . . "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc."^^ . . "19333"^^ . "00000180"^^ . . "Jeffrey Wong" . . . . . . . . "pascale.gaudet@isb-sib.ch" . "physics" . . . "http://purl.obolibrary.org/obo/ZP_$1"^^ . . . . . . . "darc" . . . . . . . "^\\d{7}$"^^ . . "Paul Schofield" . . "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)."^^ . . . "pr" . . "http://purl.obolibrary.org/obo/FLOPO_$1"^^ . . . "12969"^^ . "edennis@ucsd.edu" . _:Nbc1316da7fc24fecb8577dee5db3c6dc "cozzone@ibcp.fr" . . . . "https://www.storedb.org/?$1"^^ . . . . "^\\d{7}$"^^ . . "Fabian Schreiber" . . . . . . . . "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . . "genotype" . . "http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#"^^ . "https://www.biolegend.com/Default.aspx?ID=6664&productid="^^ . . . . . . "SCV000151292"^^ . . . "gfo" . . . . "uniprot.arba" . "dommino" . "false"^^ . "^\\d+$"^^ . "false"^^ . "true"^^ . . "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^ . . "obo" . . . "http://purl.obolibrary.org/obo/PLO_$1"^^ . . . . . . . "cho"^^ . . . . "^(MNXR\\d+|EMPTY)$"^^ . "obo" . . "true"^^ . "The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI)."^^ . "Human Reference Atlas Common Coordinate Framework Ontology" . "https://www.iedb.org/mhc/"^^ . . . . . . . "AGROVOC" . . "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID="^^ . . . "genome" . . . . . _:N9de9c5a856404f1aa6dc4444bdf57fa3 "Josef Hardi" . "yeastintron" . . . "Blue Brain Project's published data as knowledge graphs and Web Studios."^^ . "http://purl.obolibrary.org/obo/CEPH_$1"^^ . "265912"^^ . "ncats.bioplanet" . "http://purl.obolibrary.org/obo/CMO_$1"^^ . . . "laml_tcga_pub"^^ . . . . . . . . "obo" . . "CNBG_0001"^^ . "SNOMEDCT_US_2018_09_01" . . . "Sheng-Da Hsu" . . . "ontology" . "ontology" . . "quality" . . . "1868"^^ . "1354581"^^ . "http://www.jstor.org/stable/"^^ . . . "false"^^ . . "protein" . . "thesaurus" . . "https://fcs-free.org/fcs-database?$1"^^ . "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1"^^ . "tissue" . "knowledge and information systems" . . "https://www.iedb.org/epitope/$1"^^ . . . . . . . . "National Bibliography Number" . . . . "http://purl.obolibrary.org/obo/GENO_"^^ . . . . "^\\d+$"^^ . "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4,6}\\d{8,10}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . . "https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code="^^ . "wdduncan@gmail.com" . . . . . . "^[0-9A-Z]+(\\.[0-9A-Z]+)?$"^^ . . . . . "Database of Complete Genome Homologous Genes Families" . . . "http://purl.obolibrary.org/obo/MF_"^^ . "Q0VCA6"^^ . . . "false"^^ . . "genome" . "clinvar" . . "life science" . . . "obo" . . "true"^^ . . "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO)."^^ . . . . "EG10173"^^ . "infectious" . . . . "^DB\\d{5}$"^^ . . . . "Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine."^^ . "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"^^ . . "GWAS Central Phenotype" . . "flybrain.ndb" . "subject agnostic" . "nasc" . . . "chemistry" . "https://unicarb-db.expasy.org/msData/$1"^^ . "maize" . . . . . "0000049"^^ . "https://biomodels.net/vocab/idot.rdf#"^^ . . "https://www.osti.gov/biblio/"^^ . "c"^^ . . "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . . "enzymology" . "m.a.laporte@cgiar.org" . "electronic health record" . . . . . "https://nanbyodata.jp/disease/NANDO:"^^ . . . . . . "protein" . . "Chemistry resources"^^ . . "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"^^ . . . "chemistry" . . . . _:N734d9cfa9fd84fc6b5c1595bb8b23cda "Eric Duchêne" . . "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information."^^ . . . . . . "microbiology" . . "Renato Iannella" . "true"^^ . . "^000\\d{5}$"^^ . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra."^^ . "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA."^^ . . . . "SNOMEDCT_2020_03_01" . "classification" . . "small molecule" . . . "inchi" . . . . "With the DataPLANT biology ontology (DPBO), DataPLANT provides an intermediate ontology that acts as a broker and bridge between the individual researcher/domain experts and main ontology providers. DPBO enables easy and agile collection of missing vocabulary as well as relationships between terms for (meta)data annotation using DataPLANT’s Swate tool."^^ . "kegg.ligand" . "obo" . "https://prefix.cc/" . "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code."^^ . . . . . . "DrugBank Metabolite" . . "Cotton ontology from CottonGen database - June 2019"^^ . . . "Coconut ontology" . . "Ontology of units of Measure" . . . "false"^^ . . . . . "https://en.wiktionary.org/wiki/$1"^^ . "Identifiers for proposals/projects at the Joint Genome Institute"^^ . . "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object="^^ . . "obo" . "false"^^ . . "false"^^ . . . . . "https://caninecommons.cancer.gov/#/study/"^^ . . "BirdBase" . . _:Na6c73f5131054edfbc4300b3809f2683 "COI Catalogue" . . . . . "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^ . "false"^^ . "http://purl.obolibrary.org/obo/$1"^^ . . . "life science" . . "recombinant inbred rat" . "tissue" . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/"^^ . . "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature="^^ . "http://antibodyregistry.org/AB_$1"^^ . "false"^^ . . . "protein" . . "^\\d{7}$"^^ . "ontology" . . "ontology" . . . "Genomic Epidemiology Ontology" . . . . . "bs" . . . . . . . "Variation Modelling Collaboration" . . . . . . . . . . . . . "dbvar.variant" . "http://www.xmetdb.org/xmetdb/protocol/"^^ . . . "PathoPlant®" . "cryoem" . . "cell lines" . . . "label"^^ . . "International Generic Sample Number" . . . . "marine ecology" . "http://purl.obolibrary.org/obo/HAO_$1"^^ . . . . . . "http://purl.obolibrary.org/obo/OGG_"^^ . . "false"^^ . "s_mart_db" . . . . "organic chemistry" . . . "http://purl.obolibrary.org/obo/MSIO_"^^ . . . . "Homologous Vertebrate Genes Database" . "vbrc" . . . . . "false"^^ . . "^TS-\\d+$"^^ . . . . "Ontology for Biomedical Investigations" . . "empiar" . "obo" . "^(MNXM\\d+|BIOMASS|WATER)$"^^ . . . . "ontology" . "http://purl.obolibrary.org/obo/EHDAA_$1"^^ . . "https://www.internationalgenome.org/data-portal/sample/$1"^^ . . . . "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all."^^ . "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . . . . . . . . "janna.hastings@gmail.com" . "Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted."^^ . . "http://purl.obolibrary.org/obo/EPO_"^^ . . . "neurobiology" . . "false"^^ . . "As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including:\n- Research team and institution\n- The EMSL project DOI\n- Link to project data available in EMSLs Data Portal\n- Project type"^^ . . . "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names."^^ . . . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME"^^ . . . . . "SYMP" . "http://purl.obolibrary.org/obo/TO_$1"^^ . . "anatomy" . "hölzel" . . "false"^^ . "https://web.www.healthdatagateway.org/dataset/"^^ . . "0000215"^^ . . "74.186"^^ . "70"^^ . . "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^ . . "pharmgkb.disease" . . . . . . "2af339dd-a956-471f-9406-b0f74bacd579"^^ . "13"^^ . "resource metadata" . "jcm" . . "false"^^ . . . . "resource metadata" . . . . "http://reg.clinicalgenome.org/allele?hgvs=$1"^^ . . . . . . . "bioregistry.schema" . "nuclearbd" . "life science" . . . "cncb.gwh" . "biomedical science" . . . . . "https://www.kegg.jp/entry/"^^ . . "^NONHSAG\\d{5}$"^^ . . . . . . "co_347" . . . "Kim Dixon Pruitt" . . . . . . "https://bioregistry.io/fbol:"^^ . . "false"^^ . "biocyc" . "^\\d{7}$"^^ . . . . "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . . . . . "biology" . "http://geneontology.org/docs/gene-product-information-gpi-format/#$1"^^ . "https://w3id.org/linkml/$1"^^ . . . . . . . . . "sibo" . "false"^^ . "false"^^ . . . "https://bio.tools/$1"^^ . "https://www.atcc.org/products/$1"^^ . . . . . "resource metadata" . "clustering" . "MMs00000001"^^ . . . "Feature Annotation Location Description Ontology " . "Josh Moore" . . . . . . . . . . . . "relationships" . . . "life science" . . . "http://www.daml.org/2003/01/periodictable/PeriodicTable#"^^ . "molecular entity" . . "ontology" . . . "Human developmental anatomy, abstract version" . "histology" . . "false"^^ . . . . . . "fabio" . . "Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . . . . "William Hayes" . . . . . . . . . "c4o" . . . "SNOWMEDCT_US_2018_03_01" . "^\\d{7}$"^^ . . "false"^^ . "false"^^ . . "PharmacoDB Datasets" . . . "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$"^^ . . . . . "https://civicdb.org/links/sources/"^^ . . "protein" . . . . "centrally registered identifier" . . "243002_at"^^ . . . "Francesco Vitali" . . "1458400"^^ . "false"^^ . "http://www.tcdb.org/search/result.php?tc="^^ . . . "pubchem.assay" . . . . "0002058"^^ . "vbase2" . "00056"^^ . . "obo" . . . "lbctr" . . . "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."^^ . . . "An international LGBTQ+ linked data vocabulary"^^ . . . . . . . . . . . . . . . . . . . . . . . "Pierre-Yves Vandenbussche" . . . "geology" . . "https://purl.dataone.org/odo/MOSAIC_"^^ . . . . . . . "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"^^ . "https://pypi.org/project/"^^ . . "ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc."^^ . . "protein-protein interactions" . . "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)."^^ . . . . . . . . . "modeling and simulation" . . . "alleles" . "thesaurus" . "knowledge and information systems" . "false"^^ . . "protein" . "false"^^ . . . . . . . . "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . . . . "Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation."^^ . . "^K\\d+$"^^ . . "false"^^ . . "chempro.probe" . "ontology" . "^\\d{6}$"^^ . . . . . . "^CTRI/\\d{4}/\\d{2,3}/\\d+$"^^ . . "Hiroyuki Ogata" . . . . . . . . "https://europepmc.org/article/CTX/$1"^^ . . . . . . "life science" . "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions."^^ . . _:N400c4b1a400c48adac7f4fd308153dbb "Crop Ontology Helpdesk" . . "false"^^ . . "sstoss" . . . "omics" . "http://www.w3.org/ns/ssn/systems/"^^ . "life sciences" . . "National Drug File - Reference Terminology" . . "co_339" . . . "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . . "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . "false"^^ . "Sciflection" . . . . . . _:N27ee989eb2b2414eb292e2cbcd99b737 "ncictcaehelp@mail.nih.gov" . . "The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer."^^ . "false"^^ . "AAindex" . . "xl" . . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene."^^ . . . . "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^ . . "Terminology of Anatomy of Human Histology" . . "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"^^ . . . "kcris" . "methylation" . "http://purl.obolibrary.org/obo/GENEPIO_"^^ . "http://purl.obolibrary.org/obo/HOM_$1"^^ . . "112517"^^ . "false"^^ . "Dublin Core Metadata Initiative Terms" . . "chictr" . . _:N54cc659311824b238eac9306a6627e94 "Eionet Helpdesk" . . "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid="^^ . . "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . . . "false"^^ . . . "anatomy" . "dna" . . . . . . . "The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage)\n\nNote that the identifier in this semantic space is not the one used in the webpages"^^ . "life science" . . . . . . . . "Accession number of an entry from the BIND database."^^ . . . . "false"^^ . . "Joshua Orvis" . . . "00005643"^^ . . . . "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"^^ . "http://purl.obolibrary.org/obo/EMAPA_$1"^^ . . . . "nucleardb" . . . . "PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored."^^ . . "greengenes" . "^\\d{7}$"^^ . . "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . . . . . "Pathguide" . "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)."^^ . . "Influenza Sequence and Epitope Database" . . . . . "snomedct" . . . . . . . . . "http://cgsc.biology.yale.edu/Site.php?ID="^^ . . "false"^^ . "https://www.metanetx.org/chem_info/$1"^^ . "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"^^ . "false"^^ . . "Jeffrey Grethe" . . "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read."^^ . "https://ror.org/$1"^^ . "bugbase.expt" . "https://nanocommons.github.io/identifiers/registry#$1"^^ . . "NASA Open Science Data Repository Payload" . . "554"^^ . "life science" . . . . . . . . . . . . . . . . . "gorel" . . "experimental plant" . "http://purl.obolibrary.org/obo/VBO_$1"^^ . . "https://www.ncbi.nlm.nih.gov/biosystems/$1"^^ . . "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$"^^ . . . . "genomics" . . . "regulation" . "r3d100010772"^^ . . . "Bioregistry Metaregistry" . . "^nbdc\\d+$"^^ . _:N1e12b17b8ed7446da447ace8539ffd7d . "ITMCTR2023000002"^^ . . "life science" . . "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information."^^ . . . "gold standard" . . . . "EHDAA:2185"^^ . "ehdaa2" . . "false"^^ . "^\\d+$"^^ . . . "http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1"^^ . "Ontology for Parasite LifeCycle" . . . . "ncbidrs" . . . "chemical entity" . "obo" . "gene" . "http://purl.obolibrary.org/obo/APOLLO_SV_$1"^^ . "https://purl.dataone.org/odo/SALMON_$1"^^ . . . "obo" . . . . "http://purl.org/dc/dcmitype/$1"^^ . . . "https://data.4dnucleome.org/experiment-set-replicates/$1"^^ . . . . . . "^DIP(\\:)?\\-\\d{1,}[ENXS]$"^^ . "false"^^ . "false"^^ . "caro" . "https://nmrshiftdb.nmr.uni-koeln.de/molecule/"^^ . . . . . "huge" . "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^ . . "taxonomy" . "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"^^ . . . . "culture" . . "An anatomical and developmental ontology for ctenophores (Comb Jellies)"^^ . . . . "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam="^^ . . "life science" . "https://www.kew.org/data/grasses-db/www/$1"^^ . . . . . . . "vita" . "small molecule" . "An ontology of prokaryotic phenotypic and metabolic characters"^^ . . . . . "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID="^^ . . . . . . . . . "0000485"^^ . . . "molecular neuroscience" . . "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^ . "genetics" . "A0001"^^ . . . "false"^^ . . . "dylan.mcgagh@magd.ox.ac.uk" . . . . "National Uniform Claim Committee Characteristic" . . "AICARTRANSIMPCYCLO-CPLX"^^ . "false"^^ . "Identifier for a user in iNaturalist"^^ . . . . "http://purl.obolibrary.org/obo/DUO_$1"^^ . . . "^[A-Za-z_]+$"^^ . "https://www.pombase.org/gene/$1"^^ . . "SNOMEDCT_US_2023_03_01" . "false"^^ . "hao.ref" . "obo" . "grin.taxonomy" . . . "https://lincs.hms.harvard.edu/db/sm/$1"^^ . "metabolomics" . "biomedical science" . . . "Xenbase" . . "false"^^ . . . . . "0000091"^^ . . . "Linked Open Vocabularies" . "omics" . . "webelements" . "Quality"^^ . . "agriculture" . "dna" . . . "^\\d+$"^^ . . . . "BIOMD0000000048"^^ . . "SEED Reactions" . . . "false"^^ . . . "ontology" . . "W2741809807"^^ . . . "gene" . . . "transposon family" . "http://biohackathon.org/resource/faldo#$1"^^ . . . "4b848c342a4f4abc871bdf8a09a60807"^^ . "protein" . . "false"^^ . "genotype" . . . . "Hymenoptera Anatomy Reference" . "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo="^^ . . . . . "Emmanuel Guiderdoni" . . . . "Célia Michotey" . "^\\d+$"^^ . . "false"^^ . "http://purl.obolibrary.org/obo/COB_"^^ . . . "Fyler" . . . . . "ecocyc" . "http://jcggdb.jp/idb/jcggdb/$1"^^ . . . . . . "carrine.blank@umontana.edu" . . _:Ncf4fc7fd2d3c4f3ca6776004a143688b "helpdesk cropontology" . . . "https://www.ncbi.nlm.nih.gov/biosystems/"^^ . . . . . . "Yvonne Bradford" . . . . . . "Maize ontology" . . . . "dwelter.ontologist@gmail.com" . . _:N27ee989eb2b2414eb292e2cbcd99b737 . . "http://purl.obolibrary.org/obo/PLANP_$1"^^ . "LO362836C"^^ . . . "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^ . . "https://www.pharmgkb.org/variant/$1"^^ . "NCI Metathesaurus" . "https://www.dbgi.org/earth_metabolome_ontology/#$1"^^ . . "http://www.pathoplant.de/detail.php?accNo=$1"^^ . "27223"^^ . . . "MeSH" . . "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist="^^ . "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^ . . . . . . . . "sprint" . . . "bcrj" . . "Identifier for a journal article in the fossilworks website"^^ . . "ERR436051"^^ . . . "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . "http://rdfs.org/ns/void#$1"^^ . . . . "Shuichi Onami" . "Proteomics Identification Database Ontology" . . . . . . . . "gene expression" . "http://purl.obolibrary.org/obo/APOLLO_SV_"^^ . . "^A\\d{6}$"^^ . . . "Q9P0K8"^^ . . . . "genomics" . . "medical microbiology" . "ontology" . . . "BAO" . "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . . . . . "true"^^ . . . "Pathway Commons" . "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage."^^ . . "^\\d{7}$"^^ . . . "false"^^ . "obo" . "developmental biology" . . . . . "MaizeGDB" . . "obo" . "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . "MESH" . "^\\w\\d+$"^^ . . . . "MNEST029358"^^ . "data coordination" . . . "^phs[0-9]{6}(.v\\d+.p\\d+)?$"^^ . "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms."^^ . "https://nbn-resolving.org/$1"^^ . "mirnao" . . . "ontology" . . "^[CD]\\d+$"^^ . . . . . "bioinformatics" . . . . . . . . "785"^^ . . . . . . . "Ontology for Immune Epitopes" . . . "plana" . . "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id="^^ . . "https://cropontology.org/rdf/CO_333:"^^ . . . . . . "https://biopragmatics.github.io/providers/cemo/"^^ . . . "KEGG.DRUG" . . "^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$"^^ . . "https://bioregistry.io/jaxmice:"^^ . "false"^^ . . "http://www.phosphosite.org/proteinAction.do?id=$1"^^ . . "https://neurovault.org/images/"^^ . . "http://hawaii.eagle-i.net/i/$1"^^ . . . . . . . "^\\w+\\_\\d+(\\.\\d+)?$"^^ . . . . . "ontology" . "090803"^^ . . . . . . . "metabolites" . . . "false"^^ . . "^([a-z]{3,5}_)?M\\d{5}$"^^ . . . . . "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . "obo" . "ohd" . . . . . "^\\d{7}$"^^ . . . . "false"^^ . . . "dna" . . . "istransbase" . . . "http://purl.org/spar/doco/"^^ . . "life science" . "false"^^ . . . "http://purl.obolibrary.org/obo/HP_"^^ . . "false"^^ . . . . . "The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are:\n\n- [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.)\n- [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC)\n- [GENCODE](https://www.gencodegenes.org/) (uses GenBank)\n- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc)\n- [STRING](https://string-db.org/) (uses UniProt)" . "^[A-Z_0-9]+$"^^ . "P00024"^^ . "life science" . . . "dna" . . "^PRJ[DEN][A-Z]\\d+$"^^ . . . . "ontology" . . . "emi" . . "life science" . . "phenotype" . "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^ . . "http://purl.obolibrary.org/obo/GSSO_"^^ . . . "structure" . "dbpedia" . . "addgene" . . . . "pharmacist"^^ . . . . . . . . "life science" . "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps."^^ . . "12dgr161"^^ . "babelon" . "ICD10CM" . "MINID Test" . . . . . "Philipp Bucher" . . . . "326705068"^^ . . . . "This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from )"^^ . . "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene="^^ . . . . . . "^\\d+$"^^ . "The SEED" . . . . . "234"^^ . "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." . . "^\\d+$"^^ . "Michelle Giglio" . "dbd" . . . . . . "48439"^^ . "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."^^ . . . . "obo" . . "SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome."^^ . . "https://www.flymine.org/come/entry?gn=$1"^^ . "zachll@umich.edu" . . . _:N000e2f2c430b437ca9757e0c7abe8844 "PhenX Admin" . "false"^^ . . . . . "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments."^^ . "ontology" . "embryo" . . . "jla1@sanger.ac.uk" . . "rhea" . . . . . . . . "false"^^ . "ShareLoc" . . "^\\d{7}$"^^ . . "Database containing promotor sequences found in Saccharomyces cerevisiae."^^ . . . "lagonzalezmo@unal.edu.co" . . . . "http://www.w3.org/2002/07/owl#$1"^^ . "https://abrc.osu.edu/stocks/number/SALK_"^^ . . . . . . . . "genotype" . . . "ontology" . . . . "immunology" . "http://synbip.idrblab.net/data/sbp/details/"^^ . "false"^^ . . . . . . . . . "https://www.ncbi.nlm.nih.gov/genome/"^^ . . . "ChemSpiderID" . . "taxonomic classification" . . "assay" . "Contributor Role Ontology" . . "CPX-263"^^ . . "https://plants.ensembl.org/id/$1"^^ . . . . "false"^^ . "https://www.eionet.europa.eu/gemet/en/concept/$1"^^ . "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . . "protein" . "MOSAiC Ontology" . . "ped" . . "text mining" . . "nemo" . "false"^^ . . "^\\d{7}$"^^ . . "pharmacology" . . "kisao" . . . "https://bykdb.lyon.inserm.fr/data/html/annotated/$1.html"^^ . "^[a-zA-Z0-9_-]{3,}$"^^ . . . "https://modeldb.science/$1"^^ . . "pathway" . . . "Tianyi Zhao" . "false"^^ . . "PK-DB" . "false"^^ . . "VMH Gene" . "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . . . . "Trish Whetzel" . "false"^^ . . "^S\\w+(\\.)?\\w+(\\.)?$"^^ . . . . "pubchem.element" . . "life science" . . . . . . "mutation" . . . "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information."^^ . . . "http://vbrc.org/gene_detail.asp?gene_id=$1"^^ . . "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules."^^ . . . . . . . "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once."^^ . "Joint FAO/WHO Expert Committee on Food Additives" . . . "0003"^^ . "https://www.deciphergenomics.org/syndrome/"^^ . . . . . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"^^ . . "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code="^^ . . . "true"^^ . "obo" . . . . . "recombinase" . . . "arrayexpress.platform" . "https://chemprosquare.idrblab.net/data/target/details/"^^ . "bibliography" . . "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/"^^ . "Laurel Cooper" . . . "false"^^ . . . "medicinal chemistry" . . . . . . . "27267"^^ . . "Human Unidentified Gene-Encoded" . . "^DDB\\d+$"^^ . . . . "hybrid" . "obi" . . . . . . . _:N41d2d4542c2841fe918d2f7b4dec472c "Crop Ontology Helpdesk" . . "ohpi" . "LDPC0032"^^ . . . . . "false"^^ . "gene expression" . . "tred" . . "bioinformatics" . "^[A-Z0-9]+$"^^ . "obo" . "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures."^^ . . . "Dr. Alpha Tom Kodamullil" . . . "http://purl.obolibrary.org/obo/OMO_"^^ . . "phosphopoint.protein" . . . . . . "life science" . . "https://euhcvdb.lyon.inserm.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"^^ . "sabiork.compound" . . . "Merriam Webster Dictionary" . "protein" . . . . . . . "https://precision.fda.gov/uniisearch/srs/unii/$1"^^ . . "false"^^ . . "Online Mendelian Inheritance in Animals" . . . "1801.012"^^ . "biodeep" . . "pubchem_id" . "ensembl.fungi" . . "https://www.cropontology.org" . . . "GR_QTL" . . . . "worm" . . . . "^\\d+\\-\\d+\\-\\d+$"^^ . . "Lars Bertram" . "mdm" . . . "false"^^ . . . . . . . "obo" . . . . . "DrugBank Target v4" . . . "dna" . . . . . "genomics" . "pathway" . . "protein" . "false"^^ . . . "Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)"^^ . . . "false"^^ . "SABIO-RK EC Record" . . "HL7 External Code Systems" . . . . . . . "^\\d{6}$"^^ . . . "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."^^ . "biominder" . . . "ino" . "icepo" . . "neuroscience" . . . . "humanities" . "life science" . "false"^^ . . . "http://gmd.mpimp-golm.mpg.de/Spectrums/"^^ . "90801"^^ . . . . "https://w3id.org/babelon/$1"^^ . "The Integrated Chemical Environment (ICE) provides high-quality curated data and appropriate tools to support development and evaluation of new, revised, and alternative methods. ICE provides free online access to curated in vivo and in vitro test data, in silico toxicity predictions and chemical property data, reference chemical lists, and computational tools for chemical characterization and predicting toxicity.\nICE supports the following: (i) Data integration: brings together available data, including data on formulations; (ii) Results exploration: enables dynamic, graphical exploration with publication-quality graphics; (iii) Data analysis: allows characterization of data using online workflows, and (iv) FAIR data access: data are findable, accessible, interoperable, and reusable."^^ . . . . "SCTID" . . . . . "http://www.cellresource.cn/cellsearch.aspx?sc=1&where="^^ . "false"^^ . . "BioContext contains modular JSON-LD contexts for bioinformatics data." . . . "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . "digital curation" . "^[0-9]{12}$"^^ . "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1"^^ . "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions."^^ . "Susan Tweedie" . . "anatomy" . "disease" . "genecards.geneloc" . . . . "http://purl.org/biotop/biotop.owl#"^^ . . . . . . . . "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived."^^ . . "rdf" . . . . . "Tohoku University cell line catalog" . . . "co_370" . "IUPHAR_LIGAND_ID" . "1200"^^ . . . "drosophila" . "diagnosis" . . . "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."^^ . . . . . "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce"^^ . "subject agnostic" . . "https://www.probes-drugs.org/compound/"^^ . "device" . "nmrcv" . "metadata standardization" . . "KEGG Reaction Class" . "Ontology of standardized units"^^ . . "biomedical science" . . . . . . . "Regulation of Gene Expression"^^ . . . . . "true"^^ . "innatedb" . . "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1"^^ . "envo" . . . . . "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_"^^ . . . . . . . "CY077097"^^ . "Observation"^^ . . . "Amos Bairoch" . "Dorothea Iglezakis" . "smp-m3w9hbe"^^ . "dashr@lisanwanglab.org" . "false"^^ . . . . . "humIGHV025"^^ . . . . "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . . "ontology" . "plant phenotypes and traits" . . "^[0-9]*$"^^ . "http://www.kegg.jp/entry/"^^ . . "ontology" . . "d.a59037e8"^^ . . . . . . "imedvedeva@celgene.com" . . . . "https://rarediseases.org/?p="^^ . . "00000000"^^ . . . . . "slkbase" . . . . . "^\\d+$"^^ . . . . . . "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages."^^ . "SAMEA2397676"^^ . "false"^^ . "http://tables.pseudogene.org/[?species_name]/"^^ . . . . . . . "ontology" . "101775319"^^ . . "dictybase.est" . "Robert Court" . "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . . _:N84baed02742748e18efbc2915c1a74a9 . . . "false"^^ . . "MarDB" . . . . . "http://purl.obolibrary.org/obo/OMP_"^^ . . "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"^^ . . . "genomics" . . . "obo" . . "dome" . "ArrayExpress Platform" . . "cosmic.cell" . . . "https://animaldiversity.org/accounts/$1"^^ . "metlin" . . "D0001"^^ . . . "https://www.scopus.com/affil/profile.uri?afid="^^ . . . "ontoneo" . . . "terms4FAIRskills" . . . . "structural biochemistry" . "false"^^ . "obo" . . . "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_func_"^^ . . . . "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol."^^ . . . "transcript" . "http://www.kegg.jp/entry/$1"^^ . "Metabolites in the Xenobiotics Metabolism Database."^^ . . . "rdfa" . . "gene expression" . "biotop" . "http://pepbank.mgh.harvard.edu/interactions/details/"^^ . . "false"^^ . . . "obo" . . "pathway" . "AntiBody Sequence Database" . . . . . "life science" . . . . . . . "Homeostasis imbalance process ontology" . "false"^^ . . "Atsushi Yoshiki" . . . . . . . . . . "^[0-9]+:[0-9]+$"^^ . . . . "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . "false"^^ . . . "subject agnostic" . . . "https://www.brenda-enzymes.org/php/result_flat.php4?ecno="^^ . "Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database"^^ . . . "Osamu Ohara" . "structure" . "https://discover.pennsieve.io/package/"^^ . . . "jplfaria@anl.gov" . "genetic strain" . . "astd" . "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier."^^ . "ontology and terminology" . "kinetics" . "obo" . . . "Plant Experimental Conditions Ontology" . "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^ . "evolutionary biology" . . . . . . "https://sparontologies.github.io/fabio/current/fabio.html#$1"^^ . "false"^^ . . "^[1-9]\\d*$"^^ . "false"^^ . "phenotype" . "cordis.project" . "ordo.orphanet@inserm.fr" . . . "https://aftol.umn.edu/glossary?category="^^ . . . . . . . _:N20ef6feb9e1b47f89c0612370582861d "NLM Customer Service" . "phenx" . . . "data retrieval" . "Basic Register of Thesauri, Ontologies & Classifications" . "phenotype" . "^\\d+$"^^ . "http://www.dpvweb.net/dpv/showdpv/?dpvno="^^ . "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^ . . . . . . . "^\\w+$"^^ . "gene" . . "Clare Pilgrim" . . "^\\d+$"^^ . . "Martin Kuiper" . "http://purl.obolibrary.org/obo/EMAP_"^^ . . "molecular infection biology" . "MolBiC Protein" . . . . . . "massive" . . . . . . . . "Interlinking Ontology for Biological Concepts" . . . "cthoyt"^^ . "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. \nDelivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts \nand humanities, Scopus features smart tools to track, analyze and visualize research."^^ . "proteomics" . . "System Science of Biological Dynamics dataset" . . . . . "environmental science" . . . . . _:N2e4f5c23f0764470a04c3cfb1e6c4e0a "gb-admin@ncbi.nlm.nih.gov" . . . . . . "atsushi.yoshiki@riken.jp" . . "https://www.ebi.ac.uk/metabolights/$1"^^ . . "chemical" . "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. "^^ . "taxonomy" . "cells" . "an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems."^^ . . . . . . . . "microbial" . "ontology" . "https://www.datanator.info/gene/"^^ . "Henning Hermjakob" . . . . "jmcl@ebi.ac.uk" . "^\\d+$"^^ . "small molecule" . "brendanx@uw.edu" . . . . . . "structrual bioinformatics" . "biomedical science" . . . . . "MCDS_S_0000000001"^^ . "false"^^ . . . "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\n\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described."^^ . . "SLCTR/2023/010"^^ . "false"^^ . "false"^^ . . "Brett G. Olivier" . . "Gene Wiki" . "PlasmoDB" . "Saccharomyces genome database pathways" . . . "false"^^ . . . "life science" . "hpo" . . . . "A controlled vocabulary to describe phenotypic traits in plants."^^ . . _:N2dbbb1ad069d4070acf6f199211c7b8d "J.Bard@ed.ac.uk" . "SWRL enables Horn-like rules to be combined with an OWL knowledge base."^^ . "life science" . "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results)."^^ . . . . . "^OSD-\\d+$"^^ . "https://odc-sci.org/data/$1"^^ . . . . . . . . . "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae."^^ . . . "http://www.antweb.org/specimen.do?name="^^ . "scretf" . . . . "false"^^ . "structure" . "false"^^ . "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."^^ . . . . . "transcriptomics" . "SAMEA112904733"^^ . "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source."^^ . "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^ . "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . . . . "SM_UB-81"^^ . . "false"^^ . "genome" . "^\\d{6,7}$"^^ . . . . "https://integbio.jp/en/" . "bkc640"^^ . . . . "agriculture" . "transyt" . "false"^^ . "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence."^^ . . "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc="^^ . . . . "Chemical Information Ontology" . "^\\d{7}$"^^ . . . "icf" . . . "Sandra Orchard" . . . "^DAP\\d+$"^^ . . . "1000290"^^ . . "Radiation Biology Ontology" . . "15543"^^ . "ctri" . . "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . . . "^\\d+$"^^ . . . . . "^\\d{7}$"^^ . "jupp@ebi.ac.uk" . . "BioPortal Prefixes" . "http://purl.obolibrary.org/obo/YPO_"^^ . "true"^^ . . "^FOOD\\d+$"^^ . "CHEMONTID" . . . "abs" . "false"^^ . . . "http://thebiogrid.org/"^^ . . . . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/GEO_"^^ . . . . . "The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the animal semantic space correspond to animals that samples in the database are obtained from."^^ . . "gexo" . . . . . . . "registry" . . "gene" . . . . "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology."^^ . . . . . . . "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . . . . . . . "589462"^^ . "atcc" . "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+"^^ . . . "^\\w+(\\.\\d+)?(\\.\\d+)?$"^^ . . . . "^MGYA\\d+$"^^ . . . "^[1-9]\\d*$"^^ . . . . . "cdno" . "biological process" . . . . . "dg.f82a1a" . . "NA06.8D"^^ . . . "Identifier of an entry from the AAindex database."^^ . "life science" . . . "nasaosdr.hardware" . "life science" . "anatomy" . . "00000099"^^ . . . . . . . "Chris Hunter" . . "^\\d{7}$"^^ . "BioGRID" . . . "deletion" . . "veterinary medicine" . "^\\d{7}$"^^ . . "Simple Knowledge Organization System eXtension for Labels" . . . . "xsd" . . . . . "oma.grp" . "^F\\d+$"^^ . . "subject agnostic" . . . "disease" . . . . . "^\\d+$"^^ . "2.16.840"^^ . . . . "https://www.inaturalist.org/places/$1"^^ . "genetics" . . "proteomics" . . . "virology" . . . "phagedive" . . . "https://hdl.handle.net/hdl:20.500.12633/"^^ . "absd" . . . . "^(cd)?\\d{5}$"^^ . "ised" . "ontology" . . "https://www.gwascentral.org/study/"^^ . . . "ricegap" . "ICD 11 Codes" . "biomedical science" . . . "false"^^ . . "false"^^ . . . . . . . . "Publisher Item Identifier" . . "ontology" . . . "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties."^^ . "https://www.findacode.com/code.php?set=ICD10PCS&c="^^ . . "knowledge and information systems" . "false"^^ . . "DAPK1"^^ . "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium."^^ . "pain medicine" . "mutation" . "phenotype" . . "https://w3id.org/sssom/$1"^^ . . . . . . . . . "embryology" . . "wikipathways.vocab" . . "Feature Type Thesaurus" . . . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"^^ . . "vaccine" . . . . . "text mining" . "http://stitch.embl.de/interactions/$1"^^ . . "WikiPathways Ontology" . "false"^^ . . . . . "false"^^ . "disease" . "Allyson Lister" . "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode."^^ . "spider" . "computer science" . . . . "oboe" . "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . . . "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name="^^ . "https://bioregistry.io/mesh.2013:"^^ . . . . "false"^^ . . . "0000048"^^ . "false"^^ . "institution" . "virology" . . . . "false"^^ . "life science" . . "Paula.Duek@sib.swiss" . . . . . "false"^^ . "Intrinsically Disordered Proteins Ontology" . "ontology" . . "PKDB00198"^^ . . "http://usefulinc.com/ns/doap#$1"^^ . . . "AA0001"^^ . . . . "http://www.co-ode.org/ontologies/galen#"^^ . "0000411"^^ . . "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^ . . . "false"^^ . "UPPRO" . . "General Standard for Food Additives Online Database" . . . . _:Nea10c93db2cc4773a2f1c43109510bc3 "po-discuss@plantontology.org" . "COlleCtion of Open Natural ProdUcTs" . "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"^^ . "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . "protein" . "uniprot.db" . . . . . . . "Xenopus Anatomy Ontology" . . . "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally."^^ . "Rudolf T. Pillich" . "^\\w+$"^^ . "https://run.biosimulations.org/simulations/$1"^^ . . "dna" . . . . "Crop Ontology Curation Tool" . . . . "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors."^^ . . . "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . "neuron" . "https://nfdi.fiz-karlsruhe.de/ontology/NFDI_"^^ . . . . . . . . . . "LOC_Os02g13300"^^ . . . . . . "pharmacogenomics" . . "0000423"^^ . . . "The Amphioxus Development and Anatomy Ontology" . . . . "^PD\\d+$"^^ . "ncim" . "81944ba1-81d0-436e-8552-33d77a27834b"^^ . . "developed by ICARDA - Dec 2018"^^ . . "GenBank" . . "http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?winid=1&recid=$1"^^ . "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community."^^ . . . "ontology" . . . . "PhosphoPoint Kinase" . . . "http://purl.obolibrary.org/obo/MA_"^^ . . . "0001000"^^ . "ontology" . . . . . "0000712_1"^^ . . "false"^^ . . . . "obo" . "http://purl.obolibrary.org/obo/FOODON_$1"^^ . . "inaturalist.taxon" . . "Vital Sign Ontology" . . . "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1"^^ . "https://www.ebi.ac.uk/ega/studies/"^^ . . . . "https://vectorbase.org/gene/"^^ . "^\\d+$"^^ . . . . "medicine" . . . "false"^^ . . "ontology" . _:N1b21c85bc1024f35a6e8554763c3ebbe "Crop Ontology Helpdesk" . . "GO Relations" . . . . . "Foods in FooDB"^^ . . . . . . . . . "Bacillus subtilis genome sequencing project" . "http://purl.org/spar/cito/"^^ . "https://uts.nlm.nih.gov/uts/umls/concept/$1"^^ . . "cell lines" . . "^T[A-Z]\\d{7}$"^^ . . . "metascience" . . . "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."^^ . "mgnify.proj" . "https://chemprosquare.idrblab.net/data/target/details/$1"^^ . . . . . . . . . . "OSD-678"^^ . . "chemical descriptor" . "biomedical science" . "bioactivities" . . "sequence" . . . . "http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#$1"^^ . . . "BioSample" . . . . "disorders" . . . . . "co_341" . "^\\d+$"^^ . . . . . "https://lincs.hms.harvard.edu/db/datasets/$1"^^ . "56"^^ . . "ADM1"^^ . . . "https://w3id.org/aio/$1"^^ . "ViralZone" . "false"^^ . "Metabolomics Workbench Project" . . . . . . "Synthetic Binding Protein Protein Scaffold" . . . . . . "The new national clinical trials registry of the Netherlands"^^ . . "https://onderzoekmetmensen.nl/en/trial/$1"^^ . . . . "0290"^^ . . . "glycoepitope" . "^\\d{5}$"^^ . "http://purl.org/cerif/frapo/"^^ . "citation" . . "d1id" . . . . "^[a-z0-9]{5}$"^^ . "dso" . "William Hogan" . . . . . . . "data retrieval" . . . . . . . "obo" . . "Barley ontology" . . . . "fema" . . . "The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]"^^ . . . "MNXC15"^^ . . "19210-3"^^ . . . "false"^^ . . "citation" . "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID="^^ . . "0003463"^^ . "false"^^ . "life science" . . "obo" . "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . . "^[a-z0-9]{32,32}$"^^ . . "https://stemcells.nindsgenetics.org?line="^^ . . . . "^[A-Za-z0-9-]+$"^^ . . "epidemiology" . "A gazetteer constructed on ontological principles. The countries are actively maintained."^^ . . . . . "linkedin" . . . . "obo" . "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature."^^ . . "ontology" . . . . "false"^^ . "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration)."^^ . "false"^^ . . "ECOLI:CYT-D-UBIOX-CPLX"^^ . "Simplified Upper Level Ontology" . . . "gene" . "drug" . . . . "http://igsn.org/"^^ . "true"^^ . . . "https://www.rrrc.us/Strain/?x="^^ . . . . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"^^ . . "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties."^^ . "0004486"^^ . . "ychai@usc.edu" . "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^ . "ligandbook" . . . . . "MagnitudeValueType"^^ . "publishing" . . . . . "immune system" . . "phenomics" . . . . "ogata@kuicr.kyoto-u.ac.jp" . "false"^^ . "Animal TFDB Family" . . "r.court@ed.ac.uk" . . "LexicalMatching"^^ . . "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . "nextprot.family" . "International Classification of Diseases, 9th Revision, Clinical Modification" . "https://www.ebi.ac.uk/pride/archive/projects/"^^ . "G. Thomas Hayman" . . "http://bio2rdf.org/affymetrix:"^^ . "social science" . . "ontology" . "The AntiBody Sequence Database is a public dataset for antibody sequence data. It provides unique identifiers for antibody sequences, including both immunoglobulin and single-chain variable fragment sequences. These are are critical for immunological studies, and allows users to search and retrieve antibody sequences based on sequence similarity and specificity, and other biological properties."^^ . "agsc" . . "RISM Online" . "http://purl.obolibrary.org/obo/VIBSO_$1"^^ . . . "metadata" . . "phenotype" . . "fly" . . . "aop.events" . "BRIP1"^^ . . "false"^^ . . "NASA Open Science Data Repository Subject" . . . . "genome" . . . . . "Gene Ontology Rules" . . "gene" . . . . . . "OBO Foundry" . . . . . . "Taxonomic rank vocabulary" . . . . . . "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#"^^ . . . . "Human Pluripotent Stem Cell Registry" . . "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies."^^ . "plant phenotypes and traits" . . "owlstar" . . . "http://eugenes.org:7072/.bin/fbidq.html?"^^ . . "ogi" . "Fission Yeast Experimental Conditions Ontology" . . . "Unified Phenotype Ontology" . . . . . "ontology" . "^NBR\\d+$"^^ . . . "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions"^^ . "Lynn Schriml" . . "Bloomington Drosophila Stock Center" . . "experiment" . . . "ZINC is not Commercial" . . "Universal Spectrum Identifier" . . "The Simplified Upper Level Ontology (SULO) is ontology with a minimal set of classes and relations to guide the development of a personal health knowledge graph. [from homepage]"^^ . . . "ontology" . "KEGG DRUG" . . "^\\w+$"^^ . "immunology" . . "study design" . . "https://www.datascienceontology.org/concept/"^^ . . "rdf" . _:N9de9c5a856404f1aa6dc4444bdf57fa3 "johardi@stanford.edu" . . . . "^\\w+$"^^ . "Gene Ontology Registry" . . "rna" . . "The identifier for an observation in iNaturalist"^^ . . . . . "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^ . . . . "lgai.cede" . "false"^^ . "phosphosite.protein" . "uniprot.disease" . . . . . "owl" . . . "http://champ-project.org/images/ontology/cao.owl#CAO_"^^ . . . . . . "dip" . . . "nif.ext" . . "^\\d+$"^^ . . . . . . . . . . "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF)."^^ . . . "http://jcggdb.jp/idb/jcggdb/"^^ . "^\\d{7}$"^^ . . "atc" . . . . . "https://www.wormbase.org/db/seq/protein?name=$1"^^ . . "Ontology for computer aided process engineering" . "development" . . "International Classification of Diseases for Oncology" . "structure" . "genetics" . . . "CQG5"^^ . . "A representation of the variety of methods used to make clinical and phenotype measurements."^^ . "Ekaterina Chuprikova" . "STOREDB at University of Cambridge" . . "model organism" . . . . "dc.elements" . . . "pharmacogenomics" . . . . . "^[A-Z0-9*:]+$"^^ . . . "Identifier for a place in iNaturalist"^^ . "Fossilworks Taxon" . . . . "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . . . "ontology" . "false"^^ . . "https://www.storedb.org/?STOREDB:DATASET$1"^^ . "functional genomics" . "false"^^ . . . . . "obo" . . . "human" . . "M1"^^ . "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs."^^ . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"^^ . "Sabine Oesterle" . . . . "scop" . . . . . . . . . . "http://www.w3.org/2000/01/rdf-schema#$1"^^ . . . . . . "protein" . . "pharmgkb.pathways" . . . . . "dbest" . . _:N65ccae73c30e4c6baaff668b2af09913 "guqiong@mail.sysu.edu.cn" . "rs" . . "pathway" . "Mathematical modeling ontology" . . . . "proteomics" . "go.resource" . "Veterans Administration National Drug File" . "biochemistry" . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID="^^ . "expression" . . "NXPFA" . . . "Tomohiro Oga" . "true"^^ . . "transgene" . . . . . "biology" . . "Internet Standard -- IETF Request for Comments" . . "ChemIDplus" . . "agriculture" . . "spike00001"^^ . . "obo" . "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s."^^ . "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . . . "lcnaf" . "metatlas.metabolite" . . . . "rs11603840"^^ . . . . "Matthias König" . "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information."^^ . . "https://vocab.org/vann/#"^^ . "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^ . . "me@harshp.com" . . "olatdv" . "GitHub Issue" . "life science" . "subject agnostic" . . . . . . . "Consensus CDS" . "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"^^ . . . "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^ . . . . . . . . "https://labsyspharm.github.io/lspci/$1"^^ . "^GR\\:\\d+$"^^ . "^[0-9]*$"^^ . . "1000001"^^ . . . . . . . . "Genderal Ontology for Linguistic Description" . . . . . . . _:Nc7ff09a926f849c5b587faf344121bb6 . . . . "https://resolver.api.identifiers.org/resolveMirId/$1"^^ . . "Proteomics data and process provenance" . . . . "https://civicdb.org/links/gene/"^^ . . . . . "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^ . . . . "18"^^ . . "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . "false"^^ . . . . . . "3"^^ . "4DN" . . . "SNOMEDCT_US_2023_10_01" . . . "developmental biology" . . "taxonomy" . . "http://purl.obolibrary.org/obo/REO_$11"^^ . "ontology" . "morphology" . . . . . . "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models."^^ . "computer science" . . . . . "^DDInter\\d+$"^^ . "Emotion Ontology" . . "bto" . . "false"^^ . . . "https://www.ebi.ac.uk/pdbsum/"^^ . . "Human Plasma Membrane Receptome Families" . . . "dna" . . "functional genomics" . "yrcpdr" . . . . . "morphology" . "life science" . . . . "AU124"^^ . . . . . . "false"^^ . . "Wei Chen" . "Lucas Leclere" . "Cell line databases/resources"^^ . . . . "https://rapdb.dna.affrc.go.jp/locus/?name="^^ . . . . "^(ev\\:)?E\\d+$"^^ . "false"^^ . . "false"^^ . "ontology" . "^\\d{7}$"^^ . . . "^UCR\\d{5}$"^^ . . . "homosaurus" . . . "The Digital Object Identifier System is for identifying content objects in the digital environment."^^ . . . "hathitrust" . . . . . . . . . . "TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)"^^ . "life cycle stage" . . . _:N0b5ff4c94c7444bdbeeac143810f9087 "William Klimke" . "phosphosite.residue" . . "ontology" . "taxonomy" . . . . . . "Wheat ontology" . "YeTFasCo" . . "^PS\\d{5}$"^^ . . "biomedical science" . . "molbic.cellline" . . . . . . "DB14938"^^ . . "false"^^ . . . . . "rna" . "true"^^ . "128011350"^^ . "dna" . "00000000001"^^ . "^\\d{7}$"^^ . "nikolaos.moustakas@catalysis.de" . "false"^^ . . . . "yongqunh@med.umich.edu" . . . "http://www.alzgene.org/geneoverview.asp?geneid=$1"^^ . "true"^^ . . . . . "^\\d+$"^^ . "sequence" . . "Michael K. Gilson" . . . . "1710"^^ . . . . "Search the world's most comprehensive index of full-text books."^^ . . . . . "David Lynn" . . . "Unimod protein modification database for mass spectrometry" . . "obo" . . "literature curation" . "botany" . . . . "joanne.kamens@addgene.org" . . "cell lines" . "bibliography" . "toxicity" . "0000204"^^ . . . "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . . "funcbase.mouse" . . . "54"^^ . . . . . . . . "true"^^ . . "false"^^ . "interaction" . "http://purl.uniprot.org/isoforms/"^^ . "^\\d+$"^^ . . . . . . . . . "hammer"^^ . "http://purl.obolibrary.org/obo/PCL_"^^ . "^[a-zA-Z0-9_\\-]+(/.*?)?$"^^ . . "ICD9CM_2005" . . . . "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein."^^ . "SNOMED_CT" . . . . . . . "^\\d+$"^^ . "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . "http://purl.obolibrary.org/obo/FOVT_"^^ . . . "0000072"^^ . "human" . "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining."^^ . . . . "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species."^^ . "model" . . "^\\d{7}$"^^ . . "PEPhub" . "^\\d{7}$"^^ . . . . "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/"^^ . . . "rtecs" . . . "chemistry" . . "https://ssbd.riken.jp/database/project/$1"^^ . "https://www.ebi.ac.uk/thornton-srv/m-csa/search/?s=$1"^^ . "uniprot.keyword" . . "An application ontology built for beta cell genomics studies."^^ . . "false"^^ . "MarRef" . "https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_"^^ . . "Ensembl Gene" . . . . . . . . . . . . . . . . "imaging" . . . . . . "http://www.daml.org/2003/01/periodictable/PeriodicTable#$1"^^ . . . . "true"^^ . . . . "PLOSTHES" . . . "C0001"^^ . "This ontology describes system capabilities, operating ranges, and survival ranges. Please report any errors to the W3C Spatial Data on the Web Working Group via the SDW WG Public List public-sdw-wg@w3.org"^^ . . . . "biomedical science" . . "https://books.google.com/books?id=$1"^^ . "https://flybase.org/reports/$1"^^ . . "ontology" . . . "Drosophila Genomics Resource Center" . . "false"^^ . "adolphok@vcu.edu" . . "FooDB compound" . . _:Nc96d450fe9a3485c8db1be0c08048bf2 "evoc@sanbi.ac.za" . "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . . "^\\d+$"^^ . . . "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^ . . . "http://www.molbase.com/en/index.php?app=search&search_keyword="^^ . . . . . "haendel@ohsu.edu" . . . . . "emea" . "^DI-\\d{5}$"^^ . . "^\\d{4}$"^^ . . "false"^^ . . . . . . . "false"^^ . "https://www.iedb.org/receptor/$1"^^ . . . . . . "Developing Mouse Brain Atlas" . "http://purl.org/net/orth#"^^ . . . . . . "wikipedia.en" . . . "PWY3O-214"^^ . . . "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders."^^ . "fbtc" . . . "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif."^^ . . "http://purl.org/cerif/frapo/$1"^^ . . "https://www.uniprot.org/proteomes/"^^ . . "margaret.woodhouse@usda.gov" . . . . . "PM0012345"^^ . "http://purl.obolibrary.org/obo/NCIT_$1"^^ . . . . . "emolecules" . . . . . . . "tissue" . . "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"^^ . . "false"^^ . "pmdb" . "Os01g0883800"^^ . . "false"^^ . . . . "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level)."^^ . . . . . "Ontology for MicroRNA Target" . . . "973a9333-fec7-46dd-8eb5-25738f06ee54"^^ . . . . "https://www.cameo3d.org/sp/targets/target/"^^ . . . . . . "^[A-Za-z0-9+_.%-:]+$"^^ . "Cell Ontology" . . "https://cropontology.org/rdf/CO_325:"^^ . "mouse" . . . . "An ontology of minimum information regarding potential drug-drug interaction information."^^ . . . "IMGT/PRIMER-DB" . . . "protocol" . . "OTTHUMG00000169812"^^ . . . . . . "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases."^^ . . . "study design" . "https://www.metanetx.org/equa_info/$1"^^ . . "obo" . . "true"^^ . "https://www.cabi.org/cabebooks/ebook/$1"^^ . "medgen" . "gene" . _:N3257f323b5f24eeab5090d84680d8d04 . "GE86325"^^ . . . . "pathway model" . . "obo" . . . . . . "^\\w+$"^^ . . "1009107926"^^ . "annotation" . "The Bioinorganic Motif Database" . . "genome" . . . . . . . . "12345"^^ . . . . . "http://www.depod.bioss.uni-freiburg.de/showp.php?gene="^^ . . . "false"^^ . "https://mmp.sfb.uit.no/databases/marref/#/records/"^^ . "https://mycobrowser.epfl.ch/genes/"^^ . . "frbrer" . . . . . "Satoshi Fukuchi" . . . "https://www.ebi.ac.uk/ega/datasets/$1"^^ . . "corrdb" . . "antibiotic resistance" . "http://purl.obolibrary.org/obo/APO_$1"^^ . . "bioinformatics" . . . "life science" . "https://www.ebi.ac.uk/ols4/ontologies/$1" . . . "true"^^ . "neuroscience" . . "dragondb.locus" . . . "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature."^^ . "0000080"^^ . "cath.domain" . . . . . . . . "UniProt Resource" . "false"^^ . . . . . . . . . "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . . "false"^^ . . . . _:N2f847e325aeb4e769cc4780ce629c678 . . . "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . . . "provenance"^^ . "https://cropontology.org/rdf/CO_347:$1"^^ . . "^LDPC\\d+$"^^ . . "ontology" . "neuromorpho" . "Dynamic Ecological Information Management System - Site and Dataset Registry - Network" . . . "https://grch38.togovar.org/variant/"^^ . "^\\d+$"^^ . . "false"^^ . . . "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . "^[8-9]\\d{3}(/[0-3])?$"^^ . . . "https://www.vmh.life/#reaction/"^^ . . . . . . . . . "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?"^^ . "arraymap" . . . "^AT.G[0-9]{5}$"^^ . "ontology" . "false"^^ . . . . . "microbial" . . "^\\d{8}$"^^ . . "life science" . "^\\d{7}$"^^ . "Vaccine administered code set" . . . . . "https://www.ebi.ac.uk/gwas/studies/"^^ . "andreas.ruepp@helmholtz-muenchen.de" . "Mosquito insecticide resistance" . "Node Package Manager" . "obv" . . . . "data acquisition" . "http://purl.obolibrary.org/obo/GENEPIO_$1"^^ . "https://odc-sci.org/data/"^^ . "life science" . . . . . "false"^^ . . . "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . . . "The Cell Cycle DB" . "mingxun.wang@cs.ucr.edu" . . . "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^ . . . "75"^^ . "Identifiers.org Ontology"^^ . . . "small molecule" . "FAO/WHO_standards" . "FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements."^^ . "ACTRN" . . . . "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$"^^ . "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"^^ . . . . . . . . . . . . . . . "tgbugs@gmail.com" . "semantic web" . . . . "https://www.ncbi.nlm.nih.gov/probe/?term=$1"^^ . "https://biosimulations.org/projects/"^^ . "oio" . "pathway" . . . . . . . . . "mouse embryonic stem cell line" . . . . "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"^^ . . . . "cpd15380"^^ . "maxo" . "http://www.obofoundry.org/" . . . "^\\d{7}$"^^ . . "https://lotus.naturalproducts.net/compound/lotus_id/"^^ . "hovergen" . "gqzhang@sinh.ac.cn" . . . . "http://purl.obolibrary.org/obo/ECAO_"^^ . . . "000912"^^ . . "37232"^^ . . . . . . . "https://cropontology.org/rdf/CO_323:"^^ . "http://birdgenenames.org/cgnc/GeneReport?id="^^ . . "65"^^ . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid="^^ . . "wiley"^^ . . . . _:Nfbab19d7fc574378a290cb6bc16080a9 "FALDO group" . . "ATTC" . . . . . . "AberOWL" . . "0000038"^^ . . . . . "mineromero2901@ciencias.unam.mx" . "false"^^ . . . "Zhang Zhang" . "A database containing predicted viral miRNA candidate hairpins."^^ . . . . . . . "systems biology" . . . . . . "mampol" . . "https://www.nextprot.org/term/FA-"^^ . . . . . . . . . . "E-cyanobacterium model" . "gene" . _:Nb9ff211bb43b4bc4bd882e7f759848d4 "Vivian Lee" . . . . . . . . . . "nembase" . . . "http://purl.dataone.org/odo/ECSO_$1"^^ . "genome" . . . . . "Genome Aggregation Database" . _:N1e12b17b8ed7446da447ace8539ffd7d "ncithesaurus@mail.nih.gov" . . "^\\w+(\\.)?\\w+(\\.)?\\w+$"^^ . . "joel.richardson@jax.org" . "Brazilian Registry of Clinical Trials" . "anatomy" . "^NRFC\\d+$"^^ . "life science" . . "obo" . "cooperl@oregonstate.edu" . "false"^^ . . . "Jennifer Smith" . "ncbi.resource" . "pharmvar" . . . . . . . . . "https://www.uniprot.org/locations/"^^ . . . . . . . . . "metabolite" . . . "1"^^ . . . . . . . "flopo" . . . "^SAM[NED](\\w)?\\d+$"^^ . . . "HMDB" . "false"^^ . . . . . . . . "c elegans" . . . . . . "institution" . "Decentralized Identifier" . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1"^^ . "ontology" . . . "snp2tfbs" . "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available."^^ . . . . . "phenomics" . "https://www.xenbase.org/entry/"^^ . "https://www.gleif.org/lei/"^^ . . "Agronomy Ontology" . . "The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page)\nNote that the web page that resolves this trial does not correspond to the semantic space"^^ . . "life science" . . "protein" . . . "pmr" . . . "lincs.smallmolecule" . "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data."^^ . . . . . . . . . "ZINC1084"^^ . . . "24801"^^ . "interaction" . . . . . "http://www.pantree.org/node/annotationNode.jsp?id="^^ . . . . . . "virology" . . "drug interaction" . . . . "false"^^ . "false"^^ . "VFDB Genus" . . . . _:Necd84e73a13140e7a380ffb479ea75a5 "takatter@dbcls.rois.ac.jp" . . . "false"^^ . . "phenotype" . . . . . . "MetaCyc" . "disease" . . . "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1"^^ . "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder."^^ . . "sequence" . "genetics" . . "https://cellmodelpassports.sanger.ac.uk/passports/$1"^^ . "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products."^^ . "Tarcisio.Mendes@sib.swiss" . . . . . "https://cstr.cn/$1"^^ . . . "Philippe Rocca-Serra" . "anatomy" . . . . "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records."^^ . . . . "39421"^^ . "377369"^^ . . "^\\d+$"^^ . . . . . "ecmdb" . . . "^DTXSID\\d+$"^^ . "metabolomics" . . . . . "ATCC number" . "rna" . . "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . . . . . "authorList"^^ . . . "chemistry" . . . . "^\\d+$"^^ . "https://github.com/semanticchemistry/semanticchemistry" . "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^ . . "ontology" . . "http://virtualflybrain.org/reports/"^^ . "aireland@lbl.gov" . "https://bioregistry.io/metaregistry/scholia/$1"^^ . "Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]"^^ . . "Ada Hamosh" . "^\\d{7,}$"^^ . . "http://purl.uniprot.org/core/$1"^^ . . "classification" . . . . . . "registry" . . . . . . . . . . "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n"^^ . . . . . . . . . "medicine" . . . . "vdrc" . "0020"^^ . . . . . . . . . "Authorea author ID" . "https://lattes.cnpq.br/$1"^^ . "https://chemprosquare.idrblab.net/data/competitor/details/$1"^^ . . "ncro" . . . . . "^\\d+$"^^ . . . "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest."^^ . "binding site" . . . . "9-1-1 Complex"^^ . "Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models."^^ . . "Gene Ontology" . "^\\d+$"^^ . "NONCODE v3" . "false"^^ . . "https://www.jax.org/strain/"^^ . . . "false"^^ . "animal genetics" . . . . "researcher" . . . "The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage)"^^ . "false"^^ . "structural biology" . . . "artificial intelligence" . . "^[SCTAGMNU]\\d+$"^^ . "issaku@noguchi.or.jp" . . "^ECMDB\\d+$"^^ . "gene expression" . . . "developmental biology" . . "skos" . . "http://purl.obolibrary.org/obo/OBI_"^^ . . "Georgeta Bordea" . . . "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes."^^ . . . . "ecology" . . "^\\d+$"^^ . . . . . . . . . . . . "false"^^ . "^\\d+$"^^ . . "taxonomic classification" . . "ontology" . "false"^^ . . "civic.evidence" . "Jennifer L Harrow" . "Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format."^^ . . "GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio."^^ . "true"^^ . . "CAL0003079"^^ . . . "http://purl.obolibrary.org/obo/RS_"^^ . . . "remote sensing" . . . . . . "assays" . "swrl" . . . "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available."^^ . "^\\d+$"^^ . . "life science" . . . "Structural Classification of Protein - Stable Domain Identifier" . . . . . . . "https://www.discoverx.com/catalogmanagement/catalog/?searchText=$1"^^ . "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding."^^ . . "minid" . . . "tads" . . . . . . "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery."^^ . . "https://matrixdb.univ-lyon1.fr/association/$1"^^ . . . . "21723"^^ . . "^\\d{4}$"^^ . . . . . . . . . . . . "^\\d+$"^^ . . . "https://bioregistry.io/wikigenes:"^^ . . "interaction" . "botany" . . "http://www.peptideatlas.org/PASS/"^^ . . "https://medical-data-models.org/forms/"^^ . . "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . "fma" . . "obo" . . "Chromosome Ontology" . "false"^^ . "Minimal Information about any Sequence" . . "KNApSAcK" . . . "ontology" . . "http://crdd.osdd.net/servers/virsirnadb/record.php?details="^^ . . "DTXSID2021028"^^ . "violinID" . . . . "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^ . . . "false"^^ . . . . . _:Nc96d450fe9a3485c8db1be0c08048bf2 . . . "^\\d{7}$"^^ . . "damion_dooley@sfu.ca" . . "https://fungidb.org/fungidb/app/record/gene/"^^ . . "dbo" . "https://www.geonames.org/"^^ . "https://sciprofiles.com/profile/$1"^^ . "https://www.jax.org/strain/$1"^^ . . "The COVID-19 epidemiology and monitoring ontology" . . "http://purl.obolibrary.org/obo/OAE_"^^ . . "dna" . . . . . "https://glycopost.glycosmos.org/entry/"^^ . "DSSTox_Generic_SID" . . . . "http://purl.obolibrary.org/obo/UPHENO_"^^ . "Relation Ontology" . . "0000005"^^ . . . . "^\\d{7}$"^^ . . . "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key="^^ . . . . . . "ontology" . . "isrctn" . "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . "false"^^ . "true"^^ . . "annotation" . . . "^\\d+$"^^ . "UBERON" . "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis"^^ . . . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1"^^ . . . . . . . . "false"^^ . "Archival Resource Key" . . . . . "Classification of Transcription Factors in Mammalia" . . "Glottolog" . . . . . "simon.harding@igmm.ed.ac.uk" . "http://www.w3.org/ns/activitystreams#$1"^^ . . . "NIF Standard Ontology: Digital Resources" . "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved."^^ . . "https://grch38.togovar.org/variant/$1"^^ . . . . . "https://aopwiki.org/relationships/"^^ . "PPR103739"^^ . "^\\d+$"^^ . . . . "medicine" . . . . . . "dna" . . . . . "experimental condition" . . . "false"^^ . "huMAP3_04143.1"^^ . . . "kinetic model" . "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]="^^ . "taxonomy" . . . . "https://fda.report/applications/$1"^^ . "human" . . . . "Japan Chemical Substance Dictionary" . . . . "false"^^ . "enzyme" . "^[A-Za-z_0-9]+$"^^ . . "life cycle" . . "unit" . . "EUB0000221"^^ . "cas_id" . . . . "security" . "bioinformatics" . . "Genome Taxonomy Database" . . . "http://purl.obolibrary.org/obo/CIDO_$1"^^ . . "citation" . "zmp@ebi.ac.uk" . . _:Nf89cb9e92fd74e19980b1425b32a783c "Crop Ontology Helpdesk" . "sequence" . . "cordis.article" . . "false"^^ . "https://www.checklistbank.org/dataset/$1"^^ . . "http://www.wikipathways.org/instance/"^^ . . . "A vocabulary and ontology repository for agronomy and related domains." . . "2"^^ . "EMLSAT00000003403"^^ . . "false"^^ . . . . . "^DBMET\\d+$"^^ . . . . "life science" . . . . "obo" . . . . . . . "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^ . . . "false"^^ . "https://sorgerlab.github.io/famplex/$1"^^ . "flowrepository" . . "0000-0003-3738-3140" . . "277.9"^^ . . . . "90806"^^ . . "https://bioregistry.io/tkg:"^^ . . "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."^^ . . . . . "http://purl.obolibrary.org/obo/PGDSO_$1"^^ . _:Nc7ff09a926f849c5b587faf344121bb6 "biomodels-net-support@lists.sf.net" . "has URI prefix" . "assay" . "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds."^^ . . . . "The COVID-19 Infectious Disease Ontology" . "http://www.whocc.no/atcvet/atcvet_index/?code="^^ . "bioschema" . "storedb" . . . . "http://purl.obolibrary.org/obo/OPL_"^^ . "Reagent Ontology" . . . "Reactome" . . "BioCarta Pathway" . . . "barrett@ncbi.nlm.nih.gov" . . . . "genetics" . "ontology" . "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]"^^ . . . . "http://purl.obolibrary.org/obo/DDPHENO_"^^ . "lars.eisen@colostate.edu" . . . "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects."^^ . . "H3.03.00.0.00007"^^ . . . "false"^^ . . . "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession="^^ . . . . _:Neb194957c4f949aabc4fdf80b0b22646 . "genome" . "structure" . "protein" . . . . . . "epidemiology" . "ontology" . . . "^E(S|D)i\\d+-\\w$"^^ . . . "^PED\\d{5}$"^^ . . . . . "ontology" . . . . "A database for Triticeae and Avena references."^^ . . . . "Mitja M. Zdouc" . "false"^^ . . . . . "^\\d+$"^^ . "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype."^^ . "https://bioregistry.io/metaregistry/prefixcommons/$1"^^ . "https://biopragmatics.github.io/providers/diseaseclass/"^^ . . . . "456789"^^ . "false"^^ . "proteomicsdb.protein" . . . . "^Y[A-Z]{2}\\d+[CW]$"^^ . "https://www.uniprot.org/keywords/"^^ . "PGOHUM00000289843"^^ . . . . "infectious disease medicine" . . . "immunology" . "http://topdb.enzim.hu/?m=show&id=$1"^^ . . . "A structured controlled vocabulary of the development of Drosophila melanogaster."^^ . "WBGene00000001"^^ . . "WB_REF" . "46977"^^ . "omics" . . _:N04597f84a19f42f7a3ec71f7a025c792 "Crop Ontology Helpdesk" . "biology" . "michall@cc.huji.ac.il" . . "https://units-of-measurement.org/$1"^^ . "CIViC Disease" . "LCCN Permalinks are persistent URLs for bibliographic records in the LC Catalog and authority records in LC Authorities. These links are constructed using the record's LCCN (or Library of Congress Control Number), an identifier assigned by the Library of Congress to bibliographic and authority records. LCCN Permalinks are also available for citation records in the Handbook for Latin American Studies (HLAS). [from homepage]"^^ . . . . . . . . "nickf@ebi.ac.uk" . . "classification" . "Ontology for Avida digital evolution platform" . . . . . . . . _:N3b98a4a211264478917f1232ff435bb6 "David J. McLaughlin" . . "https://bioregistry.io/cmecs:"^^ . . . . . . "bspo" . . "^TCTR\\d+$"^^ . . "virgen" . "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species="^^ . . . "false"^^ . "^\\d+$"^^ . . . . . . "Aquatic Sciences and Fisheries Information System" . "G protein-coupled receptor database" . . . "http://protege.stanford.edu/plugins/owl/protege#$1"^^ . "false"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . "true"^^ . "http://exac.broadinstitute.org/variant/$1"^^ . . . . . "https://cropontology.org/rdf/CO_327:"^^ . "phs000768.v2.p1"^^ . "obo" . . . . "Life cycle stages for Mus Musculus"^^ . . "false"^^ . "http://yeastrc.org/pdr/viewProtein.do?id="^^ . "https://www.pharmgkb.org/variant/"^^ . "Daniel Himmelstein" . . . . "GeneTree" . "Franziska B. Grieder" . "GOLD metadata" . "grsdb" . . "false"^^ . . . "http://purl.obolibrary.org/obo/MRO_"^^ . . "iclc" . "0100002"^^ . . . . . . . . "false"^^ . . . . . . "epigenetics" . . "foaf" . "cell line" . "scancerrna" . "https://www.authenticus.pt/"^^ . . . "Web of Science ID (work)" . "jRCTs041220087"^^ . . . "http://purl.obolibrary.org/obo/DIDEO_"^^ . . "bioinformatics" . . . "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^ . "http://sabiork.h-its.org/reacdetails.jsp?reactid="^^ . . . . . "ppr" . "https://bioregistry.io/proteomicsdb.protein:"^^ . "^\\d+$"^^ . . . . _:Na9c31acaf1e44a54aa9421aaa582855d "Crop Ontology Helpdesk" . "^[a-z][a-zA-Z]+$"^^ . "anatomy" . . . "unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)"^^ . . . . . . . "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode="^^ . . "toprea@salud.unm.edu" . . . . . . . . "Anne Thessen" . "food" . "Animal Trait Ontology for Livestock" . . . . . "cell" . . "false"^^ . . "https://go.drugbank.com/reactions/$1"^^ . "obo" . . _:N9c235fb11e19416398c9a272c05b8505 "helpdesk@cropontology-curationtool.org" . "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . . . . . . . . "data governance" . . "obo" . . "brain" . . . . . "Chinese Clinical Trial Registry" . . . . . . "BioSimulators" . "0400109"^^ . "structure" . . . . . . . . . "^\\d+$"^^ . "Chris Sander" . "false"^^ . . . "dandi" . "John Westbrook" . "genomics" . . . "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools" . "Todd W Harris" . "TGME49_053730"^^ . . . "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools."^^ . . "aceview.worm" . . "Open Biological and Biomedical Ontologies" . . "SNOMEDCTCT_2019_03_01" . . "https://www.ebi.ac.uk/interpro/entry/pfam/$1"^^ . . "http://purl.obolibrary.org/obo/VIBSO_"^^ . "taxonomic classification" . "biomedical science" . . . . "genome" . "ontology" . . . . . . . . "https://deims.org/locations/"^^ . "Food-Biomarker Ontology" . "Sam Griffiths-Jones" . . . "bpdb" . . . . "protein" . "violinId" . "igsr" . . "SMP" . . "Cellosaurus Registry" . . . . . "^OENC\\d+$"^^ . . "hc.din" . . _:Nea10c93db2cc4773a2f1c43109510bc3 "Plant Ontology Administrators" . . . . . "bibliography" . . . "http://purl.obolibrary.org/obo/COVOC_"^^ . . . . "structure" . "anatomy" . . "https://dgrc.bio.indiana.edu/product/View?product=$1"^^ . . . "https://scicrunch.org/scicrunch/interlex/view/ilx_"^^ . "false"^^ . . . . . "anatomy" . . "subject agnostic" . . . . "http://ecoportal.lifewatch.eu" . . . . . . "mvx" . . . . "https://www.uniprot.org/diseases/"^^ . "data model" . "Shape Expression Vocabulary" . . . . "Affymetrix Probeset" . . "0.7-123"^^ . "http://www.receptors.org/nucleardb/proteins/$1"^^ . . "http://www.kegg.jp/entry/$1"^^ . "^rs\\d+$"^^ . "bioinformatics" . . . "osa-miR446"^^ . . "COSMIC Cell Lines" . "https://repeatsdb.org/structure/"^^ . "structure" . . "Chemical Analysis Ontology" . . "https://biopragmatics.github.io/providers/schem/$1"^^ . . . . . . "Descriptive Ontology for Linguistic and Cognitive Engineering" . . . "oslc" . "false"^^ . . . "^\\d+$"^^ . "true"^^ . . "^[0-9]+$"^^ . . "jesper.friis@sintef.no" . "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"^^ . . "false"^^ . . . . . . . . . "dcelem" . "https://www.ebi.ac.uk/metagenomics/samples/"^^ . . . . . . . "https://query.biodeep.cn/metabolite/"^^ . "false"^^ . . "n.lenovere@gmail.com" . "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"^^ . "http://viroligo.okstate.edu/main.php?vid=$1"^^ . "gene" . . "personalized medicine" . . "false"^^ . . "true"^^ . "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^ . . . "^ENSG\\d{11}$"^^ . . . . "obo" . . "false"^^ . "NIF Standard Ontology: Neurolex" . . "false"^^ . . . "metabolomics" . "410"^^ . . "germline" . . "bibliography" . "NIF Standard Ontology: Chemical" . . "adw" . . . . . "50943"^^ . . . . . . "life science" . "experimental condition" . . "^MSMEG\\w+$"^^ . "chempro.competitor" . "Integrated Resource for Domestic Dog" . . "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories."^^ . . "false"^^ . . "0000013"^^ . . "https://bioregistry.io/genecards.genenote:"^^ . . . "orthodb" . "umls.cui" . "false"^^ . "GrainGenes" . . . "MC" . . . . . . "SIGNOR" . "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information."^^ . . "InformAll Allergenic Food Database" . . . "subject agnostic" . "https://www.ncbi.nlm.nih.gov/gene/$1/ortholog"^^ . "Regulatory Elements Database for Drosophila" . . . . . . "false"^^ . . . . "^NCT\\d{8}$"^^ . "epidemiology" . "STUDY1040"^^ . . "Rfam database of RNA families" . . "^\\d+$"^^ . . "plant development stage" . "https://loop.frontiersin.org/people/$1/overview"^^ . "biology" . "life science" . . . . . "Multiplexed Assays of Variant Effect Database" . . . . . . . "SNOMEDCT"^^ . "transcript" . "protonet.proteincard" . "embryonic stem cell line" . . "embryo" . . "https://fairsharing.org/$1"^^ . . "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information."^^ . . . . "^\\d{4}$"^^ . . . . . . "International Standard Serial Number" . "strain" . "Ontology for simulation, modelling, and optimization" . "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . "subject agnostic" . "Simple Standard for Sharing Ontological Mappings" . . . . . . . _:N51f8a03301c741d5b216ca7d5de38061 . . "tair.locus" . "Sabrina@tislab.org" . . . "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^ . "01027931310-01022252312"^^ . "ontology" . . . "https://bioregistry.io/cubedb:"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . . "GO Chemicals" . . "sgd" . "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes."^^ . . "stem cell" . . . "edam.data" . "^[A-Z0-9]+$"^^ . . . . "anatomy" . . . "quantitative trait loci" . "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."^^ . . "https://ximbio.com/reagent/$1"^^ . . . . . "hydrogeology" . "https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail.aspx?id="^^ . . "^\\d+$"^^ . . "proteomics" . "http://purl.uniprot.org/annotation/$1"^^ . . . "^\\d+$"^^ . . "Provenance, Authoring, and Versioning Vocabulary" . . . . "CYP2A6"^^ . "Cu.me.I1"^^ . "interaction" . . "ExAC Gene" . . "http://purl.obolibrary.org/obo/ONTOAVIDA_$1"^^ . . . . . . "plant breeding" . "ontology" . "http://sweetontology.net/matrMineral/$1"^^ . "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . . . . . . . . . "biomedical science" . "attachedTo"^^ . "medicine" . . . "life science" . "embryo" . . . "merops.clan" . "protein" . . . . "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family="^^ . . . . . . . . . . "model organism" . "http://purl.obolibrary.org/obo/OMIT_"^^ . "^Rv\\d{4}(A|B|c)?$"^^ . . . . . "false"^^ . "door" . . . . . "https://www.ebi.ac.uk/complexportal/complex/"^^ . "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API."^^ . . . "Ontology of Biological and Clinical Statistics" . "https://osdr.nasa.gov/bio/repo/data/biospecimens/$1"^^ . . . . . "https://biomodels.net/vocab/idot.rdf#$1"^^ . . "https://bioregistry.io/tokue:"^^ . . . . . . . . . "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name="^^ . . "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth."^^ . "^[a-z]+(\\..*?)?$"^^ . "^\\d+$"^^ . . "Human Oral Microbiome Database" . "Identifier used by the Cancer Chemotherapy National Service Center."^^ . . . "false"^^ . . "genomics" . . . "Jacqueline.Campbell@usda.gov" . . "epigenetics" . . . . . "Raymond Lee" . "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . . . "false"^^ . . "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^ . . . . . "Zebrafish anatomy and development ontology" . . . . . . "Cell line collections (Providers)"^^ . . "taxonomy" . . . . "gene" . "http://repository.topdownproteomics.org/proteoforms/$1"^^ . "CTCAE" . "safisher@upenn.edu" . "genepio" . . . . "life science" . "PhosphoSite Curation" . . "regulation" . . . "Rita-Heuser"^^ . "^\\d{7}$"^^ . . "Daniel.Kahn@toulouse.inra.fr" . "unpd" . "https://www.ebi.ac.uk/biostudies/studies/"^^ . . "systems biology" . . "John L. Markley" . "nucleic acid" . . "Eukaryotic Linear Motif Resource" . . "https://www.inaturalist.org/users/"^^ . . . . . . "A0A009HB13"^^ . . "life science" . "Biological Collections Ontology" . "vendor" . "co_359" . . . "false"^^ . "https://biopragmatics.github.io/providers/pba/"^^ . "4019477"^^ . . "has canonical" . . . "http://stormo.wustl.edu/ScerTF/details/$1"^^ . . . . . "false"^^ . "rwinslow@jhu.edu" . "false"^^ . . "Pieter Mestdagh" . "post-translational modification" . . . . . "MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for cell lines used in assays measuring molecular bioactivity, linking them to associated compounds and proteins."^^ . "Adrien Rougny" . "taxonomy" . . "0010015"^^ . "https://omia.org/phene/omia:$1"^^ . . "^(imp|gen)\\d{5}$"^^ . "bao" . . . . "panther.family" . . . "https://www.ncbi.nlm.nih.gov/protein/"^^ . . . "http://purl.dataone.org/odo/SENSO_"^^ . . . "nasaosdr.subject" . . . " Hendrik Borgelt" . "obo" . "genatlas" . . . "WBls" . . "tgma" . . "neurophysiology" . "00100037"^^ . "a formalization of concepts and relations relevant to evolutionary comparative analysis"^^ . . . . . "aftol.category" . . . "https://www.gbif.org/species/"^^ . "bibliography" . "bel"^^ . . "0000108"^^ . "https://www.kegg.jp/entry/$1"^^ . "^\\d+$"^^ . . . . . "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition."^^ . "https://www.geonames.org/$1"^^ . . . . "study design" . . . "mmusdv" . . "^\\d+$"^^ . "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1"^^ . "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources."^^ . . . . "Scientific Evidence and Provenance Information Ontology" . . . . . . . . "^\\w+$"^^ . "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules."^^ . "0040379"^^ . "http://purl.obolibrary.org/obo/TXPO_$1"^^ . . . . "http://purl.obolibrary.org/obo/LABO_$1"^^ . . . "false"^^ . "ccle" . "https://repeatsdb.org/protein/$1"^^ . . . "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries."^^ . . "biology" . "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)."^^ . "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production."^^ . "Daniel Schober" . . . "https://cropontology.org/rdf/CO_340:$1"^^ . "disease" . . . . "nist.codata" . . . "Joanne Kamens" . . "pdthomas@usc.edu" . . . "false"^^ . "genome" . . . "Patent" . . . "LinkML" . . . . "ontology" . . "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS)"^^ . . . . "https://reporter.nih.gov/project-details/$1"^^ . "pathogen" . . "^\\d{7}$"^^ . . . "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC."^^ . . . . "https://radlex.org/RID/"^^ . . . . "tfclass" . "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . . . . . "CAPS-DB" . "wuc@udel.edu" . . . . "Developmental stages of the Zebrafish"^^ . "DDInter20"^^ . "dicom" . . . . . "false"^^ . . . "Yaroslava G Yingling" . "false"^^ . "Web Ontology Language" . . "hendrik.borgelt@tu-dortmund.de" . "jaiswalp@science.oregonstate.edu" . "true"^^ . "The main contact person for a registry" . . . "true"^^ . . . . . . . . "^IS\\w+(\\-\\d)?$"^^ . . "^\\d{7}$"^^ . . . . . "David Mendez Lopez" . . . "obo" . . . . . . . . "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^ . . "virus" . "cellopub" . "David Gloriam" . . . . . "christian.hauschke@tib.eu" . "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other."^^ . "^\\d{7,8}$"^^ . "27106865"^^ . "http://purl.obolibrary.org/obo/CIO_$1"^^ . . . "aop.stressor" . . . . "phenotype" . . "stock" . . . "developmental biology" . "bykdb" . "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id="^^ . "CryptoDB" . . . . . "eggnog" . . . "http://scop.berkeley.edu/sunid=$1"^^ . "reaction data" . "molecule" . . . . . . "ontology" . "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"^^ . . . . . "alistair.miles@linacre.ox.ac.uk" . . "harukin@protein.osaka-u.ac.jp" . "false"^^ . "http://www.humanproteomemap.org/spectrum.php?pep_id="^^ . "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli."^^ . . "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"^^ . . . . "teri.klein@stanford.edu" . "^[0-9]+$"^^ . "false"^^ . . "^rxn\\d+$"^^ . . "false"^^ . "A vocabulary about species to support the environmental research community in Arizona and New Mexico"^^ . . "phenomics" . . . "BacMap Biography" . "NCBI_GeneID" . "electronic health record" . . . "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO)." . . . "9002859"^^ . . . . . "burkesquires@gmail.com" . . . "PeptideAtlas Dataset" . "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://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . "williams.antony@epa.gov" . . . . . . . . . . . . "https://osdr.nasa.gov/bio/repo/data/subjects/$1"^^ . . . "false"^^ . . . . . . . "w3c rec" . . "false"^^ . . . "2.16.840.1.113883.6.88" . . . . . . . "^[a-z][a-z0-9_]+[a-z0-9]$"^^ . . "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid="^^ . "http://www.w3.org/2003/11/swrl#$1"^^ . . . . "fbsp" . . "false"^^ . . . . . "life science" . "http://purl.obolibrary.org/obo/OBA_$1"^^ . . "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information."^^ . "false"^^ . . . _:N624f0a74bb6a428e94c2706fa793e914 "Crop Ontology Helpdesk" . "Ilene Karsch-Mizrachi" . "multicellds.collection" . "Ceri Van Slyke" . "NLXBR" . . . . "botany" . "botany" . "bco" . . . . . . "immunology" . "antifam" . . . . . _:N08af7157802e4fe1a36022ee8ba15c2f "Stephan Schurer" . . . . . "emmo" . "^\\d{7}$"^^ . . "Data Commons" . . . "botany" . . "^\\w+$"^^ . "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases."^^ . . . . . . "transcriptomics" . . . . "frbr" . . . . . "CTRI/2023/04/052053"^^ . "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase."^^ . . . "https://ieeexplore.ieee.org/document/"^^ . "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s)."^^ . "binding site" . . . . "genome" . . . . . . . "https://gen3.theanvil.io/ga4gh/drs/v1/objects/"^^ . . . . . . "botany" . "obo" . . . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id="^^ . . . . . . . "MMsINC" . "http://oid-info.com/get/"^^ . . "^[A-Za-z][A-Za-z0-9]+$"^^ . . _:Na240e2f055ba4e10bb275bdf6f56b7b6 "Michael Lincoln" . . . . . "Gender, Sex, and Sexual Orientation Ontology" . "true"^^ . . "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$"^^ . . "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."^^ . . . . . "small molecules" . . . . "kegg_genome" . "pseudogene" . . . . . . . . . "false"^^ . "environmental science" . . . "planp" . "Cell line databases/resources"^^ . . "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . . "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names."^^ . . "Information Artifact Ontology" . . . . . . "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . "false"^^ . . "sfam" . . . "^r3d\\d{9,9}$"^^ . "social media" . "neuroscience" . . "Glycosciences.DB" . "ontology" . . . . . "false"^^ . . . "multicellds.cell_line" . "http://www.iresite.org/IRESite_web.php?page=view&entry_id="^^ . "biodiversity" . "yoh@dartmouth.edu" . . . . "mimodb" . . _:N19fbaaad31074156b5ee2d23fe33fb6a . . . "false"^^ . "genetic resource" . . "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^ . . . "2701"^^ . "^SM\\d{5}$"^^ . . . . _:N2dbbb1ad069d4070acf6f199211c7b8d "Jonathan Bard" . "genomics" . . . "false"^^ . . . . "co_337" . . . . "false"^^ . "synthetic biology" . . "^\\d{7}$"^^ . . "SugarBind" . . "https://www.iedb.org/reference/$1"^^ . . . . . . . . "https://data.4dnucleome.org/experiment-set-replicates/"^^ . . . . . . "http://open-services.net/ns/core#"^^ . "protein"^^ . . . "2966"^^ . "false"^^ . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/EPIO_"^^ . . . . . . . . . "10"^^ . "A repository of software packages written in Ruby."^^ . . "^\\d{7}$"^^ . . "^\\d+$"^^ . . "bibliometrics" . . "https://dbpedia.org/ontology/"^^ . . "https://www.holofooddata.org/animal/"^^ . . . "http://purl.unep.org/sdg/SDGIO_"^^ . "https://www.flymine.org/come/entry?gn="^^ . "cellular" . . "fao.asfis" . . . "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1"^^ . . "aftol.taxonomy" . . "true"^^ . . . "linikujp@gmail.com" . "tritrypdb" . . . . . "Linda Reha-Krantz" . . "Gramene Reference" . "https://osdr.nasa.gov/bio/repo/data/hardware/$1"^^ . . "MassBank" . . . . "structure" . "http://purl.org/spar/scoro/$1"^^ . . . . . . "kegg.orthology" . . . . . "^FB\\d{8}$"^^ . . . . "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system."^^ . "study design" . . "ardan@ebi.ac.uk" . . . . . . . . . . . . "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^ . "miRBase pre-miRNA" . . . . "H00076"^^ . . . . . . . . . . . . "HOMO_3.PE998"^^ . . . "rna" . . "kanehisa@kuicr.kyoto-u.ac.jp" . "prefixcommons" . . . "jason.stajich@ucr.edu" . "http://purl.obolibrary.org/obo/MmusDv_$1"^^ . . "obo" . "interoperability" . . "https://www.ebi.ac.uk/ena/data/view/$1"^^ . "00011461"^^ . . . . "1058367"^^ . . . . . "COG Categories" . . . . . . . . "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors."^^ . "IntAct protein interaction database" . . "dpv" . . "Judith A Blake" . . . "lcsh" . "obo" . . . . . . "Nicolas Le Novère" . . . "Ontology for vector surveillance and management" . . "gene function" . . . "^\\d+$"^^ . . "0000088"^^ . . . . . . . "false"^^ . . . . "Eukaryotic Promoter Database" . "alzforum.mutation" . . "PharmacoDB Tissues" . . . . . . . . . . "Oryza Tag Line" . "data management" . . "fbcv" . . . . . "The Drug Ontology" . "plant phenotypes and traits" . "http://ensembl.org/glossary/ENSGLOSSARY_$1"^^ . "citation" . "identifier for an article/paper at the SSRN"^^ . . "false"^^ . . . . . . . . . "false"^^ . "http://purl.obolibrary.org/obo/OGSF_"^^ . "life science" . "22132778"^^ . . . . "biomedical science" . "NIA Mouse cDNA Project" . "mgnify.samp" . . . . . . "16941567"^^ . . . . . "Animal Genome Pig QTL" . "medicine" . "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways."^^ . . . . . . . . . . . "false"^^ . . "^[0-9]+$"^^ . . "conferences" . . "4dn.replicate" . "0000062"^^ . "https://ssrn.com/abstract=$1"^^ . "NPA000001"^^ . . "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1"^^ . "life science" . "Egon Willighagen" . "araport" . . . . "proteomics" . . . . . . "^\\d{7}$"^^ . "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac="^^ . . "obo" . "https://bioregistry.io/smiles:"^^ . . "false"^^ . "false"^^ . . . _:N70395268008041129aa070422efd733c . . "https://geneontology.org/GO_REF/"^^ . . "^\\d{7}$"^^ . . . . . . . "KW-1273"^^ . "004435"^^ . . "B2067"^^ . . . "Zebrafish Experimental Conditions Ontology" . . "Nanbyo Disease Ontology" . "RepeatsDB Protein" . "^\\d+$"^^ . . . "00000532"^^ . "http://biocyc.org/getid?id=$1"^^ . "Enrique Blanco" . . "https://ngdc.cncb.ac.cn/gwh/Genome/$1/show"^^ . "Scopus Work" . "violinnet" . . "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^ . . . . . . "false"^^ . . "sisu" . "false"^^ . "WGS84 Geo Positioning" . . . . . . . . . . . "false"^^ . "citation" . . . . . "obo" . . . . . . . . . . . . . "false"^^ . "The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces."^^ . . . . . . . . . . . "false"^^ . . . . . . "Angela Kranz" . . "OS-27"^^ . "627"^^ . . . . "Danielle Thierry-Mieg" . . "Sequencing Initiative Suomi" . "virology" . "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^ . "Geomames" . . . . . "Gene"^^ . . . "Environment Ontology" . "hp" . . . . "https://w3id.org/oc/oci/"^^ . "Canadian Drug Product Database" . . . . . "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"^^ . "obo" . . . "None"^^ . . . . . "325.4"^^ . "ontology" . "mutant" . . "gc_id" . . . . "false"^^ . . . . . "cutg" . . "false"^^ . . "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^ . "false"^^ . . "true"^^ . . "NIF Standard Ontology" . "false"^^ . . "false"^^ . "grouping" . . "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . "ontology" . . . . . . . . . . . "iceberg.ime" . "UM-BBD_compID" . . "inbred rat strain" . "massbank" . . . . . . . . "https://purl.dataone.org/odo/ADCAD_"^^ . "monique.zahn@sib.swiss" . . . "^PF\\d{5}$"^^ . "^\\d+$"^^ . "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"^^ . . "https://www.chemspider.com/search?params="^^ . . "model organism database" . . "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1"^^ . "fcsfree" . "DICOM Controlled Terminology" . "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules."^^ . "20090602"^^ . "http://purl.obolibrary.org/obo/PLANA_$1"^^ . "https://bioregistry.io/gmd:"^^ . . "Functional annotations of genomes for studying gene regulation, with a primary focus on cis-regulatory elements (CREs) such as promoters and enhancers."^^ . . "markley@nmrfam.wisc.edu" . . . "people" . . "https://www.holofooddata.org/animal/$1"^^ . . . . "nlx.inv" . . "annotation" . "^[A-Za-z0-9+_.%-:]+$"^^ . . . . . "NIF Gross Anatomy" . "FEMA provides identifiers for flavor ingredients deemed safe for food use. These entities include chemical compounds and natural substances used as flavoring agents, each reviewed by the FEMA Expert Panel for GRAS (Generally Recognized As Safe) status. The identifiers link to safety data and regulatory assessments, including evaluations by the U.S. FDA and, where applicable, the Joint FAO/WHO Expert Committee on Food Additives (JECFA)."^^ . . . "https://www.sharkipedia.org/species/$1"^^ . "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"^^ . . . . . "http://www.sasbdb.org/data/$1"^^ . "http://www.ebi.ac.uk/cmpo/CMPO_"^^ . . "https://lov.linkeddata.es/dataset/lov/vocabs/$1" . "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"^^ . . "dialnet.book" . . "^[A-Z-_0-9]+$"^^ . "hgnc.genefamily" . . . . "SEED Subsystem" . "https://www.kegg.jp/entry/$1"^^ . "ontology and terminology" . . <