. "ehda" . "https://metazoa.ensembl.org/id/"^^ . . . . . "1"^^ . . . . . . . "^\\d+$"^^ . . . . . . . . "^\\d{7}$"^^ . . . . "MSH2010_2010_02_22" . "nstd102"^^ . . "biomedical science" . "scpd" . . "Tick Cell Biobank" . . . . . . . . "0000156"^^ . . . "http://www.chemspider.com/$1"^^ . "https://ximbio.com/reagent/$1"^^ . . . . "ML0224"^^ . "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid="^^ . . "SysBioCancer2022"^^ . . . . . . . "https://www.cropontology.org" . . "fishbase.species" . . "insdc.sra" . . . . . . "false"^^ . . "Thorsten Henrich" . . "life science" . . "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities."^^ . . "false"^^ . . "radiology" . . "false"^^ . "obo" . . . . . . "1755"^^ . "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1"^^ . . . . . "MESHA" . . . "48439"^^ . . . "Q13485"^^ . . . . . . . . . "true"^^ . . "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1"^^ . . . "BE0000048"^^ . . . "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics."^^ . . . . "Wyeth W. Wasserman" . . . "12"^^ . . "niaest" . . . "genome" . . . "life science" . "^\\d+$"^^ . . "Jacqueline.Campbell@usda.gov" . "false"^^ . . "ERP004492"^^ . "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue="^^ . . "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders."^^ . . . "Bacterial Tyrosine Kinase Database" . _:Na1318f2ef66144e2b3d487361929c9b5 "Stephan Schurer" . "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"^^ . "http://purl.org/dc/terms/$1"^^ . . . . "^\\d+$"^^ . . . "M58335"^^ . . "false"^^ . "interaction" . "MultiCellDS Digital snapshot" . . . . . "ontology" . . . . . "biomedical science" . "data management" . "AB0"^^ . "true"^^ . . "SNOMED_CT_US_2018_03_01" . "geodesy" . . "false"^^ . . . . . "classification" . . "gmd.ref" . . . . . . . . . "hgnc.symbol" . . . "^\\d+$"^^ . . . . "P53350"^^ . . "ontology" . . . . . . "https://aopwiki.org/stressors/$1"^^ . . "protein" . "hsa-mir-200a"^^ . "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."^^ . . . . . . . . . . . . . . . "analytical chemistry" . . . "http://purl.obolibrary.org/obo/WBPhenotype_$1"^^ . . "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . . "D0001"^^ . . "Pan African Clinical Trials Registry" . . "Groundnut ontology" . "Human Cell Atlas Ontology" . . . . "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid="^^ . . . "DEF"^^ . "false"^^ . . "subject agnostic" . "^\\d+$"^^ . . . "http://purl.obolibrary.org/obo/LPT_$1"^^ . "true"^^ . . . . . . . "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^ . "Michael Witt" . . . "http://purl.obolibrary.org/obo/CIDO_"^^ . "OSR0818"^^ . . . "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . . "https://jjj.bio.vu.nl/models/"^^ . "Patrice Buche" . "cellosaurus" . "2c6s"^^ . "false"^^ . . . . "HGNC Gene Group" . . . . . "http://www.isni.org/isni/$1"^^ . . . "nmrshiftdb2" . . "false"^^ . "http://isbndb.com/search-all.html?kw=$1"^^ . . "https://www.cellosaurus.org/CVCL_$1"^^ . . "genome" . . . . . . . . . "HGVM15354"^^ . . "EB0170"^^ . . . . . "owl" . . "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . . . "linguist" . . . "false"^^ . "https://www.biolegend.com/Default.aspx?ID=6664&productid="^^ . . . . . . "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"^^ . . "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id="^^ . . . . . . . . . . . . . . . . . "An ontology that enables the description of reviews of scientific articles and other scholarly resources."^^ . . . . "xlmod" . "chemistry" . "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1"^^ . . . . . "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . . . "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"^^ . . . "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . . "subject agnostic" . "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins."^^ . . . . . "http://purl.obolibrary.org/obo/OOSTT_"^^ . . . . . . . . . . "Sequencing Initiative Suomi" . . . "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^ . . "false"^^ . . "https://gitlab.com/"^^ . . . . . . . . "https://smid-db.org/smid/"^^ . . . "CHEBIID" . . . . "PathBank" . . . . "^\\d+$"^^ . "false"^^ . . . . . . "http://www.ontologyrepository.com/CommonCoreOntologies/$1"^^ . "Database of Macromolecular Interactions" . "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."^^ . . . . "https://www.ebi.ac.uk/interpro/entry/$1"^^ . . . . "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . . "IUPHARobj" . "structure" . "false"^^ . . "^[1-9]\\d{0,11}$"^^ . "https://doi.org/"^^ . "https://cropontology.org/rdf/CO_357:"^^ . . . "dna" . . "56"^^ . "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/"^^ . . . . . . . . . "RSNA Informatics RadLex" . "SIDER Side Effect" . "protein" . . "http://www.chemspider.com/"^^ . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID="^^ . . "The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems."^^ . . . "tgma" . "THE1B"^^ . "laia.subirats@gmail.com" . . . . "obo" . "protein" . "^[0-9]*$"^^ . . "swisslipids" . "Scientific Information Retrieval and Exchange Network" . . "https://www.ebi.ac.uk/chembl/target/inspect/"^^ . "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage)\nNote that the website uses a different identifier then the one reported in this semantic space."^^ . "botany" . . . . . "anzctr" . . "structure" . . . "false"^^ . . . . "NCBIGene" . . "false"^^ . . . . . "ontology" . "0002233"^^ . "Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle"^^ . . . "Thermo Fisher Scientific" . "0000030"^^ . . . "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^ . . . . . . "obo" . . . . . . "protein" . . "Haruki Nakamura" . . . "http://multicellds.org/MultiCellDB/"^^ . "FooDB compound" . . . . "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management."^^ . "false"^^ . "vcell" . . . "http://purl.obolibrary.org/obo/VIDO_"^^ . "false"^^ . "FundRef" . "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns."^^ . _:N3fb3a4431c224b88b89ae5c160bdea0b . . "bams" . "Uniprot ID" . . . "michel.dumontier@gmail.com" . . "^NONHSAG\\d{5}$"^^ . . "^\\d{7}$"^^ . . "NIF Standard Ontology: Brain Regions" . "https://biopragmatics.github.io/providers/diseaseclass/"^^ . . . . . "Dataset"^^ . . "Integrative and Conjugative Element Ontology" . . . "nucleotide" . . . "^\\d+$"^^ . "false"^^ . . "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . . "VB.Ob.3736.GRSM125"^^ . . . . . . "General Multilingual Environmental Thesaurus" . . . "glytoucan" . . . "string" . . "MMsINC" . "life science" . "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"^^ . . "life science" . "YRC PDR" . . . "The pattern for expanded URIs in the given resource" . . . "^OSC\\d{4}$"^^ . "AOPWiki" . . . "false"^^ . . "E-cyanobacterium Experimental Data" . . "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."^^ . "genomics" . . . "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . "http://purl.obolibrary.org/obo/RO_$1"^^ . . . . . . . . "OntoBee" . . . . . . "^[A-Za-z_0-9]+$"^^ . . . . . . . . . "gthayman@mcw.edu" . . . . . "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^ . . "http://www.bioregistry.io/"^^ . . . "10.1038/s41597-022-01807-3"^^ . "Shorthand representations of languages and their subtypes"^^ . . "None"^^ . "An ontology to capture confidence information about annotations."^^ . . . "johnbeverley2021@u.northwestern.edu" . "small molecule" . . . . "http://viaf.org/viaf/"^^ . "fishbase" . . "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid="^^ . "pathway" . . "^\\d+$"^^ . "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1"^^ . "sao" . "Drivers of human diseases including environmental, maternal and social exposures."^^ . . "A formal ontology of phenotypes observed in fission yeast."^^ . . "https://comptox.epa.gov/dashboard/"^^ . . "biosimulators" . . . "insdc.run" . . "^\\d+$"^^ . "cell biology" . "https://chemapps.stolaf.edu/jmol/jmol.php?model="^^ . . "http://www.molmovdb.org/cgi-bin/morph.cgi?ID="^^ . . "structure" . . . "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . "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."^^ . "biomedical science" . "http://purl.obolibrary.org/obo/CIO_$1"^^ . . . "jakkbl@gmail.com" . . . . "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1"^^ . . . . "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1"^^ . . "^MCDS_C_[a-zA-Z0-9]{1,10}$"^^ . . . "dhowe@zfin.org" . "gwascentral.marker" . . "https://data.4dnucleome.org/biosources/"^^ . "^phs[0-9]{6}(.v\\d+.p\\d+)?$"^^ . "^UMIN\\d+$"^^ . . "diseases" . "structrual bioinformatics" . "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . . "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^ . . . . . . "Q2207226"^^ . . "huge" . "International Classification of Diseases, 10th Revision, Clinical Modification" . . . . . . . "swisslipid" . . "The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas."^^ . . . "http://archive.gramene.org/db/ontology/search?query=EO:$1"^^ . "JWS Online" . . "http://usefulinc.com/ns/doap#$1"^^ . . . "dna" . "gramene.protein" . "Polymorphism and mutation databases"^^ . "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity."^^ . . "life science" . . . . . . "neurobiology" . . . . . . "Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business."^^ . . _:N5d72087dac0b4e7583832625be2a8b77 "Cynthia.Hake@cms.hhs.gov" . "genomics" . "A manually curated resource for the representation and annotation of metabolic pathways"^^ . . . "NIF Standard Ontology: Investigations" . . . . "^PS\\d{5}$"^^ . . . . "https://bioregistry.io/skm:"^^ . . . "https://www.flymine.org/flymine/report/ChromosomeBand/$1"^^ . . . "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$"^^ . "0000144"^^ . . . . "false"^^ . "false"^^ . "0000254"^^ . "https://www.datanator.info/gene/$1"^^ . . . . . . "^\\w+$"^^ . . "^\\d+$"^^ . "animal husbandry" . . . . "http://www.geneontology.org/formats/oboInOwl#$1"^^ . . "false"^^ . . "Internet Engineering Task Force Language Tag" . "iro" . . "mgiglio@som.umaryland.edu" . . . . . . . "linguistics" . . . . . . "false"^^ . "false"^^ . . "false"^^ . "^[0-9]+$"^^ . . "^\\d+$"^^ . . . "false"^^ . "3dmet" . "xmetdb" . "^\\d{7}$"^^ . "gfrishkoff@gsu.edu" . "dispositions" . . "Cell line collections"^^ . . . "false"^^ . . . . . . "0000046"^^ . . . "http://iflastandards.info/ns/fr/frbr/frbrer/$1"^^ . . . . . . . . . . . . . . . . "ontology" . . . . "false"^^ . "Cell line collections"^^ . . "phismith@buffalo.edu" . . . "http://www.hprd.org/protein/"^^ . . "false"^^ . . "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information."^^ . "https://rism.online/"^^ . . "GXA Gene" . "Metabolic Encyclopedia of metabolic and other pathways" . . . . . "biomedical science" . "ontology" . "Mouse Developmental Stages" . . "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . . . "CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof"^^ . "Francesco Vitali" . "gene" . "^\\d{6}$"^^ . "DBCAT000600"^^ . . . . . "uo" . . . . "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . . "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."^^ . . "https://w3id.org/biolink/vocab/$1"^^ . . . . "^\\w+$"^^ . _:Ne143752cb0494165a80506d4055c9935 "Usha Mahadevan" . . . "4685"^^ . . . "^[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}$"^^ . . . . . . "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$"^^ . . . "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research."^^ . . . . . . "genbank" . . . "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:"^^ . . . "^\\d{7}$"^^ . . "CHEBI" . . . . . "true"^^ . . . . "false"^^ . . "SCV000151292"^^ . . . "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/"^^ . . . . . . . . "microarray" . . "protein" . . . . "^\\d+$"^^ . . "structure" . . . "true"^^ . . . "^[1-9]\\d{0,6}$"^^ . . "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts."^^ . . . "ontology" . . "structure" . . . . . . . . . "false"^^ . . . . . . "Protein Ensemble Database" . . "taxonomy" . "Contains entries for various database identifiers" . . . "subject agnostic" . _:N63039258d8394671ab2a7d78a1a6f639 "Onard Mejino" . . "lipid" . . "false"^^ . "Asset Description Metadata Schema Vocabulary" . "tobias.schulze@ufz.de" . . . . . . . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . "ontology" . "protein" . . . . . . "false"^^ . . . . "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF."^^ . "RDF Schema" . . "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa."^^ . "protein" . "Enzo Life Sciences is an antibody vendor."^^ . . . . "inxight" . . "dna" . . . . . "false"^^ . . . . "0778"^^ . . . . "14"^^ . . . . "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^ . . . . . "ontology" . "^\\d+$"^^ . . _:N5e9d6f9c29114d7cadb47cb07c2bba26 "whocc@fhi.no" . "GitHub is an online host of Git source code repositories."^^ . . . _:Ncf7b1863fd0f41e39b83ba6561066181 "First DataBank Customer Support" . . . . . . . . . "https://protists.ensembl.org/id/$1"^^ . . "life science" . "bacmap.biog" . "http://www.signaling-gateway.org/molecule/query?afcsid="^^ . "LSM-6306"^^ . "http://gmd.mpimp-golm.mpg.de/Analytes/$1"^^ . "Adriano Rutz" . . . . . "emaps" . . . "bioinformatics" . . . "omia" . "The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website)"^^ . "data management" . "https://www-is.biotoul.fr/scripts/ficheIS.php?name="^^ . . . "Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000."^^ . "false"^^ . "Brazilian Registry of Clinical Trials" . . . . "false"^^ . "^\\d{7}$"^^ . . . . "http://virtualflybrain.org/reports/$1"^^ . . "computational biology" . . . "UCR00513"^^ . . "molmovdb" . . "true"^^ . "systems biology" . "false"^^ . . "gnomad" . "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . . "obo" . . . . "Hathi Trust Digital Library" . . . "oai:cwi.nl:4725"^^ . "gramene.taxonomy" . . "RNA SSTRAND" . . "proteomics" . . . "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . . "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . . "https://fungidb.org/fungidb/app/record/gene/"^^ . "Open Citation Identifier" . "deepak.unni3@lbl.gov" . "http://purl.obolibrary.org/obo/TAHE_$1"^^ . . . "https://w3id.org/reproduceme#"^^ . . . . "9-1-1 Complex"^^ . . "ontology" . . "https://precision.fda.gov/uniisearch/srs/unii/$1"^^ . "An ontology covering the taxonomy of teleosts (bony fish)"^^ . . "interaction" . . . "ECCODE" . . "^\\d{7}$"^^ . . . . . . . . . "false"^^ . . . . . "umbbd.reaction" . . . . _:N8337d36cca6e4d828dddf715871da434 . . "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+$"^^ . . "Information about the C57BL/6J. Includes genetic background and disease data."^^ . . . . . . "silvio.peroni@unibo.it" . . . "MycoBrowser marinum" . . . . . . . "bactibase" . . . "906801"^^ . "protein" . . . "234"^^ . "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy."^^ . "^\\d+$"^^ . "Tim Robertson" . . "structure" . "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing."^^ . . . . . . . . . "436605"^^ . . . . . . "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them."^^ . . "false"^^ . . "^SIGNOR\\-[A-Z]+\\d+$"^^ . "Frederique Lisacek" . . . . "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"^^ . . "https://web.expasy.org/abcd/ABCD_"^^ . . "dna" . "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."^^ . . . "Ontology of RNA Sequencing" . "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."^^ . . . "obo" . "dal.alghamdi92@gmail.com" . . "http://biobanknetwork.telethon.it/Sample/View?sampleId="^^ . "0000062"^^ . . . "Integrated Canine Data Commons" . . "https://reactome.org/content/detail/"^^ . "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." . . . . "http://purl.obolibrary.org/obo/PLANA_$1"^^ . . . "SM00015"^^ . "Tohoku University cell line catalog" . . "matus.kalas@uib.no" . "http://purl.obolibrary.org/obo/RNAO_"^^ . . "^[0-9]+$"^^ . . "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1"^^ . . . . . . . "earth science" . . "Ontology of Organizational Structures of Trauma centers and Trauma systems" . . "https://mobidb.org/$1"^^ . "PED00017e001"^^ . "agsd" . "^\\d{7}$"^^ . "An organization" . . "gxa.expt" . . . . . . . . "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . "ontology" . . "false"^^ . "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/"^^ . . . . . . . . . . . "Vitis ontology" . "Mouse Tumor Biology Database" . . . . . "^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$"^^ . . . . . . . . . . . . "napp" . . "^PA\\w+$"^^ . . . . "^T3D\\d+$"^^ . . . "false"^^ . . "wormbase" . _:Nfa27ad29e54a4380a53d16f8436fcf43 "Jonathan Bard" . "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump"^^ . "frim1"^^ . . "^IRCT\\d+N\\d+$"^^ . . "^\\d{7}$"^^ . . "functional genomics" . "^MMP\\d+.\\d+$"^^ . . . "^\\d+$"^^ . "rsk00410"^^ . . . "imaging" . . . . . "drug repositioning" . . "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid="^^ . "ICARDA - TDv5 - Sept 2018"^^ . "descriptor" . . . "NCBI Taxonomy" . . . "^\\d+$"^^ . "glycomedb" . . . . . "obo" . "Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank."^^ . "Distributed Archives for Neurophysiology Data Integration" . . "to" . . . . . . "Golm Metabolome Database Reference Substance" . . "https://cropontology.org/rdf/CO_346:"^^ . . "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."^^ . "dna" . . . "life science" . . "life science" . . "s_mart_db" . . . . "International Protein Index" . . . "life science" . . "luana.licata@gmail.com" . "UBREL" . . "Mental Functioning Ontology" . . . "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_"^^ . . . . . "obo" . . "http://purl.org/dc/dcmitype/$1"^^ . "http://www.isni.org/isni/"^^ . . . . . . . . "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"^^ . "^\\d+$"^^ . "false"^^ . "ontology" . "UniProt Cross-ref database" . "0000001"^^ . . "COL3A1"^^ . . . "Willy Wong" . . "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]."^^ . "00020007"^^ . . "cito" . . . "https://athena.ohdsi.org/search-terms/terms/$1"^^ . . . . . . . "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . "protein" . "^[a-z]+(\\-[a-z]+)*$"^^ . "0116"^^ . . "0000001"^^ . . . . . . . . . "http://purl.obolibrary.org/obo/HsapDv_$1"^^ . . "00050"^^ . "false"^^ . . "https://fairsharing.org/organisations/$1"^^ . . . "chebi" . "false"^^ . . . "http://uri.neuinfo.org/nif/nifstd/nifext_$1"^^ . . . "^\\d{7}$"^^ . . . . "zeco" . . . "MI0026471"^^ . . . . "LK99"^^ . . . . . . . . . . "Habronattus courtship" . "^\\S+$"^^ . . "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^ . . . "false"^^ . . . . "^(ENSFM|ENSGTV:)\\d+$"^^ . . . . . . "https://biofactoid.org/document/$1"^^ . "https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md"^^ . . "^[A-Za-z]+$"^^ . _:N445dae3d588d4d9a9aeaf49bf3252e62 "curator@inoh.org" . "noaa" . . . . "https://bioregistry.io/abs:"^^ . . "cmpo" . . . . . . . . . . . . . . . "785"^^ . . . . "RCV000033555.3"^^ . "https://www.worldwildlife.org/ecoregions/"^^ . . . . . . . . . "false"^^ . "anatomy" . . "^URS[0-9A-F]{10}(\\_\\d+)?$"^^ . . _:N90eef15507124f0fa1fb1d0dc3a6358d "Hajo Rijgersberg" . "NCITm" . . . . . . . "Encyclopedia of DNA Elements" . . "Cooperative Patent Classification" . . "100000"^^ . . "false"^^ . . "bitbucket" . . . "ILX" . . . . . "https://www.novusbio.com/products/"^^ . "false"^^ . "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . . "BirdBase" . . . . . . . "https://www.ebi.ac.uk/chembl/entity/$1"^^ . "221058"^^ . "^\\d+$"^^ . . "MNXM1723"^^ . "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . "^[\\w\\-.]{3,}$"^^ . . . "mgi" . . . . . . . "^[a-zA-Z0-9\\-:#\\.]+$"^^ . . . . "depod@embl.de" . . . . . . "prediction" . "http://www.cathdb.info/domain/"^^ . . "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."^^ . . "ctd.chemical" . . "transportdb" . . . . "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)."^^ . "false"^^ . . . . "false"^^ . . . . "https://bioregistry.io/rebase:"^^ . . "10b38aaf-b977-4950-85b8-f4775f66658d"^^ . "https://lincs.hms.harvard.edu/db/antibodies/$1"^^ . "^SL-\\d+$"^^ . "chemistry" . . . . . . . "https://bioregistry.io/chemspider:"^^ . . "^\\d+$"^^ . "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id="^^ . "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . "true"^^ . . "epigenomics" . . "tarbase" . . . "Europe PMC Preprints" . "tanja.bekhuis@tcbinfosci.com" . "obo" . "anatomy" . . . . "Cell Line Ontology" . "MM00040"^^ . "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium."^^ . . . . . . "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^ . . . . . "^C\\d+$"^^ . "ontology" . . "ontology" . "http://bigg.ucsd.edu/models/$1"^^ . . "chemical" . "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs."^^ . . . "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^ . . . . "Draft version"^^ . "gene" . "VegBank" . . . "chemistry" . "^\\d+$"^^ . . "Fernanda Dorea" . . "https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:"^^ . . . . "^\\d+$"^^ . "^Q[A-Z0-9]+$"^^ . . "civic.aid" . . "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."^^ . . . . . "swissregulon" . "A subspace of Metabolic Atlas for reactions."^^ . . . . "neurobiology" . "https://bioregistry.io/cldb:"^^ . . . . "classification" . . "https://www.sharkipedia.org/species/$1"^^ . . "obo" . "CAS_RN" . "https://drs.microbiomedata.org/objects/$1"^^ . "false"^^ . "ird.segment" . "http://purl.obolibrary.org/obo/MFMO_$1"^^ . . "https://bioregistry.io/geonames.feature:"^^ . . . . . . "false"^^ . . . . . . . . . . "ontology and terminology" . "NCBI_Taxon_ID" . . "^\\d{7}$"^^ . . . "false"^^ . "GFAM" . . "617102"^^ . "ontology and terminology" . "cath.superfamily" . . . "^\\w+$"^^ . "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . "olatdv" . . . "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/"^^ . "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information."^^ . "eupath" . . . . . . . "Common Anatomy Reference Ontology" . . "violinnet" . "ontology" . . "^\\d+$"^^ . "obo" . . . . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . . . "Catalogue of Life" . . . "^TA\\d+$"^^ . . "000140" . . "cryoem" . "^\\d+$"^^ . . . "https://ensaiosclinicos.gov.br/rg/"^^ . "http://purl.unep.org/sdg/SDGIO_"^^ . . "Virtual International Authority File" . "genecards.genenote" . "nkos" . "genome" . "https://dbpedia.org/ontology/$1"^^ . "obo" . "http://en.wikipedia.org/wiki/$1"^^ . . . . . . . . . . "chebi" . . "biodiversity" . "nanotechnology" . "^\\d{7}$"^^ . . . "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles."^^ . "false"^^ . . . . . . . "http://www.w3.org/ns/dcat#$1"^^ . . . . "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:"^^ . . "GT10"^^ . "obo" . . . . . "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid="^^ . "interaction" . "^\\d+-\\d+$"^^ . "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."^^ . . "http://qudt.org/schema/qudt#$1"^^ . "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML."^^ . . "16129"^^ . . . . . . "mfo" . . . . "https://cropontology.org/rdf/CO_324:$1"^^ . "Data Science Ontology" . . "0000029"^^ . . . "Genomic Distribution of structural Superfamilies" . "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum"^^ . . . . . "ontology" . . "NIF Dysfunction" . "false"^^ . . . "biomedical science" . . . . "Melanoma Molecular Map Project Biomaps" . "ecology" . . . "preclinical studies" . "molecules" . . . . . "109082"^^ . "Sorghum TDv5 - Oct 2019"^^ . . . . . "dr.shorthair@pm.me" . . "false"^^ . . "Korean Clinical Research Information Service" . . . . . . . . "biochemistry" . "Nathan Baker" . . "Mingxun Wang" . . . . . . . . . "ppdb@gifu-u.ac.jp" . . "https://books.google.com/books?id=$1"^^ . . "agriculture" . . "neurondb" . "kegg.reaction" . . . . . . . . "apaonto" . "^[0-9][A-Za-z0-9]{3}$"^^ . . . . . . . . . "1004" . . "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . "The set of prefixes used in the Cellosaurus resource" . . "unigene" . . "signor" . . "0005926"^^ . . . "https://repo.napdi.org/study/"^^ . "idoo" . . "ontology" . . . . . . . "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities."^^ . . . . . "ontology" . "https://bioregistry.io/wos:"^^ . "immunology" . . . "FBbi" . "pesticides" . . . "0000205"^^ . . . . . "Name-to-Thing" . "SCC111"^^ . . "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."^^ . . "molecular biology" . . . . "http://purl.obolibrary.org/obo/EPIO_$1"^^ . . . "https://www.addexbio.com/productdetail?pid=$1"^^ . "http://ddinter.scbdd.com/ddinter/interact/"^^ . "1000001"^^ . "https://cn.dataone.org/cn/v2/resolve/{$1}"^^ . . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . . . "sharesAuthorInstitutionWith"^^ . . _:Nf868a8126b794489804014ace3e076a6 . "life science" . . "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier."^^ . . . . "false"^^ . "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]"^^ . "cognitive neuroscience" . . "http://purl.obolibrary.org/obo/LPT_"^^ . . "ae8c77fe-e6c8-44d5-8265-4a38c637bbef"^^ . . . . . . . "The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB."^^ . . "mgnify.proj" . . . "0290"^^ . "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants."^^ . "http://purl.org/dc/terms/"^^ . . . "obo" . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . . . "oostt" . . "false"^^ . "biochemistry" . . . "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species."^^ . "https://biomedit.ch/rdf/sphn-ontology/sphn#"^^ . "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules."^^ . "ASRP1423"^^ . . . . . . . "MGgn0008978"^^ . . . "http://www.receptors.org/nucleardb/proteins/$1"^^ . . . . . . . "MassBank" . . "preclinical studies" . "wbls" . "false"^^ . . . . "^bt\\d+$"^^ . "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."^^ . . . "true"^^ . . . . . _:N24a01489849c4a15ac69df989dd73b05 "radlex-feedback@lists.rsna.org" . "agriculture" . . "data model" . "http://purl.obolibrary.org/obo/OMO_"^^ . . "^\\d\\w+$"^^ . . . "false"^^ . . . . . . . "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . . "kcris" . . . . . . "GCA_000155495.1"^^ . "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"^^ . "^\\w+$"^^ . "ontology" . "SL-0002"^^ . . "ontology" . "International Standard Serial Number" . . . . . . . . . . . "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . . . "lipidmaps" . "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object="^^ . . . . . . . . "https://www.ebi.ac.uk/ols/ontologies/symp/terms?iri=http://purl.obolibrary.org/obo/SYMP_$1"^^ . . "viaf" . . "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems."^^ . "vbase2" . "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . . . "Homologous Organ Groups" . "https://www.worldcat.org/oclc/$1"^^ . "false"^^ . . . . "^\\d+$"^^ . "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."^^ . . . "CID" . "diapriid@gmail.com" . . "biomedical science" . "mamo" . . . . "Woody Plant Ontology ontology" . "Marc Ciriello" . . . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1="^^ . "NCI Pathway Interaction Database: Pathway" . "development" . . . . "NLXORG" . . . . "protein" . . "https://cropontology.org/rdf/CO_345:$1"^^ . . "false"^^ . "life science" . "https://lincs.hms.harvard.edu/db/sm/$1"^^ . "http://open-services.net/ns/core#"^^ . . "https://www.uniprot.org/database/$1"^^ . "mauno.vihinen@med.lu.se" . . . "mpidb" . . "^\\d{7}$"^^ . . . "^\\d+$"^^ . . "image" . . "E-cyanobacterium rule" . . . . "^\\d+$"^^ . . . . . . "^\\d{8}$"^^ . . . "true"^^ . . "cordis.article" . "disease" . "http://purl.obolibrary.org/obo/PECO_$1"^^ . . . "Li7"^^ . "mesh.2012" . . "https://ssbd.riken.jp/database/dataset/$1"^^ . . "false"^^ . "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln="^^ . . "ricegap" . "^\\d+$"^^ . . "SpBase" . "Terminology of Anatomy of Human Histology" . "ontology" . "virology" . . "brenda" . . . . . "label"^^ . . . "https://bioregistry.io/odam:"^^ . "http://www.noncode.org/NONCODERv3/ncrna.php?ncid="^^ . . . . . . . . . . . . . . "3792"^^ . . "false"^^ . . "genome" . . . . . . . . "https://fairsharing.org/$1" . "npo" . . . . "Transporter Classification Database" . "http://purl.org/spar/biro/"^^ . . . "iNaturalist Taxonomy" . . . . . . . . "false"^^ . "false"^^ . . . . . "MGnify Analysis" . . . . . . "dna" . . "life science" . . . . . . "vsmo" . . . . "Sample processing and separation techniques" . . . "false"^^ . . . "hsdb" . . . "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . . . . . . "false"^^ . "life science" . "structure" . . . . . . "Leszek@missouri.edu" . "ontology" . . . . . "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. " . "SABIO-RK" . "Molecular database for the identification of fungi" . "ontology" . "ontology" . . . . "NCBI Genome" . . . "https://aopwiki.org/stressors/"^^ . . "http://arabidopsis.org/servlets/TairObject?accession=AASequence:"^^ . "Nucleotide Sequence Database" . . . "IPP900099"^^ . . "https://gold.jgi.doe.gov/resolver?id=$1"^^ . . . . "true"^^ . . "scr" . . . "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."^^ . "Oryzabase Strain" . "SEQF1003"^^ . "http://purl.obolibrary.org/obo/TADS_$1"^^ . . "http://purl.obolibrary.org/obo/FOVT_"^^ . "https://portal.gdc.cancer.gov/cases/$1"^^ . . "pubchem_id" . "http://purl.obolibrary.org/obo/CHIRO_"^^ . "ontology" . . "PolBase" . . . . "false"^^ . . "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."^^ . "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^ . . . "http://purl.obolibrary.org/obo/SCDO_$1"^^ . . . . . . . "https://www.alzforum.org/mutations/"^^ . . . . "https://cropontology.org/rdf/CO_325:$1"^^ . "life science" . . "Computational and Informatics Resources for Glycoscience" . "Allotrope Merged Ontology Suite" . "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_"^^ . . . . "obo" . . "fcb" . "DBrodbelt@RVC.AC.UK" . "19"^^ . . "http://purl.obolibrary.org/obo/VBO_"^^ . "The Statistical Methods Ontology" . . "BRENDA Tissue Ontology" . "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"^^ . "https://bioregistry.io/cst:"^^ . . . . . "Cellular Microscopy Phenotype Ontology" . . . . . . "did" . . . . . . . "registry" . . "MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats."^^ . "^\\w+$"^^ . . . . . "false"^^ . . . "https://www.biozol.de/en/product/$1"^^ . . "swrl" . . "true"^^ . "false"^^ . . "false"^^ . . . . . . "false"^^ . "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . "nlx.dys" . "syoid" . . "26753"^^ . . "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^ . . . "GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources"^^ . "false"^^ . . "SAMEA2397676"^^ . . . . . . . . "biochemistry" . "India Clinical Trials Registry" . "life science" . . . "proteomics" . . . "gene" . . "false"^^ . "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"^^ . "00007294"^^ . "maizegdb.locus" . . . . "WiCell Research Institute Cell Collection" . . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . . "151022"^^ . "000000024"^^ . . "true"^^ . "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . "genome" . . . . "dna" . "genomics" . "PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains."^^ . "http://purl.obolibrary.org/obo/VTO_"^^ . "http://eugenes.org:7072/.bin/fbidq.html?$1"^^ . "BRIP1"^^ . . . . "Description of Plant Viruses" . . . . "bgee@sib.swiss" . "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . "Publication Provenance Prefixes" . . . "obo" . . . "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)."^^ . . "time" . . . . . "https://cropontology.org/rdf/CO_347:$1"^^ . . . "https://hpscreg.eu/cell-line/$1"^^ . . . "false"^^ . . "ontology" . . "37"^^ . "^PWY\\w{2}\\-\\d{3}$"^^ . . "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#"^^ . "anatomy" . . . . . . "http://www.pathwaycommons.org/pc/record2.do?id=$1"^^ . "http://www.ecogene.org/gene/"^^ . . . "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"^^ . . . . . . . "m.a.laporte@cgiar.org" . . . . "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule="^^ . . . . "CORDIS Project" . . . "rna" . "Wasila Dahdul" . . "^\\d+$"^^ . "60141"^^ . . . . . . "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."^^ . "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/"^^ . "pathguide" . "false"^^ . . "false"^^ . . . . "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . . . . . . . . . "FaceBase Data Repository" . "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes"^^ . "epidemiology" . . "MarDB" . "obo" . . . . "http://pepbank.mgh.harvard.edu/interactions/details/$1"^^ . . . . . "https://bioregistry.io/$1:$2" . . "ontology" . "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . . . . . "dbvar.study" . "nutritional science" . . "^\\d+$"^^ . . . "dron" . . . "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . . . . . . . . "enm" . . . . . "doqcs.pathway" . . . . "ocid" . "http://purl.obolibrary.org/obo/SIBO_"^^ . . . . . . . . . "obo" . . "genome" . "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1"^^ . "false"^^ . . "glycomics" . . . . "tRNA Gene Database" . . "ontology" . . . "GitLab" . "1"^^ . "false"^^ . . . . . "pdumdv" . . . . . . . . "^C\\d+$"^^ . . "^\\d{7}$"^^ . . . "Molecular Interaction Database" . "https://www.ebi.ac.uk/metabolights/"^^ . . . . . . "Anatomical Therapeutic Chemical Classification System" . . "subject agnostic" . . . . "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1"^^ . "https://www.kegg.jp/entry/"^^ . "^\\d+$"^^ . "has local unique identifier pattern" . . . "https://www.wwpdb.org/pdb?id=$1"^^ . "bioinformatics" . "^\\w+(\\.)?(\\d+)?$"^^ . "false"^^ . . "https://www.datanator.info/metabolite/"^^ . . . . . . . . "FoodEx2 is a comprehensive food classification and description system aimed at covering the need to describe food in data collections across different food safety domains."^^ . "ChEMBL" . "gold" . "^\\d{7}$"^^ . . . . "HD+118-001"^^ . . "transcriptomics" . . "https://cropontology.org/rdf/CO_325:"^^ . . "provenance"^^ . "http://www.sequenceontology.org/miso/current_release/term/SO:$1"^^ . "http://purl.obolibrary.org/obo/T4FS_$1"^^ . . "wikidata" . . "LO362836C"^^ . . "soybase" . . . "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . . . . "mcc" . "false"^^ . . . . "farming systems research" . . . . . . . "Clytia hemisphaerica Development and Anatomy Ontology" . . . "http://edamontology.org/data_$1" . . "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance."^^ . . . "false"^^ . . "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^ . "protein" . . . . "gene" . "biomedical science" . . . "false"^^ . "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . "IMGT/PRIMER-DB" . . "HBG004341"^^ . "https://www.animalgenome.org/CorrDB/q/?id=CorrID:"^^ . "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."^^ . . . . . . "false"^^ . "sep" . . . . "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . . . . . . . . "false"^^ . . "COG_Cluster" . "igsr" . . "false"^^ . "urn:nbn:fi:tkk-004781"^^ . . "peff" . "co_336" . . . "0000041"^^ . "The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved." . . "HGNC_GROUP" . . . . . . . "true"^^ . "BioStudies database" . "biomedical science" . "000009"^^ . . "6"^^ . . . . . "^[a-zA-Z0-9_-]{3,}$"^^ . . . . "Drosophila gross anatomy" . . . . . . . "ngl" . . . "broad" . . . "false"^^ . "An ontology to standardize research output of nutritional epidemiologic studies."^^ . . . . . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . . . "ontology" . "Chris Stoeckert" . . . . . "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . "false"^^ . . "0000547"^^ . "agricola" . "comparative neurobiology" . . "^\\d{7}$"^^ . "ontology" . . . "NCI2004_11_17" . "LIPID_MAPS_class" . . . "false"^^ . "rexo" . . "mimodb" . . _:N3fd66af97ee34c39bf4eee3c715172e6 . . . . "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."^^ . . "https://hdl.handle.net/hdl:20.500.12633/"^^ . . . . "false"^^ . . "1915"^^ . . "http://purl.obolibrary.org/obo/VSMO_"^^ . . . "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."^^ . "^\\d+$"^^ . "histology" . "gene" . . "^PKDB[0-9]{5}$"^^ . . . . "life science" . . . "biomedical science" . "https://www.ebi.ac.uk/intact/search?query="^^ . . . . "dbg2introns" . . "plant breeding" . "PyPI" . . . "RiceNetDB miRNA" . . . "https://covid19.sfb.uit.no/api/records/"^^ . "pao" . . . . "^DB\\d{5}$"^^ . . . . . . "^(Q|P)\\d+$"^^ . . . . "Lars Holm Nielsen" . . . . "meddra" . . . . . . . "tao" . . "http://purl.obolibrary.org/obo/MC_$1"^^ . . "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id="^^ . "An ontology of human and animal behaviours and behavioural phenotypes"^^ . . . . "20021"^^ . "fma" . "^\\d+$"^^ . "https://medlineplus.gov/genetics/condition/"^^ . . . "true"^^ . . . . "false"^^ . "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . . . . . "protein" . "^\\d+$"^^ . . . "0000139"^^ . . . "chemistry" . . . "metanetx.reaction" . "hmdb" . "KEGG_DRUG_GROUP" . "Daniel Himmelstein" . . "https://bioregistry.io/ccdc:"^^ . . "ontology" . "^[a-zA-Z0-9_\\-]+(/.*?)?$"^^ . "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^ . "slm" . "Models developed with the Virtual Cell (VCell) software prorgam."^^ . . . . . . _:Nc19f7ac97d0d4258a3699439291a2c7b "custserv@nlm.nih.gov" . . "bernd.mueller@zbmed.de" . "orphanet" . . . "^[A-Z0-9]{6,7}$"^^ . . . . . "An issue in any public repository on GitHub."^^ . . . "https://www.scopus.com/sourceid/$1"^^ . . . . "Geomames" . . . "subject agnostic" . "false"^^ . . . . . . "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."^^ . . . "metabolomics" . . . . . "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . "ACM1_HUMAN"^^ . "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1"^^ . . "comparative genomics" . "H-InvDb Protein" . . "KC-0979"^^ . . . . "21692"^^ . . . . . . . "GWAS Catalog" . "false"^^ . "Al Kikhney" . "nmr" . . . . . "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . "mKIAA4200"^^ . . "^\\d{7}$"^^ . . "hl7.v3codesystem" . . . . . "The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year."^^ . "keilbeck@genetics.utah.edu" . "https://bioregistry.io/dragondb.protein:"^^ . . . . . . "nucleotide" . "FAIRsharing Subject Ontology" . . "true"^^ . . . . "^\\d{7}$"^^ . "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records."^^ . . "n2t" . "health science" . . "Open Data Commons for Traumatic Brain Injury" . . . . "PaxDb Protein" . "life science" . "KEGG_DGROUP" . . "00000022"^^ . . . . . "cellosaurus.resource" . . . . . . . . . . . "structural biology" . . . "true"^^ . "Pankaj Jaiswal" . . . "dna" . "panther.pathway" . . "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species="^^ . "statistics" . . . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes."^^ . "cl" . . . . . . . . "vandf" . . . . . "^([3-5][A-Z])\\w+[^A-Z][0-9]$"^^ . . . "^\\w+$"^^ . . . "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . . "^RBR-\\w+$"^^ . . . "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."^^ . "https://www.findacode.com/code.php?set=ICD10PCS&c="^^ . . . . . "edam.topic" . "Foundational Model of Anatomy" . "^T\\d{3}$"^^ . . . "gateway" . . . . "biology" . "300108/p3934_A-172"^^ . . . "false"^^ . . . "life science" . . . . _:N65c4a0766aa745e488f8e29b39bbe993 "pbrooks@hcfa.gov" . "reaction" . . . . "mirnao" . . . "LTS0004651"^^ . "false"^^ . . . "http://www.radiomics.org/RO/"^^ . . . . . "protein" . . . . "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"^^ . "preclinical studies" . "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . . . "Philippe Le Mercier" . . . . . "physiology" . "domain" . . . . . "Animal Genome Chicken QTL" . . . . . . "orphanet.ordo" . . "odor" . . "gene expression" . "^\\d+$"^^ . . . . . . . _:N65c4a0766aa745e488f8e29b39bbe993 . "e.arnaud@cgiar.org" . . . . "pmap.substratedb" . . "false"^^ . "stefanie.seltmann@ibmt.fraunhofer.de" . . "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . . "c0001"^^ . . . "microbiology" . . "bacdive" . "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:"^^ . . . "false"^^ . "epd" . "obo" . . . . . "Identifier for a place in iNaturalist"^^ . . . . . "genewiki" . . . . . . . "^[0-9]+$"^^ . . . . . . . "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."^^ . "Alberto Traverso" . . "life science" . . . "FlyBase Gene" . . "https://www.checklistbank.org/dataset/3LR/taxon/"^^ . "life science" . . . . "ensembl.bacteria" . "HMS Library of Integrated Network-based Cellular Signatures Antibodies" . . . . "0000574"^^ . "agriculture" . . . . . . "false"^^ . . _:Ne143752cb0494165a80506d4055c9935 "usha@molecularconnections.com" . . . . "https://www.sigmaaldrich.com/US/en/product/sigma/"^^ . . "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . . . . . "Data Catalog" . "gene" . . "ontology" . . "ProteomeXchange" . . . "vario" . "http://purl.obolibrary.org/obo/SCDO_"^^ . . . "false"^^ . "Observation"^^ . "Pearl millet ontology" . . . . . . "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."^^ . "OMIT" . . . . "false"^^ . "10531"^^ . . . "https://www.ncbi.nlm.nih.gov/medgen/"^^ . . . "http://purl.obolibrary.org/obo/OBI_$1"^^ . "true"^^ . "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement."^^ . "4dn.biosource" . . "mat" . "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . . . "https://www.inaturalist.org/taxa/"^^ . . . "The upper level ontology upon which OBO Foundry ontologies are built."^^ . . . "EJH014"^^ . "http://lipidbank.jp/cgi-bin/detail.cgi?id="^^ . . . . "^\\d+$"^^ . . "E. coli Metabolite Database" . "An ontology representation of the LIPIDMAPS nomenclature classification."^^ . . . "https://meshb.nlm.nih.gov/record/ui?ui="^^ . "false"^^ . . "https://proteinensemble.org/"^^ . . . . . "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."^^ . . "cgsc" . . . . "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop="^^ . "http://purl.obolibrary.org/obo/CDAO_"^^ . . . . . . "ontology" . "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . . . . . . . . . "https://amzn.com/"^^ . . . "interaction" . "false"^^ . . . "ontology" . . . "nicolas.matentzoglu@gmail.com" . . . . "http://purl.org/dc/elements/1.1/"^^ . . . "genome" . . . . . . "seinet" . "http://www.yeastract.com/view.php?existing=locus&orfname="^^ . "transcriptomics" . "genome" . . . "0007114"^^ . "NLXFUNC covers terms for cognitive function."^^ . "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"^^ . "jrct" . "^MSMEG\\w+$"^^ . . . . . . . . . . "true"^^ . . . . . _:N85ddaefd50244628bbfdeb33140cc7f3 . "49"^^ . . . . . . . . . . "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."^^ . . "NITE Biological Resource Center" . . "true"^^ . "https://proteininformationresource.org/cgi-bin/resid?id=$1"^^ . "obo" . . . . . . . . "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$"^^ . . . . "ontology" . "uc001rvw.5"^^ . . "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^ . . . "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1"^^ . . "6819"^^ . "PubChem_Compound_CID" . . . "AY209920"^^ . "easychair.cfp" . . "SNR17A"^^ . . . "Bob Thacker" . . "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]"^^ . . . . "false"^^ . . "^\\d+$"^^ . . . . . . "^[A-Za-z-0-9]+$"^^ . . . . . . . "Sugar Kelp trait ontology" . . . . . "obo" . "foodb.compound" . "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)"^^ . . "634515043"^^ . . . "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1"^^ . . . . "http://vocab.getty.edu/page/tgn/"^^ . "983"^^ . "false"^^ . . . "williams.antony@epa.gov" . . "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"^^ . "taxonomy" . "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . . "http://purl.enanomapper.org/onto/ENM_"^^ . . . . . . . . "Plasmodium Life Cycle" . . "http://solgenomics.net/phenome/locus_display.pl?locus_id="^^ . "epidemiology" . "co_331" . "ATL98012"^^ . . . "^DB-\\d{4}$"^^ . "^[1-9]\\d{5}$"^^ . . . . "1981638"^^ . . . . "false"^^ . "DICOM Controlled Terminology" . . . . . . . . . . . "biomedical science" . . "false"^^ . . . . . . "https://cropontology.org/rdf/CO_320:"^^ . "Cell line databases/resources"^^ . . . . . . "As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including:\n- Research team and institution\n- The EMSL project DOI\n- Link to project data available in EMSLs Data Portal\n- Project type"^^ . . . "http://purl.obolibrary.org/obo/ONS_"^^ . . . "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val="^^ . . . . . . . . . . . . . "Mike Cherry" . . "grin.taxonomy" . . "comparative genomics" . . "^EP\\d{4}$"^^ . . . "false"^^ . . . "clao" . "01.01.005"^^ . . "Coconut ontology" . . . . . "senso" . "lpt" . "anatomy" . . "^\\d{7}$"^^ . "false"^^ . "epidemiology" . . "genomics" . . . "ontology" . . "agriculture" . . "Fission Yeast Phenotype Ontology" . . . "Leafsnap" . . . "Protein Model Portal" . . "Pathogen Transmission Ontology" . . "^\\w+$"^^ . . . . . . "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."^^ . . . . "0002989"^^ . "70"^^ . . "structural biology" . "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . . . . . . . "false"^^ . . "http://www.lipidmaps.org/data/LMSDRecord.php?LMID="^^ . "http://purl.obolibrary.org/obo/PRIDE_$1"^^ . . . "HEX1"^^ . "http://www.bindingdb.org/compact/"^^ . "wos" . "DataCollection"^^ . . . _:N5ec95b5321a64fbf81ad8855bbb6b18c . "Anatomical Therapeutic Chemical Vetinary" . . . . . . . . . . . . . "giardiadb" . . "abs" . . . "Jie Zheng" . . . . "epigenetics" . . . "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes."^^ . "computational neuroscience" . . . . "hepro" . "https://bioregistry.io/resolve/github/issue/"^^ . "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer"^^ . "chebi"^^ . . "life science" . "0000001"^^ . "Scientific Event Ontology" . . . . . "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$"^^ . . . "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://www.ncbi.nlm.nih.gov/medgen/$1"^^ . "http://linkedlifedata.com/resource/umls/id/$1"^^ . . . . . . . "Tom Gillespie" . "Maxwell L. Neal" . . . "genome" . . . "phenomics" . . "obo" . . . "life science" . . "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . "A type for entries in the Bioregistry's collections" . . "Terry.Hayamizu@jax.org" . . _:N969e51e760e143a396fffef623989a13 "CTCAE Help" . "ATCC(dna)" . "ontology" . "false"^^ . "cameo" . "https://www.re3data.org/repository/"^^ . . . . "https://lincs.hms.harvard.edu/db/cells/"^^ . . . . "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^ . . . . . . "Brachiaria ontology" . "owlstar" . . . . . . . . "false"^^ . . "obo" . . "^\\d+$"^^ . "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID="^^ . . . . . . "life science" . . "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^ . "false"^^ . "https://www.ebi.ac.uk/ols/ontologies/clo/terms?short_form=CLO_"^^ . . . . . . . "Andreas Ruepp" . . "AC00963334"^^ . . "http://purl.obolibrary.org/obo/GEO_$1"^^ . . "^\\d+$"^^ . . . "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines." . "chemistry" . "http://purl.obolibrary.org/obo/TXPO_$1"^^ . "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."^^ . "false"^^ . . . . . . "MESH_SUPPLEMENTAL_RECORD_UI" . . "E-MEXP-1712"^^ . "AllSomeInterpretation"^^ . "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . . . . . . . . "Lebanon Clinical Trials Registry" . "http://pepbank.mgh.harvard.edu/interactions/details/"^^ . . . . . "safisher@upenn.edu" . . "microbial" . "false"^^ . "obo" . . . . . . . . . "torsten.schwede@unibas.ch" . . . . . . . "ligandexpo" . . "obo" . "life science" . "SR0000178"^^ . "false"^^ . . . "data visualization" . . "A user of FAIRsharing"^^ . . . . "GitHub Pull Request" . . . . . . . . "https://gudmap.org/id/$1"^^ . . "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."^^ . . . . . . "http://purl.org/spar/deo/"^^ . . . . . "https://purl.uniprot.org/uniprot/"^^ . "false"^^ . . . . . . . "http://uri.neuinfo.org/nif/nifstd/nifext_"^^ . "Orphanet Rare Disease Ontology" . . . . . . "false"^^ . . "life science" . . . . . . . . "life science" . "false"^^ . "https://s3.us-east-2.amazonaws.com/lg.cede/"^^ . . . . . . "http://purl.obolibrary.org/obo/CRO_"^^ . . "http://www.w3.org/2003/11/swrl#$1"^^ . . "Apple Ontology" . . "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"^^ . . . "ontology" . . "^\\d{7}$"^^ . . . . "false"^^ . . "genomics" . . . . . . . "TTHERM_00648910"^^ . "ontology" . . "Observational Medical Outcomes Partnership" . "systems biology" . . . "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . . "dsm4" . . "http://data.crossref.org/fundingdata/funder/10.13039/$1"^^ . . "habronattus" . . . . . . . . . "https://bioportal.bioontology.org/ontologies/$1" . . "2555646"^^ . . . "licebase" . "^\\d+$"^^ . . "statistics" . "REPRODUCE-ME Ontology" . . . . "https://proteinensemble.org/"^^ . . . . "omics" . "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$"^^ . . . "true"^^ . "ontology" . . . . . . "false"^^ . "MMP02954345.1"^^ . . . "Benjamin M. Gyori" . . . . "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . . _:N3f1d8c950822411f8d6e8a3817a284fb "albertgoldfain@gmail.com" . . "false"^^ . . . . "^HGVM\\d+$"^^ . "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."^^ . . . . . . . . "^\\S+$"^^ . . "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."^^ . "https://www.ncbi.nlm.nih.gov/snp/"^^ . . . "0000189"^^ . . . . . "https://www.ncbi.nlm.nih.gov/nlmcatalog/"^^ . . "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)."^^ . . . "taxonomy" . . . . . . "life science" . . . . . . . . "Chemical Information Ontology" . . "miw023@ucsd.edu" . . . . . "false"^^ . . . "http://hawaii.eagle-i.net/i/$1"^^ . . "http://champ-project.org/images/ontology/cao.owl#CAO_$1"^^ . "fairsharing.organization" . . "Plant Anatomy Ontology" . . _:N861bf4e2c6fc4484bca1e8e0d37f5ee6 "edd@usefulinc.com" . . "https://www.ebi.ac.uk/interpro/set/pfam/"^^ . . . . . "nutritional science" . "biology" . . . "cordis.project" . . "000017"^^ . . . . . . . . . . . "false"^^ . . . . . . . "genome" . . . . "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."^^ . . . . . "http://www.cellresource.cn/cellsearch.aspx?sc=1&where="^^ . . . . . . "http://purl.obolibrary.org/obo/MO_"^^ . . . . "regulation" . "Sugar Kelp trait ontology"^^ . "anatomy" . . . "http://purl.obolibrary.org/obo/PROCO_$1"^^ . . "raymond@caltech.edu" . "computer science" . . . "Data Commons" . "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"^^ . . . . "Cell Signaling Technology Antibody" . "https://massbank.jp/RecordDisplay?id="^^ . . . . . . "5688061"^^ . . . "bcio" . . . . . . "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."^^ . "Genetic Testing Registry" . "977869"^^ . . "http://www.vbase2.org/vgene.php?id="^^ . . . . . . . . . "dbo" . . . "http://cellimagelibrary.org/images/$1"^^ . . "https://jrct.niph.go.jp/en-latest-detail/"^^ . "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character."^^ . "A gazetteer constructed on ontological principles"^^ . . . . . . . . "http://id.nlm.nih.gov/mesh/vocab#"^^ . . "subject agnostic" . "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations."^^ . "pathway" . . . . . . . "false"^^ . "27223"^^ . "deo" . . "^\\d{5}$"^^ . "Harry Caufield" . . . "^[A-Z_]{3}[0-9]{4,}$"^^ . . . . . "false"^^ . . "https://cropontology.org/rdf/CO_326:$1"^^ . . . . . . . . "pass2" . . . . "Jessica Kissinger" . "^\\d{7}$"^^ . "11303"^^ . "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."^^ . . . "botany" . "https://www.fishbase.ca/summary/"^^ . . . . . . "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."^^ . "cognitive neuroscience" . "G00123"^^ . "^SEQF\\d+$"^^ . "ProtoNet Cluster" . . "Homeostasis imbalance process ontology" . . . . . . . "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary"^^ . . "biochemistry" . . "^\\d+$"^^ . "5ede4273-b26c-4ea4-adb7-3ce294ab3397"^^ . . "false"^^ . "https://www.rebuildingakidney.org/id/"^^ . . . "anatomy" . "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."^^ . . . "High-quality Automated and Manual Annotation of microbial Proteomes" . . "https://bartoc.org/" . "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . . . "http://www.w3.org/ns/shacl#"^^ . "^\\d{7}$"^^ . . . "http://www.w3.org/2001/XMLSchema#"^^ . . "false"^^ . . . . "Assists in resolving data across cloud resources."^^ . . "structural bioinformatcs" . "75121530"^^ . . "obo" . . "true"^^ . "false"^^ . . "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1"^^ . "life science" . "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1"^^ . . "false"^^ . . . . "http://purl.obolibrary.org/obo/LBO_"^^ . "false"^^ . . . . . "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . . "pina" . . . . . "oma.grp" . . "https://www.ncbi.nlm.nih.gov/gene/"^^ . "International repository of Adverse Outcome Pathways."^^ . "http://www.alanwood.net/pesticides/$1.html"^^ . . . . . . . . "false"^^ . . . "EC" . . "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^ . . "http://purl.obolibrary.org/obo/XLMOD_$1"^^ . . . . . "mwitt@purdue.edu" . . . "mathematics" . . . "http://erop.inbi.ras.ru/result2.php?PepName=$1"^^ . . . "biology" . "Eric W. Deutsch" . . . "ontology" . "false"^^ . . "obo" . . . "http://purl.obolibrary.org/obo/TAO_$1"^^ . "C. elegans ORFeome cloning project" . . . . . "true"^^ . . . . . "ontology" . . . "http://www.ecogene.org/gene/$1"^^ . . . . . . . . . . . . "laml_tcga_pub"^^ . "obo" . . . "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses."^^ . . . "literalForm"^^ . . . "structure" . . . . "mathematics" . . . . "UDB000691"^^ . . . . . "biomedical science" . "ENSFM00500000270089"^^ . . . . "anatomy" . . . . "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes."^^ . . "https://cropontology.org/rdf/CO_367:$1"^^ . "preclinical studies" . . "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept"^^ . . . . . . "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets."^^ . "Genetics Home Reference" . . "celia.michotey@inrae.fr" . "has identifier space owner" . "NeuroLex Dysfunction" . "timrobertson100@gmail.com" . "medicine" . . . "ApiDB_PlasmoDB" . . . . . "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. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies."^^ . "life science" . . . . "false"^^ . . . . "Ontology for MicroRNA Target" . "1199"^^ . . . "http://www.ebi.ac.uk/cmpo/CMPO_"^^ . . "https://spdx.org/licenses/"^^ . . . "plwhetzel@gmail.com" . . "pathway" . . . "Asiyah Yu Lin" . "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project."^^ . . . "obo" . . "ontology" . "Cellosaurus identifeirs for publications, like Pubmed"^^ . . "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . . . "false"^^ . "paxdb.protein" . . "^(SMP|PW)\\d+$"^^ . "ontology" . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_anat_"^^ . . "Biotin_biosynthesis"^^ . "small molecule" . "46"^^ . _:N3fb3a4431c224b88b89ae5c160bdea0b "julie@igbmc.u-strasbg.fr" . . . . . . "false"^^ . . . . _:N9cd6b83be62b4cb9b98b539a5a594414 . "comparative genomics" . "metabolomics" . . . "http://thebiogrid.org/"^^ . . . "https://bioregistry.io/kerafast:"^^ . "NLFFF Database" . "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#"^^ . . . "agrovoc" . . . . . "biopesticides" . . . "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . . . "amalik@ebi.ac.uk" . . . _:N78b29c3077bc42a897068be98e924ec9 "datex@efsa.europa.eu" . "virsirna" . . . . . "genomics" . "true"^^ . . . . . "decipher" . . . . . "ontology" . . "https://cropontology.org/rdf/CO_360:$1"^^ . "1458400"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_qual_"^^ . . "false"^^ . . . . "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."^^ . "M77F7JM"^^ . "dna" . "sequence" . "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"^^ . . "https://tools.ietf.org/rfc/rfc$1"^^ . . . "https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:"^^ . . . . "ontology" . . . "ENSG00000169174"^^ . . "http://www.wikidata.org/entity/$1" . . . . . . . . . "ontology and terminology" . . . . "DragonDB Protein" . "biomedical science" . . . . . . "http://purl.obolibrary.org/obo/MICRO_$1"^^ . . . . . "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."^^ . "small molecule" . "uniprot.resource" . "biology" . . . . . "http://purl.obolibrary.org/obo/MF_$1"^^ . . "false"^^ . . . . . "ICD9CM_2006" . . . . . . . . "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world."^^ . "A vocabulary about species to support the environmental research community in Arizona and New Mexico"^^ . . "ontology" . . . . . . . . "false"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"^^ . . "00030692-0FE1-4A1B-955E-A2E55D659267"^^ . . . "false"^^ . . "false"^^ . . . . "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"^^ . "bioinformatics" . "XML Schema Definition" . . "co_340" . . "Add"^^ . . "PubMed" . . "Ontology of Arthropod Circulatory Systems" . "Human developmental anatomy, abstract" . . . . "life science" . "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1"^^ . . "false"^^ . . "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide"^^ . "biomedical science" . "https://www.genome.jp/virushostdb/"^^ . . . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/MPATH_$1"^^ . . "http://purl.obolibrary.org/obo/TAHH_$1"^^ . . "dcat" . . . . . "^\\d{7}$"^^ . "^\\d+$"^^ . "^\\d{4,}$"^^ . "Symptom Ontology" . "http://purl.obolibrary.org/obo/NOMEN_"^^ . . . "pathway" . "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id="^^ . "allergome" . . . "3355"^^ . "GiardiaDB" . "0101963"^^ . . "https://bioregistry.io/metaregistry/biocontext/$1" . . . . . . . . "http://purl.obolibrary.org/obo/OHMI_$1"^^ . "ontology" . "Don Gilbert" . . . "false"^^ . . . "false"^^ . "life science" . . "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . "false"^^ . "openalex" . "http://purl.org/spar/deo/$1"^^ . . . . "Compositional Dietary Nutrition Ontology" . "ontology" . "0001011"^^ . . "^DDInter\\d+$"^^ . "obo" . "National Center for Biotechnology Information Registry" . . "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.\r\n\r\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."^^ . "SNOMED CT (International Edition)" . _:N30b084992577444d9e24bda5c34d200d "maria.herrero@kcl.ac.uk" . "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id="^^ . . . "Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021"^^ . "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^ . "Philipp Bucher" . . . . . . . . . "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"^^ . . . "atmospheric science" . "false"^^ . . "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way."^^ . . . "false"^^ . . . "lutz.fischer@tu-berlin.de" . . . . . "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^ . "false"^^ . . "ChemIDplus" . . . "^HMDB\\d+$"^^ . "duo" . . . . "1868"^^ . . "false"^^ . . "spp" . . . . "false"^^ . "true"^^ . . . "ydpm" . "life science" . . . . . "http://scipion.i2pc.es/ontology/CRYOEM_"^^ . . . ""^^ . . "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . _:Na1d50c8b474d4223829b097d73a654cf "mb4@sanger.ac.uk" . "doi"^^ . "International Nonproprietary Names" . "kegg.metagenome" . "true"^^ . . . "adms" . . . "Carlos Oscar S. Sorzano" . . "has canonical" . . . . . "vfdb.genus" . . . "http://www.ontologyrepository.com/CommonCoreOntologies/"^^ . . . . . "https://www.hipsci.org/lines/#/lines/"^^ . "software engineering" . . . "Geonamaes" . . . "International Classification of Diseases for Oncology" . "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging"^^ . . . . . . . "sgd" . "clinical veterinary medicine" . "developmental biology" . . . "https://www.uniprot.org/tissues/"^^ . . "organic molecular chemistry" . "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1"^^ . . . . "NCI Thesaurus" . . . "false"^^ . "lincs.smallmolecule" . "clinical trials" . . . . . "0471491039"^^ . "https://disprot.org/$1"^^ . "https://www.ebi.ac.uk/arrayexpress/experiments/"^^ . "agilent.probe" . . "chemical" . . . . . . . "false"^^ . . "1046"^^ . "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . . "unipathway.compound" . . . "http://purl.obolibrary.org/obo/CARO_$1"^^ . "zmp@ebi.ac.uk" . "false"^^ . . "true"^^ . . . "0000984"^^ . . . "^[m,M]{2}[0-9]{5}[0-9]*$"^^ . . "http://www-snorna.biotoul.fr/plus.php?id="^^ . . "UK Universities and Colleges Admissions Service" . . . "https://cordis.europa.eu/project/id/"^^ . . "MetaNetX compartment" . "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . . . "colonatlas" . "biology" . "rnacentral" . . . "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id="^^ . . "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^ . "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data."^^ . "miriam"^^ . . . "life science" . . . "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment."^^ . "life science" . "^BAMSC\\d+$"^^ . "http://www.onto-med.de/ontologies/gfo.owl#"^^ . . . . . . . . . "Gene Expression Ontology"^^ . "https://gnomad.broadinstitute.org/variant/"^^ . . . . . . . . . . "https://europepmc.org/article/CTX/$1"^^ . . . . "chictr" . "dunand@lrsv.ups-tlse.fr" . . "NPC139585"^^ . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$"^^ . . . . . "subject agnostic" . . . "Biofactoid" . . . "^CE\\d{5}$"^^ . "false"^^ . . . . . . . . . "classification" . "false"^^ . . . . . . . "classification" . . . "^\\d{3}$"^^ . . . "https://envipath.org/package/"^^ . . . . . . . . . "Database of the dielectric properties of biological tissues."^^ . . . "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept"^^ . "Molbase" . "subject agnostic" . . . . "https://sparontologies.github.io/fabio/current/fabio.html#$1"^^ . . "aism" . "Cephalopod Ontology" . . "false"^^ . . . "http://www.arachnoserver.org/toxincard.html?id="^^ . . . "^MAR\\d{5}$"^^ . . . . . . "Bgee gene" . . "ontology" . "http://purl.obolibrary.org/obo/OAE_"^^ . . . . "300165/p13898_2106T"^^ . "antibodyregistry" . "https://www.ebi.ac.uk/ena/browser/view/"^^ . . . . . . . . "Cell line databases/resources"^^ . . "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"^^ . . . "ctd.gene" . . . "glygen" . "^\\d+$"^^ . "LBCTR2023015204"^^ . "ido" . "https://registry.bio2kg.org/resource/$1" . . "dna" . "Salk Institute for Biological Studies" . "http://purl.obolibrary.org/obo/NBO_$1"^^ . . "gexo" . . . "ontology" . "false"^^ . . . . "col.taiwan" . . "interaction" . "false"^^ . "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."^^ . "vaccines" . . . "molecule" . "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^ . . "MGnify Project" . . . . . _:N109b855995034d6c8ba73623667eb8de "Crop Ontology Helpdesk" . . "false"^^ . "ontology" . . . "100101"^^ . . "planp" . _:N04608afe5638414c957c0d37ef14401e "Crop Ontology Helpdesk" . . . . "^\\d+$"^^ . . "clinvar.variant" . "obo" . . _:Nf7c461b564cb4893b44e4de8a8f9a78c . . . . "Protein Model Database" . . "false"^^ . . . "Clare Pilgrim" . . . . . . . . . "Toxic Process Ontology" . "PdumDv" . "The Drug-Drug Interactions Ontology" . . "biomedical science" . "http://purl.obolibrary.org/obo/CMO_$1"^^ . . . . . . . . . . . . . . "upa" . "http://www.chemspider.com/inchikey=$1"^^ . "^\\d{7}$"^^ . . "agriculture" . "ontology" . . . . "http://purl.obolibrary.org/obo/OPL_$1"^^ . . . . . . "http://purl.obolibrary.org/obo/COLAO_$1"^^ . "cpga" . . . "merops.family" . . . . . "developmental biology" . "Circular double stranded DNA sequences composed" . . . . . . . . . "cell lines" . "plana" . "MSMEG_3769"^^ . "co_322" . . . "vendor" . . "false"^^ . . . . . "http://www.pharmgkb.org/pathway/$1"^^ . . "obo" . "tgbugs@gmail.com" . "biomedical science" . "biology" . "peptideatlas" . . "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$"^^ . . . . . . . . . . "ontology" . . . . . . . "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . "http://purl.obolibrary.org/obo/IAO_"^^ . . . . . . . . . "life science" . . . . . "^GLDS-\\d+$"^^ . "00023232"^^ . "has resolver formatter" . . . "Protein Ensemble Database ensemble" . . . . "ecyano.rule" . . "false"^^ . . "1"^^ . . "medicine" . . . . "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases."^^ . "https://neurovault.org/images/"^^ . "^\\d+$"^^ . . "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"^^ . "Chicken Gene Nomenclature Consortium" . "false"^^ . "Imanis Life Sciences cell line products" . . . . . . "richard@cyganiak.de" . "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^ . . "false"^^ . "data management" . "The Echinoderm Anatomy and Development Ontology" . "431472"^^ . . "0000983"^^ . . "https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1"^^ . "life science" . "obo" . "microbiology" . . "https://www.pharmvar.org/gene/"^^ . . . . . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . "http://snomed.info/id/"^^ . . . "National Experimental Cell Resource Sharing Platform" . . . "https://abrc.osu.edu/stocks/number/SALK_"^^ . "^SAM[NED](\\w)?\\d+$"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . . "4dn.replicate" . . "Jesper Friis" . . "Philippe.Lemercier@sib.swiss" . . . . "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition."^^ . . . . "false"^^ . "^[0-9][A-Za-z0-9]{3}$"^^ . . . "Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications."^^ . . . . . . "life science" . . . . . "false"^^ . "SNOMEDCT_US_2019_03_01" . . . . . . . . . . "https://reactome.org/content/detail/$1"^^ . . . . . "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. "^^ . . "protein" . . "anatomy" . . "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."^^ . . . "true"^^ . "bioRxiv" . . . "door" . "pharmacy" . . "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."^^ . "nje5@georgetown.edu" . . . "knowledge and information systems" . "earth science" . . . . "Gene Ontology Database references" . . "https://www.webelements.com/"^^ . . . "false"^^ . . "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1"^^ . . . "GWAS Central Study" . . "false"^^ . "false"^^ . "biomedical science" . "crop2ml" . "satyasahoo@ieee.org" . . "ACH-000001"^^ . "^RCV\\d+(\\.\\d+)?$"^^ . . . . . . "depod" . . . . . "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . . "zfs" . . "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . . . "preclinical studies" . "http://purl.obolibrary.org/obo/ICO_"^^ . "false"^^ . "genome" . . . . . "TRQ"^^ . . "^\\d+$"^^ . . "life science" . . . . . . . . "health" . . "EAWAG Biocatalysis/Biodegradation Database" . . . . _:N5cdc25bb742a4a0ca1a1623643d8be92 "Crop Ontology Helpdesk" . . . . . _:Na143d7469e704dd6892346f194336bca "slarson@ncmir.ucsd.edu" . . "ontology" . . "app-d678n-tottori"^^ . . "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . . . . . . . "grid.225360.0"^^ . . . "bco" . "http://purl.obolibrary.org/obo/MMO_"^^ . . "BindingDB is the first public database of protein-small molecule affinity data."^^ . . . . . . . . "adcad" . "Joint Genome Institute Proposals" . "kegg.orthology" . . "evm" . . . "^(T0\\d+|\\w{3,5})$"^^ . "http://purl.obolibrary.org/obo/PSO_$1"^^ . . . "materials informatics" . "COMBINE specifications" . "100"^^ . "^[0-9]+$"^^ . . . "classyfire" . . . . "CHEBI" . . . "http://pax-db.org/#!protein/$1"^^ . . "MeSH 2012" . "SBGN Bricks data and ontology" . . "bioinformatics" . . . "31253.11.sciencedb.j00001.00123"^^ . . "bioinformatics" . . . . "Rice annotation Project database" . "protein" . . . . . . . . . . "oid" . . "semapv" . "iso15926" . . . . "http://exac.broadinstitute.org/variant/"^^ . "https://www.picb.ac.cn/limore/cellLines/single?para="^^ . "MESH" . . . "false"^^ . . . . "STOREDB at University of Cambridge" . . . . . . . . "ontology" . "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."^^ . . "fisheries science" . "f.quaglia@ibiom.cnr.it" . "https://cropontology.org/rdf/CO_359:"^^ . . "http://www.molbase.com/en/index.php?app=search&search_keyword="^^ . . . . "drug discovery" . "GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals"^^ . . . . . . "http://purl.obolibrary.org/obo/BCO_$1"^^ . . . "CLO" . . . . . . . . . . "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line="^^ . . . . . "Contributor Role Ontology" . . "CAE46076"^^ . "http://www.icd9data.com/getICD9Code.ashx?icd9="^^ . "genome" . . . "protein" . . . . "https://odc-sci.org/data/"^^ . "metabolomics" . "http://www.w3.org/2008/05/skos-xl#$1"^^ . "http://www.treefam.org/family/$1"^^ . "homd.taxon" . . "Hypertension Ontology" . "Cell Version Control Repository" . . . "life science" . "Jakob Voß" . . . . . . . . "IPI"^^ . "https://mips.helmholtz-muenchen.de/corum/?id=$1"^^ . . "GlyTouCan" . . "dna" . . . . . "life science" . . "false"^^ . "siren" . . "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"^^ . . . "https://repeatsdb.org/protein/"^^ . "dragondb.protein" . "https://www.cbioportal.org/study/summary?id=$1"^^ . "^[A-Za-z0-9]+$"^^ . "http://ascl.net/$1"^^ . . . . . "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification."^^ . "social and behavioural science" . . "terms4FAIRskills" . "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . . . "The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters"^^ . "MC" . . "Simplified molecular-input line-entry system" . . "false"^^ . . . . . "http://purl.obolibrary.org/obo/PECO_"^^ . . . "Zhiliang Hu" . "https://fairsharing.org/users/"^^ . . . . . . "0000138"^^ . . "phytozome.locus" . "life science" . . . "PANTHER Pathway" . "false"^^ . . . . . . . "trait" . . "^[AEP]-\\w{4}-\\d+$"^^ . "^\\d{7}$"^^ . "haendel@ohsu.edu" . "domain" . "hsa-let-7a-2-3p"^^ . . . . . . "pmid" . . . "reagents" . . . . "https://www.gwascentral.org/marker/"^^ . . . . "false"^^ . "^\\d{7}$"^^ . . "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . . "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . "envipath" . "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^ . . "BAC045"^^ . . "http://purl.obolibrary.org/obo/YPO_"^^ . "https://mmp.sfb.uit.no/databases/mardb/#/records/"^^ . "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1"^^ . . . . "false"^^ . "https://molmedb.upol.cz/mol/$1"^^ . . . "0002502"^^ . "sed-ml.level-1.version-1"^^ . "helpdesk@cropontology-curationtool.org" . "https://www.ncbi.nlm.nih.gov/pubmed/"^^ . . . . . . . "cpt" . . . . "Logical Observation Identifiers Names and Codes" . "false"^^ . "5282"^^ . . . "^\\d+$"^^ . "fbbt" . . . "false"^^ . "Prefix Commons" . . "^[a-zA-Z]+.+$"^^ . . "noncodev4.gene" . . "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. "^^ . "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"^^ . "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^ . "Christophe Dunand" . . "^SKIP\\d+$"^^ . . "Pol Castellano Escuder" . "^\\d{7}$"^^ . "0000001"^^ . "uniprot.taxonomy" . "0000000"^^ . "0000001"^^ . . . . . "ABC"^^ . . . . "sider.drug" . "Diagnostic and Statistical Manual of Mental Disorders (5th Edition)" . . "px" . . . . . . . . "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$"^^ . . . . "RGD Disease Ontology" . . . . . . "ZINC is not Commercial" . "ontology" . "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$"^^ . . . "interaction" . "obo" . . . "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."^^ . "false"^^ . . "^\\d+$"^^ . . "PR" . . . "rnavdb" . "structural biology" . . . . . . "emdb" . "^\\d+$"^^ . "3000887619"^^ . . . . . . . . "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . "Search the world's most comprehensive index of full-text books."^^ . "^\\d+$"^^ . . . . . . . _:N90eef15507124f0fa1fb1d0dc3a6358d . . . "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."^^ . . "fobi" . . . "Common Science and Technology Resources" . "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/"^^ . . "interaction" . "Drosophila RNAi Screening Center" . "van_slyke@zfin.org" . . . "http://purl.obolibrary.org/obo/TRANS_$1"^^ . . . "lotus" . . "life science" . "true"^^ . . . . . . "false"^^ . . . . "Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website)"^^ . "dg.anv0" . . "knowledge and information systems" . . . . "^\\d{7}$"^^ . . . . "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . . "arraymap" . . . "true"^^ . . "Entrez Gene" . "aop.stressor" . . . "toprea@salud.unm.edu" . . . . "venom" . . . "false"^^ . . . "false"^^ . . "bibliography" . . . . . "false"^^ . . . "https://bioregistry.io/mesh.2012:"^^ . . . . "mmp.cat" . . . . . . "uniprot.db" . "false"^^ . . . . "confident.series" . . . . . "NIF Standard Ontology: External" . "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId="^^ . . . . . . . "mark@gersteinlab.org" . . . . . . "subtiwiki" . . . . . "4685"^^ . . "Electron Microscopy Data Bank" . . "false"^^ . . "Web Ontology Language" . . . . . "https://www.ebi.ac.uk/pdbsum/$1"^^ . . . . "mass spectrometry" . . . . . . . . "KEGG.EDRUG" . . . . "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . . . "false"^^ . . "uniprot.location" . . "google.patent" . "food chemistry" . "go.chebi" . . . . . . "http://purl.obolibrary.org/obo/FAO_$1"^^ . . . . "Database of Aligned Ribosomal Complexes" . "mondo" . . "XUO" . . . . . . . "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . . . . . . . "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/"^^ . . . "http://purl.obolibrary.org/obo/ARO_$1"^^ . . . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/GENEPIO_"^^ . . . _:N4ba9bf54b1f64ef4ada718c40befdb0f . "gemet" . . . . . "false"^^ . "^\\w+$"^^ . . "^TF\\w+$"^^ . . "^\\d+$"^^ . . "Sweet Potato ontology" . . . . . _:N3e849f93fd6b41c098a77a2e4cc1935b "Crop Ontology Helpdesk" . "false"^^ . "false"^^ . . "Mental Disease Ontology" . "UniProt journal" . . . "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"^^ . . "http://purl.obolibrary.org/obo/LBO_$1"^^ . . "vipr" . "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1"^^ . . . . . . "ontology" . . "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege."^^ . "knowledge and information systems" . "https://w3id.org/seo#"^^ . "^\\d{7}$"^^ . . "obo" . "false"^^ . "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."^^ . "0000003"^^ . . "false"^^ . "Conference Ontology" . "^\\d{7}$"^^ . . . "https://www.jax.org/strain/"^^ . "false"^^ . . . . . . "0002058"^^ . . "false"^^ . . . . . . . "rebec" . "0000025"^^ . . "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"^^ . . . . . "http://purl.obolibrary.org/obo/AAO_"^^ . . . . "miriam" . . "environmental science" . "^\\d{7}$"^^ . "dragondb.locus" . "unichem" . "life science" . . "computational biology" . . . "biomedical science" . . . "structure" . "http://purl.obolibrary.org/obo/MIRNAO_"^^ . . "Activity"^^ . "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^ . . "Barley ontology" . . "false"^^ . "PGOHUM00000289843"^^ . "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)."^^ . . . "http://purl.bioontology.org/ontology/HCPCS/"^^ . . . . . . . . . "^\\d+$"^^ . "http://www.w3.org/ns/shacl#$1"^^ . . . . "clinvar.variation" . . . . . . "bsu:BSU01340"^^ . . "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . "PIR Superfamily Classification System" . "Manually curated collections of resources stored in the bioregistry"^^ . . . "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."^^ . "PXD000500"^^ . . . "Ribocentre is designed to contain comprehensive information of all natural ribozymes."^^ . "iceberg.ime" . "ToxoDB" . . . "Metabolomics Workbench Study" . "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . . . . "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"^^ . "https://viralzone.expasy.org/$1"^^ . "false"^^ . . . . . "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^ . "false"^^ . "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp"^^ . . . . . . . "rna" . "^UPI[A-F0-9]{10}$"^^ . . "https://biosimulations.org/projects/"^^ . . . _:N07ee20961bd84fde8ab67f99edea1dcc "custserv@nlm.nih.gov" . "ontology" . . "http://www.gramene.org/db/protein/protein_search?protein_id="^^ . "gene" . . . "false"^^ . . . "0000590"^^ . . . "fbcv" . . . "ontology" . . "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_"^^ . "false"^^ . "life science" . "cheminf" . . "http://vocabularies.bridgedb.org/ops#"^^ . "MMs00000001"^^ . . . . "^\\d+$"^^ . . . "9606"^^ . . . . . . . "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym="^^ . . "ped.ensemble" . . . "false"^^ . "Sharkipedia Trait" . . . . . . . . . "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms."^^ . "^\\d{4}$"^^ . . "European Genome-phenome Archive Study" . . . . "structure" . "http://purl.obolibrary.org/obo/FYPO_$1"^^ . . "http://purl.bioontology.org/ontology/NDDF/"^^ . "Prefixes mentioned on the _external_ list on the FHIR [Code Systems](https://hl7.org/fhir/terminologies-systems.html) page. This list is mostly complete. Notably, some entries that have not been curated:\n\n- HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460))\n- [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries\n- [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_\n- [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_\n- [MDC](https://www.iso.org/standard/37890.html) (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation" . . . . . . . . . "ontology" . . . . "false"^^ . . "false"^^ . . . "false"^^ . "^[0-9a-zA-Z]+$"^^ . "bioinformatics" . "false"^^ . "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . . "developmental biology" . . "wbbt" . . . "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."^^ . . "http://edamontology.org/format_"^^ . . . "false"^^ . . . "ons" . . . "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis."^^ . . . "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."^^ . "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."^^ . "AA0001"^^ . . . . "http://scop.berkeley.edu/sccs=$1"^^ . "HMS LINCS Cell" . . . "Alzheimer Gene Database" . . . . . "structure" . . "life science" . . . "false"^^ . "false"^^ . . . . . "WBls" . . . "^[a-z0-9]{32,32}$"^^ . . . . . "dc" . "https://sorgerlab.github.io/famplex/$1"^^ . . . . . "false"^^ . . . "enzyme" . . "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/"^^ . "mobidb" . "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples."^^ . . . "http://purl.obolibrary.org/obo/OHD_$1"^^ . "obo" . . . "TS-0285"^^ . . "OBO Metadata Ontology" . "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^ . . . . "Exposure ontology" . . . . "Provenance, Authoring, and Versioning Vocabulary" . . "Suggested Ontology for Pharmacogenomics" . "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id="^^ . . . "2170610"^^ . "Selventa legacy complex namespace used with the Biological Expression Language"^^ . "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). \r\n\r\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."^^ . . "false"^^ . "pazar" . . "false"^^ . "https://www.kegg.jp/entry/"^^ . . . . . . "false"^^ . "civic.vgid" . . . "genome" . "Identifier for an entity in open tree of life"^^ . "Tobias Schulze" . . "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."^^ . "virsi1909"^^ . "biomedical science" . . . "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . . . _:N9d883e0538e84fd7be2772fc9707b557 . . "^\\d+$"^^ . . "false"^^ . . . "false"^^ . . . "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id="^^ . . . . . "false"^^ . . "false"^^ . "structure" . "cutg" . "AberOWL" . "hsa00190"^^ . . . "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1"^^ . . "^\\d+$"^^ . "metabolites" . . . . . . . . . "http://purl.dataone.org/odo/ECSO_"^^ . "statistics" . . . . . . . . . . . . "false"^^ . . . "obo" . . . "obo" . "NodeShape"^^ . . "Cell line collections"^^ . . "proteomics" . . . "biology" . "^\\d+$"^^ . . . . . . "inaturalist.observation" . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id="^^ . . . . "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . "https://bioregistry.io/wikigenes:"^^ . . . "false"^^ . . . . "RSC3"^^ . . . . "https://biopragmatics.github.io/providers/msigdb/$1"^^ . "obo" . "^RF\\d{5}$"^^ . . "8639.1"^^ . . . "false"^^ . . "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."^^ . . "rgd.qtl" . . . . "762"^^ . . "vmc" . . . . "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"^^ . "50018"^^ . . "molecular physical chemistry" . . "estdab" . "feature"^^ . . . . . "false"^^ . "subject agnostic" . . "Wikidata" . "^WBRNAi\\d{8}$"^^ . "ehdaa" . . "SMP0000219"^^ . . . . "^\\d+$"^^ . . "http://www.jcvi.org/mpidb/experiment.php?interaction_id="^^ . . "Pathguide contains information about 325 biological related resources and molecular interaction related resources."^^ . . "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public."^^ . . . . . . . "2.1.1"^^ . "bioinformatics" . . . . "https://models.physiomeproject.org/exposure/$1"^^ . . "^\\d{7}$"^^ . "medicine" . "infectious disease medicine" . . . "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"^^ . . "E-MTAB-2037"^^ . "5601141"^^ . . "Nonribosomal Peptides Database" . . "589462"^^ . . "Erik van Nimwegen" . "obo" . . . . "skip" . "http://purl.obolibrary.org/obo/TAXRANK_"^^ . "http://purl.org/spar/datacite/"^^ . "edong@umich.edu" . . . "ttd.target" . . . "0003463"^^ . . "obo" . . "^\\d{7}$"^^ . "false"^^ . . . "huang@southalabama.edu" . "https://cropontology.org/rdf/CO_335:$1"^^ . . . "^[A-Z]+[0-9]+(\\.\\d+)?$"^^ . . . "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation."^^ . . "IID00001"^^ . . . "immunology" . . . "ProGlycProt" . "jfernand@um.es" . . . . "zfa" . . "https://www.ebi.ac.uk/QuickGO/GProtein?ac="^^ . . . . "Cowpea ontology" . . . "developed by ICARDA - Dec 2018"^^ . . "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . "false"^^ . . . . . "5112"^^ . . "NIF Cell" . "^[A-Z_0-9]+$"^^ . . . . . "http://www.w3.org/ns/adms#"^^ . . . . . "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1"^^ . "Allergy"^^ . . . . . "molecular biology" . "obo" . . . . . . . . . . . . "carrine.blank@umontana.edu" . "NanoParticle Ontology" . . . . "GenBank" . . . "Disease Drivers Ontology" . . "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"^^ . . "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . "Bacillus subtilis genome sequencing project" . "http://purl.obolibrary.org/obo/PRIDE_"^^ . "gene" . . . . . "bioinformatics" . "comparative genomics" . . . . "ElementNumber"^^ . . "panther.family" . "https://bioregistry.io/metaregistry/ncbi/$1"^^ . . . "publishing" . . "00000"^^ . . "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."^^ . . . "00100005"^^ . . . . . "chemistry" . . . "obo" . "chemistry" . . "http://purl.bioontology.org/ontology/VANDF/"^^ . "false"^^ . . . . . "https://w3id.org/seo#$1"^^ . "ontology" . . . . "dictyBase" . . "Spectra Hash Code" . . . . "life science" . . . "Anatomical Entity Ontology" . . . . . . . "organic chemistry" . "subject agnostic" . . . "^\\d+$"^^ . . "https://www.checklistbank.org/dataset/"^^ . "cheminformatics" . "http://qudt.org/schema/qudt#"^^ . "https://biofactoid.org/document/"^^ . . . . . "CASRAI Contributor Roles Taxonomy" . "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function."^^ . "^\\d{7}$"^^ . . . . . "zoology" . . "development" . "obo_rel" . . "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."^^ . . . . . "http://purl.obolibrary.org/obo/SEP_"^^ . "002678"^^ . . . "go.resource" . "http://purl.obolibrary.org/obo/MOP_"^^ . . . . . . . . . . . . "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="^^ . . . "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"^^ . . . "https://www.fishbase.ca/summary/$1"^^ . . . . . . . . . . . . . . . "https://www.re3data.org/repository/$1" . "false"^^ . "0000049"^^ . "http://www.wikipathways.org/instance/$1"^^ . "version control" . . . "ontology" . . . "dna" . . "Silvio C.E. Tosatto" . . "false"^^ . . "ModelDB concept" . "dg.4dfc" . . . "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid="^^ . "ontology" . "false"^^ . "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities."^^ . . "protein" . . . . . . . . . . . . . . . "https://ssbd.riken.jp/database/project/"^^ . "Semantic Web Context" . "false"^^ . . . "false"^^ . . . . "citlalli.mejiaalmonte@gmail.com" . . "UniProt Chain" . . "https://cropontology.org/rdf/CO_360:"^^ . . . . "Microarray experimental conditions" . "false"^^ . "0000546"^^ . . . . . . . "Foods in FooDB"^^ . . . "An ontology of minimum information regarding potential drug-drug interaction information."^^ . . . . . "Ontology about the development and life stages of the C. elegans"^^ . . . . "STOREDB at University of Cambridge" . "http://viaf.org/viaf/$1"^^ . "bioinformatics" . . "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."^^ . "SNOMEDCT_US_2019_09_01" . . "The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure."^^ . "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."^^ . . . . "https://reporter.nih.gov/project-details/$1"^^ . . . . . . . . . . "false"^^ . . "^G\\d+$"^^ . . "lbctr" . "false"^^ . . . . "tccd" . . "knowledge and information systems" . . "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"^^ . "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."^^ . . . "LOC_Os01g49190.1"^^ . "http://purl.obolibrary.org/obo/TXPO_"^^ . . . "The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies."^^ . "Dublin Core Elements (1.1)" . . . "biodiversity" . . "Pseudomonas Genome Database" . "uniprot.ptm" . "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."^^ . "life science" . "gobpid" . . . . . . "life science" . "https://rarediseases.info.nih.gov/diseases/$1/index"^^ . . "botany" . . "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"^^ . _:Nd63930629486424d9f521aa61488154a . "https://commonchemistry.cas.org/detail?cas_rn="^^ . . "false"^^ . "Brain Architecture Knowledge Management System Neuroanatomical Ontology" . . . "fungidb" . "mba" . . "sopharm" . "protein" . "https://www.uniprot.org/locations/$1"^^ . . "pharmgkb.disease" . "life science" . . "^FOOD\\d+$"^^ . "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:"^^ . "obo" . . "false"^^ . . . "31"^^ . "The ISRCTN registry is a primary clinical trial registry recognised by WHO and ICMJE that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage)"^^ . . "anatomy" . . . "https://www.pharmvar.org/gene/$1"^^ . "false"^^ . . . "Topology Data Bank of Transmembrane Proteins" . . . "molecular biology" . . . . "preclinical studies" . . . "discoverx" . . "http://purl.obolibrary.org/obo/EMAP_$1"^^ . "structure" . . . "https://www.vmh.life/#gene/"^^ . "NCBI_GeneID" . "genome" . "false"^^ . . "bioinformatics" . "http://purl.obolibrary.org/obo/DERMO_"^^ . . . "^\\d{1,9}$"^^ . "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."^^ . "BIOZIL" . . . . . "https://eol.org/pages/$1"^^ . . "ontology" . "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"^^ . "Jianjiong Gao" . "^CLPUB\\d+$"^^ . "https://cropontology.org/rdf/CO_365:"^^ . "https://fungidb.org/fungidb/app/record/gene/$1"^^ . . "sequence" . . . "nfdi4chem.cao" . "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . . . . . . . "^PPR\\d+$"^^ . "ontology" . "OSR00185W"^^ . . "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^ . . "^HBG\\d+$"^^ . . . . . "^[a-z_A-Z0-9]+$"^^ . . "http://aims.fao.org/aos/agrovoc/c_$1"^^ . "Ecological terms"^^ . "^SLCTR/\\d{4}/\\d+$"^^ . . . . . "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^ . "ontology" . . . "salk" . . . . . "Application ontology for entities related to insecticide resistance in mosquitos"^^ . "315.1"^^ . "jaxmice" . . "trichdb" . "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"^^ . "biomedical science" . . . . "cellular neuroscience" . . "Subcellular Anatomy Ontology" . . "life science" . "595"^^ . . "ontology" . "systems biology" . "https://www.uniprot.org/arba/$1"^^ . "http://purl.obolibrary.org/obo/CHMO_$1"^^ . . . "microbiome" . . . "^NCT\\d{8}$"^^ . "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"^^ . "^MF_\\d+$"^^ . . "Coriell Institute for Medical Research" . . . . . . "obo" . . . . . "^\\d+$"^^ . "https://www.uniprot.org/database/$1" . "ontology" . . . . . . . . "https://www.wikidata.org" . . . "https://github.com/biolink/biolink-model" . . . "0100010"^^ . . "exac.variant" . . . . "https://cropontology.org/rdf/CO_345:"^^ . . . . . "genetics" . _:N07ee20961bd84fde8ab67f99edea1dcc "NLM Customer Service" . "small molecule" . . "http://purl.obolibrary.org/obo/ECAO_$1"^^ . . . "PDB Structure" . . "Image Data Resource" . "http://id.who.int/icd/entity/"^^ . . . "yid" . "casspc" . "dandi" . . "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity."^^ . . . "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.pharmgkb.org/gene/$1"^^ . "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . . . . . . "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^ . . "false"^^ . . . . . . . . . . "Ontology of Physics for Biology" . . . "gc_id" . "false"^^ . "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . . . . . . "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."^^ . . . "ontology" . . . . . . . "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster="^^ . . . "Complex Portal" . . "http://darcsite.genzentrum.lmu.de/darc/view.php?id="^^ . . "https://cropontology.org/rdf/CO_327:$1"^^ . . "FOOD00020"^^ . "21723"^^ . . . . . "http://purl.obolibrary.org/obo/HOM_"^^ . "cell_biolabs" . . . "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"^^ . . . . "Bioregistry Collections" . . "http://purl.obolibrary.org/obo/NOMEN_$1"^^ . . . . . "sedml.format" . . . . . . "^\\d+$"^^ . . . . "false"^^ . . "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein="^^ . . "biomedical science" . . "genomics" . "false"^^ . . . "^(ev\\:)?E\\d+$"^^ . "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" . . . . . "unipathway.reaction" . "Rice Genome Annotation Project" . "false"^^ . . . "lncipedia" . . . . . . "000000341"^^ . "false"^^ . . "^KW-\\d{4}$"^^ . "0000858"^^ . . . "iceberg.element" . . . . . "^\\d{7}$"^^ . "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id="^^ . . . . . . . "A set of guides on implementing various processes within hospitals or healthcare systems."^^ . . . . "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."^^ . . . "ontology" . "http://repository.topdownproteomics.org/proteoforms/$1"^^ . . . . . . "false"^^ . . "brendanx@uw.edu" . . "CH_001923"^^ . "C063233"^^ . "Omar Harb" . "biomedical science" . . "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=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 Drosophila data."^^ . . . . "natural history" . . . "FuncBase Fly" . . . "https://thebiogrid.org/interaction/$1"^^ . . "Person"^^ . . "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . . "1"^^ . "term"^^ . . . . . . "068078"^^ .