"https://nanocommons.github.io/identifiers/registry#$1"^^ . . "sgn" . . . . . "Cell Biolabs cell line products" . "Jakob Voß" . "clinvar.submitter" . "dggr" . . . "https://www.jax.org/strain/"^^ . . . . . . "mpath" . . . "https://www.sharkipedia.org/traits/$1"^^ . "ND50028"^^ . "ontology" . . . . "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER."^^ . _:Ncec661c1c76848d8a02c89fa39775417 "nospam@iandavis.com" . . "annotation" . . "scdo" . . . . "false"^^ . . . . . . . . . "false"^^ . "HBG004341"^^ . "false"^^ . "Michael K. Gilson" . . "Protein Alignment organised as Structural Superfamily" . "ecolexicon" . . . . "life sciences" . . . "Nicole Vasilevsky" . "life science" . _:N8f287a15652444e6a1ab1f96fade6ae1 . "NCATS Drugs" . . . "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1"^^ . . . . . . . "agriculture" . . . . . . . "PhosphoSite Protein" . . . "SYMP" . . . . . "53784"^^ . . . . "mge" . . . . . . . "IUPAC Gold Book Compendium of Chemical Terminology" . . . . "Human Protein Reference Database" . "http://purl.obolibrary.org/obo/AMPHX_"^^ . . . . "UMR7315"^^ . "protein" . . . "^[A-Za-z0-9]+$"^^ . . . "^\\d+$"^^ . "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . . . "Database of RNA Junctions and Kissing loop Structures" . . . . . "botany" . "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products."^^ . "ontology" . . . . . . "panorama" . "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"^^ . . . . . . . . "false"^^ . . "0000000"^^ . . . "cells" . . . . "chemical entity" . "noncodev4.gene" . "ontology" . . "protein" . . . . "AberOWL" . . . . "ontology" . . . . "http://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF."^^ . . . . . . "http://purl.obolibrary.org/obo/SO_"^^ . "ontology" . . . . "Alpha Tom Kodamullil" . "genetics" . . . "knowledge and information systems" . . . "David Sehnal" . . . . . "obo" . . . . . . . . "^[A-Za-z 0-9]+$"^^ . "RE" . . . . "food" . "histology" . . . . "protein" . . . . "MaizeGDB Locus" . . . . . . "^\\d*$"^^ . . . . "030719"^^ . . "CYP2A6"^^ . . . . . . "life science" . . "^\\d+$"^^ . "Basic Formal Ontology" . "gramene.growthstage" . "false"^^ . . . . . . . . "0000071"^^ . "unipathway" . . . "Alan Rubin" . . "Ada Hamosh" . "0778"^^ . . . . "teresa.k.attwood@manchester.ac.uk" . . . . "https://bioregistry.io/vipr:"^^ . . . . "90901"^^ . . . . . . . . . . . . . "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1"^^ . "http://purl.jp/bio/4/id/$1"^^ . . . "false"^^ . . . . . . . . . . "CHEBI" . "biology" . "^\\d+$"^^ . "AKR-270"^^ . . . "mesh.2013" . "http://purl.obolibrary.org/obo/ATO_$1"^^ . . "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases."^^ . "^CHEMBL\\d+$"^^ . . . "false"^^ . . . . . . . . "loqate" . . . "Shuichi Onami" . . . "interaction" . "gene expression" . . . . "http://www.iclc.it/details/det_list.php?line_id="^^ . "uberon"^^ . . "Rice Metabolic Pathways" . "^\\d+$"^^ . . "genetics" . . . . "false"^^ . "http://purl.obolibrary.org/obo/YPO_$1"^^ . "rbeavis@thegpm.org" . . . . "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$"^^ . . "pathway" . "anatomy" . . . . "0000001"^^ . "NCBI_Taxon_ID" . "interaction" . . . . . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . . . . . . . "Minimum PDDI Information Ontology" . "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species."^^ . . "Selventa legacy chemical namespace used with the Biological Expression Language"^^ . . . . . . . "phylomedb" . . . . "characterisation data heat" . . . . "frbr" . . . _:Nae36e2aebfee4e58acbcb8a52f217512 . "http://www.genome.jp/dbget-bin/www_bget?cpd:"^^ . . . . "PELNAW"^^ . . . . "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://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"^^ . "https://eds.gene.le.ac.uk/home.php?select_db=$1"^^ . . . . . . "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . _:N675fee80caff42db81030ecf60b6eab2 . . "life sciences" . "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^ . "Anne Thessen" . . . "seo" . . . . "false"^^ . . "Degradome Database" . . "Pazar Transcription Factor" . . . "^[SED]R[APRSXZ]\\d+$"^^ . . "https://www.cancerrxgene.org/translation/Drug/$1"^^ . "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . . "genomics" . . . "http://pax-db.org/#!species/"^^ . "http://purl.bioontology.org/ontology/NDDF/$1"^^ . . . "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands."^^ . "4685"^^ . . . . . . . . "00005643"^^ . . . . "https://senselab.med.yale.edu/ModelDB/ModelList?id=$1"^^ . "icdc" . . . . . . . . "virology" . . "http://mods.rna.albany.edu/mods/modifications/view/"^^ . "^\\d+$"^^ . "nikolaos.moustakas@catalysis.de" . . "false"^^ . "hmdb" . . "false"^^ . "ARBA00000001"^^ . . "SysBioCancer2022"^^ . . "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid="^^ . . . . . . "true"^^ . "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$"^^ . . . . . . . "biomedical science" . "srvoss@uky.edu" . "gorel" . "272"^^ . . "ArrayExpress Platform" . "ChEMBL-Targets" . . . . "RF00230"^^ . "citation" . . . "false"^^ . "Sanger Cell Model Passports" . . . . . . "br/1"^^ . "https://creativecommons.org/ns#$1"^^ . . "https://pk-db.com/data/$1"^^ . "transposon" . . . "faseb list" . . . "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"^^ . . "true"^^ . . . . . . . . . "interoperability" . . . "life science" . . . . "false"^^ . . . . _:N9e47917e61904b6ca52093f043990cdc . . . "anatomy" . . . "UMLSSG" . . . "odrl" . . . . "cameo" . "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"^^ . . . . "stem cell" . "false"^^ . . . "bspo" . . . "obo" . . "ontology" . "swh" . "Hymenoptera Anatomy Ontology" . . "food" . "hhe@ebi.ac.uk" . . "KW-1273"^^ . "The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage)"^^ . "^\\d{7}$"^^ . . . . "The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities."^^ . . . . "obo" . . "false"^^ . "stefanie.seltmann@ibmt.fraunhofer.de" . . "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$"^^ . . . . . . "structure" . . . "http://www.iclc.it/details/det_list.php?line_id=$1"^^ . "wes_schafer@merck.com" . "dna" . . . . "WikiPathways" . . "asap" . . "https://www.ebi.ac.uk/biomodels/"^^ . "Dan Brickley" . "linguistics" . "biology" . . . "^\\d{1,7}\\-\\d{2}\\-\\d$"^^ . . . . . . . "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . "false"^^ . . . "RIKEN Bioresource Center Cell Bank" . "^[A-Z0-9]{6,7}$"^^ . . "false"^^ . . . . . . . "NM_006262"^^ . . . "0000001"^^ . "life science" . . . . . "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes."^^ . "semantic web" . . "genomics" . . "false"^^ . . _:Nbbc79547cdff4e5c9df18bd7c99700af . "gene" . "false"^^ . . "contact@bacdive.de" . . . "idr" . "mfmo" . "dsm-v" . . "https://biosimulations.org/projects/$1"^^ . . . "Identifier for an animal, plant, or microorganism from the fossilworks website"^^ . . . . . . . . . . . . . "https://rfam.org/family/"^^ . "medicinal chemistry" . . . "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"^^ . . . . . . . . . "idoden" . . "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . . . "^WB[A-Z][a-z]+\\d+$"^^ . . . "false"^^ . . . "false"^^ . . . . _:N452d5df5d4174c6ea0a4aed0f83019b6 . "false"^^ . . . "kegg.dgroup" . . "^\\d+$"^^ . . . "false"^^ . "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$"^^ . . "https://www.fishbase.ca/summary/"^^ . . . "false"^^ . _:Nd45bb82a739d443a9a81f0bffd8efefc "helpdesk@cropontology-curationtool.org" . . . . . "obo" . "Chemspider" . . . . . . . . . . . . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"^^ . . "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries."^^ . . "^\\d{6}$"^^ . . . "Health Canada Drug Identification Number" . . "NLXORG" . "bioportal" . . "https://cropontology.org/rdf/CO_330:"^^ . . . . "^[A-Za-z0-9\\-\\_]+$"^^ . . . . . "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . . "ViolinNet" . "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."^^ . "life science" . . . . "protein" . "https://bioregistry.io/ipi:"^^ . "X58356"^^ . . . . . . "BioPortal Prefixes" . . "ontology" . . . . "noncodev3" . . "https://bioregistry.io/imgt.primerdb:"^^ . . . . . . . "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/)]"^^ . "http://www.whocc.no/atc_ddd_index/?code=$1"^^ . "http://www.w3.org/2002/07/owl#$1"^^ . . "http://www.w3.org/ns/prov#"^^ . "SugarBind" . "false"^^ . . "PROSITE" . "^MIRT\\d{6}$"^^ . . . . . "false"^^ . . . . . . "phenotype" . . "phenotype" . . "life science" . . "obo" . "false"^^ . . . . "obo" . . . "data model" . . . . "^\\d+$"^^ . . "konigmatt@googlemail.com" . "life science" . . . . . . . . "CQG5"^^ . "peco" . . "https://www.vmh.life/#reaction/$1"^^ . . "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines." . . . . . . . "http://purl.obolibrary.org/obo/TAHH_"^^ . . . "ontology" . . . . "eu89h" . "mesh.vocab" . _:N554742b5d5ea45529b998c824a4e7c6a . . . . . . "mathematical model" . . "wikipathways" . . "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"^^ . . . . . . "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"^^ . . . "meghan.balk@gmail.com" . "ror" . "false"^^ . "anatomy" . . "https://aopwiki.org/relationships/"^^ . . . . . "engineering science" . . . . . "The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/)."^^ . . . "protein" . "http://purl.obolibrary.org/obo/PW_"^^ . "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . . . . "epigenetics" . "co_323" . . "grin" . . . "true"^^ . . . . . "G17689DH"^^ . "http://purl.obolibrary.org/obo/MAXO_$1"^^ . . . "phenotype" . "^\\w+$"^^ . . "environmental science" . "genome" . . . . . . "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]."^^ . "pathway" . . . "Health Procedure Ontology" . . . . . . . . "^\\d+$"^^ . . "^\\d{7}$"^^ . "https://cropontology.org/rdf/CO_339:"^^ . "https://tree.opentreeoflife.org/taxonomy/browse?id="^^ . "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^ . "The World-2DPAGE database" . . "nxr" . "https://senselab.med.yale.edu/ModelDB/ModelList?id="^^ . . "bmrb.restraint" . "4900"^^ . "Glycosciences.DB" . "rna" . "https://pb.apf.edu.au/phenbank/strain.html?id=$1"^^ . "Radiomics Ontology" . "sequence feature" . . . "^\\d{7}$"^^ . "false"^^ . . "ecology" . "ontology" . . . "topics" . "http://www.kegg.jp/entry/"^^ . "http://purl.obolibrary.org/obo/OBIB_"^^ . . "false"^^ . . "Proteomics data and process provenance" . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . "biomedical science" . . . . "Zach Landis-Lewis" . . . "LDS-1110"^^ . "^\\d{7}$"^^ . "adeans@psu.edu" . "biomedical science" . . . "http://purl.obolibrary.org/obo/ZP_"^^ . . . . "obo" . _:N29cffc1ec179407e8925a065fa656ab4 "FALDO group" . . . . . . "mi" . . . . . . "small molecule" . "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"^^ . "ontology" . . "http://purl.obolibrary.org/obo/TAHE_$1"^^ . "G02681"^^ . . . . . . "https://www.mavedb.org/#/experiments/urn:mavedb:$1"^^ . . "http://www.bioinfo.org/NONCODEv4/show_rna.php?id="^^ . "botany" . "false"^^ . . "Illumina Probe Identifier" . . . "ACTRN" . "false"^^ . "false"^^ . "pfey@northwestern.edu" . "^\\d{7}$"^^ . "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary."^^ . . . "project management" . "geochemistry" . "^\\d+$"^^ . . . "M0001"^^ . . . . . . "life science" . . . "https://pk-db.com/data/"^^ . "Common Bean ontology" . . "http://purl.obolibrary.org/obo/CIDO_"^^ . "tigrfam" . . . . "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana."^^ . "dbvar.variant" . "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"^^ . "tissue" . . "hc.din" . "^\\d{7}$"^^ . . . . . . . "seed.reaction" . "life science" . . . "http://purl.obolibrary.org/obo/CDAO_$1"^^ . "transcriptomics" . . . "abcd" . . . . . "developmental biology" . . "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS."^^ . "Genomics Cohorts Knowledge Ontology" . . "QJ51RV02"^^ . . . . . . . . "cell" . . . . . . . "AOPWiki (Key Event Relationship)" . . . . . . . . "https://cropontology.org/rdf/CO_350:$1"^^ . . "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers."^^ . . . "report" . "genomics" . "knowledge and information systems" . . . . . "taxonomy" . . "http://purl.org/spar/datacite/"^^ . "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)"^^ . . . . "http://w3id.org/nfdi4ing/metadata4ing#$1"^^ . . . "hidden markov model" . "false"^^ . . "https://www.flymine.org/flymine/report/ChromosomeBand/$1"^^ . "http://purl.obolibrary.org/obo/SIBO_"^^ . . "false"^^ . . . . "https://registry.identifiers.org/registry/"^^ . . . "SNOMEDCT_US_2023_11_01" . . "Jawahar Swaminathan" . . "http://fossilworks.org/?a=referenceInfo&reference_no="^^ . "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis."^^ . . "Global Research Identifier Database" . . . . "DisProt region" . . . . . "facebase" . . . . . . "sedml.language" . . . "vfb" . . . . . . . . "https://dgrc.bio.indiana.edu/product/View?product="^^ . . "ontology" . . . . . "false"^^ . . "RCB0002"^^ . . . . "false"^^ . "dsonensh@odu.edu" . . "annotation" . "64ba"^^ . "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId="^^ . . . "topics" . . "Human Genome Variation Society Nomenclature" . "molecular biology" . . . . "bioRxiv" . . . "model organism" . "^(\\d{8}|(\\w+\\d+\\w+))$"^^ . . . "barrett@ncbi.nlm.nih.gov" . . . . . "false"^^ . . "obo" . "2000191"^^ . . . . . "00050"^^ . . . "Database for Prokaryotic Operons" . "brain imaging" . . . . . . . . "http://igsn.org/"^^ . "Pierre-Marie Allard" . . . "https://www.ncbi.nlm.nih.gov/nuccore/"^^ . "subject agnostic" . "CC2(C)C\\1CCC(C)/C=C/12"^^ . . . "false"^^ . . . . "SNR17A"^^ . "Blue Brain Project Topological sampling Knowledge Graph" . "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories."^^ . "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"^^ . . "nif_subcellular" . . . . "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^ . . . . . . "classification" . . "^c\\d+$"^^ . . . . "protocol" . . . "http://purl.obolibrary.org/obo/DINTO_"^^ . "model" . . "^\\d{7}$"^^ . "sbml.level-3.version-2"^^ . . "http://purl.obolibrary.org/obo/ENVO_"^^ . . . "https://terminology.hl7.org/CodeSystem-v3-"^^ . . "FundRef" . . . . . . . . . "laia.subirats@gmail.com" . . . . . . "false"^^ . . "0009089"^^ . . "false"^^ . "http://purl.obolibrary.org/obo/SIBO_$1"^^ . . "genomics" . . . . "ontology" . . "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"^^ . . "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease."^^ . "embryonic stem cell line" . "bacdive" . . . "^HMDB\\d+$"^^ . "false"^^ . "pypi" . . . "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . "diagnosis" . . "biochemistry" . . . . . . "alan.rubin@wehi.edu.au" . "Applied Biological Materials cell line products" . "Ontology for computer aided process engineering" . . . "functional genomics" . . "structural biology" . . . "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1"^^ . . . . . "gitlab" . . "http://purl.obolibrary.org/obo/PLANA_$1"^^ . . "1000100"^^ . "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view."^^ . . "http://purl.obolibrary.org/obo/SBO_"^^ . . . "obo" . "Alzforum_mut" . "structure" . . "9606"^^ . . . "aaeA"^^ . . "false"^^ . "phylogeny" . "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1"^^ . "^[0-9]+$"^^ . "https://www.ensembl.org/id/"^^ . "HOSAPI0399"^^ . "Vocabulary used in the RDF representation of SBML models."^^ . . "proteomics" . . "438782"^^ . "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE."^^ . "https://cameochemicals.noaa.gov/chemical/$1"^^ . "0005926"^^ . "^[0-9a-fA-F]{32}$"^^ . "sisu" . . "http://viaf.org/viaf/$1"^^ . "genomics" . . . . "LIPID_MAPS_class" . . . . "genprop" . . . "health science" . . . "Charles Ettensohn" . . . . "montana.smith@pnnl.gov" . "^[A-Z]+[0-9]+$"^^ . . "ontology" . . . "^8\\d{4}$"^^ . "small molecule" . "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id="^^ . . . . "neuroscience" . . . "false"^^ . . . . "Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project." . . . "mfomd" . "UMLS" . "false"^^ . . . "^\\d+$"^^ . . "false"^^ . . . "^\\d{7}$"^^ . . "qtldb" . . . . . . "http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1"^^ . . "Unified Code for Units of Measure" . . . "false"^^ . "Database of human Major Histocompatibility Complex" . "UM-BBD_ruleID" . . _:N80cbcd52618948a5867f9c33561a4aeb "Jan Willis, NLM" . . "Project"^^ . . . . . . "^\\d+$"^^ . . . "235" . "International repository of Adverse Outcome Pathways."^^ . "chembl" . . . . . "life cycle" . . "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1"^^ . . . "false"^^ . . . . . "Identifier for a journal article in the fossilworks website"^^ . "https://www.re3data.org/repository/"^^ . . "false"^^ . "dna" . "http://www.phosphosite.org/siteAction.do?id="^^ . . . "A structured controlled vocabulary for the anatomy of fungi."^^ . . . . . . . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/DDPHENO_$1"^^ . . "S6"^^ . . "prov" . . "CPD-10330"^^ . "75"^^ . . "Jörg Wicker" . . "0001"^^ . . "unit" . "https://models.physiomeproject.org/exposure/$1"^^ . . . "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . . . "false"^^ . "structrual bioinformatics" . . . "M3G stands for “Metadata Management and distribution system for Multiple GNSS Networks”. M3G allows to upload, validate, and distribute GNSS station metadata such as IGS-style site logs, information about local networks, DOIs, nominal data provision, data licenses attached to the daily RINEX data, etc..."^^ . "https://web.expasy.org/abcd/ABCD_$1"^^ . "^PTN\\d{9}$"^^ . "https://zenodo.org/record/"^^ . . "aaindex" . "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research."^^ . . . "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . . "ECMDB" . . . "false"^^ . "natural history" . "structure" . . . . "time" . "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used."^^ . . . . . "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"^^ . . . . . "^\\d{8}$"^^ . . "GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio."^^ . "Pfam Clans" . "w3c rec" . . "http://purl.obolibrary.org/obo/SLSO_"^^ . . . . "https://www.xenbase.org/entry/$1"^^ . "fungorum" . . "obo" . . _:N02215f8b79c94205b423321cccd2c962 "Crop Ontology Helpdesk" . "ontology" . "biomedical science" . . "false"^^ . . . . "false"^^ . . . . . . "ontology" . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"^^ . . . . . . . . "MSH2010_2010_02_22" . . . "https://gudmap.org/id/"^^ . . "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . . . . . . "rna" . "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"^^ . . . . "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms"^^ . "cell" . . . "0001807"^^ . "NINDS Human Cell and Data Repository" . . . . "Elizabeth Arnaud" . . "https://cropontology.org/rdf/CO_326:$1"^^ . "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort."^^ . . . . "284196006"^^ . . . . . . . . "obo" . . . . . . . . . . "^[0-9]+$"^^ . . . "database" . . . "bel" . "medicine" . "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme."^^ . . . . "Gavin Sherlock" . . . . . "animal" . . "ECMDB00005"^^ . "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id="^^ . . . . "voc4cat" . "Hazardous Substances Data Bank" . . . "http://purl.obolibrary.org/obo/ORNASEQ_"^^ . "enzymology" . "80001"^^ . "anatomy" . . . . . . . "nlfff" . "false"^^ . . "Insect Resistance Ontology" . . "Yvonne Bradford" . . "d.e.starns@liv.ac.uk" . . . "The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals."^^ . . "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"^^ . "http://purl.obolibrary.org/obo/T4FS_"^^ . . . . . "judith.blake@jax.org" . . . . "to" . "social science" . . . "Protein Model Portal" . "gaz" . . . . . . "yongqunh@med.umich.edu" . . _:N833306e1b1f5424d97974ffc4ab537e9 "Crop Ontology Helpdesk" . . "http://purl.obolibrary.org/obo/NGBO_"^^ . . . "co_370" . . "false"^^ . "genome" . "biology" . "Nucleotide Sequence Database" . "Merck Millipore (EMD Millipore)" . . "Kim Dixon Pruitt" . . . . "A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots."^^ . . . "FDB002100"^^ . "^DI-\\d{5}$"^^ . . "^\\d+$"^^ . . . "HOSO is an ontology of informational entities and processes related to healthcare organizations and services."^^ . "S000002493"^^ . . . . "skos" . . . . . . . . "chemical" . . . "structure" . . "nif.ext" . "Cowpea Trait Dictionary in template v5 - IITA - August 2015"^^ . "noaa" . "http://igsn.org/$1"^^ . . "biology" . . . . "false"^^ . . "^TC\\d+$"^^ . "commoncoreontology" . . "3966782"^^ . "https://civicdb.org/links/sources/"^^ . "MEROPS Clan" . . . . _:N8f287a15652444e6a1ab1f96fade6ae1 "Jan Willis, NLM" . . "ontology" . . . . "life science" . "NLXSUB" . . "https://www.kegg.jp/entry/"^^ . . . "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"^^ . . . . . . . . . . . . "authorea.author" . "rna-seq" . . "https://www.gwascentral.org/phenotype/"^^ . . . . "biomedical science" . "false"^^ . . "https://cropontology.org/rdf/CO_325:"^^ . . . . . "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . . . "Wormpep" . . . . "https://jrct.niph.go.jp/en-latest-detail/$1"^^ . . "toni.gabaldon@crg.eu" . . . . . "^\\d+$"^^ . . . . . . . "true"^^ . "^AC[0-9]{8}$"^^ . "^\\d{10}$"^^ . . . "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^ . "https://www.gwascentral.org/marker/$1"^^ . "occo" . . "medgen" . . . "urgi-contact@versailles.inra.fr" . . . "mathematical model" . . "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it."^^ . . "map" . . _:Ne38cefa1b7b748d98dc227b75908f096 . . "Cancer Cell Line Encyclopedia Cells" . "We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage)"^^ . "fungi" . . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"^^ . . . . "https://web.expasy.org/abcd/ABCD_"^^ . . . "false"^^ . "ontology" . . . . . . . . . "0000091"^^ . . "^[0-9]+$"^^ . . "false"^^ . . "biomedical science" . "smpdb" . "mirte" . "https://ocid.ontochem.com/prefname?ocid="^^ . . . "false"^^ . . . . "https://knowledge.lonza.com/cell?id=$1"^^ . . . . . . "https://www.geonames.org/"^^ . "false"^^ . . . "bibliography" . "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research."^^ . "^\\d+$"^^ . "false"^^ . . . . "life science" . "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$"^^ . "PANTHER Pathway Component" . . . . . . "gene expression" . . "Vital Sign Ontology" . "true"^^ . . . . "environmental science" . . . . "mathematics" . "101"^^ . . "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. "^^ . "obo" . . . . . . "bsweeney@ebi.ac.uk" . . . . "complexportal" . "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative."^^ . "oryzabase.gene" . "https://www.thermofisher.com/antibody/product/"^^ . . _:N80cbcd52618948a5867f9c33561a4aeb . . "GCF_000005845.2"^^ . . "ontology" . "http://geneontology.org/docs/gene-product-information-gpi-format/#$1"^^ . . "Cellosaurus Registry" . "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid="^^ . . . "neuroscience" . "Pierre Grenon" . "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . "EMLSAT00000003403"^^ . . "a.kikhney@embl-hamburg.de" . . "d.a59037e8"^^ . . "dbmhc" . . "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . . . . . . . . . "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^ . . . "has reviewer" . . "https://bioregistry.io/spike.map:"^^ . . . . . . "Assists in resolving data across cloud resources."^^ . . . . "BRIP1"^^ . . "DTXSID2021028"^^ . "damion_dooley@sfu.ca" . "proteomics" . . . "https://openalex.org/$1"^^ . "plant phenotypes and traits" . . . . . . . . . . . "agriculture" . . . . . "^\\d{7}$"^^ . . . "dylan.mcgagh@magd.ox.ac.uk" . "AT4G01080"^^ . . "life science" . . . "System Science of Biological Dynamics dataset" . . "fossilworks.journal" . "bioinformatics" . . . . . . "false"^^ . . . . . . . . . "oma.protein" . . . "davidos@ebi.ac.uk" . . . . . "^\\d{8}$"^^ . . . . . . "disease" . . "strain" . . "tto" . . "The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library"^^ . . . . . . . "240-17-488-3-4-12"^^ . . . . . . . . . . . . "ohara@kazusa.or.jp" . . . "strain" . . "http://purl.org/spar/cito/"^^ . "Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation."^^ . . . . . . "^\\d{7}$"^^ . . . "false"^^ . . . _:N560c1b9b384a4f05be40aadc76ea025d . . . . "experiment" . . . . . "Spider Ontology" . . . "C12345"^^ . "^\\d+$"^^ . . "^TF\\w+$"^^ . "HGNC Gene Group" . . "http://degradome.uniovi.es/cgi-bin/protease/$1"^^ . . . . . _:N67bba369e0514790a627d10e8fd5af6d "radlex-feedback@lists.rsna.org" . "cognition" . "BioSimulators" . . . . . "false"^^ . . . . . . _:N8e7200565e95498cbc33e59130e8e542 . . . "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."^^ . "DragonDB Allele" . . . "Maude Pupin" . "WB" . "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"^^ . "Metabolic Encyclopedia for Pathway/Genome Databases" . . . "sean@arabidopsis.org.uk" . . "knowledge and information systems" . . "false"^^ . . . . . "Phenoscape Publication" . . . . . . "Transporter Classification Database" . . . . . . "https://bioregistry.io/hssp:"^^ . . "Immune Epitope Database" . . "demographics" . . . . . "https://w3id.org/nmdc/"^^ . . . . . _:Na498744430974b0f965343f882a62ba4 . . . "false"^^ . . . . "610"^^ . . "4447"^^ . "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"^^ . . "Unique Ingredient Identifier" . "openWEMI Vocabulary" . . . "shoshana@sickkids.ca" . "^\\d+$"^^ . "bioinformatics" . "publishing" . . . . . . _:N554742b5d5ea45529b998c824a4e7c6a "j.bard@ed.ac.uk" . . . . . . . . . . . . "http://www.w3.org/ns/dcat#"^^ . "mir" . . . . . . "http://www.kegg.jp/entry/$1"^^ . . . . . "homologous" . . . . "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . "bibliography" . "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^ . "disease" . . . . "false"^^ . . "biochemistry" . "false"^^ . . . . "rs121909098"^^ . "https://registry.identifiers.org/registry?query=MIR:"^^ . . . . "The DevTox Project harmonizes the nomenclature used to describe developmental anomalies in laboratory animals, assists in the visual recognition of developmental anomalies with the aid of photographs, and provides a historical control database of developmental effects in laboratory animals."^^ . . "LINCS Small Molecule" . . "Lin Huang" . . . . . "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration)."^^ . . . "gdc" . . . . "^\\d+$"^^ . "ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG)."^^ . . . "livestock" . "Joel Richardson" . . . "sequence alignment" . "PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them."^^ . . "molecular function" . . "GlyGen Computational and Informatics Resources for Glycoscience" . . . . "ontology" . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_res_"^^ . "assay" . . . . . . "model organism database" . _:Nc8de2d34560649929fc1996dfc57b425 "Crop Ontology Helpdesk" . . "false"^^ . "European Food Information Resource Network" . . . . . "protein" . . "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus."^^ . "ALX-210-175"^^ . . . "ontology" . . "mental health" . . . "false"^^ . . . "false"^^ . "CALM1"^^ . . . . "Brian Aevermann" . "reactome.pathway" . "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"^^ . "CLV_MEL_PAP_1"^^ . "http://terminology.hl7.org/CodeSystem/v2-$1"^^ . . . "prediction" . . . . . . "595"^^ . "SPIKE Map" . . . "structure" . "^\\d+$"^^ . . . "life science" . . "Rafael Richards" . . "Michael Feolo" . . "AURKA"^^ . . . "STOREDB at University of Cambridge" . . . . . . . . . . . . . "^ML\\w+$"^^ . "protein families" . . . . "bactibase" . . . . . . . . . . . "http://purl.obolibrary.org/obo/NIF_CELL_"^^ . . "protein" . . "^[a-z][a-z0-9_]+[a-z0-9]$"^^ . . "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery."^^ . . . "mesh" . "http://purl.obolibrary.org/obo/HTN_$1"^^ . . . . . . . . . "^[\\w\\d\\.-]*$"^^ . . . "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."^^ . . . . "^(?:\\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\\d+)?)$"^^ . "http://purl.obolibrary.org/obo/CL_"^^ . "life science" . "wosid" . . "TTDS00056"^^ . . "Functional Requirements for Bibliographic Records" . . . "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id="^^ . "ark" . . . . . "false"^^ . "^\\d+$"^^ . "ontology" . "EAWAG Biocatalysis/Biodegradation Database" . . "olatdv" . . "centrally registered identifier" . "Rice Genome Annotation Project" . . . . "http://autism.mindspec.org/GeneDetail/"^^ . . "myco.smeg" . "clinical studies" . . . . . "false"^^ . . . . . . "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.\n\nNote that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States."^^ . . . . "Datasets inside StoreDB"^^ . "drugs" . . . . "^\\d{7}$"^^ . . . . . . . . . . . . . . "http://purl.obolibrary.org/obo/CHEBI_$1"^^ . . . . . . . "^NOR\\d+$"^^ . . "http://purl.obolibrary.org/obo/CTENO_$1"^^ . . "false"^^ . . "https://metacyc.org/compound?orgid=META&id=$1"^^ . "blast" . "https://www.re3data.org/repository/$1"^^ . "rna" . . . . . . . "https://mediadive.dsmz.de/medium/"^^ . "An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date."^^ . . "Ontology for Biomedical Investigations" . . . . . "https://www.drugbank.ca/categories/"^^ . . . "false"^^ . . "207LH0002X"^^ . "uniprot.chain" . . . "interfil" . "cells" . . . . . . "https://www.inaturalist.org/users/$1"^^ . . . . . . . "https://vac.niaid.nih.gov/view?id=$1"^^ . . . . "ontology" . . . "false"^^ . . "agriculture" . . . "classification" . . "^K\\d+$"^^ . "cbioportal" . . . . . "A type for entries in the Bioregistry's collections" . . . . "false"^^ . . "FlyBase Gene" . . "GlycoNAVI" . . . . "^\\d{7}$"^^ . "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies."^^ . . "database management" . . "0000609"^^ . . "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes."^^ . "https://cropontology.org/rdf/CO_343:"^^ . . . . . . . "https://www.ndexbio.org/viewer/networks/$1"^^ . . . . . . . "medicine" . . "time" . . . "cellbank.australia" . "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1"^^ . . . "Internet Standard -- IETF Request for Comments" . "deepak.unni3@gmail.com" . "5046"^^ . "false"^^ . . . . . "Identifier used by the Cancer Chemotherapy National Service Center."^^ . . . . . . "https://scicrunch.org/resolver/RRID:NXR_$1"^^ . . "environmental science" . . . "http://search.sisuproject.fi/#/variant/"^^ . . . "Integrated Taxonomic Information System" . "100"^^ . . "431472"^^ . "metadata" . . . . "false"^^ . . . . . . "doi" . "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName="^^ . . . . . . . "ProtoNet Cluster" . . "MRA-253"^^ . . "false"^^ . . . . "faseb list" . "https://bioregistry.io/elm:"^^ . . "Veterans Administration National Drug File" . . . . . "https://www.ncbi.nlm.nih.gov/datasets/genome/"^^ . . "^[1-9]\\d*$"^^ . . "pubchem.substance" . . . . . "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations."^^ . "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid="^^ . "^\\d{7}$"^^ . . "fbrf" . . . "MEDRA" . . "Prefix Commons" . "https://www.langual.org/langual_thesaurus.asp?termid=$1"^^ . "Cellular Microscopy Phenotype Ontology" . "orphanet" . "biomedical science" . . . . . . . . . . "http://purl.obolibrary.org/obo/TXPO_$1"^^ . . . "GlycoEpitope" . "Genome Properties" . . "clingene" . . . . . "gold" . . . . "^(imp|gen)\\d{5}$"^^ . . . . "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^ . . . "^\\d{1,5}$"^^ . . "GL50803_102438"^^ . . "nucleotide" . . . "http://purl.obolibrary.org/obo/COVIDO_"^^ . . . . . . "^\\d{7}$"^^ . "https://www.uniprot.org/arba/"^^ . . . "obo" . . "ITMCTR2023000002"^^ . "GR_PROTEIN" . . "biology" . . . . "senso" . "health science" . "dna" . "https://purl.dataone.org/odo/SALMON_$1"^^ . . "classification" . "genome" . . . . . "Variation Modelling Collaboration" . . "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^ . "RSNA Informatics RadLex" . . . . "false"^^ . "small molecule" . . . . . "http://purl.obolibrary.org/obo/FOVT_"^^ . . . "hoso" . . "^\\d+$"^^ . "anatomy" . "false"^^ . . . "PRINTS compendium of protein fingerprints" . "civic.evidence" . . "false"^^ . . . . "nbdc01071"^^ . "false"^^ . "swo" . "graph" . . . . . . . . . . . . . . "NCBI Registry" . "http://purl.obolibrary.org/obo/GNO_$1"^^ . . . . "http://id.nlm.nih.gov/mesh/vocab#"^^ . "WP732"^^ . . . . . "biology" . "protocol" . . "https://lincs.hms.harvard.edu/db/datasets/"^^ . . "Jackson Laboratories Strain" . . . . _:N6f930f1da65341b9bb1888984de2ebb0 "ICARDA Ethiopia" . . . . . . . . . . "false"^^ . "false"^^ . . . "https://hpscreg.eu/cell-line/"^^ . . . "^\\d+$"^^ . "ido" . . . . . . . . . . . _:Ne2eb2958e37a46608ca817d8e0d9ba50 "tim.vandermeersch@gmail.com" . . "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0="^^ . . "Gender, Sex, and Sexual Orientation Ontology" . . "^\\d{7}$"^^ . . "NONCODE v4 Gene" . . . . "false"^^ . . . . "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie="^^ . . "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)."^^ . "Ontology of Host-Microbiome Interactions" . . . . . "hgnc" . "http://cerevisiae.oridb.org/details.php?id="^^ . "ontology" . "co_346" . "^\\d+$"^^ . "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. "^^ . . . "wormmart" . . . . . "The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format"^^ . . "life science" . . . "bibliometrics" . . "false"^^ . . "false"^^ . . "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1"^^ . . "^\\d{5,}$"^^ . . "Cell line collections (Providers)"^^ . . . "R00100"^^ . . . "LG Chemical Entity Detection Dataset (LGCEDe)" . . . "Natural Product Activity and Species Source Database" . . . "Crop Ontology Curation Tool" . "biomagresbank" . . . . "environmental science" . "pscdb" . . "Cell line databases/resources"^^ . "December 2019"^^ . . "false"^^ . . . . . . . . . "covoc" . "door" . . . . . "pathway" . . . . "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"^^ . . . "false"^^ . . "false"^^ . . "tricdb" . "Berkeley Drosophila Genome Project EST database" . "false"^^ . . . "genomics" . . . . "HMS Library of Integrated Network-based Cellular Signatures Antibodies" . "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^ . . . . "https://aopwiki.org/aops/$1"^^ . . . . . "https://www.sharkipedia.org/trends/"^^ . . . . . . "subject agnostic" . . . "brain" . . . . "obo" . . . _:Na8edbc95dc9943cead4287a28ea4f5dc "j@deltaflow.com" . "0000198"^^ . . "SASDAX8"^^ . "UCSC Genome Browser" . . "gene" . . . . "https://aopwiki.org/aops/"^^ . . "false"^^ . . "wasila.dahdul@usd.edu" . "classification" . . . . "PathBank" . "^[A-Za-z0-9]+$"^^ . . . "report" . "Occupation Ontology" . . . . . . . . . "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"^^ . "0010034"^^ . "identifier of a compound in the UniChem database"^^ . . "true"^^ . "msigdb" . . "Catalytic Site Atlas" . . "has resolver formatter" . "Toni Gabaldón" . . . . . . . . . "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."^^ . . . . . . . . . "pav" . . "Philip.Stroemert@tib.eu" . . . "DBMET02292"^^ . "co_322" . "Genetic and Rare Diseases Information Center" . . "http://purl.obolibrary.org/obo/OBCS_$1"^^ . "protein" . . . . . . "Simon D Harding" . "ExO" . "Joachim Kopka" . "multicellds.snapshot" . . . . "MetaNetX chemical" . . "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1"^^ . . . . . . . . . . . . "^\\d+$"^^ . . . "systems biology" . . . _:Na753bc128ae04b158307c2af391f4ddf "INOH curators" . "ontology" . . "https://w3id.org/babelon/"^^ . "56305849200"^^ . . "bioinformatics" . . . . "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^ . . . "TA_H3"^^ . "992"^^ . "https://packagist.org/packages/"^^ . . "structure" . "Selventa Families" . . . . . "1354581"^^ . "MedlinePlus Health Topics" . . . "ubio.namebank" . . . . . . . . "Omar Harb" . . "false"^^ . . "Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).\n\nLandis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf"^^ . "false"^^ . . . . "ppdb@gifu-u.ac.jp" . . "false"^^ . . . "kristian.axelsen@sib.swiss" . "dashr" . . . . . "cryopreserved" . . "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id="^^ . . "false"^^ . "145"^^ . "Thomas Lütteke" . "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR)."^^ . . . . . . "ega.study" . "bibliography" . "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"^^ . . . . "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^ . "tgbugs@gmail.com" . . . . . "Ctibor Škuta" . "nih initiative" . . . . . "Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver."^^ . "ontology" . . "^[A-Za-z]+\\/[0-9]+$"^^ . "^ENSG\\d{11}$"^^ . . . . . "pathway" . . "true"^^ . . "vac" . . "phenotype" . . . "life science" . . . "chemical" . "A vocabulary about species to support the environmental research community in Arizona and New Mexico"^^ . . . . . "NIAID ChemDB ID" . . "Bloomington Drosophila Stock Center" . "anatomy" . "false"^^ . . . . . . . . . "gene" . . "molecular biology" . . "false"^^ . . . "biocuration" . . . . "Resources mentioned in \"Sharing biological data: why, when, and how\"" . "false"^^ . "https://protists.ensembl.org/id/"^^ . . . "https://bioregistry.io/pocketome:"^^ . . . "https://gudmap.org/id/$1"^^ . . "1"^^ . "phenotype" . . . . . . . . "MolMeDB" . . . "false"^^ . . "false"^^ . "https://grants.nih.gov/stem_cells/registry/current.htm?ID="^^ . . "pdbj" . . "Integbio" . "omics data analysis" . "NLXORG covers organisms."^^ . "pso" . . "dpo" . "^\\d+$"^^ . . "^\\d+$"^^ . "http://pepbank.mgh.harvard.edu/interactions/details/"^^ . . "FooDB compound" . "arxiv" . . . . "ontology" . "perkinelmer" . . . "merops.family" . "^PTM-\\d{4}$"^^ . . "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)"^^ . . . "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC="^^ . . "http://purl.org/dc/dcmitype/$1"^^ . "false"^^ . . "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$"^^ . . . "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . . . "false"^^ . . . . "culture" . . "NCBI Taxonomy" . "obo" . "life science" . . . . . "^\\d+$"^^ . . "behavior" . . "Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business."^^ . . "^\\d+$"^^ . . "PharmacoDB Cells" . "true"^^ . . "https://panoramaweb.org/$1.url"^^ . "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession="^^ . "Wheat ontology" . . . "http://www.phosphosite.org/proteinAction.do?id="^^ . . . . . . "Yiming Bao" . . . "ontology" . "NIF Standard Ontology: Subcellular Entities" . "false"^^ . . . . . . "The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included."^^ . . "Hypertension Ontology" . "Job Dekker" . "K00001"^^ . . "ontology" . . . . . . . . . "structure" . . . . . "LinkML" . "https://openalex.org/"^^ . . "Southwestern Environmental Information Network" . "false"^^ . "https://easychair.org/cfp/topic.cgi?tid="^^ . . "vegbank" . "false"^^ . . "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"^^ . . . "CIViC variant" . "worldavatar.compchem" . . . "nuclearbd" . . . . . . . . "67035"^^ . . "https://www.ebi.ac.uk/metagenomics/samples/"^^ . . . "biomedical science" . . "false"^^ . . . "marine environment" . "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:"^^ . . "^PA\\d+$"^^ . "Cell line collections (Providers)"^^ . . "FBdv" . "upa" . . . . "biology" . . . "false"^^ . . "runBioSimulations" . "Probes and Drugs" . . "rnavdb" . "vdrc" . "http://purl.obolibrary.org/obo/IAO_"^^ . . "EC_CODE" . . "https://www.ncbi.nlm.nih.gov/cdd?term="^^ . . "ncro" . "Variable"^^ . "homologene" . . "radiomics" . . . "omics" . . "nmckenna@bcm.edu" . . . "^NX_\\w+$"^^ . . "protein" . . . "venom" . "ontology" . "The State of Alaska's Salmon and People Ontology" . . . . "pgx" . "rx00408"^^ . . "09200010"^^ . . . "fbtc" . . "Matúš Kalaš" . "Bactibase" . "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry."^^ . . . . "Giorgio Ascoli" . "false"^^ . . . . "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution."^^ . "oma.hog" . "ontology" . . "allele" . . . . "^\\d+$"^^ . . "systems biology" . "protocol" . . . "http://www.marinespecies.org/aphia.php?p=taxdetails&id="^^ . . . "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"^^ . . . . "BioData Catalyst" . . . "Collembola Anatomy Ontology" . . . "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^ . . "UPa" . . . "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . . . "UPPRO" . "http://purl.obolibrary.org/obo/PGDSO_$1"^^ . . "molecules" . . "https://biopragmatics.github.io/providers/pba/"^^ . "ISA1083-2"^^ . "mim.ps" . . "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . . . . "agsc" . . . . . "^(cl|tum)\\d+$"^^ . . "Maize gross anatomy"^^ . . . "Geographical Entity Ontology" . . "https://biopragmatics.github.io/providers/dmba/$1"^^ . "gnomad" . "go.chebi" . "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^ . . . . . . . . . "00020134"^^ . . . "ontology" . . . . . "false"^^ . . . "genetics" . . "Cellular Phenotypes" . . "TIGR protein families" . . "cultured cell" . . . "ArachnoServer" . . . . "bibliography" . "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . "https://bioregistry.io/medlineplus:"^^ . "^\\d{7}$"^^ . "phenotype" . . . "RiceNetDB Reaction" . . . . . "transportdb" . . "false"^^ . . . . . . "https://bartoc.org/en/node/"^^ . "^\\d{1,5}$"^^ . . "0000001"^^ . "COG Pathways" . . . "anatomy" . . . . . "small molecule" . . . "lipidomics" . "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."^^ . . . "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1"^^ . "false"^^ . . . . "mco" . "0000001"^^ . . "skip" . . . "knowledge and information systems" . "pfam.clan" . . . . . . "nucleic acid" . _:Nbbc79547cdff4e5c9df18bd7c99700af "michael.lincoln@med.va.gov" . "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id="^^ . "baseDimensionEnumeration"^^ . "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . . . . . "assays" . . "blast" . . "true"^^ . "http://purl.obolibrary.org/obo/TRANS_$1"^^ . . . . . "SIGNOR Relation" . . . "torsten.schwede@unibas.ch" . . "Stephen R. Heller" . . . "^MMP\\d+.\\d+$"^^ . . . . . . . . . . . . . "493771"^^ . . . . "disease" . . . . . . . . . "http://purl.obolibrary.org/obo/FIX_"^^ . . "PSI Extended File Format" . . . . . . "false"^^ . . . "structure" . "life cycle stage" . . . . "rrid" . . . . . "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates."^^ . . . "^PIRSF\\d{6}$"^^ . . "http://purl.obolibrary.org/obo/ZFS_$1"^^ . "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder."^^ . . . . . . . . . . . . "COlleCtion of Open Natural ProdUcTs" . . . . . "Activity"^^ . "false"^^ . "MeSH 2013" . . "false"^^ . . "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . "02069237"^^ . . "true"^^ . "molecular function" . "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"^^ . . . . . . . "rgd.qtl" . . . "bioinformatics" . "classification" . . "Measurement method ontology" . "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components."^^ . "metadata" . . . "https://odc-tbi.org/data/$1"^^ . . "ehdaa" . . "gene" . . "ped.ensemble" . . "ABE-0009634"^^ . . "https://www.discoverx.com/?post_type=product&s=$1"^^ . . . . "false"^^ . "false"^^ . . "Analyses of microbiome data within MGnify"^^ . . . . . . . "The tRNA Gene DataBase Curated by Experts \"tRNADB-CE\" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones."^^ . . . "^\\d+$"^^ . . . . . "enviPath" . . "lagonzalezmo@unal.edu.co" . _:N999a3379cbec462b80acdd3f8d0a25df "GenBank Support" . . "false"^^ . "false"^^ . "^[a-z_A-Z0-9]+$"^^ . . . . . . . "ontology" . . "false"^^ . "^\\d+$"^^ . "JRC Data Catalogue" . . "0000171"^^ . "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:"^^ . "datanator.gene" . "EP0311"^^ . . . . . . "seed.compound" . "An ontology of physico-chemical methods and properties."^^ . . . "46946"^^ . "life science" . "214100"^^ . . . . . . . "https://www.ebi.ac.uk/biosamples/sample/$1"^^ . . . . . . . "4201PAT-CCTCC00348"^^ . . "topdb" . "BioPortal" . . "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1"^^ . . . . "false"^^ . "https://permalink.obvsg.at/"^^ . "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"^^ . "bmrb" . . "^\\w+$"^^ . . . . . "ecoliwiki" . "Akhilesh Pandey" . . . . . . . . "https://web.expasy.org/cellosaurus/cellopub/$1"^^ . . . . . . "^\\d{7}$"^^ . . _:N23ddc6feb53a4e3faf299933d3451260 "Bert Van Nuffelen" . "^PMC\\d+(\\.\\d+)?$"^^ . . "^\\d{7}$"^^ . . "^\\d{8}$"^^ . "A language for validating RDF graphs against a set of conditions"^^ . "life science" . . "HGNC_GROUP" . . . "false"^^ . . . . . . . . . . "Wikipedia" . "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups"^^ . . . . "epidemiology" . "life science" . . "Q0VCA6"^^ . . "chemistry" . . . . . "vz" . . . "false"^^ . . "kaggle" . . "metadata" . . "98"^^ . . "terms4FAIRskills" . . . . "Human developmental anatomy, timed version" . . . . "https://www.ebi.ac.uk/gxa/experiments/$1"^^ . . . "true"^^ . . "homd.seq" . "false"^^ . . . . . . . . . . . . "^N[0-9]{10}$"^^ . . . "ontology" . . "false"^^ . "neuroscience" . . . . . . . . . "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination."^^ . "false"^^ . . . . "envo" . . . . . "^[0-9\\.]+$"^^ . . . . . . . . "polbase" . . "rna_sstrand" . . _:N833306e1b1f5424d97974ffc4ab537e9 "helpdesk@cropontology-curationtool.org" . . . . "vso" . "false"^^ . . . . . "biomodels.vocabulary" . . . . "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . . . . . . . . "https://w3id.org/semapv/vocab/"^^ . "Ensembl" . "genome" . "Plasmodium Life Cycle" . . . "nathan.baker@pnnl.gov" . . . . "http://www.bioassayontology.org/bao#BAO_"^^ . . . "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^ . "nlx.chem" . "http://purl.obolibrary.org/obo/COVOC_$1"^^ . . . . . . "FOOD00020"^^ . . "pirsf" . . "^[A-Za-z0-9\\-\\/]+$"^^ . "ohpi" . "Allan Spradling" . . . "http://biocyc.org/getid?id="^^ . "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . . "dbgap" . "false"^^ . . . . "gmd.analyte" . . . . . . . . . "life science" . "UniProt Diseases" . . . "http://www.arachnoserver.org/toxincard.html?id="^^ . . . . "https://datanator.info/reaction/"^^ . "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee."^^ . . . . . "microbial" . "immunology" . "Protein Ontology" . . . . . . . . . "cell biology" . "somatic" . . . "edam.data" . . . "false"^^ . "environmental science" . "infectious disease medicine" . . . . "^[A-Z]{6}(\\d{2})?$"^^ . . "gene" . . "industry" . "gecko" . . "false"^^ . . . . "EDI_244000"^^ . "Mouse adult gross anatomy" . . "ontology" . "^G[0-9]{5}[A-Z]{2}$"^^ . . "dclunie@dclunie.com" . . . "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession="^^ . "false"^^ . . "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^ . "^\\d{3}-\\d{3}-\\d$"^^ . . . . . . . "storedb.study" . . . . . "true"^^ . "German Clinical Trials Register" . . . . . "comparative genomics" . "grsdb" . "B-5720-2018"^^ . "false"^^ . . "molecules" . "sequence" . . . . "TAIR Gene" . . . . . . _:N02215f8b79c94205b423321cccd2c962 "helpdesk@cropontology-curationtool.org" . . . "false"^^ . . . "The data cube vocabulary" . . "nbn" . . "false"^^ . "ontology" . . "http://purl.obolibrary.org/obo/EPO_"^^ . "obo" . . "^\\d+$"^^ . . . . . . "Terminology for Description of Dynamics" . . . . . "disease" . "LINCS Protein" . . . "^UCR\\d{5}$"^^ . . . . "http://biocyc.org/getid?id=$1"^^ . "Martin Kuiper" . . "MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides"^^ . . . "false"^^ . . . "genome" . "envipath" . "https://www.ncbi.nlm.nih.gov/medgen/"^^ . . "0000041"^^ . . "reto" . "ontology" . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/ICEO_"^^ . . "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs)."^^ . . . . . . "https://jjj.bio.vu.nl/models/"^^ . "https://www.biocatalogue.org/services/$1"^^ . . . . . . . . "VFDB Gene" . "Ontology for Chemical Kinetic Reaction Mechanisms" . . . "CRISP Thesaurus" . "salmon" . . "false"^^ . "obo" . "http://uri.neuinfo.org/nif/nifstd/nifext_"^^ . . . . . "pfam" . . "4dn.biosource" . . . "hospital" . . "FBgn0011293"^^ . . "cognition" . . . "transgenic" . . . . . . "structure" . "obo" . . . . . . . . "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?"^^ . "false"^^ . "http://purl.obolibrary.org/obo/VSAO_"^^ . "Structural Classification of Protein - Stable Domain Identifier" . "ontology" . "structure" . . . "veNOG12876"^^ . . "ikufareva@ucsd.edu" . "Diseases Database" . "dna" . . "mirex" . . . . . . . "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus="^^ . . . . . . "Jesper Friis" . "geography" . . "https://www.ebi.ac.uk/miriam/main/$1"^^ . "https://dandiarchive.org/dandiset/"^^ . _:Nae36e2aebfee4e58acbcb8a52f217512 "Ramesh Verna" . . . . . "false"^^ . . . . "chickenqtldb" . "https://nztcs.org.nz/nztcs-species/$1"^^ . "^PWY\\w{2}\\-\\d{3}$"^^ . . "ontology" . . "^COG\\d+$"^^ . . . "protein" . "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."^^ . "protein" . . . . "world2dpage" . "https://identifiers.org/$1:$2" . "ChEBI"^^ . "Will Simpson" . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_dys_"^^ . . . . "http://www.bootstrep.eu/ontology/GRO#$1"^^ . . "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes."^^ . . . "http://purl.obolibrary.org/obo/MOD_$1"^^ . . . . . "publication" . "ontology and terminology" . . . . "https://registry.bio2kg.org/resource/$1" . "biotools" . . . . . . "obo" . "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i="^^ . "BioTools" . . . . . . "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^ . . . "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results."^^ . . . "https://bioregistry.io/pmap.substratedb:"^^ . . _:N3b58243ab27745cdb371ab0bc0d041b0 "Intellectual.PropertyServices@ama-assn.org" . . . . "Human Oral Microbiome Database" . . . "http://purl.obolibrary.org/obo/DDANAT_$1"^^ . . . "structure" . "http://thebiogrid.org/$1"^^ . . . . . "http://www.vbase2.org/vgene.php?id="^^ . "funcbase.human" . . . . "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1"^^ . "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules."^^ . "http://purl.obolibrary.org/obo/MFOEM_$1"^^ . "monique.zahn@sib.swiss" . "veterinary medicine" . . . "ontology" . "DDInter20"^^ . . . "obo" . . . . . . . . "familyName"^^ . "rapdb.transcript" . . . . . . . "plant phenotypes and traits" . . "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment."^^ . . . . . . "structure" . . "Uberon" . . "false"^^ . "phenotype" . . "RNA SSTRAND" . "https://flowrepository.org/id/$1"^^ . . . . "ontology" . . . . . . . . "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM."^^ . "mice" . "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . . . . "biofactoid" . . . . . . . . "molecular biology" . . . "D053716"^^ . . . . . "false"^^ . "Hathi Trust Digital Library" . . . . . . "https://fungidb.org/fungidb/app/record/gene/$1"^^ . "1150"^^ . "https://www.disprot.org/idpo/IDPO:"^^ . . "propreo" . . . . "hyou@sjtu.edu.cn" . . "true"^^ . . "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences."^^ . . . . . . . . . . . . "^\\d{5}$"^^ . . . . . "false"^^ . . "engelsta@ohsu.edu" . "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1"^^ . "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1"^^ . "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"^^ . . "YAL001C"^^ . . . . . "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1"^^ . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id="^^ . _:N13aaee59b0414bc887f8a768b19c3f7d "vlee@ebi.ac.uk" . "agriculture" . "https://w3id.org/aio/"^^ . . . "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes."^^ . . "^10.\\w{4}/\\w{10}$"^^ . . "Wes Schafer" . . . . "Properties and classes used for protein annotation"^^ . "atcc" . . . . . . "plant phenotypes and traits" . . . "^\\d+$"^^ . . . . "icd10" . "2170610"^^ . . "obo" . . "biomedical science" . . "SNOMED_CT_US_2018_03_01" . . . . "epidemiology" . . "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$"^^ . . "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id="^^ . . "mbaudis@me.com" . "A type for entries in the Bioregistry's registry." . "comparative genomics" . . . . . . . . . . . . "Perry Miller" . . "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F"^^ . "Daniel Kahn" . "Mental Functioning Ontology" . . . "G00054MO"^^ . "https://mmp.sfb.uit.no/databases/marref/#/records/"^^ . "Jacqueline.Campbell@usda.gov" . . . . . "Fission Yeast Experimental Conditions Ontology" . . . . "kegg.disease" . "genomics" . . . . "false"^^ . . . "Repository of packages for the R programming language"^^ . "MOL000160"^^ . . "https://togoid.dbcls.jp/" . "^\\d+$"^^ . . "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit."^^ . "imsr_em" . . . . . "false"^^ . . "DRSC05221"^^ . . "0005452"^^ . . _:N4c3dffe6e39b4106a71dd32df9563225 "Animal Diversity Web technical staff" . "^\\S+$"^^ . . . . . "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."^^ . . "4685"^^ . . "immunology" . . . "https://datanator.info/reaction/$1"^^ . "genome" . "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified."^^ . . . . . . "obo" . . . . . "enzyme" . _:N39ed82037cb5445ab076272c9b940c48 "Alain J. Cozzone" . . . "A application driven Epilepsy Ontology with official terms from the ILAE."^^ . "nhcdr" . . . . . "Microarray experimental conditions" . . "life science" . . "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases."^^ . . "false"^^ . "noaa.cameo" . "Orphanet" . "^\\w+$"^^ . . . . . "^DDB\\d+$"^^ . . . . . . . . "OGI.owl" . "Marcin Pawel Joachimiak" . . "ontology" . . . . "gene" . . . . "syoid" . . . . "Integrated Resource for Domestic Dog" . . "protein" . "taxonomy" . . "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"^^ . . "true"^^ . . . . . . . "http://sideeffects.embl.de/drugs/"^^ . . . "The Comprehensive R Archive Network" . . . . "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences."^^ . . . "bel"^^ . . . . "fly" . "https://www.enzolifesciences.com/"^^ . "false"^^ . "rdfs" . . "obo" . "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . . "Andrea Jacobs" . . . "true"^^ . "^LSM-\\d+$"^^ . "https://cropontology.org/rdf/CO_370:"^^ . . . . . "^PA\\d+$"^^ . "ontology" . . "data visualization" . . . . . "false"^^ . . "life science" . . . "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^ . . "https://sparontologies.github.io/fabio/current/fabio.html#$1"^^ . . "help-swissmodel@unibas.ch" . . . . "Pathogen Transmission Ontology" . "https://sciflection.com/"^^ . "epidemiology" . . "Current Procedural Terminology" . . . . "http://aims.fao.org/aos/agrovoc/c_"^^ . "^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\\d+$"^^ . . "The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans."^^ . "The International Standard Book Number (ISBN) is for identifying printed books."^^ . . "biology" . . . . . . . "measurement" . . . . . "3"^^ . . . . . . . . . . . . "00000003"^^ . "https://stemcells.nindsgenetics.org?line="^^ . "http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1"^^ . "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . . "mouse" . . "http://purl.obolibrary.org/obo/PLO_$1"^^ . . . "xco" . "obo" . . . . . "lbctr" . "false"^^ . . . "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts."^^ . "Draft version"^^ . . . . "https://www.addexbio.com/productdetail?pid="^^ . . "false"^^ . . . "BioAssay Ontology" . . "https://bioregistry.io/zazuko:"^^ . . . . . . . . . "http://www.pharmgkb.org/pathway/$1"^^ . "lincs.cell" . . . . . . . . . . . "https://civicdb.org/links/variant_group/"^^ . . . "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid="^^ . . "phenotype" . . . . . . . . . . "biodiversity" . . "biomedical science" . "phenomics" . "metabolights" . . . "gene expression" . "life science" . . "dna" . "T06648"^^ . . . "http://id.who.int/icd/entity/"^^ . . . . . . . . . "genotype" . "false"^^ . . . . "independent variable" . . . "plant phenotypes and traits" . . . . . "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"^^ . . . "jgoll@emmes.com" . "http://ctdbase.org/detail.go?type=gene&acc="^^ . . "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID="^^ . "false"^^ . "http://www.orpha.net/ORDO/Orphanet_$1"^^ . . . . . . . . . . . "biomedical science" . "true"^^ . . . . . "Allen Institute Ontologies" . . "aphidbase.transcript" . . . "http://purl.obolibrary.org/obo/VIDO_"^^ . . "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id="^^ . "Multiplexed Assays of Variant Effect Database" . . . . . . "http://purl.org/vocab/frbr/core#$1"^^ . . . . . "biomedical science" . . . "disease" . . . . . . . . . "false"^^ . "ProDom" . . "http://database.deepsolar.space:18080/dbs/nlfff/"^^ . . . . . "true"^^ . "chemistry" . "annotation" . . . "dispositions" . . . "Small Angle Scattering Biological Data Bank" . . . . "7123"^^ . . . . "obo" . . . "GWAS Central Study" . "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid="^^ . . . . "The identifier for an observation in iNaturalist"^^ . _:Nd5000726c51a442e95b8c79d186a8132 . . "false"^^ . "ProteomicsDB Peptide" . . . . . . "Description of a Project" . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . . . . . . "^[a-zA-Z0-9-_]+$"^^ . _:Nc8de2d34560649929fc1996dfc57b425 . . . "Anne.Morgat@sib.swiss" . . . "RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project."^^ . "false"^^ . "structural biology" . "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."^^ . . "AAC"^^ . . . . . "reaction data" . . . . . . "Adrien Rougny" . . . . . "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^ . "functional genomics" . . . "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"^^ . . "^PD\\d{6}$"^^ . . "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$"^^ . "robert.hoehndorf@kaust.edu.sa" . . "CropMRespository is a database of soil and crop biophysical process models."^^ . . . "http://purl.obolibrary.org/obo/OlatDv_"^^ . . . . . . "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . . . "cell biology" . . . "functional genomics" . . . . . "https://biomodels.net/vocab/idot.rdf#"^^ . "WBRNAi00086878"^^ . "genepio" . "chemistry" . . . . . . . "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . . "pubchem.element" . "bibliography" . "http://www.ebi.ac.uk/efo/EFO_"^^ . "ecosystem" . "go.chemicals" . "Identifier for a user in iNaturalist"^^ . "animal model" . . "icd10pcs" . "^AT.G[0-9]{5}$"^^ . . "gold.meta" . "data management" . "knowledge graph" . . . . "ontology" . . . . "rna" . . . "Microbial Conditions Ontology is an ontology..."^^ . . . . "glycoproteomics" . . "^\\d+$"^^ . . . "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"^^ . . . "Sergio José Rodríguez Méndez" . . "MT"^^ . . . "John L. Markley" . . . . . "Europe PMC Preprints" . "dcterms" . "physiology" . . . . . . "http://bcrj.org.br/celula/$1"^^ . . "https://animaldiversity.org/accounts/"^^ . . . . "false"^^ . . . . "false"^^ . . . . "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4,6}\\d{8,10}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . "^\\d{7}$"^^ . . . "ygob" . . . . "protein" . . . . . . . "Geomames" . "Nicolas Matentzoglu" . . "earth science" . . "false"^^ . . "publication" . . "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions."^^ . . . . "0000003"^^ . . . "obo" . . "quality" . . . . . . "cgd7_230"^^ . "XUO" . "^\\d+$"^^ . . . "Identifier for a species on the noaa fisheries website"^^ . . "Time Ontology in OWL" . "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis"^^ . . . . "obo" . . "https://www.pharmvar.org/gene/$1"^^ . "pathbank" . . . "false"^^ . . . . . . . . "computational biology" . . . . . . "http://classyfire.wishartlab.com/tax_nodes/C$1"^^ . "33607"^^ . "5"^^ . . . . "https://bbp.epfl.ch/nexus/web/studios/public/$1"^^ . _:N1699cf1ea2754508a32e555023a392e4 "AGROVOC Team" . "false"^^ . . "375364"^^ . "false"^^ . . . . . "rna" . "c4o" . . "Mosquito gross anatomy ontology" . "Nicolas Le Novere" . "food" . "^\\d+$"^^ . "Database of biopesticides maintained by the University of Hertfordshire "^^ . "ncit" . . . . . . "model organism" . . . "worfdb" . "http://purl.obolibrary.org/obo/CMO_$1"^^ . . . "https://metazoa.ensembl.org/id/$1"^^ . . "perriere@biomserv.univ-lyon1.fr" . . "1000003"^^ . . . . . . . "http://purl.obolibrary.org/obo/IDOMAL_"^^ . . . . . . . "false"^^ . "novus" . "Irina Medvedeva" . "lcnaf" . . . . "food" . "A formal ontology of phenotypes observed in fission yeast."^^ . . "Motonori Ota" . . "^\\d{7}$"^^ . "false"^^ . . "false"^^ . "Plant Transcription Factor Database" . . "true"^^ . "https://cordis.europa.eu/project/id/$1"^^ . . . "Sequence types and features ontology" . . . . . . "botany" . . "Linda Reha-Krantz" . . . "cell types" . . . "^CH_\\d+$"^^ . . . . . . "Social Insect Behavior Ontology" . "adms" . . "Meng LIU" . . "http://purl.obolibrary.org/obo/FBSP_$1"^^ . . . "false"^^ . . . . "The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage)"^^ . . . . "pharmgkb.drug" . . . . . "pathway" . . "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$"^^ . . "^[A-Za-z0-9]+$"^^ . "false"^^ . "DSMZCellDive" . "pharmgkb.pathways" . . "classification" . . . . "57"^^ . . . "^\\d{7}$"^^ . . . . . "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1="^^ . . . "^FR\\-FCM\\-\\w{4}$"^^ . . "false"^^ . "http://purl.obolibrary.org/obo/NCIT_$1"^^ . . "life science" . . "ontology" . . . . . . . . . "^\\d{7}$"^^ . . . . . . . "NMRShiftDB structure" . "HIT000195363"^^ . . "false"^^ . . . . "http://viaf.org/viaf/"^^ . "https://foodb.ca/foods/$1"^^ . "dna" . . "CA981206459"^^ . "virus" . _:Nc5649c0b3ba24647bf32bddea5052c76 . . . "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein."^^ . . . . . . . . . "exo" . . . . . . . . "people" . . . . "ontology" . . "^\\d+$"^^ . "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records."^^ . "clinical data" . "neuroscience" . "biology" . . . . . "classification" . . . . . . "MedDRA" . "chemistry" . "83088"^^ . "JCRB1355"^^ . . "database management" . . "pmap.cutdb" . . . "0000046"^^ . . . . "Online Computer Library Center WorldCat" . "https://www.ebi.ac.uk/intact/search?query=$1"^^ . "obo" . . "anne.morgat@sib.swiss" . . "A0118748"^^ . . . "RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale. "^^ . . "gamete" . "^\\w+$"^^ . "ricegap" . . . "Gmelins Handbuch der anorganischen Chemie" . . "http://uri.neuinfo.org/nif/nifstd/nlx_anat_"^^ . . . . "1433C_TOBAC_1_252"^^ . . . "http://planttfdb.cbi.pku.edu.cn/tf.php?uid="^^ . "alpha.tom.kodamullil@scai.fraunhofer.de" . . "D.Schomburg@tu-braunschweig.de" . . "RoleInTime"^^ . . . . . . . . "life science" . "https://schema.org/"^^ . . "foodb" . . . . "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval."^^ . . . . "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web"^^ . . "BCRTi001-A"^^ . . "reactions" . . "false"^^ . "false"^^ . "Protein and Associated NucleotideDomains with Inferred Trees" . "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^ . "^T3\\d+$"^^ . "^[dp]\\.[a-z0-9]{8}$"^^ . . "http://purl.obolibrary.org/obo/COLAO_$1"^^ . "chemistry" . "data acquisition" . . "ontology" . . . . . "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies."^^ . . . "centrally registered identifier" . . . . . . "^\\d{7}$"^^ . . "https://www.pirbright.ac.uk/node/$1"^^ . . . . . . "medicine" . . "taxonomy" . "JGI Phytozome" . . "obo" . . . . "Blake A Sweeney" . "^\\d{7}$"^^ . "http://genomics.senescence.info/genes/details.php?id=$1"^^ . "ontology" . . "araport" . . "database" . "Animal Genome Pig QTL" . . "^\\d{7}$"^^ . . . "co_330" . . "lcsh" . . "0000128"^^ . . "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials."^^ . . "ontology" . "^\\w+$"^^ . "http://www.unimod.org/modifications_view.php?editid1="^^ . "4238"^^ . "dhba" . "http://purl.obolibrary.org/obo/ONE_"^^ . . . . . "The Behaviour Change Intervention Ontology" . "3905431"^^ . . "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1"^^ . . . . "false"^^ . "false"^^ . . . "gene" . . . . "false"^^ . . "http://purl.obolibrary.org/obo/REX_"^^ . . . . . . . . . _:N586e7aba53ab4b68932778362bfd0f96 "Matt Berriman" . . . "Ismail Fliss" . . . "0001114"^^ . . . . . "frbr"^^ . . . "vendor" . . . . . . . . . . . . . . "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . . . . . . "Richard Scheuermann" . . "http://www.w3.org/2003/01/geo/wgs84_pos#$1"^^ . "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . . . "^bkc[0-9]*$"^^ . . . "Victoria K. Jenkins" . . . . . . . . . . . "A vocabulary for annotating vocabulary descriptions" . "false"^^ . . . . "^[a-z]+(\\..*?)?$"^^ . "A modeling paradigm-specific registry of prefixes and their URL expansions" . . . "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references."^^ . . . . . . "ontology" . . . . "^\\d{4}$"^^ . . "https://rnacentral.org/rna/"^^ . . "regulation" . _:Nbe62732905da46fa8b5b42f91dc55de9 "Edd Wilder-James" . . "Symposium"^^ . . . "E-MEXP-1712"^^ . "trnadbce" . . . . "http://purl.obolibrary.org/obo/RXNO_$1"^^ . "PDC000351"^^ . . . "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . . . . "BiGG Model" . . . "^\\d{7}$"^^ . . . "obo" . . "false"^^ . . "ontology" . . "togoid" . . "Research Resource Identification" . . . "infection" . "^[0-9]+$"^^ . "A hierarchical classification of congenital heart disease "^^ . . . . "GCA_000155495.1"^^ . . "Kyoto Encyclopedia of Genes and Genomes" . . . _:N44ea25e78e4a4c21a4fc2751279240af "Cynthia Hake" . . . . . . . "bind" . . "false"^^ . . . . . . . "meetings" . "ontology" . "Kyoto Stock Center" . "life science" . . . . . "gene" . "flybrain.ndb" . "publications" . . . "w3c rec" . . . "https://horizondiscovery.com/en/search?searchterm=$1"^^ . "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id="^^ . . "^[1-9]\\d*$"^^ . "https://w3id.org/nfdi4cat/voc4cat_"^^ . . . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . . . . . "smart" . . . "cheminformatics" . . "false"^^ . "mcc" . . "tRNA Gene Database" . . . "300165/p13898_2106T"^^ . . . . "Social Behavior in insects"^^ . . . . . . "Philipp.Bucher@sib.swiss" . . . . . . "obo" . "subject agnostic" . "TR0000001"^^ . "false"^^ . . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes."^^ . . . "data model" . . . . . "literature curation" . . "true"^^ . "Upinder S. Bhalla" . "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents."^^ . "Cell line collections (Providers)"^^ . . "citexplore" . . . "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"^^ . . "false"^^ . . . . . "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets"^^ . . . "NodeShape"^^ . "Search Tool for Retrieval of Interacting Genes/Proteins" . . "ontology" . . "pride" . . "MagnitudeValueType"^^ . . "life science" . "https://www.ebi.ac.uk/gxa/experiments/"^^ . . . . "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc="^^ . "measurement" . . "fish" . . . . "http://purl.obolibrary.org/obo/ZEA_"^^ . . . "https://www.isrctn.com/"^^ . . "molecular biology" . . . "wgs84" . . "Nathan Edwards" . . "biomedical science" . . "http://hawaii.eagle-i.net/i/"^^ . "obo" . . . . . . "http://purl.obolibrary.org/obo/MIRNAO_"^^ . . . "Signaling Pathways Project" . . . . "^\\w\\d+$"^^ . "false"^^ . "0000509"^^ . . "data transformation" . "Coli Genetic Stock Center" . . . "assay" . . "DUO is an ontology which represent data use conditions."^^ . "Spectra Hash Code" . "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname="^^ . "imsr_tac" . "https://jrct.niph.go.jp/en-latest-detail/"^^ . . . "^\\d+$"^^ . . . "Woody Plant Ontology ontology" . "^\\d{7}$"^^ . . . . . "obo" . . "ontology" . . "secondary_attack_rate"^^ . "lincs" . "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections."^^ . "https://rfam.org/family/$1"^^ . "molecular chemistry" . . . "ontology" . . . . . "ontology" . . . . . "http://noctua.geneontology.org/editor/graph/gomodel:"^^ . "XML Schema Definition" . . . . . . . "https://thebiogrid.org/interaction/$1"^^ . "obo" . . . . "false"^^ . . "https://www.wormbase.org/db/seq/protein?name=$1"^^ . . . "http://purl.obolibrary.org/obo/XLMOD_"^^ . . . "electron microscopy" . "HPSI0114i-bezi_1"^^ . . . . . . "http://snomed.info/id/$1"^^ . . . . "biomedical science" . . "Cell line collections (Providers)"^^ . . "Information Artifact Ontology" . . . "false"^^ . . . . "life science" . "phenotype" . . "CTD Chemical" . . . . . "obo" . "Yoshiharu Y. Yamamoto" . . "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database."^^ . . . . . . . "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1"^^ . . . "GPIb_IX_V"^^ . "gene" . "Identifiers.org" . . "DirectiveInformationContentEntity"^^ . . . . . "virology" . . . . "EcoliWiki from EcoliHub" . . . "^[a-z0-9]+:[A-Za-z0-9.\\-:]+$"^^ . "phylogeny" . . . . . . . . "Inge.Jonassen@uib.no" . . . . . "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes."^^ . . . "https://pharmacodb.ca/datasets/$1"^^ . . "SP_DI" . . . "OpenCitations Corpus" . "Quantities, Units, Dimensions, and Types Ontology" . . . . . "infectious" . "13"^^ . . . . . . "true"^^ . . . . "false"^^ . . . . "An organization" . "skm" . . . . . "https://www.brenda-enzymes.de/ligand.php?brenda_group_id="^^ . . . "^\\d+$"^^ . "ICD9" . "protein" . . "false"^^ . "genome" . . . "false"^^ . . "UniProtKB_VAR" . "data management" . _:N4c3dffe6e39b4106a71dd32df9563225 . "bitbucket" . . "molecular infection biology" . . "approved drug" . "Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID]"^^ . . "0000080"^^ . . _:N4abb5ec25bc84b7794aa116c6e227a95 "chebi-help@ebi.ac.uk" . "LCL-2085"^^ . "phenotype" . . "https://www.kegg.jp/entry/$1"^^ . . . . "Pol Castellano Escuder" . "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors."^^ . . "ontology" . "false"^^ . . . . . "life science" . "false"^^ . "http://purl.obolibrary.org/obo/AAO_"^^ . . "eugenes" . "Integrated Microbial Genomes Gene" . "protein" . "citation" . . "false"^^ . . . . . "^\\d+$"^^ . . "PMC3084216"^^ . "http://purl.obolibrary.org/obo/GALLONT_$1"^^ . "eukaryotic" . "0000196"^^ . . . "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"^^ . "panther.pathway" . "mriffle@u.washington.edu" . "https://comptox.epa.gov/dashboard/"^^ . "http://purl.obolibrary.org/obo/ECAO_$1"^^ . . . . "Mouse Developmental Anatomy Ontology with Theiler Stage" . "subject agnostic" . . "https://www.worldwildlife.org/ecoregions/"^^ . "LO362836C"^^ . "Leszek@missouri.edu" . . . . . . "http://www.chemspider.com/Chemical-Structure.$1.html"^^ . "DDB_G0267522"^^ . "knowledge and information systems" . . . "00020007"^^ . . "MESHA" . "false"^^ . . . "obo" . . "umls.sty" . . . "phenotype" . "CranioMaxilloFacial ontology" . "n2t" . . "longevity" . "https://www.uniprot.org/tissues/$1"^^ . . "http://cegg.unige.ch/orthodb/results?searchtext=$1"^^ . . . . . . . . . . . "Eschmeyer's Catalog of Fishes" . . . "^\\d+$"^^ . "ApiDB_PlasmoDB" . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1"^^ . . . . . . . "antibody" . . "TaxonomyID" . "marie-paule.lefranc@umontpellier.fr" . "000000012281955X"^^ . . "0745-4570"^^ . "01467"^^ . . "http://erop.inbi.ras.ru/result2.php?PepName=$1"^^ . "World Wildlife Fund Ecoregion" . "Pennsieve" . . . "bibo" . "Population and Community Ontology" . . "^casent\\d+(\\-D\\d+)?$"^^ . . "https://civicdb.org/links/variant/"^^ . . . . . . . . "http://purl.obolibrary.org/obo/DIDEO_$1"^^ . . . . . . . . "http://www.alzgene.org/geneoverview.asp?geneid="^^ . "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."^^ . "ontology" . . . . . "false"^^ . "life science" . "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries"^^ . . "http://yeastrc.org/pdr/viewProtein.do?id="^^ . . "neurolex" . "life science" . . "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"^^ . . . . . . "1-55516888-G-GA"^^ . "false"^^ . . "citation" . . . . . "Affymetrix Probeset" . . "^\\d+$"^^ . . . "chembl.cell" . . "proteomics" . . "semantic web" . . . "false"^^ . . . . "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"^^ . _:N452d5df5d4174c6ea0a4aed0f83019b6 "Vladimir Mironov" . . . . "http://purl.obolibrary.org/obo/CDNO_$1"^^ . . . . "Mouse Developmental Stages" . "^IPR\\d{6}$"^^ . "^\\d{7}$"^^ . "ecyano.entity" . . . "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"^^ . . . "https://www.uniprot.org/proteomes/$1"^^ . . . "post-transcriptional modification" . "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration."^^ . . . . . . "Wikidata" . "TAO_RETIRED" . . "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1"^^ . . . . . "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . . . . . . "https://civicdb.org/links/diseases/$1"^^ . . "Gene Ontology Causal Assembly Model" . . "https://www.rhea-db.org/rhea/"^^ . "co_325" . . "adverse reaction" . . "nuclear" . "http://purl.obolibrary.org/obo/UPHENO_$1"^^ . . "MMs00000001"^^ . "false"^^ . . . . . . . "Martin Pospíšek" . . . "genetic" . . . "ChiCTR2300070727"^^ . . . . . . . . "type"^^ . "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"^^ . "help@emdatabank.org" . "Structural Classification of Proteins - Unique Identifier" . . . "https://www.facebase.org/data/record/#1/isa:dataset/accession="^^ . . "^NONHSAG\\d{5}$"^^ . . . . "yid" . "ontology" . . . . . . . "phenomics" . . . "mint" . "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."^^ . . . "http://www.cathdb.info/domain/"^^ . "health science" . "epidemiology" . "http://purl.obolibrary.org/obo/TAO_"^^ . . . . . . . "https://www.gleif.org/lei/"^^ . "NeuroLex Anatomy" . . . . "protein" . "http://www.gramene.org/db/literature/pub_search?ref_id="^^ . . "dg.4dfc" . "emolecules" . . . . . . . "1"^^ . "^(5?)\\d{7}$"^^ . . . "obo" . . . . . "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^ . . . . . "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST)."^^ . . "global health" . . "http://www.w3.org/2000/01/rdf-schema#$1"^^ . "cmo" . . "protein trap" . . . "ontology" . . . "^\\d+$"^^ . . "Alistair Miles" . . . . . "dbSNP Reference SNP number" . . . . . . . . . "obo" . . . . "f.quaglia@ibiom.cnr.it" . "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available."^^ . . . "false"^^ . . "Evidence and Conclusion Ontology" . . "RXCUI" . "Karen R. Christie" . . . . . . . . . . . . . . "http://purl.obolibrary.org/obo/PROPREO_"^^ . . "ICEberg integrative and mobilizable element" . "http://purl.obolibrary.org/obo/ORNASEQ_$1"^^ . . . . . . . "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps."^^ . . . "0000001"^^ . . . . . . . . . . "46"^^ . "ensembl.metazoa" . . . "https://bykdb.ibcp.fr/data/html/annotated/$1.html"^^ . "genomics" . . . "000410"^^ . "obo" . "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"^^ . . . . "euclinicaltrials" . . . . . . . . "transcriptomics" . "obo" . . . "ontology" . "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible." . . "^DG\\d+$"^^ . "phenotype" . . "resource metadata" . "sphn" . . . . "MNXM1723"^^ . . . "disease" . "PROV Namespace" . . . . . . . . "liumeng94@sjtu.edu.cn" . "false"^^ . . "http://ddinter.scbdd.com/ddinter/drug-detail/"^^ . . . "clinical LABoratory Ontology" . . . . . "false"^^ . "John G Tate" . "https://cameochemicals.noaa.gov/chemical/"^^ . "citation" . . "r3d100014165" . . . "plant phenotypes and traits" . "Paul Flicek" . . . "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . "https://bioregistry.io/hovergen:"^^ . . . "addiehl@buffalo.edu" . "00103"^^ . "Nathan Baker" . . _:Nb210a71e511f4cbfa454a654c89797e8 . . . "ontology and terminology" . . . "geographical location" . . . . . . . "lonza" . . "life science" . . . "botany" . . "PRIDE Controlled Vocabulary" . . . . . . "https://www.rebuildingakidney.org/id/"^^ . . . "aism" . "12e8LH"^^ . . . . . . . . "omics" . . "https://disprot.org/"^^ . "http://ratmap.org/Showgene.php?gene_stable_id="^^ . . . "DBSALT001211"^^ . . "ontology" . "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas="^^ . . "WGS-95-1333"^^ . . . . "false"^^ . . "true"^^ . . "http://purl.obolibrary.org/obo/LEPAO_$1"^^ . "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."^^ . "Human Proteome Map" . . "PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2"^^ . . . . "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"^^ . . . . "life science" . . . . . . . "https://www.drugbank.ca/categories/$1"^^ . . . . . . "gene" . . "https://bioregistry.io/registry/$1"^^ . . . . . "gene expression" . . . "biolink" . "Meghan Balk" . . . . . . "recombinant inbred rat" . . . "The data sources used in xrefs in the ChEBI ontology. More information in the \"Data Sources\" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx)." . _:N66cf499252324c29a5fea5f7bf331f08 "sschurer@med.miami.edu" . "http://ecoliwiki.net/colipedia/index.php/$1:Gene"^^ . "https://scicrunch.org/resolver/RRID:NXR_"^^ . "bibliography" . . . "pancreatic islet" . . . . . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . "pubmed" . . "dna" . . "adverse reaction" . . . "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI)."^^ . "https://www.yeastgenome.org/locus/$1"^^ . . . . "life science" . . . . . . "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^ . . "10194"^^ . . . "ontology" . . "^[CD]\\d+$"^^ . . . "^H\\d+$"^^ . "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm"^^ . . "Fossilworks Journal" . "qudt" . . . "COMBINE specifications" . . . "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . . . . "11061"^^ . "^([3-5][A-Z])\\w+[^A-Z][0-9]$"^^ . "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^ . . "100291"^^ . . . . "true"^^ . . . "fao" . . "An ontology to support disciplinary annotation of Arctic Data Center datasets."^^ . . . . . "SNOMEDCT_US_2019_03_01" . "software engineering" . . . "0000086"^^ . . "pathway" . . . . "co_341" . . "epidemiology" . "Close to 5K Categorizations for drugs, similar to ATCC."^^ . . . "subject agnostic" . "^MAM\\d{5}\\w$"^^ . "http://purl.obolibrary.org/obo/FIX_$1"^^ . "false"^^ . "Ontological Interpretations for Web Property Graphs" . "SNOMEDCTCT_2019_03_01" . . "development" . . "MycoBrowser marinum" . . . . "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"^^ . . . . "https://www.alzforum.org/mutations/"^^ . . . "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union."^^ . . . . . . . . . "classification" . . . . . . . "Fiona M McCarthy" . "human genetics" . . "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^ . "bioinformatics" . "https://bioregistry.io/phosphopoint.kinase:"^^ . "anatomy" . . "cvdo" . . "https://www.wwpdb.org/pdb?id="^^ . _:N0e9622e07aba42a0b14922d6456e5c09 "helpdesk cropontology" . "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode."^^ . "sequence" . . "trans" . . . . . "pathway" . . . . "IntAct protein interaction database" . "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1"^^ . . . "Event (INOH pathway ontology)" . . "false"^^ . . "Molecular Interaction Database" . "worm" . . . . . . "Medaka Developmental Stages" . "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality."^^ . . . . . . . "Ontology of Adverse Events" . . "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels."^^ . . . . . "^\\d+$"^^ . . . . . . "https://www.fisheries.noaa.gov/species/"^^ . "https://w3id.org/oc/meta/$1"^^ . . "^tgv[0-9]+$"^^ . . . . . . "DrugBank" . "false"^^ . "https://prefix.zazuko.com/prefix/$1:" . "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics."^^ . . . . "civic.variant" . "OncoMX Dataset" . . . . . . . . . . "vmc" . "^\\d{6}$"^^ . "http://purl.obolibrary.org/obo/CMO_"^^ . . . "small molecule" . . "^[A-Za-z0-9\\/]+$"^^ . . . "SchemaDefinition"^^ . . "obo" . . . . . "^.+$"^^ . . "true"^^ . . . "katy@indiana.edu" . . . . . . . "https://proteininformationresource.org/cgi-bin/resid?id=$1"^^ . "genomics" . . . . "Dengue Fever Ontology" . . . . . . . . "0000079"^^ . . "GPCR Natural Variants database" . . . . . "12969"^^ . "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation."^^ . "Vertebrate Skeletal Anatomy Ontology" . "Internet Engineering Task Force Language Tag" . . "bsg-000052"^^ . "false"^^ . . . . "MM00040"^^ . "patent" . . . "msaier@ucsd.edu" . . "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families."^^ . . . . "cell line" . . . . "false"^^ . "^\\d+$"^^ . "homd.taxon" . . "life cycle" . . "life cycle" . "http://purl.org/ontology/bibo/$1"^^ . . . "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. "^^ . "Regulatory Elements Database for Drosophila" . . "false"^^ . . "anatomy" . "Don Gilbert" . "ConfIDent Event Series" . . "medlineplus" . . . . . . . . . . . . . . "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1"^^ . "dictybase.est" . . "http://purl.obolibrary.org/obo/GSSO_$1"^^ . . . . . . "FlyBase Controlled Vocabulary" . . "http://purl.obolibrary.org/obo/EPIO_"^^ . "https://www.disprot.org/"^^ . . . "omim" . . "The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer."^^ . . "false"^^ . . . . . . . "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"^^ . "neuroname" . . . . . . "Gramene QTL" . . . . "https://biopragmatics.github.io/providers/hog/"^^ . . . "CoVoc Coronavirus Vocabulary" . . . . "orthodb" . "frederique.lisacek@isb-sib.ch" . "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId="^^ . "protein" . . "MediaDive Ingredient" . "https://www.emsl.pnnl.gov/project/"^^ . "false"^^ . . . "10b38aaf-b977-4950-85b8-f4775f66658d"^^ . . . . "drug interaction" . . "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment."^^ . . . . "This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage)"^^ . . "XB-GENE-922462"^^ . . . "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1"^^ . "^\\w+(\\.\\d+)?(\\.\\d+)?$"^^ . . . . . . . . . . . "0005"^^ . "false"^^ . . . "false"^^ . "This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family."^^ . . . "^\\d+$"^^ . "ccle" . "Role Ontology" . . "^\\d{7}$"^^ . "Clinical Trials Information System" . "false"^^ . "life science" . "false"^^ . . "behavior" . . . . "ncbitaxon" . "^MGYA\\d+$"^^ . . . . . "biosystems" . . "true"^^ . . . "data set" . "^DRSC\\d+$"^^ . "9861/3"^^ . . "ontology" . "ndex" . . "biomedical science" . "false"^^ . "false"^^ . . . "obv" . . "Integrative and Conjugative Element Ontology" . "phenomics" . . . . . . . "http://www.pathwaycommons.org/pc/record2.do?id=$1"^^ . . "http://www.oid-info.com/get/2.16.840.1.113883.6" . . "^\\d{7}$"^^ . "mcro" . "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."^^ . "true"^^ . . . "physics" . . "false"^^ . . "biodiversity" . "Liver Cancer Model Repository" . . "biomedical science" . . "https://bacteria.ensembl.org/id/"^^ . "^[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}$"^^ . "82"^^ . . . . . "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . "https://bioregistry.io/cabri:"^^ . "co_347" . "botany" . "Pier Luigi Buttigieg" . "http://purl.obolibrary.org/obo/LEPAO_"^^ . "protein" . . . . . . "matthias.samwald@meduniwien.ac.at" . . . . . . "PIRSF000100"^^ . "false"^^ . . "Sierra Moxon" . . . . . "hydrogeology" . . . . "cteno" . "https://bartoc.org/en/node/$1"^^ . . . "flymine.chromosome" . . . "The Python Package Index (PyPI) is a repository for Python packages."^^ . "life science" . . "^\\d{7}$"^^ . . "^\\d+$"^^ . "hl7.v3codesystem" . "biomedical science" . "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" . . . . . . . . "Lindsay Cowell" . "SFB_COVID19_MW286762"^^ . . . "ENCSR163RYW"^^ . . . "biomedical science" . "Danielle Thierry-Mieg" . . . . "hl7.v2codesystem" . . . . . "https://bioregistry.io/leafsnap:"^^ . . "obo" . "http://www.genome.jp/dbget-bin/www_bget?aaindex:"^^ . "BRAF"^^ . . . . "http://www.kegg.jp/entry/$1"^^ . "ontology" . "pmr" . . . . "^[0-9X\\-]+$"^^ . . . "biology" . . . . "plant phenotypes and traits" . "http://www.narcis.nl/publication/RecordID/$1"^^ . . . "A registry of life science prefxes"^^ . "5fde96bdc5f1aa9ff0cce18a"^^ . "http://ddinter.scbdd.com/ddinter/interact/"^^ . "ped" . . "Teresa K. Attwood" . . "Observational Medical Outcomes Partnership" . . . . . . . . . . "https://mged.sourceforge.net/ontologies/MGEDontology.php#"^^ . . . . "10020.2"^^ . . . "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^ . "^[A-Za-z]+$"^^ . . . . "http://purl.org/spar/bido/$1"^^ . "bitterdb.rec" . . . . . . . "false"^^ . "https://www.ncbi.nlm.nih.gov/snp/"^^ . . . . . "Urmas Kõljalg" . "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term="^^ . "ontology and terminology" . . "vuid" . "false"^^ . "http://bioportal.bioontology.org/ontologies/$1"^^ . "title"^^ . . "http://biomeddb.org/Disease/Details?DISEASEID="^^ . "0000015"^^ . "https://signor.uniroma2.it/relation_result.php?id=$1"^^ . "icd11" . "stian@soiland-reyes.com" . "ae8c77fe-e6c8-44d5-8265-4a38c637bbef"^^ . . "Asset Description Metadata Schema Vocabulary" . . . "Bioregistry Metaregistry" . . . "computational biology" . . . . "^P(X|R)D\\d{6}$"^^ . "https://www.ncbi.nlm.nih.gov/cdd?term=$1"^^ . "protein" . "atfdb.family" . . "false"^^ . "A type for entries in the Bioregistry's metaregistry." . . "ontology" . "http://usefulinc.com/ns/doap#$1"^^ . . . . . "animal physiology" . "false"^^ . "NIF Standard Ontology: Digital Resources" . "protein" . "General Formal Ontology" . "pharmacology" . . . . "transcript" . . . . . "cell biology" . . "http://purl.obolibrary.org/obo/NBO_"^^ . "rxnorm" . . . "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$"^^ . . . . . . . . "D001151"^^ . . . "true"^^ . . "mass spectrum" . "go.gpi" . "http://purl.obolibrary.org/obo/GEO_$1"^^ . . "Leen Vandepitte" . "bork@embl.de" . . "modeling and simulation" . . . . . . . . "inaturalist.observation" . "false"^^ . . "PSEEN0001"^^ . . . . . . . . . "pathoplant" . . . . . . "100000"^^ . . "alfred" . . . "phenotype" . . "anatomy" . . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene."^^ . . "172"^^ . "^[0-9]+$"^^ . . . "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . "false"^^ . . . "UM-BBD_compID" . "https://www.ebi.ac.uk/interpro/genomeproperties/#"^^ . . . . "Software Package Repositories" . "redfly" . _:N586e7aba53ab4b68932778362bfd0f96 "mb4@sanger.ac.uk" . . "gene function" . . . . "ontology" . . . . . . "nztcs" . "https://bioregistry.io/resolve/github/issue/$1"^^ . "http://purl.obolibrary.org/obo/ICEO_$1"^^ . "^\\d{7}$"^^ . . . . . . "ontology" . "Cowpea ontology" . . "ena" . . . "CIAT Common bean trait dictionary - version August 2014"^^ . . . . "false"^^ . "^[1-9][0-9]*$"^^ . . . . "epidemiology" . "Biofactoid" . "false"^^ . "David Lynn" . . . . . . "^\\d+$"^^ . "Gramene Growth Stage Ontology" . . "Sweet Potato ontology" . . . . _:Nbde6269f4f6443d69a8fb868ba8954f9 . "xpo" . . . . "Hans Ienasescu" . . . "sequence variant" . . "true"^^ . . . . . . "http://purl.bioontology.org/ontology/HOIP/HOIP_"^^ . . "biological process" . . . . "ontology" . . . . . . "https://commonchemistry.cas.org/detail?cas_rn="^^ . "AS000060"^^ . . . "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . . . . . . . . "000204"^^ . . . "genomics" . . . . . "phylogenetics" . . . . . . "dlxc" . . . . . . "clinical trials" . . "rtecs" . . "video resource" . . "^PDC\\d+$"^^ . . . . . . "https://models.physiomeproject.org/workspace/$1"^^ . "Sunflower ontology" . . . . "The Digital Object Identifier System is for identifying content objects in the digital environment."^^ . . . . "mpio" . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME"^^ . . . . . "^(\\w){3}$"^^ . . . . . . "http://psb.kobic.re.kr/STAP/refinement1/result.php?search="^^ . . . . . "medical informatics" . . "edda" . "PA448710"^^ . . . . . "grassbase" . . . . "Thomas Keane" . "https://catalog.hathitrust.org/Record/"^^ . "false"^^ . . "^[a-zA-Z_][a-zA-Z0-9\\-_]+$"^^ . . "Birgit Kersten" . . . "structure" . "jla1@sanger.ac.uk" . "https://www.datanator.info/gene/$1"^^ . "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments."^^ . "4dn.replicate" . "https://plants.ensembl.org/id/"^^ . "elspeth@genenames.org" . "15"^^ . . . . . "false"^^ . "Maggot" . "http://purl.bioontology.org/ontology/VANDF/"^^ . . "iceberg.family" . "chemical in the database supplied by Pesticide Action Network North America"^^ . "^EG\\d+$"^^ . . . . "^\\d+$"^^ . . . . "dragondb.dna" . . . "Identifier for an entity in open tree of life"^^ . . "WD_Entity" . . . . . "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"^^ . . "false"^^ . . . . "3792"^^ . "Genetic and Rare Diseases Information Center" . "BT20_BREAST"^^ . . "Ontology for the Anatomy of the Insect SkeletoMuscular system" . "AGRICOLA_ID" . . "sider.effect" . "Taconic Biosciences" . . "transgenic" . "Common Terminology Criteria for Adverse Events" . . . . . "true"^^ . . "subject agnostic" . . "npass" . . . "Castor bean ontology" . "obo" . . "molecule" . . . . "SNOMEDCT_US_2020_03_01" . . "false"^^ . "239287"^^ . . . . . . . "hsa-mir-200a"^^ . "general & upper" . . . . "A download link for the given resource" . "phenotype" . "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid="^^ . . . "knowledge representation" . . "^(Gi|Gc)\\d+$"^^ . "ontology" . . "DRKS00031815"^^ . . . . "Image Data Resource" . "50943"^^ . . . . "subject agnostic" . . "https://amzn.com/"^^ . "false"^^ . . "false"^^ . . . "false"^^ . . . . "3D Metabolites" . . . "unite" . . . "The Cell Cycle DB" . . "merops.clan" . . "^\\d+$"^^ . "microbial" . "KEGG_DGROUP" . "http://purl.obolibrary.org/obo/DDANAT_"^^ . "^BAMSC\\d+$"^^ . "otl" . "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . "Workflow"^^ . "http://vbrc.org/gene_detail.asp?gene_id=$1"^^ . . . "https://cropontology.org/rdf/CO_338:"^^ . "dip" . . "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO="^^ . "Clare Pilgrim" . "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"^^ . . . . . "classification" . "anatomy" . . . . . . . . . . "mex" . "false"^^ . . "^\\w+\\_\\w+$"^^ . "phylogenomics" . . . . . "https://repeatsdb.org/structure/"^^ . "protein" . _:N3e69e1e263a943b3837d9bf1b0810d0d "yingqin@rti.org" . . . . . . . . . . "A user of FAIRsharing"^^ . . . . . "ZFA_RETIRED" . "This collection contains various brain atlases from the Allen Institute." . . "opb" . "https://www.flymine.org/flymine/report/ChromosomeBand/"^^ . . . "anatomy" . "BAO" . "MIPModDB" . . . . . "drugbank.metabolite" . . "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^ . "https://go.drugbank.com/reactions/$1"^^ . . . . "life science" . "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^ . . . . . "false"^^ . "patient care" . "0010316"^^ . "https://cstr.cn/$1"^^ . . "false"^^ . . "https://tetrahymena.vet.cornell.edu/display.php?stockid=$1"^^ . "^[A-Z_]{3}[0-9]{4,}$"^^ . . . . . . "ncbibook" . "ecso" . . . . "cellrepo" . "RETIRED_EHDAA2" . . "BioNumbers" . "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."^^ . . "MaizeGDB" . . . . . "false"^^ . . . . . "^\\d{7}$"^^ . . . . . . "xenbase" . . "epidemiology" . "gc_id" . . "pao" . "false"^^ . "A0001"^^ . . "IUPHARfam" . "funding agencies" . . "http://dicom.nema.org/resources/ontology/DCM/$1"^^ . "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:"^^ . . . . "Candida Genome Database" . "https://www.ebi.ac.uk/ena/browser/view/"^^ . . . . . . . . . "^[A-Z]{1,2}\\d{5}$"^^ . . . "Web Elements" . . . . . . . "75"^^ . . . "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001)."^^ . "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^ . "SciCrunch Registry" . . "false"^^ . "0000440"^^ . . . . . "chemdb" . "Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan."^^ . . . . "6017782"^^ . . . . . . . . . "5fce9b7300001250"^^ . . . "false"^^ . "The Drug-Drug Interactions Ontology" . "false"^^ . . "BioCarta Pathway" . "https://biofactoid.org/document/"^^ . "1968"^^ . . . "Add"^^ . . . . . "^L\\d+$"^^ . . . "disease process modeling" . . "agriculture" . . "false"^^ . . . . "obo" . "omx.dataset" . "relationships" . . . . . . "0000000"^^ . . "http://purl.obolibrary.org/obo/CTO_$1"^^ . . "BiGG Reaction" . . . "interaction" . "Q9UKQ2"^^ . "ricenetdb.mirna" . "sequence" . "A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada."^^ . "ken.sd.hsu@gmail.com" . . "data model" . . . "The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants."^^ . . . . . "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id="^^ . "31623"^^ . "LK99"^^ . . . . . "EDAM Ontology" . . "French National Center for Scientific Research - Research Group Identifier" . . . "metabolite" . "dna" . . "dg5b0d" . "rnao" . . . . "https://www.storedb.org/?"^^ . "http://w3id.org/owlstar/"^^ . . . "http://purl.obolibrary.org/obo/AfPO_$1"^^ . "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . . . . . . "Ensembl Glossary" . . "090924"^^ . "pw" . . . . . . . . . "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " . "Interlab Cell Line Collection" . . "^\\w+$"^^ . "^TS-\\d{4}$"^^ . "https://www.phenxtoolkit.org/protocols/view/"^^ . . . "sequence annotation" . _:N44ea25e78e4a4c21a4fc2751279240af "Cynthia.Hake@cms.hhs.gov" . . . . "chemistry" . . "Human Metabolome Database" . . . . . . . . "http://purl.org/linked-data/cube#"^^ . . . . . "Torsten Schwede" . "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID="^^ . "stefan.kuhn@dmu.ac.uk" . "190000021540"^^ . . "ORCiD" . . "anatomy" . . "^\\w+$"^^ . . . "false"^^ . . "http://purl.obolibrary.org/obo/VIDO_$1"^^ . . "Genomic Epidemiology Ontology" . . . . . . "FungiDB" . "pruitt@ncbi.nlm.nih.gov" . . . "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif."^^ . "https://www.ebi.ac.uk/complexportal/complex/"^^ . . "https://www.wormbase.org/get?name="^^ . . . "jak@ucop.edu" . . . "obo" . "false"^^ . . . . "http://purl.obolibrary.org/obo/IAO_$1"^^ . . . . . . . "ontology" . "gmd" . "http://purl.obolibrary.org/obo/FBcv_$1"^^ . . . "false"^^ . . . "false"^^ . "http://swissregulon.unibas.ch/query/$1"^^ . . . . . "d4akea1"^^ . . "^\\d+$"^^ . . "obo" . "annotation" . "drosophila" . "biology" . . "communication science" . . . "http://purl.obolibrary.org/obo/AEO_"^^ . "abm" . . "Gi07796"^^ . . . . . . . "protein" . "https://integbio.jp/dbcatalog/en/record/$1"^^ . . . . "roleo" . . "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies."^^ . . . . . "https://sorgerlab.github.io/famplex/"^^ . . . . . . . . . . . . . . "ontology" . "^\\d{7}$"^^ . . "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"^^ . "evolutionary biology" . "proteomics" . . "http://purl.obolibrary.org/obo/FBSP_"^^ . . "https://biopragmatics.github.io/providers/msigdb/"^^ . "genome" . . . "obo" . "cutg" . . . "http://agroportal.lirmm.fr/ontologies/$1" . . . . . . . . "plo" . . . . "http://purl.obolibrary.org/obo/HsapDv_$1"^^ . "omics" . "https://www.biorxiv.org/content/10.1101/"^^ . . . . . "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing."^^ . "0110974"^^ . "Feature Annotation Location Description Ontology " . . . "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . "wdduncan@gmail.com" . "Trushar Shah" . . _:N23ddc6feb53a4e3faf299933d3451260 . "http://noctua.geneontology.org/editor/graph/gomodel:$1"^^ . . . "CY077097"^^ . . _:Nc8116353cdbb47418cccd7d79b6ca2a2 . "biological sample" . "gene" . "biomedical science" . "SubtiWiki" . "http://purl.obolibrary.org/obo/MI_$1"^^ . "biomedical science" . "false"^^ . . . "A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. "^^ . . . . . . "AADB12"^^ . "^UMIN\\d+$"^^ . "drug discovery" . . "Infectious Disease Ontology" . . "true"^^ . . "Academic Event Ontology" . "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . . "false"^^ . "false"^^ . "biology" . . "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . . "feature"^^ . . . . . "Database containing promotor sequences found in Saccharomyces cerevisiae."^^ . . . "life science" . . . . . . . . "provides for" . . "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$"^^ . . "http://purl.obolibrary.org/obo/ONE_$1"^^ . "false"^^ . . . "https://www.cellrepo.com/repositories/$1"^^ . . . . "https://www.storedb.org/store_v3/study.jsp?studyId="^^ . "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes"^^ . . "life science" . . . "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain."^^ . . . "http://purl.org/spar/biro/"^^ . "chictr" . . . . "CIViC Molecular Profile" . "SNOMEDCT_US_2020_09_01" . "obo" . "obo" . . . . "ontology" . . "Guy Perrière" . . "ontology" . "structure" . . . . . "small molecule" . "subject agnostic" . . . "botany" . . . . "pharmacodb.tissue" . "BIOMD" . "co_324" . "centrally registered identifier" . . . . . "Resource Description Framework" . . . "^\\d+$"^^ . . "environmental material" . . . . "provenance"^^ . . . . "Sofia Robb" . . "botany" . . "cell" . "ontology" . "false"^^ . . . . . "false"^^ . "Cell Line Database" . . . . . "alleles" . "^\\d+$"^^ . . "https://www.abcam.com/$1.html"^^ . . "life science" . . "BioKC (Biological Knowledge Curation), is a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML)."^^ . . "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database."^^ . . "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid="^^ . "lectins/172"^^ . . . "false"^^ . "Cellosaurus Registry" . . . "https://www.genome.jp/virushostdb/$1"^^ . "igsn" . . "mizrachi@ncbi.nlm.nih.gov" . . "sequence" . . . "cancer" . "obo" . . . "obo" . . . "^[A-Za-z]+$"^^ . . "Descriptive Ontology for Linguistic and Cognitive Engineering" . . . "https://coconut.naturalproducts.net/compound/coconut_id/"^^ . "ncbi.assembly" . . "http://sabiork.h-its.org/newSearch?q=ecnumber:$1"^^ . _:Nb5cf4dffbb9545e5b5258205b63dabd6 . "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology."^^ . . . . _:Nf2777a2942e4414f95db524e51c78f67 "kninomiya-mope@g.ecc.u-tokyo.ac.jp" . "SNOMEDCT_2020_03_01" . . . "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^ . . . "false"^^ . "corum" . . . "Kenan Azam" . . "Database of Quantitative Cellular Signaling: Model" . . . . . "trait" . . . . . "http://purl.obolibrary.org/obo/MIRO_$1"^^ . "nlx.br" . "https://www.semion.io/Author/$1"^^ . "Allergome" . "A vocabulary in LOV gathers definitions of a set of classes and properties (together simply called terms of the vocabulary), useful to describe specific types of things, or things in a given domain or industry, or things at large but for a specific usage. Terms of vocabularies also provide the links in linked data, in the above case between a Person and a City. The definitions of terms provided by the vocabularies bring clear semantics to descriptions and links, thanks to the formal language they use (some dialect of RDF such as RDFS or OWL). In short, vocabularies provide the semantic glue enabling Data to become meaningful Data. [from https://lov.linkeddata.es/dataset/lov/about]" . "genotyping" . "Yeast Deletion and the Mitochondrial Proteomics Project" . . "0001079"^^ . . . . "EDAM Topic" . . . "International Classification of Diseases, 9th Revision" . "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId="^^ . . "transcriptomics" . "obo" . . "protein" . "true"^^ . . "false"^^ . "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines."^^ . . . "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . "biosample" . . "life cycle" . . . . . . . "LNC" . . "alignment" . "eo" . . . "https://metazoa.ensembl.org/id/"^^ . "An ontology to capture confidence information about annotations."^^ . "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API."^^ . "DICOM Controlled Terminology"^^ . . . . . . . . . "https://chemkg.github.io/chemrof/$1"^^ . "^RC\\d+$"^^ . "dna" . . . "PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets."^^ . . "0000013"^^ . . . . . . . . . . . . "ontology" . "ricenetdb.reaction" . "false"^^ . "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" . "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid="^^ . . . "obo" . . . . "false"^^ . . "ideal" . . . "lewis.geer@nih.gov" . . . . "^MSMEG\\w+$"^^ . "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\"."^^ . . "Cell line collections (Providers)"^^ . . . . . "developmental biology" . . . "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"^^ . "Q13485"^^ . "Eric P. Nawrocki" . . . "Antibody Registry" . "https://www.pesticideinfo.org/chemical/"^^ . . . "text mining" . . . . "bugbase.protocol" . . . "scop.sccs" . . . "ontology" . "BitterDB Compound" . . . . "jrc-eurl-ecvam-chemagora"^^ . "health science" . . . . "https://bioregistry.io/metaregistry/"^^ . . . "312.33"^^ . _:Nb5cf4dffbb9545e5b5258205b63dabd6 "Heinrich Herre" . "host" . "36"^^ . . . . . . . . . "co_335" . "EG10173"^^ . "WormBase" . . "kronkcj@mail.uc.edu" . "^\\d+$"^^ . . . "mass spectrometry assay" . . . "Damion Dooley" . . . . "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id="^^ . . . "false"^^ . . . "miro" . . . . . "computer science" . . . . "subject agnostic" . . . "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data."^^ . . "false"^^ . "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^ . . . "http://purl.obolibrary.org/obo/MF_"^^ . . . "http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml"^^ . . "https://biopragmatics.github.io/providers/uniprot.ptm/"^^ . . . . "reagent" . . . "http://multicellds.org/MultiCellDB/$1"^^ . . . "MIPF0000002"^^ . "SABIO-RK" . . . "Todd M Lowe" . . . "SMP" . . "phenotype" . "hog" . . . . . . . . . . . . "modeling and simulation" . "Ensembl Plants" . . . . . . . . "false"^^ . "phenotype" . . . . . "human" . "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23"^^ . "protein" . "ontology" . . . . . . . . "PASS01237"^^ . . "Mathias Brochhausen" . "https://caninecommons.cancer.gov/#/study/"^^ . . . . . . . "jcggdb" . "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key="^^ . . . "structrual bioinformatics" . "structure" . . . "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1"^^ . . "^\\d{7}$"^^ . "bioinformatics" . . "nlm" . "https://www.hipsci.org/lines/#/lines/$1"^^ . . "A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research.\n\nRadLex provides the foundation for vital data resources used in radiology:\n\n- The LOINC/RSNA Radiology Playbook\n- RadElement Common Data Elements\n-RadReport Radiology Reporting Templates\n\nThe development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project."^^ . "IP" . "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query="^^ . . . . . . . . . . . . . "sebastien.moretti@sib.swiss" . "^P\\d+$"^^ . . . . "data retrieval" . "citation" . . "^D\\d+$"^^ . . . . . . . "protein" . . . . . . "http://purl.obolibrary.org/obo/ZFA_"^^ . "rna" . "iceberg.ime" . "http://www.ncbi.nlm.nih.gov/clinvar/$1"^^ . . "A subspace of Metabolic Atlas for compartment-specific records for metabolites."^^ . "false"^^ . "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage."^^ . . . "^\\d{7}$"^^ . . "http://www.onto-med.de/ontologies/gfo.owl#"^^ . . . . . . . "Cell line collections (Providers)"^^ . "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms."^^ . . "uniprot.var" . . "https://dbpedia.org/ontology/"^^ . "Integbio" . . . "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available."^^ . . . . . "^[0-9]+$"^^ . . . . . "ctibor.skuta@img.cas.cz" . "J. Michael Cherry" . . . . "^[1-9][0-9]{14}$"^^ . . . . "1174"^^ . . . "gemet" . "false"^^ . . . . . . . "http://aims.fao.org/aos/agrovoc/c_$1"^^ . . . . . . . "https://gitlab.com/$1"^^ . . . . . "SCV000151292"^^ . . . "http://vita.mbc.nctu.edu.tw/search.php?acc="^^ . . . "anatomy" . . "HOMD Sequence Metainformation" . "reaction data" . . . "GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match."^^ . . . . . "false"^^ . "metlin" . "google.scholar" . . . . . . . "false"^^ . . . . "http://purl.unep.org/sdg/SDGIO_$1"^^ . . . . . . "^\\d+$"^^ . . "5112"^^ . "ontology" . . "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences."^^ . . . "true"^^ . . . "Astrophysics Source Code Library" . . . . . . "Open Data for Access and Mining" . "pathway" . "Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys."^^ . "dna" . . . "chemistry" . . . . . "comparative genomics" . . . . "Metabolic Atlas" . "Leszek Vincent" . . . . . . "http://dictybase.org/gene/"^^ . "http://multicellds.org/MultiCellDB/"^^ . . "Ontology of Precision Medicine and Investigation" . "unit" . "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . . . . . . "genome" . . . . "obo" . . . "InChIKey" . . "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid="^^ . . "salamander" . "disprot.region" . . . . "https://cropontology.org/rdf/CO_360:$1"^^ . "Dublin Core Elements (1.1)" . . "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf="^^ . "https://www.ncbi.nlm.nih.gov/sra/"^^ . "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]"^^ . "http://purl.obolibrary.org/obo/CHMO_"^^ . . . "Roman Laskowski" . "https://viperdb.org/Info_Page.php?VDB=$1"^^ . "biocuration" . . . . . . . "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"^^ . "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms."^^ . . . . . "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/"^^ . "GALEN" . "NIF Cell" . . . . . . . . "PM0012345"^^ . "cco" . "genomics" . . . . "Medical Subject Headings" . . . "false"^^ . "glycopost" . . . . . "sweetrealm" . "ontology" . "subject agnostic" . "functional genomics" . "^\\d{6,8}$"^^ . . . "obo" . . . . . . . . . "Xenbase" . . . . . "BEI Resources" . . . . . "^\\d{7}$"^^ . "swissregulon" . "^cpd\\d+$"^^ . . "ontology" . . "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/"^^ . . . . . "false"^^ . "ATL98012"^^ . "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1"^^ . . . "ndc" . "linkml" . "pathway" . . "MGnify Analysis" . . . . "An ontology of prokaryotic phenotypic and metabolic characters"^^ . "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . "funcbase.mouse" . "life science" . . "false"^^ . . . . "Data Use Ontology" . "metabolites" . . "classification" . "false"^^ . "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name="^^ . . "https://ximbio.com/reagent/"^^ . . . . . . "false"^^ . . . "ontology" . . . . . . . . "merops.entry" . "MicroScope" . "European Medicines Evaluation Agency" . "https://reporter.nih.gov/project-details/"^^ . "jax" . . . . "JMChandonia@lbl.gov" . "STOREDB at University of Cambridge" . . . "http://zfin.org/$1"^^ . "http://purl.obolibrary.org/obo/PdumDv_"^^ . "major histocompatibility complex" . "enzyme" . . "life science" . . . . . . "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege."^^ . . . . "obo" . . . . . . . "false"^^ . . . "Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species."^^ . "materials informatics" . . . "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^ . . . . "false"^^ . . . . . "A repository of software packages written in Javascript, TypeScript, and related."^^ . . "obo" . . . . "Enzo Life Sciences" . . "ACTRN12623000498695"^^ . "phenotype" . . "protozoan" . . . "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^ . . . "https://units-of-measurement.org/$1"^^ . _:N0e9622e07aba42a0b14922d6456e5c09 "helpdesk@cropontology-curationtool.org" . . . . . . . . . "clinvar.variant" . . "Biological Spatial Ontology" . . "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . . "false"^^ . "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits."^^ . . . . . . "Variation Ontology" . . . . . "ontology" . . . . . . . . . "Stress Knowledge Map" . . "28"^^ . . "https://bio.tools/"^^ . "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources."^^ . . . . . . . . . "life science" . "plant phenotypes and traits" . "Ardan Patwardhan" . "ecosystem science" . . "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation."^^ . . . . "3304"^^ . "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g="^^ . . . . . "systems biology" . . . . . . "false"^^ . "ncbigene" . . "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes."^^ . . "Lindsey.Anderson@pnnl.gov" . . . "interaction" . "http://www.ubio.org/browser/details.php?namebankID="^^ . . "^\\d{8}$"^^ . . . . . "false"^^ . . . . . . "false"^^ . . _:N0b8e586b4b274c769184d4708ff70754 "helpdesk@cropontology-curationtool.org" . "agriculture" . "ASPL0000349247"^^ . "^\\d+$"^^ . . . . . . "0000022"^^ . . . "molecular entity" . . . . "slso" . . "MOSAiC Ontology" . "translational medicine" . . . "gomf" . . . "PharmGKB Disease" . . "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read."^^ . . . "glycomapsdb" . . "cemo" . . . "ychai@usc.edu" . . "ecology" . . . . . "botany" . . . . "kegg.compound" . . . . . . . "4DN"^^ . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid="^^ . "PR000001"^^ . . . . . . . "http://purl.obolibrary.org/obo/VSAO_$1"^^ . "Archival Resource Key" . . . "http://data.crossref.org/fundingdata/funder/10.13039/$1"^^ . "Nikos C. Kyrpides" . "http://biomodels.net/rdf/vocabulary.rdf#"^^ . . . "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms" . . . . . "https://cropontology.org/rdf/CO_338:$1"^^ . . . "The upper level ontology upon which OBO Foundry ontologies are built."^^ . "false"^^ . . . "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/EPIO_$1"^^ . "Zoë May Pendlington" . . . "^\\d+$"^^ . . "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1"^^ . . . "Rfam database of RNA families" . "CutDB" . . . . "^\\d{7}$"^^ . . "bone" . . . . "false"^^ . . . . "http://aber-owl.net/ontology/$1/#/Browse/" . "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons."^^ . . . . "PharmacoDB Tissues" . _:Nf670dc591a464c0e95466a2df952cb59 . . "mpjensen@buffalo.edu" . . "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^ . . "^PAp[0-9]{8}$"^^ . "^\\d{8}$"^^ . . "false"^^ . . . "GRIN URL" . . . "genome" . . "false"^^ . "agriculture" . "classification" . "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes."^^ . . "sequence feature" . "sequence" . . "^\\d+$"^^ . "false"^^ . "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" . . . "Homeostasis imbalance process ontology" . . "http://cegg.unige.ch/orthodb/results?searchtext="^^ . "life science" . "false"^^ . . . . "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^ . . . . . "true"^^ . "^[0-9]{8}$"^^ . "bioinformatics" . . . "NP_012345"^^ . . . . "pubchem.aid" . . . "icldb" . . "niaest" . . "https://cropontology.org/rdf/CO_359:"^^ . "domain" . "bio.tools" . . "ahamosh@jhmi.edu" . . "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins."^^ . . . . . "nci.drug" . . "biology" . "^\\d{7}$"^^ . . . . . . . "http://n2t.net/ark:"^^ . . "https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md"^^ . "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."^^ . . . . . . . . . "mouse strain" . "obo" . . "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."^^ . . "life science" . . "amalik@ebi.ac.uk" . . . . . "https://cropontology.org/rdf/CO_322:$1"^^ . . . . . . "scomp" . . . "preclinical studies" . . "https://abrc.osu.edu/stocks/number/SALK_"^^ . . . . "https://prefix.zazuko.com/prefix/$1:"^^ . . . . . "false"^^ . . "https://www.gbif.org/species/$1"^^ . "neXtProt family" . . . . "Li-San Wang" . "http://virtualflybrain.org/reports/$1"^^ . "PUBCHEM_CID" . "dentistry" . "brain regions" . . "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"^^ . . . . . "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools."^^ . "https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm"^^ . . "http://purl.obolibrary.org/obo/STATO_"^^ . "ontology" . . . "false"^^ . . . "Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant."^^ . "vto" . . "http://iflastandards.info/ns/fr/frbr/frbrer/"^^ . "false"^^ . . . "biology" . . . . "Selventa legacy protein family namespace used with the Biological Expression Language"^^ . "https://w3id.org/nfdi4cat/voc4cat_$1"^^ . . . . "biomedical science" . . . . . . . . "https://www.uniprot.org/uniref/$1"^^ . . . "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^ . . . "EchoBASE post-genomic database for Escherichia coli" . "p.buttigieg@gmail.com" . "^\\d{7}$"^^ . . . "Rat Genome Database" . . "wmueller@gbf.de" . "FullySpecifiedAtom"^^ . . . "obo" . "ontology" . "https://www.bgee.org/gene/"^^ . "tumor" . . . "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an="^^ . "structure" . "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"^^ . . "m.a.laporte@cgiar.org" . . . "NRFC051"^^ . . . . . . "ZFIN" . "CIViC Source" . "informatics" . . . "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"^^ . . "protein" . . . "shuichi@hgc.jp" . . . . . . . "William Hayes" . "anatomy" . "https://disprot.org/$1"^^ . . . . . . "Handle" . . "structure" . . . "0290"^^ . . "KEGG Module" . "^\\d+$"^^ . "crossref.funder" . "comparative genomics" . . . . "C. elegans phenotype" . . . . "autdb" . . . . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information."^^ . . "https://bioregistry.io/proteomicsdb.protein:"^^ . . "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1"^^ . . . "ybradford@zfin.org" . "life science" . . . "ontology" . "false"^^ . "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"^^ . "https://rpcec.sld.cu/en/trials/$1"^^ . "biology" . "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."^^ . . "false"^^ . . "Samuel Friedman" . "an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems."^^ . "https://www.webofscience.com/wos/woscc/full-record/WOS:$1"^^ . . . . "Ontology of rat strains"^^ . . "^\\d+$"^^ . "2019-08-03_00000089_1"^^ . . "Pubchem" . . . "http://purl.obolibrary.org/obo/COVOC_"^^ . . . . . . . . . . "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=$1"^^ . . "structural bioinformatics" . . . . . "genetic resource" . . . "false"^^ . . . "http://purl.obolibrary.org/obo/HEPRO_$1"^^ . "hso" . . . "health science" . . "rscheuermann@jcvi.org" . . "jfernand@um.es" . "daniel.wilson@uni-hamburg.de" . "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid="^^ . . . . "http://purl.obolibrary.org/obo/TADS_$1"^^ . . . . "http://bactibase.hammamilab.org/$1"^^ . . "Nicholas Furnham" . "977869"^^ . . . . "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"^^ . _:N14aec72fb9624574a7835e3cbcbfd5e9 . . . "http://purl.obolibrary.org/obo/PAO_"^^ . . . . . "life cycle" . _:N9b7f1cbc7ff94c8baf5784763220d782 "cs@firstdatabank.com" . "Ambystoma Genetic Stock Center" . . . "image" . "https://labsyspharm.github.io/lspci/$1"^^ . "^[0-9]{12}$"^^ . . . "true"^^ . "http://www.ncbi.nlm.nih.gov/clinvar?term="^^ . . . . . "schem" . "false"^^ . . . "http://www.isni.org/isni/$1"^^ . . "false"^^ . . "conferences" . . "https://www.isrctn.com/$1"^^ . . "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources."^^ . . . "COG Categories" . "gsso" . "NIST Chemistry WebBook" . . . "false"^^ . "genetic strain" . . . . . . . . "http://ratmap.org/Showgene.php?gene_stable_id=$1"^^ . "https://bioregistry.io/bacmap.map:"^^ . "UPC04349"^^ . "false"^^ . . . "wyeth@cmmt.ubc.ca" . . "http://open-services.net/ns/core#$1"^^ . "obo" . . "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms."^^ . "false"^^ . . . "KEGG Compound" . "obi" . . . . . . . . . . "Publishing Workflow Ontology" . "http://purl.bioontology.org/ontology/VANDF/$1"^^ . . . . . "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . "https://w3id.org/aio/$1"^^ . . _:Na498744430974b0f965343f882a62ba4 "Jonathan Bard" . . "Medaka fish anatomy and development" . "AA0001"^^ . . "^\\d{8}$"^^ . "false"^^ . . "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond."^^ . . . . . "true"^^ . "true"^^ . . . . "MESH_DESCRIPTOR_UI" . "false"^^ . "true"^^ . "FBtr0084214"^^ . . "LIPID_MAPS_instance" . . . . . . "false"^^ . . . . . . "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"^^ . . . . "ISCW007415"^^ . . . "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1"^^ . . "OSC1416"^^ . "^HIX\\d{7}(\\.\\d+)?$"^^ . "taxonomy" . "https://id.loc.gov/authorities/$1"^^ . . . . "ontology" . . "false"^^ . . . "karr@mssm.edu" . "medicine" . "273"^^ . . . . . . . . . . . . . . "vt" . "life science" . . "vsdb" . "12"^^ . . . "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1"^^ . . . . "BugBase Protocol" . "^[A-Z]+[A-Z-0-9]{2,}$"^^ . . . "^(ev\\:)?E\\d+$"^^ . "GiardiaDB" . "false"^^ . . . . "^DAP\\d+$"^^ . . "ontology" . "AGRO" . "http://data.crossref.org/fundingdata/funder/10.13039/"^^ . . . . . "policy" . . . . "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query="^^ . . . . . "Physico-chemical methods and properties" . . "genomics" . . . "C34"^^ . "https://bioregistry.io/cmecs:"^^ . "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables"^^ . "reaction" . . . "ProteomicsDB Protein" . . . . "http://purl.bioontology.org/ontology/HCPCS/$1"^^ . . . "life cycle stage" . "astrophysics and astronomy" . "false"^^ . . . . "medicinal chemistry" . "https://bioregistry.io/pesticides:"^^ . . . "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry."^^ . . . . . . . . . . . "GitLab" . "Andrew G. McArthur" . "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data."^^ . . "Logical Observation Identifiers Names and Codes" . "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank."^^ . "http://www.coloncanceratlas.org/search_cell_line?cell_line="^^ . "mmo" . . . "LSM-6306"^^ . . . "ISBN-13" . . . "collagenmutdb" . . "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . . . . . . . . "dna" . "P683" . "Brachiaria ontology" . "Plant Growth and Development Stage" . . . . "EGAD00000000001"^^ . "true"^^ . "false"^^ . . "Oryzabase Mutant" . . . . "http://uri.neuinfo.org/nif/nifstd/birnlex_"^^ . "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^ . . . . "false"^^ . . . "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^ . . "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1"^^ . . . "John Garavelli" . . "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)"^^ . "ontology" . . . . . . "false"^^ . "NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet.\n\nKnowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004)."^^ . "ChemDB" . "life science" . "structure" . "false"^^ . . "metatlas.reaction" . "0000000"^^ . . "life science" . "radiology" . . . "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place."^^ . . "http://purl.obolibrary.org/obo/XLMOD_$1"^^ . "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id="^^ . . . "http://purl.obolibrary.org/obo/NCIT_"^^ . . . . . . "molecule" . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes."^^ . . "UM-BBD_enzymeID" . . "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra."^^ . . "F-SNP" . "CIViC Disease" . . . "Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate."^^ . . . . . . "This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website)"^^ . . . "ontology" . . . "GLDS-141"^^ . . . "United States Patent and Trademark Office" . "ontology" . . . _:Nfbe0e8521e37434badd542c98d5cadea . "http://metnetonline.org/browse_pathway2.php?pthID=$1"^^ . . . . "^MAR\\d{5}$"^^ . . . "101"^^ . "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession="^^ . . "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features."^^ . . "Laurent Duret" . . . "https://idr.openmicroscopy.org/search/?query=Name:idr"^^ . . "gc" . "life science" . "https://www.ncbi.nlm.nih.gov/medgen/$1"^^ . "This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects."^^ . "WormBase RNAi" . . "ecology" . . . "nickf@ebi.ac.uk" . . . "^UPI[A-F0-9]{10}$"^^ . . . "virology" . "false"^^ . "ricenetdb.gene" . . . . "protein" . "https://catalog.hathitrust.org/Record/$1"^^ . . "Amos.Bairoch@sib.swiss" . . "^\\d+$"^^ . . . "https://uts.nlm.nih.gov/uts/umls/concept/$1"^^ . "KEGG BRITE" . "http://www.bind.ca/Action?identifier=bindid&idsearch="^^ . . "BioCatalogue Service" . . . "Cell line collections (Providers)"^^ . . . "d.craik@imb.uq.edu.au" . . "dna" . "false"^^ . . . . . . "ontology" . "neuronames" . . . "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae."^^ . . . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid="^^ . . . "co_336" . . . . . . . . . . . . "chromium"^^ . "Pantelis Topalis" . "ProtClustDB" . "classyfire" . "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"^^ . . . . "infection" . . . "https://precision.fda.gov/uniisearch/srs/unii/$1"^^ . "EMEA/H/C/000181"^^ . "http://www.informatics.jax.org/accession/MGI:$1"^^ . . "http://func.mshri.on.ca/human/genes/list_functional_scores/"^^ . . . . . "cp390@cam.ac.uk" . "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."^^ . . "A collaborative project intended to create an encyclopedia documenting all living species known to science"^^ . . . "Protein Structural Change Database" . "http://www.w3.org/2008/05/skos-xl#$1"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_qual_"^^ . . . "protein" . "animal husbandry" . . . "tair.locus" . "https://www.uniprot.org/keywords/"^^ . "false"^^ . . . "dicom" . . . . "https://radlex.org/RID/$1"^^ . "^\\d{7}$"^^ . "false"^^ . _:N560c1b9b384a4f05be40aadc76ea025d "chinhda@alleninstitute.org" . . "classification" . . . "https://pypi.org/project/"^^ . . "3532759"^^ . "https://archive.softwareheritage.org/browse/swh:"^^ . "has resource example" . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/CTO_"^^ . "NCBI Data Repository Service" . . . . . "genomics" . "life science" . "ontology" . "MIMAT0046872"^^ . "ontology" . . "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]."^^ . "Cardiovascular Disease Ontology" . "false"^^ . . "human" . "biosimulations" . . "false"^^ . . . "false"^^ . . . "^\\d{6}$"^^ . "https://prefix.zazuko.com/$1:$2" . "cell biology" . "http://purl.obolibrary.org/obo/VariO_"^^ . "DragonDB DNA" . "https://www.genenames.org/data/gene-symbol-report/#!/symbol/"^^ . "spar" . "crop2ml" . . . . "^\\d{7}$"^^ . . "allele" . . . . . . "cell" . . . "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:"^^ . . . "data management" . . . . . . "taxonomy" . . . . "subject agnostic" . . . "false"^^ . . . . . . . "ontology" . . . "publons.researcher" . "CH_001923"^^ . . . . . . . . . "https://uts.nlm.nih.gov/uts/umls/semantic-network/"^^ . . . . "obo" . "Product number for the European Medicines Agency"^^ . "true"^^ . . . _:N67bba369e0514790a627d10e8fd5af6d "Radiological Society of North America" . . . . "SRX000007"^^ . . . . . . "drugs" . "http://purl.obolibrary.org/obo/AfPO_"^^ . "protein" . "sequence" . . . . . . . . "OUYCCCASQSFEME-MRVPVSSYSA-N"^^ . . . . . "false"^^ . . . . . "The anatomy of the Tick, Families: Ixodidae, Argassidae"^^ . . . . "human" . . "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . . "Teleost Anatomy Ontology" . "csa" . . "http://purl.obolibrary.org/obo/REO_$11"^^ . "life science" . . "ElementNumber"^^ . . . . . "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information."^^ . . "CSP2005" . "anatomy" . "http://www.kegg.jp/entry/"^^ . . . "quality" . "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"^^ . . "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies."^^ . . "recombinant host" . . . . "network model" . . . "^\\d{8}$"^^ . "https://www.ebi.ac.uk/pdbe/entry/emdb/"^^ . . . . . . . . . . . . . . . . . . . . "food" . . "https://www.ribocentre.org/docs/"^^ . . . . . . . "https://cropontology.org/rdf/CO_367:$1"^^ . . . "2"^^ . "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications."^^ . "^NPC\\d+$"^^ . "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques."^^ . "http://purl.obolibrary.org/obo/ZECO_"^^ . . . . "Decentralized Biomedical Ontology" . . "100"^^ . . . "cell biology" . . . "ctd.chemical" . . "false"^^ . . . . "ICARDA - TDv5 - Sept 2018"^^ . . . . . "echobase" . "gmd.ref" . . . "nlx.inv" . "A registry of commonly used prefixes in the life sciences and linked data. The source data for this registry is a spreadsheet on Google called the Life Science Registry. This registry was previously known as Prefix Commons and was available at https://prefixcommons.org." . "false"^^ . . "Saccharomyces Genome Database" . . "0000088"^^ . "molbase.sheffield" . _:Nc8de2d34560649929fc1996dfc57b425 "helpdesk@cropontology-curationtool.org" . "RiceNetDB miRNA" . "https://nanocommons.github.io/identifiers/registry#"^^ . . . . . "Database of Genotypes and Phenotypes" . . "http://purl.obolibrary.org/obo/PROCO_"^^ . _:Na753bc128ae04b158307c2af391f4ddf . "is deprecated" . "ontology" . . . "orthologous" . "Peter Karp" . . . "http://www.probonto.org/ontology#PROB_"^^ . . "TAIR Protein" . "cropping systems" . "^EMD-\\d{4,5}$"^^ . "expression data" . . "UniProt Protein" . "Scholia Registry" . . . . "structure" . "false"^^ . . "Human Dephosphorylation Database" . "SABIO-RK Reaction" . "cordis.project" . "^[a-z0-9]+$"^^ . . . . . . . . . . . "electronic health record" . "Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank."^^ . "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . . "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database."^^ . . . . . . "life science" . . . . "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)"^^ . . . "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . . "AddexBio cell line products" . "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue."^^ . "https://bioregistry.io/ppdb:"^^ . "000004"^^ . "MSBNK-IPB_Halle-PB000166"^^ . . "IA"^^ . "0000550"^^ . . "resource metadata" . . "5ede4273-b26c-4ea4-adb7-3ce294ab3397"^^ . . "^[a-zA-Z0-9_\\.]+$"^^ . . . "nutritional science" . . "Dictyostelium discoideum anatomy" . . "false"^^ . . . . . "ICD-11" . "CASID" . "nmr" . "false"^^ . . . "ontology" . . . "chemistry" . . . . . "cell" . . "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view."^^ . . . . . "ICDO" . . . . "^\\w+$"^^ . . . "true"^^ . "hj@uestc.edu.cn" . . . . . . . . . . . . . "Gene Normal Tissue Expression" . "BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format."^^ . . "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways."^^ . . "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier."^^ . "diseasesdb" . "true"^^ . . "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract."^^ . "life science" . "spar" . "false"^^ . . . . . . "Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]"^^ . . "https://aopwiki.org/stressors/$1"^^ . . "true"^^ . "tarbase" . "mutation" . . . . "obo" . "^\\d{7}$"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_"^^ . . . . . "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)."^^ . . "Ontology for genetic interval" . "http://vbrc.org/gene_detail.asp?gene_id="^^ . . "icepo" . . . . "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value="^^ . "false"^^ . . . . . "Philippine Health Research Registry" . . . "genetics" . . . . . "sep" . . . . . . . "FlyBase internal citation identifiers"^^ . . "Darren Natale" . . "Human Brain Atlas" . . "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species."^^ . . . "fbcv" . . . "false"^^ . "metabolite" . . "obo" . "encode" . "H3.03.00.0.00007"^^ . . . "^\\d{8}$"^^ . "domain" . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/"^^ . . "http://exac.broadinstitute.org/gene/"^^ . "panther.family" . "owl" . "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide."^^ . "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function."^^ . . . "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^ . "genomics" . "^ChiCTR\\d+$"^^ . . "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries."^^ . . . . . . "nlx" . . . . "GWAS Catalog" . . . . . "International Classification of Diseases for Oncology" . "geogeo" . . . . . "Dataset"^^ . "http://purl.org/net/orth#"^^ . "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC="^^ . . "Toby J Gibson" . . . . . "^[a-zA-Z]+.+$"^^ . . "http://purl.obolibrary.org/obo/BTO_"^^ . "citlalli.mejiaalmonte@gmail.com" . . . . . "fernanda.farinelli@gmail.com" . . "small molecule" . "insdc.run" . . . "0007404"^^ . "4DNESWX1J3QU"^^ . . . "0000449"^^ . . . "AMDEFA"^^ . . . . "psdo" . . "idomal" . . . . "RPCEC00000423"^^ . . "r.huntley@ucl.ac.uk" . . . . "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^ . . . . "ontology" . "77"^^ . . . . . . . "harkemaj@msu.edu" . "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."^^ . . . . "virology" . "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins."^^ . "https://lobid.org/gnd/"^^ . . "biochemistry" . "Proteomic Data Commons" . "BTO" . . "http://purl.obolibrary.org/obo/MMO_$1"^^ . . . . . . . "lars.holm.nielsen@cern.ch" . "https://biokb.lcsb.uni.lu/fact/"^^ . . "https://bioregistry.io/reo:"^^ . "timrobertson100@gmail.com" . . . . "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept"^^ . . . . "transcriptomics" . "https://uts.nlm.nih.gov/uts/umls/concept/"^^ . "^\\d{7}$"^^ . . . . "fabio" . . "biomedical science" . . "clinical studies" . . "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"^^ . . "A subspace of Metabolic Atlas for reactions."^^ . "lindsey.anderson@pnnl.gov" . . "http://www.wikidata.org/entity/"^^ . . . "^GenProp\\d+$"^^ . "false"^^ . "Biocompute Object" . . "PD000596"^^ . . . . "https://www.scopus.com/affil/profile.uri?afid="^^ . . . . . . "xuo" . . "http://www.w3.org/2000/01/rdf-schema#"^^ . "TRQ"^^ . . . . . . . . . . . "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1"^^ . . . . . . . . . . "ontology" . "clinvar.record" . . . "200906038218908385"^^ . "Traits and phenotypes of flowering plants occurring in digitized Floras"^^ . . "http://cerevisiae.oridb.org/details.php?id=$1"^^ . "https://www.xenbase.org/entry/"^^ . . "obo" . . . "obo" . . . "Software"^^ . "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object="^^ . "bartoc" . "morphology" . . . "rutgeraldo@gmail.com" . . "false"^^ . . . "brain" . . . . "http://purl.obolibrary.org/obo/SLSO_$1"^^ . "false"^^ . . . "regulation of gene expression" . . "ontology" . "https://bacdive.dsmz.de/strain/$1"^^ . "expression" . . "reagents" . . "https://data.terra.bio/ga4gh/drs/v1/objects/"^^ . "^\\d{7}$"^^ . . "social and behavioural science" . . "0000008"^^ . . "CATH superfamily" . . "obo" . "drugbank.salt" . . . . . . . . . "neurodegeneration" . . . . "false"^^ . . . "^F\\d+$"^^ . "https://cropontology.org/rdf/CO_322:"^^ . "chemical" . "https://www.biolegend.com/Default.aspx?ID=6664&productid="^^ . . . . "MarDB" . . . . . "SNOMED CT (International Edition)" . . "innatedb" . "false"^^ . "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families."^^ . . "sheepqtldb" . . "MNXC15"^^ . . . . . . . . . . . . "structure" . . "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts."^^ . . . . . . . . . "https://vectorbase.org/gene/$1"^^ . . . . . . "http://www.ontology-of-units-of-measure.org/resource/om-2/"^^ . . "David Gloriam" . "Jeremy D. Glasner" . _:N35b9ad34ce8c47dd8af00d082157e04c "LOINC Support" . . "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation."^^ . . "ccle.cell" . . . . "obo" . "hgmd" . . . . . "life science" . . . . "01625"^^ . . . . . . "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN="^^ . . "SNOMEDCT_US_2018_09_01" . "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp="^^ . "CHEMONTID" . . . . "2A"^^ . . _:Ncec661c1c76848d8a02c89fa39775417 "Ian Davis" . . "chemistry" . . . . "http://edamontology.org/data_$1" . . "ontology" . "reaction data" . "https://biokb.lcsb.uni.lu/fact/$1"^^ . "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line="^^ . . "life science" . "http://exac.broadinstitute.org/transcript/"^^ . . . . . . . . . . "AURKA"^^ . . "gene" . . . . . "vmhreaction" . . . "85163"^^ . "http://purl.obolibrary.org/obo/CARO_$1"^^ . "http://purl.obolibrary.org/obo/TGMA_"^^ . . "0000010"^^ . "http://purl.obolibrary.org/obo/OHMI_"^^ . "Marc_Ciriello@hms.harvard.edu" . . . . "biomedical science" . . "http://purl.obolibrary.org/obo/GOREL_$1"^^ . . . . . . "biology" . "PubMed" . "VHOG_RETIRED" . "PrefixOrTermMapping"^^ . . "https://biosimulators.org/simulators/"^^ . . "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species."^^ . . . "registry" . . . "biology" . . . . . . . "^\\d{7}$"^^ . . "biomedical science" . . . . "Erik Segerdell" . . . "Gramene Taxonomy" . . . "bioinformatics" . "foodex2" . "ontology" . "protein acetylation" . . . "virology" . "Homologous Organ Groups" . "genomics" . . . "CIViC Evidence" . "^[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}$"^^ . "URGI Contact" . "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . . . "India Clinical Trials Registry" . "000000159"^^ . . . . "human health" . "068078"^^ . "https://www.kegg.jp/entry/"^^ . "Flora Phenotype Ontology" . . . . "report" . "http://purl.obolibrary.org/obo/MC_$1"^^ . . . . . "biology" . . . . . "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"^^ . "21877"^^ . "^\\d+$"^^ . . . "false"^^ . "GrainGenes" . "^\\d+$"^^ . . "http://purl.obolibrary.org/obo/ONTONEO_"^^ . . . "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . . . . . "^[AEP]-\\w{4}-\\d+$"^^ . "life science" . . . . . "http://purl.obolibrary.org/obo/PGDSO_"^^ . "This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files."^^ . "gene" . . . "protein" . "CorrDB" . "ontology" . "http://purl.obolibrary.org/obo/OPMI_"^^ . . . . "Sabrina@tislab.org" . . "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/"^^ . "sty" . "gwascentral.phenotype" . "Crates.io" . . "0040379"^^ . . . . "Polymorphism and mutation databases"^^ . "human disease model" . . . . . . "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs."^^ . "false"^^ . . . . . "life science" . . "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds."^^ . . "http://en.wikipedia.org/wiki/$1"^^ . . . . "^\\d{7}$"^^ . "false"^^ . . "^\\w+$"^^ . . . . . . "https://www.ncbi.nlm.nih.gov/nuccore/"^^ . . . . . . . . "00005254"^^ . . . "https://www.ncbi.nlm.nih.gov/nucleotide/$1"^^ . . "false"^^ . "The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes."^^ . . . . "http://purl.obolibrary.org/obo/HEPRO_"^^ . . . . . . . . . "false"^^ . . "mmrrc" . "small molecule" . . . . "false"^^ . "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"^^ . . "^\\w+$"^^ . . . "https://mobidb.org/"^^ . "false"^^ . . . . . "ecology" . . "ontology" . "bold.taxonomy" . . . . "false"^^ . . . . . "The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response."^^ . . . . "https://pubchem.ncbi.nlm.nih.gov/element/$1"^^ . . "https://bioregistry.io/registry/$1" . . "https://www.genenames.org/cgi-bin/genefamilies/set/"^^ . "nist" . "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1"^^ . . . . . "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."^^ . . . . . . "European Registry of Materials" . "false"^^ . . . . "drug development" . . . . . . . . . "http://multicellds.org/MultiCellDB/"^^ . . "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"^^ . . "life science" . . . "phosphopoint.kinase" . . "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries."^^ . "EDDA Study Designs Taxonomy" . "experimentally determined" . . . . . . . . "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . . . . . . "https://glygen.org/glycan/"^^ . "Cathy H. Wu" . "19757"^^ . . . . . "SNOMEDCT_US_2016_03_01" . "life science" . . "http://purl.obolibrary.org/obo/MICRO_$1"^^ . . "life science" . "insdc.gcf" . . . . . "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name="^^ . "lipid" . "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form."^^ . . "http://www.sasbdb.org/data/"^^ . "obo" . . . . "simon.harding@igmm.ed.ac.uk" . "RiceNetDB Protein" . . . "^BSU\\d{5}$"^^ . . . . . . . "genetics" . "Benchmark Energy & Geometry Database" . . . _:N66cf499252324c29a5fea5f7bf331f08 . . "http://purl.obolibrary.org/obo/FOODON_"^^ . . "^\\d+$"^^ . . . "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis."^^ . . . . "https://www.storedb.org/?STOREDB:DATASET$1"^^ . "obo" . . . . "false"^^ . . "RSC3"^^ . "registry" . "Minimal Information about any Sequence" . "narcis" . . . . . . "drsbello@gmail.com" . "^\\d+$"^^ . "false"^^ . . . . . . . . . . . "Etsuko Yasugi" . . . . . "dna" . . "obo" . . . "false"^^ . . . . . "https://scicrunch.org/resolver/RRID:$1_$2" . "Cell Signaling Technology Pathways" . "biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology" . . . . "http://purl.obolibrary.org/obo/SEP_"^^ . "60316"^^ . "BBA0001"^^ . "http://www.gramene.org/db/literature/pub_search?ref_id=$1"^^ . . "Biosapiens Protein Feature Ontology" . . . "The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)"^^ . "dandi" . "a formalization of concepts and relations relevant to evolutionary comparative analysis"^^ . . . . . "diagnosis" . "experimental measurement" . "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands."^^ . "kerafast" . "false"^^ . . . . "sustainability" . . "ontology" . "^ILMN_\\d+$"^^ . . . . . . "immunology" . "5HT3Arano"^^ . "genetic polymorphism" . . . . . . . . . . . "drugbank.reaction" . "false"^^ . . . . . . "false"^^ . . "Pesticide Properties DataBase" . . . "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology."^^ . . "^\\d{7}$"^^ . "malaria" . "doqcs.pathway" . . . "ontology" . . . . "^\\d{7}$"^^ . "metabolomics" . . _:N15f1101e5afe405f9d53181d2c5a6e24 . . "ZINC is not Commercial" . "AEO_RETIRED" . "00000105"^^ . "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task="^^ . "structure" . . "obo" . . . . . "false"^^ . . "Genomic Distribution of structural Superfamilies" . "http://purl.obolibrary.org/obo/NCRO_$1"^^ . . . "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins."^^ . . "immds"^^ . . . "0000215"^^ . "life science" . . "4DN" . "systems biology" . . "agriculture" . . "proteomics" . . . . . "cell lines" . . . . . "false"^^ . . "true"^^ . . . . "dna" . "literature curation" . "0000123"^^ . . . . "IUPHAR_LIGAND" . . . "Influenza Sequence and Epitope Database" . "JCGG-STR008690"^^ . . . "Database of experimentally verified IRES structures" . . "A repository of software packages written in PHP."^^ . . "http://virtualflybrain.org/reports/"^^ . . . . "gramene.qtl" . "DevTox" . . "https://www.wormbase.org/db/seq/protein?name="^^ . . "huge" . "http://www.jstor.org/stable/"^^ . . . . . . . "hgnc.family" . . . . . . "ontology" . . "false"^^ . . "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc="^^ . "false"^^ . "https://www.aapc.com/codes/cpt-codes/$1"^^ . . "2701"^^ . . "false"^^ . . . "A terminology for the skills necessary to make data FAIR and to keep it FAIR."^^ . . . "false"^^ . "Phy000CLXM_RAT"^^ . "ontology" . "http://www.ontologyrepository.com/CommonCoreOntologies/$1"^^ . . . . "http://purl.obolibrary.org/obo/SCDO_$1"^^ . . . "^\\d{7}$"^^ . "ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases."^^ . "biomedical science" . . . "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . "model" . . . "EAWAG Biocatalysis/Biodegradation Database" . . . . . "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID="^^ . . . . . . . . . . . . . . . "biology" . "International Classification of Diseases, 9th Revision, Clinical Modification" . . . . "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^ . "Fungal gross anatomy" . . "life science" . . "false"^^ . . . "http://lisanwanglab.org/DASHR/entry/$1"^^ . . . . . . . . "plant phenotypes and traits" . . "false"^^ . "http://biomeddb.org/Disease/Details?DISEASEID=$1"^^ . . "niaid.chemdb" . . . . "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon."^^ . "biochemistry" . "http://www.proteinatlas.org/$1"^^ . . . . . "genome" . . . "https://pubchem.ncbi.nlm.nih.gov/bioassay/"^^ . "GR_GENE" . . . "uniprot.kw" . "developmental biology" . "micro rna" . "pathogen" . "http://purl.obolibrary.org/obo/ExO_$1"^^ . . "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode="^^ . . . "4b848c342a4f4abc871bdf8a09a60807"^^ . . . . . . . . . . . . . "false"^^ . . . "life science" . "Imke Tammen" . . "National Drug File - Reference Terminology" . "lepao" . "http://purl.enanomapper.org/onto/ENM_$1"^^ . . . . "pieter.mestdagh@ugent.be" . . . . . "false"^^ . "0376"^^ . "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^ . . "^E(S|D)i\\d+-\\w$"^^ . . . . . "amoebadb" . "life science" . . . "Lynn Schriml" . "life science" . "false"^^ . . "1000290"^^ . "human disease" . "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^ . . . . . "biopesticides" . "biomedical science" . "molecular structure" . . . . . . . . . . . "http://www.w3.org/ns/shacl#$1"^^ . . . "0000021"^^ . . . . "proteomics" . . . . . . "http://purl.org/dc/dcmitype/"^^ . "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."^^ . . "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS)"^^ . "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web."^^ . . . "Common Anatomy Reference Ontology" . "metacyc.reaction" . "adult" . "synthetic biology" . "^\\d{7}$"^^ . . "bibliography" . "interaction" . . . . _:N1d19e00ba7954d99888290da420c49d2 . . . "http://purl.obolibrary.org/obo/OGG_$1"^^ . "pdbsum" . . . . . "a.39.1.1"^^ . "^\\d+$"^^ . . . "genome" . . . . "0459895"^^ . . "false"^^ . . . . "8668"^^ . . . . . . "The S/MAR transaction DataBase" . . "https://biopragmatics.github.io/providers/bs/"^^ . . . "Human Medical Genetics" . "00000674"^^ . "assay" . . "false"^^ . "false"^^ . . "obo" . . . . . "Michal Linial" . "PMCID" . "semapv" . . . . "false"^^ . . "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . . . . . . . . "subject agnostic" . . . . . "biological process" . "ontology" . "agriculture" . . . . "Nematode & Neglected Genomics" . "bibliography" . "agriculture" . . "false"^^ . "false"^^ . . "bioinformatics" . . . "protein structure" . "ugis@ebi.ac.uk" . . "nucleotide" . . . "false"^^ . "miszcz@amu.edu.pl" . . "disease" . . . "Blue Brain Project's published data as knowledge graphs and Web Studios."^^ . . . "Swiss National Clinical Trials Portal" . "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId="^^ . "^\\d{7}$"^^ . "small molecule" . . "NCT" . "http://ecoportal.lifewatch.eu" . . . . . . "proglyc" . . . . "9781584885658"^^ . . . "http://purl.obolibrary.org/obo/ECTO_"^^ . "epio" . . . . . . "^\\w+$"^^ . . "Stian Soiland-Reyes" . . . "http://biohackathon.org/resource/faldo#"^^ . . . "false"^^ . . . . . . . . . . . . "NLX" . . "^ERM[0-9]{8}$"^^ . . "LigandBook" . "https://animaldiversity.org/accounts/$1"^^ . "^ENSG\\d{11}$"^^ . . . . "^[a-z0-9]{32,32}$"^^ . "https://reactome.org/content/detail/"^^ . "https://bioregistry.io/beiresources:"^^ . . . "Gene"^^ . "false"^^ . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . . . . . "nsv3875336"^^ . . . "4140"^^ . "International Histocompatibility Workshop cell lines" . . . . . "^\\w+$"^^ . . "https://hl7.org/fhir/us/"^^ . . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"^^ . . "FlyMine Chromosome Band" . "^A\\d+$"^^ . . . "http://edamontology.org/data_$1"^^ . . "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects."^^ . . . "MetaCyc" . "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1"^^ . . . . . . . . . "Langua aLimentaria Thesaurus" . . . . . . . "identifier for a fungus taxon in Index Fungorum"^^ . . "probonto" . . "agriculture" . . . . . "http://vegbank.org/cite/$1"^^ . . . "false"^^ . "obo" . "pavel.hobza@uochb.cas.cz" . "https://biocomputeobject.org/BCO_"^^ . . . "ontology" . "http://standards.iso.org/iso/15926/part14/"^^ . . "LiceBase" . . "false"^^ . . . . . . . "false"^^ . . . . . . "bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate."^^ . . _:N898d99e86be74a7b95d64696be1ba50b "helpdesk@cropontology-curationtool.org" . . "https://w3id.org/sssom/$1"^^ . "OntoBee" . "uniprot.db" . "408"^^ . . . . . . "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research)."^^ . . . . "Siqian He" . "atol" . . "oecd.template" . "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^ . . "An ontology to describe entities related to cardiovascular diseases"^^ . "http://www.pathoplant.de/detail.php?accNo="^^ . "subject agnostic" . . "https://metacyc.org/META/NEW-IMAGE?object="^^ . . "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded."^^ . . . "algorithm" . . . . "traumatology" . . "systems biology" . . . . "http://www.cathdb.info/cathnode/$1"^^ . . . "https://pharmacodb.ca/datasets/"^^ . . . "drugbank" . "Network of Different Plant Genomic Research Projects" . . . . . . . . . "http://purl.obolibrary.org/obo/OMP_$1"^^ . . . "subject agnostic" . . . . . . . "Expression"^^ . . "https://www.scopus.com/sourceid/"^^ . "false"^^ . . . . . "31253.11.sciencedb.j00001.00123"^^ . "^phs[0-9]{6}(.v\\d+.p\\d+)?$"^^ . . . _:N615b517125c946639821d2766320e103 "info@who.int" . "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . . . . . . "life science" . . "502930"^^ . . . . "Dr. Alpha Tom Kodamullil" . "MatrixDB" . . . "https://mged.sourceforge.net/ontologies/MGEDontology.php#$1"^^ . . "Workspace (Git repository) for modeling projects managed by the Physiome Model Repository"^^ . . . "mcourtot@gmail.com" . . "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#"^^ . "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources."^^ . . "false"^^ . "^\\d{4}-\\d{3}[\\dX]$"^^ . "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."^^ . "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina."^^ . . . . "Catalogue of Life" . _:Nb6b37a7b77e34a5eb7eefc59be1db2d7 . . . . . "^\\d+$"^^ . . . . . . . . . "pathway model" . . . "false"^^ . . . . "http://www.ecogene.org/gene/$1"^^ . . . . . . "0001"^^ . "interaction" . "knowledge and information systems" . "hcao" . "AgentIdentifierScheme"^^ . "arba" . . . . . "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins."^^ . . . . "selventa" . "scopus.author" . . . . "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d"^^ . . . . "^\\d{3}$"^^ . . . . . . "^\\d+$"^^ . . . . . "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN="^^ . . "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1"^^ . . . . . . "eropmoscow" . . . "protein" . "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies."^^ . . . . . . "^\\d{7}$"^^ . "4892"^^ . . "fetus" . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene."^^ . "G77500AY"^^ . . "false"^^ . . "biomedical science" . . . . . . "Michael Baudis" . . "Document Components Ontology" . . . "biology" . "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information."^^ . . . . . "Adrien Coulet" . . . "glida.ligand" . "gramene.ref" . . "false"^^ . . . . . "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^ . . "Bilateria anatomy" . "smtifahim@gmail.com" . . "life science" . "BirdBase" . . "https://bacdive.dsmz.de/strain/"^^ . . . . . . . "http://ctdbase.org/detail.go?type=disease&db=MESH&acc="^^ . "eVOC (Expressed Sequence Annotation for Humans)" . . . "https://cropontology.org/rdf/CO_350:"^^ . . "ontology" . "https://www.atcc.org/products/"^^ . . "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . "pubchem.cell" . . "Andy Deans" . "false"^^ . "SM00015"^^ . . . . "https://www.ebi.ac.uk/pride/archive/projects/$1"^^ . "SwissProt" . . "deepak.unni3@lbl.gov" . . . . "funcbase.yeast" . "Google Scholar Researcher" . . "^\\d+$"^^ . "miRBase Families" . "1.10.10.200"^^ . . "https://www.semion.io/Author/"^^ . "biomedical science" . . "^VB\\.[A-Za-z][A-Za-z]\\..*$"^^ . . "hdl" . . . "false"^^ . "https://biopragmatics.github.io/providers/hba/"^^ . "^(T0\\d+|\\w{3,5})$"^^ . . . "7345"^^ . "knowledge and information systems" . "vcell"^^ . "CAE46076"^^ . . . . "^\\d+$"^^ . "adenovirus" . . . "ontology" . . "MarRef" . "pathway model" . . "http://purl.dataone.org/odo/SENSO_$1"^^ . . "LINCS_LDP" . . . . . . . . "PicTar" . . . . . . . . . "https://www.e-cyanobacterium.org/bcs/entity/"^^ . "uniprot.isoform" . "false"^^ . "PNS12@cam.ac.uk" . "vfdb.gene" . "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . . "https://www.swisslipids.org/#/entity/SLM:"^^ . . . "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."^^ . "false"^^ . . "epidemiology" . . "FAIRsharing Organization" . "377550"^^ . . . . "http://purl.obolibrary.org/obo/OAE_$1"^^ . "^\\d+$"^^ . . . "^[0-9]+$"^^ . "fypo" . . "https://www.ncbi.nlm.nih.gov/gtr/conditions/"^^ . "Coconut ontology" . "https://cropontology.org/rdf/CO_356:"^^ . . . "nlx.dys" . . . . . . . . "Sample processing and separation techniques" . . "false"^^ . "LOC_Os02g13300"^^ . "comparative genomics" . "0100002"^^ . . "http://www.gramene.org/db/ontology/search?id=GRO:$1"^^ . "noncodev4.rna" . . "data analysis service" . . . "https://odc-tbi.org/data/"^^ . . "false"^^ . . "http://purl.obolibrary.org/obo/ICO_$1"^^ . "https://www.alliancegenome.org/accession/$1"^^ . . "false"^^ . . "P0DP23"^^ . . "Health Canada Natural Product Number" . . . "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID="^^ . . "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1"^^ . . "obo" . . . . "^Q[A-Z0-9]+$"^^ . . . . . . "agriculture" . "co_331" . . . "http://purl.obolibrary.org/obo/TRANS_"^^ . . . . . "mgilson@health.ucsd.edu" . . . . "true"^^ . . "life sciences" . . . . . . "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."^^ . . . . . "medicine" . . . "genome" . "primary health care" . . . . "rna" . . . "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . . "https://mmp.sfb.uit.no/databases/marfun/#/records/"^^ . . . . . "false"^^ . . "ontology" . "The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated."^^ . "subject agnostic" . "http://europepmc.org/articles/"^^ . "39421"^^ . "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^ . . "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities."^^ . "Developmental stages of the Zebrafish"^^ . . "Linguist" . . "data science" . . "regulation" . "false"^^ . . . . "enzyme" . . . . . . "knowledge and information systems" . . . . "false"^^ . . "Chris Sander" . . . . "HUGO Gene Nomenclature Committee" . "c.orengo@ucl.ac.uk" . "ricenetdb.protein" . . "^\\d+$"^^ . "enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products."^^ . . . "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced."^^ . "http://arabidopsis.org/servlets/TairObject?accession=Gene:"^^ . "false"^^ . "plwhetzel@gmail.com" . . . "siren" . "false"^^ . . . . . . "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id="^^ . "Jaime Huerta-Cepas" . . . "false"^^ . "Metabolic Encyclopedia of metabolic and other pathways" . . . . . . . "false"^^ . . "https://data.who.int/countries/"^^ . "BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it."^^ . . "5UTR_107_ENST00000517291.2"^^ . "uniprot.location" . . "F0001"^^ . "1178"^^ . "Laboratory of Systems Pharmacology Compound" . "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites."^^ . . . . . . . . . "zfa" . . "2-s2.0-0030770923"^^ . "developmental biology" . "genome" . . "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^ . . . . "life science" . . . "https://bioregistry.io/resolve/github/pull/"^^ . . . "irct" . . "chris.ponting@ed.ac.uk" . "false"^^ . . . "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^ . . . "false"^^ . "MEROPS Family" . . "false"^^ . . . "pharmgkb.gene" . . "^\\d+$"^^ . . . . . . . "Jeffrey A. Detras" . . . "Jie Zheng" . . . . . . . . "ontology" . "false"^^ . "ontology" . "Guide to Pharmacology Ligand" . . . . "chemistry" . "false"^^ . . "Toxin and Toxin Target Database" . "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id="^^ . . . "Raimond Winslow" . "SNOMEDCT_US_2023_10_01" . "http://purl.obolibrary.org/obo/CVDO_"^^ . . . "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . "https://herv.img.cas.cz/s/$1"^^ . "http://purl.obolibrary.org/obo/BTO_$1"^^ . . "https://bioregistry.io/cnrs:"^^ . . "PolBase" . . . "experimental measurement" . "sbo" . . "bioinformatics" . . . . . . . . "http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1"^^ . . . . . . "^\\d+$"^^ . "NAD%20biosynthesis"^^ . "Ugis Sarkans" . "identifier of an entry in the NCI Drug Dictionary"^^ . . "life science" . . . . "http://lisanwanglab.org/DASHR/entry/"^^ . . . "opl" . . "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made."^^ . . . . "http://purl.obolibrary.org/obo/VSMO_"^^ . . . "rna" . "database" . . . . . . . . "gcst" . . . "sstoss" . . "life science" . . "false"^^ . . . . . "The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data."^^ . . . . . . "hssp" . . . "scholia.resource" . . . . . . . . "1801.012"^^ . . . "false"^^ . "Virus Pathogen Resource" . "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID="^^ . "subject agnostic" . . . "rat model" . . . . . . . "topfind" . . . . . "Endeavor"^^ . . "life science" . . . . . . "http://nava.liacs.nl/cgi-bin/nava.py?id="^^ . . . . . . "grouping" . "Ontology of Genetic Susceptibility Factor" . "Description of Plant Viruses" . "^[A-Z0-9]+$"^^ . "biocuration" . . . . . . "treefam" . . . . "906801"^^ . . . . . . "false"^^ . . . . . . . . "Selventa Diseases" . "transgenic" . . "http://www.kegg.jp/entry/$1"^^ . . . "sugarbind" . . . . . . . "Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database"^^ . . . . "ENSG00000169174"^^ . "small molecule" . "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$"^^ . "PRJDB3"^^ . _:N865ae216243546ca96f93a846edbb7bc . . . . "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid="^^ . "life science" . "AgroPortal" . . "hgnc.genefamily" . "^DIP(\\:)?\\-\\d{1,}[ENXS]$"^^ . . . . _:Nad2e205775ec4086893d6f8fac120366 "Stephanie Bocs Sidibe" . "biological process" . . "omiabis" . . . "2h6o"^^ . . . . "http://purl.obolibrary.org/obo/OVAE_$1"^^ . . "false"^^ . . "owl" . . . "true"^^ . . . "epidemiology" . . . . "animal physiology" . . "cancer" . . . . "^\\d+$"^^ . _:Ne69efea612ad4b3ba46ab98730596773 "helpdesk@cropontology-curationtool.org" . "false"^^ . . "gemma.l.holliday@gmail.com" . . . "kegg_genomes" . "Melek Chaouch" . . . . . . . . . . . . . . . . . "ontology" . . . "Method"^^ . "chemistry" . . . "inchikey" . "entrez" . "obo" . "property" . . "dbest" . . . "false"^^ . . "github" . . "Ontology of Arthropod Circulatory Systems" . . . "AGROVOC" . . . . "Korean Cell Line Bank" . "stn" . "http://purl.obolibrary.org/obo/OHMI_$1"^^ . . . "The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science."^^ . "MMP3888430"^^ . . "life science" . "EBI-366083"^^ . "Habronattus courtship" . . . "registry" . . . . "life science" . . . "^\\d{4}\\-\\d{6}\\-\\d{2}$"^^ . "EcoCyc" . "false"^^ . "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id="^^ . "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."^^ . . . "analysis" . . "mod" . . . . . . "45539"^^ . "conferences" . . . "https://swbiodiversity.org/seinet/taxa/index.php?taxon="^^ . "dictybase.gene" . . "UMLS_ICD9CM_2005_AUI" . "20003"^^ . . "FAIRsharing" . . . . "shareloc" . . "pkdb" . . . . "babelon" . "pathway" . . "434"^^ . . "^\\d{7}$"^^ . . . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/"^^ . . . . . . . "^\\d{7}$"^^ . "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . "cdpd" . "http://purl.obolibrary.org/obo/COB_"^^ . . . . "interaction" . . "EUCTR" . "geno" . . "http://purl.obolibrary.org/obo/ERO_$1"^^ . . . . "protein" . "TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them."^^ . . . . . "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"^^ . . . . . "^\\d+$"^^ . . . . . . . . . "SNOMEDCTCT_2018_03_01" . "https://www.checklistbank.org/dataset/3LR/taxon/"^^ . "deoxyribonucleic acid" . . . "false"^^ . "protein" . . "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"^^ . "anatomy" . "http://metlin.scripps.edu/metabo_info.php?molid=$1"^^ . "1458400"^^ . . . . "morphology" . "false"^^ . . . . "Luis A. Gonzalez-Montana" . "https://www.metabolome-express.org/datasetview.php?datasetid="^^ . "21723"^^ . "https://www.wormbase.org/species/c_elegans/rnai/$1"^^ . "vann" . . . . . . "http://purl.obolibrary.org/obo/GEO_"^^ . . "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^ . . . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra."^^ . "^[a-z][a-zA-Z]+$"^^ . . . "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic."^^ . "^\\d{7}$"^^ . . . . . "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid="^^ . . . "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^ . . "small molecules" . . . . "false"^^ . . "^\\w+_COVID19_[-\\w]+$"^^ . . . "GLAndersen@lbl.gov" . . . "co_320" . . . "academy" . . . . . "disease" . "0000088"^^ . . . "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID="^^ . . . . . . "medicine" . . "/53355/cl010066723"^^ . . . . "http://www.nematodes.org/nembase4/cluster.php?cluster="^^ . . "ontology" . . . . . . . . . . . . . . . . "obo" . "uniprot.arba" . "roundworm" . . . "tgd" . . "wicell" . . . "http://purl.obolibrary.org/obo/OMIABIS_$1"^^ . . "computational biology" . . . . . . "^\\d+$"^^ . . . . . . . . "tfclass" . "study design" . "false"^^ . . "epigenetics" . "ontology" . . "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+"^^ . . "http://pax-db.org/#!species/$1"^^ . . . "fishbase" . . . . "ato" . . . . . . . . . . "phenotype" . . "false"^^ . "0000001"^^ . . . . . "Martin Ramirez" . "^\\d+$"^^ . "life science" . . "cpc" . "relationships" . "bt0001"^^ . "schema" . . "systems biology" . "model" . "life science" . "health science" . . "3hB06"^^ . . "pharmacodb.cell" . . . "ab-1-ha"^^ . "genome" . . "ensembl.protist" . . . . . "genetic construct" . . . "genomics" . . "AffyProbeset" . . . "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^ . "napdi" . . . . "PA447218"^^ . . "ontology" . . . . . . "NCI Thesaurus" . "dna" . "microarray" . "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn="^^ . "https://www.flymine.org/come/entry?gn="^^ . "gene" . . "http://www.isni.org/isni/"^^ . . . . "50583"^^ . "biorxiv" . . . "SIGNOR-252737"^^ . . "ontology" . . "https://www.diseasesdatabase.com/ddb$1.htm"^^ . . . . . "false"^^ . "life science" . . "http://foodb.ca/compounds/"^^ . . "RCV000033555.3"^^ . . . . . . "Browser for the periodic table of the elements"^^ . . "ctd.disease" . . "^[0-9]+$"^^ . "http://purl.obolibrary.org/obo/MFMO_$1"^^ . "http://purl.obolibrary.org/obo/MPIO_$1"^^ . . "organic chemistry" . "^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . "SitEx" . . . . . . . . . . . . . "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC="^^ . "false"^^ . . "ACH-000001"^^ . "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"^^ . "A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)" . "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . . "false"^^ . . "^\\d+$"^^ . "Kristian Axelsen" . . "ontology" . "chemistry" . "http://multicellds.org/MultiCellDB/$1"^^ . . "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^ . . "hpath" . "Katy Börner" . "false"^^ . . "559"^^ . . . . "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID="^^ . . "catalogs" . . "iceberg.ice" . . . . . . . "false"^^ . . "biology" . . "Job.Dekker@umassmed.edu" . "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^ . . . . . . . "darc" . . "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^ . . "enzyme" . "zazuko" . "https://tools.ietf.org/rfc/rfc"^^ . . . . . . . . . "clinvar.variation" . "https://www.ebi.ac.uk/gwas/studies/"^^ . . "ontology" . "numpy"^^ . . . "ontology" . . . . "hendrik.borgelt@tu-dortmund.de" . . . . . . "namerxn" . . "78"^^ . . . . . . . . . . . . . . . . "^\\w+$"^^ . . . "classification" . . . "false"^^ . "taxon" . "pain medicine" . . . . . "SNOMEDCTCT" . "life science" . . "protein interaction" . . . "false"^^ . . . "http://www.pantree.org/node/annotationNode.jsp?id=$1"^^ . . . . . . . "0000125"^^ . "mirTarBase" . . . "phenotype" . . "^\\d{7}$"^^ . . "http://purl.obolibrary.org/obo/HTN_"^^ . . . . . . "oae" . "life-cycle" . . "http://www.t3db.org/toxins/"^^ . . "mgriffit@wustl.edu" . "^.*/.*$"^^ . "pharmvar" . . "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^ . "https://www.webelements.com/$1"^^ . . . . "Identifier for a species in iNaturalist"^^ . "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project."^^ . . "^\\w{5}\\.\\d{2}\\..*$"^^ . . . . . "^Y[A-Z]{2}\\d+[CW]$"^^ . . . "HMS LINCS Cell" . . "classification" . . "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n"^^ . . . . . . . "huanglin36@mail.sysu.edu.cn" . "Enzo Life Sciences is an antibody vendor."^^ . . . "false"^^ . . . . "false"^^ . . . . "geneotype" . "000000341"^^ . . . "false"^^ . . . . "^DBSALT\\d{6}$"^^ . . "false"^^ . "Mark Jensen" . . "mathematics" . . . . . . . . . "^EGAD\\d{11}$"^^ . "https://data.who.int/countries/$1"^^ . "electroencephalography" . . . "false"^^ . _:N1d19e00ba7954d99888290da420c49d2 "wbug@ncmir.ucsd.edu" . "https://www.cellosaurus.org/CVCL_"^^ . "false"^^ . . "0007114"^^ . . . . . . "gene expression" . . . . . . . "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00"^^ . . . "BIND accession number" . . . "FooDB Food" . . "ls-c35719-120"^^ . _:N0b947b7b473b4387b084765374d32e99 . . "ncats.drug" . . . . . "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. "^^ . "0032571"^^ . "C6155"^^ . . "data model" . . "false"^^ . . . . "phenotype" . "The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. [from homepage]"^^ . "PaxDb Protein" . "strain" . "network model" . . . . . "dictybase" . . . . . "Eric W. Deutsch" . "Organization" . "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'."^^ . . "https://www.ebi.ac.uk/metabolights/"^^ . "G00123"^^ . "re3data" . . "Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)"^^ . . "^\\d+$"^^ . "1a24"^^ . "Telethon Network of Genetic Biobanks" . . . . "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."^^ . . . "Mouse Brain Atlas" . . . . . "https://cropontology.org/rdf/CO_356:$1"^^ . "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^ . . "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . _:N080da5f29fdd435f9aaec76ffbd54dbb . "false"^^ . . . "small molecule" . "false"^^ . "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^ . "^[A-Za-z0-9]+$"^^ . "biomedical science" . "ontology" . . "false"^^ . . . . . "clinicaltrials" . . . "lter" . "cst" . "false"^^ . "MTHICD9_2006" . . . "false"^^ . "obo_rel" . . . "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"^^ . . "false"^^ . "false"^^ . "false"^^ . . . . . . . "dna" . . . . "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name="^^ . "ontology" . . . . . . . "^RID\\d+$"^^ . . . "genomics" . . "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links."^^ . . "oci" . . . . "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use." . "https://www.biocatalogue.org/services/"^^ . "false"^^ . . . "Deutsche Sammlung von Mikroorganismen und Zellkulturen" . . "false"^^ . "^Rv\\d{4}(A|B|c)?$"^^ . "metadata standardization" . . "https://data.4dnucleome.org/biosources/"^^ . . . . . . . "false"^^ . "http://purl.org/spar/scoro/$1"^^ . . . "citation" . . . . "Alzheimer's Disease Ontology" . "chemistry" . . "michall@cc.huji.ac.il" . . . . . . . . "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id="^^ . "identifier for an organisation in author affiliations per Scopus"^^ . . . . "false"^^ . "NCBI_taxid" . "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc."^^ . . "A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources."^^ . . . "rdf" . "physiology" . . . . . "090803"^^ . "http://purl.obolibrary.org/obo/NGBO_$1"^^ . "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . . "UK Universities and Colleges Admissions Service" . "http://purl.org/spar/deo/"^^ . . "classification" . . . "UniProtKB" . . . . . "false"^^ . "https://www.animalgenome.org/CorrDB/q/?id=CorrID:"^^ . "genecards.genenote" . . . . . "jakkbl@gmail.com" . _:N29cffc1ec179407e8925a065fa656ab4 "faldo@googlegroups.com" . . . . "issaku@noguchi.or.jp" . . . "http://purl.obolibrary.org/obo/DUO_"^^ . "nando" . "preclinical studies" . . . . . "chemical descriptor" . "http://bitterdb.agri.huji.ac.il/Receptor.php?id="^^ . . . . . "1009107926"^^ . . "taxonomy" . . . . "T039"^^ . . "biominder" . "728"^^ . "atmospheric science" . . "http://purl.org/dc/elements/1.1/$1"^^ . "organic chemistry" . . . "tol.webproj" . . "life science" . "db-object-id"^^ . . . . "chemistry" . . . . "botany" . . "Human Chromosome Ontology" . . "life science" . "otol" . . "nje5@georgetown.edu" . . _:Nbf80f06127494db5b73251968072335a "Crop Ontology Helpdesk" . "protein complexes" . "0000001"^^ . . "BCRC Strain Collection Catalog" . . "http://www.pathoplant.de/detail.php?accNo=$1"^^ . "aeon" . . . . "^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$"^^ . "Packagist" . . "classification" . "dsmz_mutz-id:ACC 291"^^ . . "physics" . . "iceberg.cime" . "50-00-0"^^ . "csd" . . . "https://rnaloops.cs.put.poznan.pl/search/details/"^^ . "^\\d+$"^^ . "http://www.hprd.org/protein/"^^ . . . . . . . . . "http://www.ifomis.org/bfo/1.1/snap#$1"^^ . "https://abrc.osu.edu/stocks/number/SALK_$1"^^ . . . "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo="^^ . . . . . . . . . "16129"^^ . . . . . . . . . "Alan Wood's Pesticides" . . . . . . "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.)."^^ . "sabiork.reaction" . . . "false"^^ . "10142"^^ . . . . . "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability."^^ . "gene" . . "^\\d{7}$"^^ . "botany" . "0000184"^^ . "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . . "Haruki Nakamura" . . "1"^^ . . . "Brain Architecture Knowledge Management System Neuroanatomical Ontology" . "http://www.w3.org/2008/05/skos-xl#"^^ . . "bs" . "mirbase" . "74.186"^^ . . "Josh Moore" . . . . "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id="^^ . . "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information."^^ . "civic.assertion" . . "Birgit Meldal" . . "http://purl.obolibrary.org/obo/CRO_"^^ . . . . . . . "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1"^^ . "ontology" . . "http://purl.obolibrary.org/obo/HP_"^^ . . . . . . "cell lines" . . . . . . . "natural product" . . . "http://purl.obolibrary.org/obo/EO_"^^ . . . . . "^m\\w+$"^^ . "massbank" . . "ccds" . . . "MetaCyc Reaction" . "protein" . . . "^SEQF\\d+$"^^ . . . "Grape Ontology including OIV and bioversity descriptors. INRA July 2017"^^ . "https://go.drugbank.com/salts/$1"^^ . "Eukaryotic Promoter Database" . . . . . . "oid" . . . . . . . . . . "FBbt_root" . "aeo" . "https://bioregistry.io/matrixdb.association:"^^ . . "vita" . "70"^^ . "data governance" . . . "r0001"^^ . . "FBbt" . . . . . "false"^^ . "obo" . . . "Cell line databases/resources"^^ . . . "affy.probeset" . . . . . . "hco" . . . . "false"^^ . "C2584994"^^ . . . . . "Data Catalog" . . "gene" . . "bcrj" . . "Synapse Data Repository" . "entiminae@gmail.com" . "knapsack" . . . "false"^^ . "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$"^^ . . . . . . . . "https://www.ncbi.nlm.nih.gov/dbvar/variants/"^^ . . . "data retrieval" . "medical informatics" . . . . "proteomics" . . "Q5BJF6-3"^^ . . "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . . . . . . . "ChemSpiderID" . . . . . . "^\\d+/.+$"^^ . . "dg.6vts" . "http://purl.obolibrary.org/obo/MmusDv_$1"^^ . . "false"^^ . . "KEGG_REACTION" . "lipidbank" . "chembl" . . . "oban" . . . . "http://purl.obolibrary.org/obo/HsapDv_"^^ . . . . "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."^^ . "scretf" . . "resource metadata" . . . . . . . . "ro" . . . "http://purl.obolibrary.org/obo/RO_$1"^^ . "false"^^ . . . "spar" . . "W2741809807"^^ . . "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . "ontology" . _:N121f99ad90c846da8913ff92b247ea48 "biomodels-net-support@lists.sf.net" . "Yosef Shiloh" . . . "RxNorm" . . "false"^^ . . _:N14aec72fb9624574a7835e3cbcbfd5e9 "Steven John Zimmerly" . "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . "Michael Y Galperin" . . . "^JCGG-STR\\d{6}$"^^ . . . "Peter D'Eustachio" . . "plant phenotypes and traits" . . . . "https://loinc.org/"^^ . . "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record."^^ . "false"^^ . . "Citation Counting and Context Characterisation Ontology" . . . . . "agriculture" . . . . "imr" . . . "ClinicalTrials.gov" . "mental health" . "scoro" . "Michel Dumontier" . . . "http://cutdb.burnham.org/relation/show/"^^ . . . "http://www.sasbdb.org/data/$1"^^ . . "Vendor for assays, cells, and antibodies"^^ . . . "Tissue List" . . . "Marie-Paule Lefranc" . "Enzyme Commission Code" . . . "drug repositioning" . . . . . "protein" . "phylogenetics" . "ontology" . "biomedical science" . . . "fossilworks.taxon" . "mathematics" . . . . "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . . "18030"^^ . "0007807"^^ . "eolife" . "^\\d{8}$"^^ . "qtl" . . . "biology" . . "computational biology" . "behavior" . . . . . . . "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."^^ . . . . "Zebrafish Information Network Gene" . . . . "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^ . . . . . "false"^^ . . "cell biology" . . . "NCBI_GeneID" . . "false"^^ . "0000389"^^ . . . "Minimal Viable Identifier" . . "^PA\\w+$"^^ . . "receptome.family" . . "^\\d{7}$"^^ . . . . . . "ontology" . . "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^ . "https://viralzone.expasy.org/$1"^^ . . "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS)."^^ . . "false"^^ . . "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^ . . "^\\w+$"^^ . . . "https://cropontology.org/rdf/CO_345:$1"^^ . "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications."^^ . "classification" . . "false"^^ . "https://www.osti.gov/biblio/$1"^^ . . "^\\d+$"^^ . . "life science" . . "Food-Drug interactions automatically extracted from scientific literature"^^ . . "false"^^ . . "^\\d+$"^^ . "epilepsy" . . . . "IUPHAR_GPCR" . "false"^^ . "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . "protein" . "protein" . "https://morpheus.gitlab.io/models/$1"^^ . "Saccharomyces cerevisiae promoter database" . . . "false"^^ . "^\\d{7}$"^^ . "obo" . . . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id="^^ . . . "http://unite.ut.ee/bl_forw.php?nimi=$1"^^ . . . . . . . . "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"^^ . . "false"^^ . . "^\\d{7}$"^^ . "R-BTA-418592"^^ . "pencehe@oneonta.edu" . . . . . . "Morpheus model repository" . "signor" . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_inv_"^^ . . . . . "BatchelorC@rsc.org" . "^\\d{7}$"^^ . . . "false"^^ . . . . . "https://scicrunch.org/scicrunch/interlex/view/ilx_$1"^^ . "https://github.com/prefixcommons/biocontext" . "4D Nucleome Data Portal Biosource" . "glenn.king@imb.uq.edu.au" . "568815597"^^ . "^\\d+$"^^ . . . "MESHC" . . . "Prefixes useful in annotating documentation provenance." . . . "ECOCYC"^^ . . . . . "thesaurus" . . . "MCDS_C_0000000001"^^ . . . "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1"^^ . . "gendis" . . "^\\d{7}$"^^ . . . . "botany" . . "^\\d\\w+$"^^ . . . . . . "protein" . "Unified Medical Language System Atomic Unique Identifier" . . "peptideatlas.dataset" . . "metagenomics" . . . . . "false"^^ . . "phenotype" . . . . "https://dblp.org/pid/"^^ . "biologics" . "false"^^ . "Christine.Pourcel@u-psud.fr" . . . "UDB000691"^^ . "^\\d{3}\\.\\d{2}$"^^ . "transposon insertion" . . . . "false"^^ . . . "GM17027"^^ . "nfdi4chem.osmo" . . "biomedical science" . . . . . . . "false"^^ . . "^\\d+$"^^ . . "https://www.ebi.ac.uk/interpro/entry/InterPro/$1"^^ . "http://bacmap.wishartlab.com/organisms/"^^ . . . . . "ontology" . . . "chemical" . . . "celia.michotey@inrae.fr" . "0011140"^^ . "http://ciliate.org/index.php/feature/details/"^^ . "000009"^^ . . . . "NIST Chemistry WebBook" . "false"^^ . "false"^^ . . . "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s."^^ . "^\\d{7}$"^^ . . "Identifiers for relationships between proteins and complexes, along with their type and provenance"^^ . . . "Bgee gene" . "true"^^ . . "^\\d+$"^^ . . "obo" . "life science" . . "structure" . . . . "false"^^ . "NCBITaxon" . . . . . . . "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . . . "ENSGT00550000074763"^^ . . "biomedical science" . "^\\d+$"^^ . "preclinical studies" . . . "genome" . . . "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries."^^ . . "0154"^^ . "http://purl.obolibrary.org/obo/TGMA_$1"^^ . . "false"^^ . . . "cognitive neuroscience" . . "metagenomics" . "food" . . . . . . . "artificial intelligence" . . . . "transcriptomics" . "^EBI\\-[0-9]+$"^^ . "disease" . "false"^^ . . . "SNOMED_CT" . . "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world."^^ . "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications)."^^ . . "cog.category" . . "mutant" . . . "drsanv0" . "nextprot.family" . "^[A-Z]{1,3}-\\d{4}-(19|20)\\d\\d$"^^ . "protein-protein interactions" . . "broad" . "https://bartoc.org/en/node/$1" . "5013"^^ . . "sdgio" . "^\\d{7}$"^^ . . . "The localization and quantitation atlas of the yeast proteome" . . . . "CAL0003079"^^ . . "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)" . "srodriguez142857@gmail.com" . "gene" . "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"^^ . . . "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. "^^ . . "https://cropontology.org/rdf/CO_365:"^^ . "data model" . . . . . "anatomy" . . "obo" . . "0221"^^ . . "imp10873"^^ . . . . . "model organism" . "computational biology" . "protein" . . . "Austrian Library Network" . "^\\d+$"^^ . . "gaoj@mskcc.org" . . "troy_pells@yahoo.ca" . . . . . . . "subject agnostic" . "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information."^^ . . . . . . "OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX."^^ . . "utrdb" . . . . . . "0000144"^^ . . _:N648de9a3c9414188aeff24d0e23085c4 . . . "http://www.kegg.jp/entry/"^^ . "https://cropontology.org/rdf/CO_324:"^^ . "Luis González-Montaña" . "http://purl.obolibrary.org/obo/PROPREO_$1"^^ . . . "life science" . "genomics" . . . . "https://www.dsmz.de/collection/catalogue/details/culture/$1"^^ . . . . "dermatology" . "https://www.fao.org/fishery/en/species/"^^ . . . . . "false"^^ . . . "iNaturalist Taxonomy" . . . "ivan@w3.org" . . "NIF Standard Ontology: OEN Terms in Neurolex" . . . "Anatomical Entity Ontology" . "0001410"^^ . "E-cyanobacterium model" . . "^\\d+$"^^ . . . . . . . . . . . . . . "gene" . "ProtoNet ProteinCard" . "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"^^ . . . "KEGG Environ" . "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem="^^ . . . "http://biohackathon.org/resource/hco#$1"^^ . . "https://civicdb.org/links/molecular_profile/$1"^^ . . . . . "genetics" . "epidemiology" . "cell line" . . "Biolink Model" . . . "Chris P. Ponting" . . . "^[0-9]+$"^^ . . "toxoplasma" . . . "benjamin_gyori@hms.harvard.edu" . . . . . . . "Property"^^ . . . "^(ENSFM|ENSGTV:)\\d+$"^^ . "genetics" . . "preclinical studies" . . . . . . . "^\\d{7}$"^^ . . "neuromorpho" . . "eVOC mouse development stage" . . . . . "ontology" . . . . . "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . "Adriano Rutz" . "steven.marsh@ucl.ac.uk" . "canal"^^ . . "CC-BY-1.0"^^ . . . "h2o"^^ . . . "UCR00226"^^ . . . . . "^[0-9A-Za-z\\-.]+$"^^ . . . "MSMEG_3769"^^ . . . . "false"^^ . "http://purl.obolibrary.org/obo/FBbi_"^^ . . . . "http://purl.obolibrary.org/obo/OVAE_"^^ . . . . . . . . "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^ . . . "Cell Version Control Repository" . . . . "https://europepmc.org/article/CBA/$1"^^ . . . "Aisling Doyle" . "biodiversity" . . "false"^^ . . . . "discoverx" . . . "github.issue" . . . . . . . "General Multilingual Environmental Thesaurus" . "false"^^ . "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments."^^ . . . . . . "JRBC Cell Bank" . . "A database for Triticeae and Avena references."^^ . . . "proteomics" . . . "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"^^ . . . . . . . "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"^^ . . "NeuronDB" . . "agriculture" . . "mgi" . . . . . . . "mass spectrometry" . . . . . . "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp="^^ . . . "life science" . "https://biopragmatics.github.io/providers/sfam/"^^ . . . . . "interaction" . . . "NASA GeneLab" . "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."^^ . "rna" . . "8639.1"^^ . . "civic.aid" . . "https://lincs.hms.harvard.edu/db/sm/"^^ . . "hba" . "Evan Patterson" . . . "gavin.thomas@york.ac.uk" . . . . "Frédéric Bastian" . "21692"^^ . "tcdb" . . . "https://www.cbioportal.org/study/summary?id="^^ . . "sequence" . . "https://transyt.bio.di.uminho.pt/reactions/"^^ . "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"^^ . . "disdriv" . "^\\d+(-\\d+)?$"^^ . . . "pmp" . . . "oridb.schizo" . . . "https://civicdb.org/links/variant_group/$1"^^ . . "5601141"^^ . . "false"^^ . "http://purl.obolibrary.org/obo/EMAP_$1"^^ . "817732"^^ . . . . . . "63189"^^ . . . "^[0-9]{9}$"^^ . . . "pspub" . "^[0-9][A-Za-z0-9]{3}$"^^ . . "genome" . "^rs[0-9]+$"^^ . "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist="^^ . "quantitative genetics" . . "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id="^^ . . . "The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces."^^ . "ontology" . "SNOMEDCT_2010_1_31" . . . . "ms" . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code="^^ . "H-InvDb Locus" . . "^GE\\d+$"^^ . . . . . "gene" . . . "^PKDB[0-9]{5}$"^^ . "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary."^^ . . . "zfs" . . . . . . "genomics" . "Citlalli Mejía-Almonte" . "phrr" . "protein" . . . "138488"^^ . "nlx.qual" . "https://bioregistry.io/mesh.2012:"^^ . "po" . . . . . "atcvet" . "182"^^ . . . "gpmdb" . "Registry" . . "^[A-Z0-9]+$"^^ . "kenan@ucsd.edu" . . . . "Robert Druzinsky" . . "Basic Register of Thesauri, Ontologies & Classifications" . "https://www.datanator.info/gene/"^^ . . "http://www.imgt.org/ligmdb/view?id="^^ . . "https://pdc.cancer.gov/pdc/study/$1"^^ . "https://discover.pennsieve.io/package/"^^ . "genome-wide association study" . "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id="^^ . . . "https://www.findacode.com/code.php?set=ICD10PCS&c="^^ . "http://purl.obolibrary.org/obo/AEON_"^^ . "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."^^ . . . . . "Trish Whetzel" . "false"^^ . "false"^^ . . . . . "http://purl.unep.org/sdg/SDGIO_"^^ . . "ADM1"^^ . . . "Malaria Ontology" . . . . "osti.article" . "molecular dynamics" . . . "structure" . "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"^^ . _:N6f930f1da65341b9bb1888984de2ebb0 . "https://massbank.jp/RecordDisplay?id=$1"^^ . . "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1"^^ . "false"^^ . . . "0019171"^^ . . "http://addgene.org/$1"^^ . . . . . . . . "clinvar.submission" . . "^\\d+$"^^ . . . . . "^\\d{8}$"^^ . . . . "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins."^^ . "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . "^\\d+$"^^ . . . . "false"^^ . "https://www.genecards.org/cgi-bin/carddisp.pl?gene="^^ . "https://w3id.org/reproduceme#"^^ . . "https://hdl.handle.net/hdl:20.500.12582/"^^ . "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#"^^ . "00000532"^^ . . "http://www.w3.org/2004/02/skos/core#$1"^^ . . "obo" . . . . . "mutation" . . . "person" . "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1"^^ . . . "stap" . . . "JAX Mice" . . . . . "Pierre Cosson" . . "false"^^ . "false"^^ . . "alteration" . "http://hdl.handle.net/"^^ . "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^ . "https://cropontology.org/rdf/CO_347:"^^ . . . . . . . "mathias.uhlen@scilifelab.se" . "sgd" . . "https://cropontology.org/rdf/CO_335:"^^ . "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . . . . . . . "^[0-9a-z_-]+$"^^ . "false"^^ . "CIViC Therapy" . . _:N9dbce4005f294750b1a88391f8505532 "kasschau@cgrb.oregonstate.edu" . "SNOMEDCT_US" . . "false"^^ . "Provenance, Authoring, and Versioning Vocabulary" . "gene expression" . . . "FlyBase Reference Report" . . . . "https://www.ebi.ac.uk/pdbsum/$1"^^ . "false"^^ . "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass="^^ . . . . . . . "Lebanon Clinical Trials Registry" . "Ontology about the development and life stages of the C. elegans"^^ . . . "rdf" . "rebase" . "protein" . . "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures."^^ . . . . . "http://purl.obolibrary.org/obo/XCO_$1"^^ . "^PED\\d{5}$"^^ . . . . . "ontology" . . "https://www.metanetx.org/equa_info/"^^ . . . . "00000001"^^ . "ontology" . "^[a-zA-Z0-9_\\-]+(/.*?)?$"^^ . . "https://gnss-metadata.eu/MOID/$1"^^ . . . . "false"^^ . . "Unipathway" . . "structure" . . . . "https://www.rhea-db.org/rhea/$1"^^ . . . "Genomic Data Commons Data Portal" . . . "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI."^^ . . . "http://uri.neuinfo.org/nif/nifstd/$1"^^ . . "false"^^ . "structure" . "KEGG Glycan" . . "expression data" . . . _:N898d99e86be74a7b95d64696be1ba50b "Crop Ontology Helpdesk" . . "^[A-Z]C\\d{1,3}$"^^ . "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^ . . . "developmental biology" . . . . "wawong@gmail.com" . . . "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France)."^^ . . . . . . "http://purl.obolibrary.org/obo/MA_$1"^^ . . . . . "cadsr" . . "https://hamap.expasy.org/unirule/"^^ . . . "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."^^ . . . . . . "kegg.pathway" . . . "transport and kinetic data" . . "biochemistry" . . . . . . . . . "false"^^ . "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"^^ . "Biotin_biosynthesis"^^ . "environmental science" . "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones."^^ . . "false"^^ . . . . "KEGG Reaction Class" . "false"^^ . "https://www.gleif.org/lei/$1"^^ . . . . "http://func.mshri.on.ca/mouse/genes/list_functional_scores/"^^ . . "comparative genomics" . . "^\\d+$"^^ . "http://gmd.mpimp-golm.mpg.de/Spectrums/"^^ . . "The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure."^^ . . . . . . . "genome" . "Christine Orengo" . . "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning."^^ . . . . . "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^ . "structure" . "false"^^ . . . . . "research" . "Aclame" . . "basic science" . "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR."^^ . "false"^^ . . . . . . . . . "^\\d+$"^^ . . "https://www.perkinelmer.com/searchresult?searchName="^^ . . "^(LCL|LDC|ES|LSC|LPC)-\\d+$"^^ . . "VFG2154"^^ . "genome" . "pancreas" . . "structural biology" . . . . . "Pathguide" . "ontology" . . . . . " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries."^^ . . . . "Bibliographic Reference Ontology" . _:N448b82cbd59945169b3836f32e3eefba "Michael J. Adams" . "https://bioregistry.io/cellbank.australia:"^^ . . "http://purl.obolibrary.org/obo/TO_$1"^^ . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1"^^ . . . . . . . . . "CL070"^^ . "life science" . "stoeckrt@pcbi.upenn.edu" . "false"^^ . . "iev" . . . . "j.a.moore@dundee.ac.uk" . . . . "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects."^^ . "^\\d+$"^^ . . "experimental condition" . . "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-"^^ . . "true"^^ . "developmental biology" . . . . "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q="^^ . . . . . "Pathway Commons" . "Ontology of standardized units"^^ . . "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082"^^ . . . . "false"^^ . "SWRL enables Horn-like rules to be combined with an OWL knowledge base."^^ . . . . "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^ . . "metabolomics" . "identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/)"^^ . "https://www.merckmillipore.com/catalogue/item/"^^ . . "http://purl.obolibrary.org/obo/LPT_$1"^^ . . . "genetics" . . . . . . . "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access."^^ . . . . "false"^^ . "0001707"^^ . . . . . "PubMed" . . . . "20560"^^ . "http://purl.obolibrary.org/obo/AERO_"^^ . . "http://www.gramene.org/db/protein/protein_search?protein_id=$1"^^ . . "http://iflastandards.info/ns/fr/frbr/frbrer/$1"^^ . . "FuTRES Ontology of Vertebrate Traits" . . . . . "cell" . "00000098"^^ . . . "http://w3id.org/nfdi4ing/metadata4ing#"^^ . . . . . . . "true"^^ . . "false"^^ . "software engineering" . "^[0-9][A-Za-z0-9]{3}$"^^ . . . . "WGS84 Geo Positioning" . . . . . . . "false"^^ . . "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^ . "EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823"^^ . . "ehda" . "An ontology supporting data modeling in WikiPathways"^^ . . "life science" . . "medicine" . "pierre-alain.binz@chuv.ch" . . "obo" . . "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography."^^ . "false"^^ . "CiteXplore" . "antibodies" . "meetings" . "Christopher Baker" . "false"^^ . . "false"^^ . . . . . . "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization."^^ . "https://www.authorea.com/users/$1"^^ . . . . . . "pdc.study" . . . . . . "https://www.google.com/patents/$1"^^ . "https://europepmc.org/article/CTX/$1"^^ . "obo" . _:Ne1468601788e47eca2b22312b36a1bba "UK Food Standard Agency" . . . "http://www.conoserver.org/?page=card&table=protein&id="^^ . . . . . "https://publons.com/publon/$1"^^ . . "gene expression" . . . . . . . . "http://purl.obolibrary.org/obo/UBERON_"^^ . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes."^^ . . . "mtbd" . "https://www.alliancegenome.org/accession/"^^ . . . . . "NIFSTD" . . "Colorectal Cancer Atlas" . . . . "https://www.scopus.com/authid/detail.uri?authorId="^^ . . . . . . . _:N99631d09d986422da1d50c116ee97530 "pierre.sprumont@unifr.ch" . "wbphenotype" . . "http://www.pocketome.org/files/$1.html"^^ . . . "^\\d{7}$"^^ . . "http://purl.obolibrary.org/obo/HAO_$1"^^ . "1484"^^ . "false"^^ . . . "http://purl.org/spar/bido/"^^ . . "NLXFUNC" . . . . . "Cotton ontology from CottonGen database - June 2019"^^ . . "atc" . . "^\\d+$"^^ . . . "sequence" . . . . "life science" . . . . "http://autism.mindspec.org/GeneDetail/$1"^^ . . . . . "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein."^^ . "ma" . . . . . . "genome" . "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources."^^ . . . "Database of Sequence Tagged Sites" . . . "https://ontology.iedb.org/ontology/ONTIE_$1"^^ . "http://vita.mbc.nctu.edu.tw/search.php?acc=$1"^^ . . "neurophysiology" . . "ontology" . . . "false"^^ . "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data."^^ . . "Regulation of Transcription Ontology" . . . . . . . "biology" . "1h68"^^ . "mouse" . . . . "National Uniform Claim Committee Characteristic" . . . . . "https://w3id.org/reproduceme#$1"^^ . . "EasyChair Call for Paper" . . "quality" . "false"^^ . . "cell line" . . . "http://www.w3.org/2003/11/swrl#"^^ . "Hs635"^^ . . . "drug interaction" . . . . "^\\d+$"^^ . "fbbt" . . . . "0000390"^^ . "1257009"^^ . . . . . "http://www.interfil.org/details.php?id=$1"^^ . . "functional genomics" . . "classification" . . . . "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^ . . . . "demographics" . . "https://bioregistry.io/metaregistry/prefixcommons/$1"^^ . . . "^\\d{7}$"^^ . "glyconavi" . . "molecular structure" . . . . . . "^\\d+$"^^ . . . "biochemistry" . "^[1-9][0-9]*$"^^ . "true"^^ . . . . . "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . . . "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1"^^ . . . "https://herv.img.cas.cz/s/"^^ . . "toxicity" . . . "Q47475003"^^ . . . . . "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships."^^ . . . . . "false"^^ . "AB_262044"^^ . "ThoracicArtery"^^ . . "E12768"^^ . "The TCTR was estabished in 2009 and has been operated by Clinical Research Collaboration Network (CRCN), an organization under the Medical Research Foundation, which is a non-profit organization, and financially supported by Thailand Center of Excellence for Life Sciences (TCELS). CRCN has been retitled the Medical Research Network (MedResNet) since June 15, 2012. (from homepage)"^^ . . . "^\\d+$"^^ . "ENSG00000136147"^^ . "^\\w+$"^^ . . "http://purl.obolibrary.org/obo/MAT_"^^ . "proteomics" . . "genomics" . . . . "true"^^ . . . "Scopus Work" . . "false"^^ . . . "tgn" . . . "biological sample annotation" . . . . . "Oryza Tag Line" . "SPAR Ontologies" . "patricia.siguier@univ-tlse3.fr" . . . . . . "Digital Object Identifier" . . "Sorghum ontology" . "maxo" . . "umls.st" . . . . . "expression data" . "anatomy" . . "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . . . . . . "life science" . . "CE28239"^^ . "genome" . "http://www.crop2ml.org/cropmdb/$1"^^ . "^M\\d+$"^^ . . "hannele.laivuori@helsinki.fi" . "hbvar" . . . "https://sciflection.com/$1"^^ . . . "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands."^^ . . "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors."^^ . . "http://geneontology.org/" . . "apid.interactions" . "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"^^ . "Web Annotation Ontology" . . . . . "http://purl.obolibrary.org/obo/ZFS_"^^ . . . . "http://oncotree.mskcc.org/api/tumorTypes/search/code/"^^ . "Tribolium Genome Database -- Insertion" . . . . . . "developed by ICARDA - Dec 2018"^^ . . . "preclinical studies" . "false"^^ . . . . . . . . . . "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . "false"^^ . . . "ecyano.rule" . . . . . "DSSTox substance" . . "apaonto" . . . . . . . . "Proteoform Atlas" . "life science" . . . . "Selventa Complexes" . "^\\d{7}$"^^ . "false"^^ . "genome" . "biomedical science" . "http://purl.bioontology.org/ontology/npo#NPO_"^^ . "jorvis@gmail.com" . . . . "jens.klump@csiro.au" . . . . . "http://purl.obolibrary.org/obo/VBO_$1"^^ . . . "false"^^ . . "Rosemary Shrestha" . "false"^^ . . . . "^\\d{8}$"^^ . "Chemical Entities of Biological Interest" . "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1"^^ . _:Nfa653585832f480d92bb1b122af31629 "eVOC mailing list" . "^\\d+$"^^ . . . "^\\d+$"^^ . . . . . . . . . "text mining" . "Yossih@tauex.tau.ac.il" . "http://purl.obolibrary.org/obo/TAHH_$1"^^ . "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"^^ . . "translational medicine" . "DB-0174" . . . . . . . . . "false"^^ . "kopka@mpimp-golm.mpg.de" . . "false"^^ . . "^[1-9][0-9]*$"^^ . "^bt\\d+$"^^ . "Life cycle stages for Human"^^ . "false"^^ . . "Ontology for Nutritional Epidemiology" . "ontology" . . "reaction data" . "000140" . . . "European Mouse Mutant Archive" . . . "http://purl.obolibrary.org/obo/GENO_$1"^^ . "Harry Caufield" . . "false"^^ . . . . . . . . "toprea@salud.unm.edu" . "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"^^ . "false"^^ . . . "experiment" . "349124"^^ . . . . . . "Golm Metabolome Database GC-MS spectra" . "http://www.w3.org/2001/XMLSchema#$1"^^ . . . . "https://vac.niaid.nih.gov/view?id="^^ . "slctr" . . _:Ne69efea612ad4b3ba46ab98730596773 "Crop Ontology Helpdesk" . "CAMEO Chemicals ID" . . . . "gene expression" . "22-46615880-T-C"^^ . . . . . . . . . . . . . . . . . . . "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions."^^ . . . . "disease" . "virus" . "beiresources" . . _:N999a3379cbec462b80acdd3f8d0a25df . . . . . . . "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . . . "ontology" . . "Mauno Vihinen" . . "NeuroLex Dysfunction" . "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law."^^ . . . "Mammalia Polymorphism Database" . "5277619"^^ . "http://purl.obolibrary.org/obo/WBPhenotype_$1"^^ . . "http://lincsportal.ccs.miami.edu/cells/#/view/$1"^^ . "AAA35559"^^ . . . . _:Na97d430be7184cf8b6ff1a06628e1cb0 "Crop Ontology Helpdesk" . "International Molecular Exchange" . "ordb" . . "0000047"^^ . . "plant phenotypes and traits" . . . "reproduceme" . "false"^^ . "GlyTouCan" . . "http://www.antweb.org/specimen.do?name=$1"^^ . "assay" . . "^\\d{8}$"^^ . . "false"^^ . "D00123"^^ . . . . "NBC00001"^^ . . . "EC number" . . . . . "^\\d+$"^^ . "GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E."^^ . . . . . "Paula.Duek@sib.swiss" . . . . "^\\w+$"^^ . "identifier for a physical constant"^^ . "https://www.authorea.com/users/"^^ . . "bgee.gene" . . "NONHSAT000001"^^ . "mobidb" . "obo" . "http://purl.obolibrary.org/obo/ECAO_"^^ . "biomedical science" . . "01406"^^ . "https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?short_form=NMR:"^^ . "https://e-cyanobacterium.org/bcs/rule/$1"^^ . . "229233"^^ . . "^LGCEDe-S-\\d{9}$"^^ . . . . . "http://purl.obolibrary.org/obo/SPD_$1"^^ . "false"^^ . "http://www.cathdb.info/cathnode/"^^ . . "dna" . "UniRef" . . . . . "http://purl.obolibrary.org/obo/EHDAA2_$1"^^ . "Animal Genome Size Database" . "ddanat" . "molecular microbiology" . "https://doulix.com/biomodules/$1"^^ . . . . . "ZFA description."^^ . "bioinformatics" . "false"^^ . . "International repository of Adverse Outcome Pathways."^^ . _:Nad2f9fd8a95c45bf99bbdc790171afb0 "usha@molecularconnections.com" . . "MCDS_S_0000000001"^^ . . . . "00000443"^^ . "http://www.w3.org/ns/oa#"^^ . . . "gene expression" . "false"^^ . . "biochemistry" . . "^\\d{7}$"^^ . . . . . . . "NCI2004_11_17" . "InTextReferencePointer"^^ . . . . . . . . "Bryce Mecum" . . . "medicine" . "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific."^^ . . . "identifier for a source/publication venue (journal, conference, etc) in Scopus"^^ . . . . . "ontology" . . . . "false"^^ . "OMA Group" . "life science" . "https://bioregistry.io/tkg:"^^ . . . . "^[1-9][0-9]{3,6}$"^^ . . . . . . "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . . . . "mimodb" . . . . . . . . "food" . . . "ShareLoc" . "biomedical science" . "pina" . . . . . "0000000"^^ . "false"^^ . "loggerhead" . "http://purl.obolibrary.org/obo/PCL_"^^ . "w3c rec" . . . . . "NCIT_Thesaurus" . . . . "ChecklistBank" . . "false"^^ . "biopixie" . . "^\\d{7}$"^^ . "pesticides" . . "false"^^ . "0001017"^^ . "false"^^ . . "https://bioregistry.io/chemspider:"^^ . . . . "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . . "^\\d{7}$"^^ . . _:Naa56318ac26547a6b2bc62f503f794a6 "SEP developers via the PSI and MSI mailing lists" . "http://purl.obolibrary.org/obo/DUO_$1"^^ . "https://www.langual.org/langual_thesaurus.asp?termid="^^ . . . . _:N898d99e86be74a7b95d64696be1ba50b . . "BioSchemas" . . "rdf" . . "https://cropontology.org/rdf/CO_324:$1"^^ . "exac.gene" . "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . "^(VT)?\\d{7}$"^^ . . . . "OncoTree" . . . "TGME49_053730"^^ . . "Banco de Celulas do Rio de Janeiro" . . "http://www.chemspider.com/"^^ . . . . "t3db" . . "http://purl.obolibrary.org/obo/MPATH_"^^ . "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^ . "http://edamontology.org/topic_$1"^^ . . "PubChem Element" . "drsc" . . . . "false"^^ . . . . "false"^^ . . . . . . . "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"^^ . . . . . . . . "jaxmice" . "Zazuko Prefix Server" . . . . "https://www.storedb.org/?STOREDB:DATASET"^^ . "GT10"^^ . . . . "Andreas Ledl" . "Animal natural history and life history" . "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms."^^ . "ontology" . . . "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc."^^ . "Schema.org" . "ogg" . "reagent" . . . . . . _:Nb17ffaa62b3744119234c8e614e3fe61 "Anita Ghebeles" . "http://www.drugtargetontology.org/dto/DTO_"^^ . . . . . "http://www.w3.org/ns/shex#$1"^^ . . . "false"^^ . "cstr" . "http://purl.obolibrary.org/obo/ECO_$1"^^ . . . "Cross-linker reagents ontology" . "ERR436051"^^ . . "http://exac.broadinstitute.org/variant/$1"^^ . . "Veterinary Nomenclature" . . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID="^^ . . . . "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . . "ontology" . "IUPHARobj" . "ontology" . . "The Virus Infectious Disease Ontology" . "om" . "^\\d+$"^^ . . . . . "anatomy" . "machine learning" . _:Nd1e9b7f7d97d4a2a83127f2390a8ce15 "helpdesk@cropontology-curationtool.org" . "vega" . . . . . "metadata" . "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^ . . "mental health" . "life science" . "data retrieval" . . . . . . . . . . "oma.grp" . . . . "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1"^^ . . . . "Colin Batchelor" . "Rebecca Jackson" . "^[0-9]{4}$"^^ . "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER."^^ . . . . "annotation" . "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^ . "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^ . "http://purl.obolibrary.org/obo/OAE_"^^ . . . . "miapa" . . "neurology" . "http://avis.princeton.edu/pixie/viewgraph.php?graphID="^^ . . . . . "0001655"^^ . "0000252"^^ . . "dmendez@ebi.ac.uk" . "paxdb.protein" . . . . . "http://www.proteinmodelportal.org/query/uniprot/$1"^^ . "https://www.ebi.ac.uk/intact/interaction/"^^ . "Q9P0K8"^^ . . . . . . . . . . . . . "obo" . . . . . . . "23"^^ . . "0000012b-5661-2f63-2f73-b43980000000"^^ . "http://www.bootstrep.eu/ontology/GRO#"^^ . . . . . . . . . . _:Ncec661c1c76848d8a02c89fa39775417 . . "http://open-services.net/ns/core#"^^ . . . . . . "alzgene" . . . . "12DICHLORETHDEG-PWY"^^ . "false"^^ . "^[AEP]-\\w{4}-\\d+$"^^ . . . . . . . . "HUMAN16963"^^ . . _:Nbf80f06127494db5b73251968072335a "helpdesk@cropontology-curationtool.org" . . "https://www.ebi.ac.uk/biomodels/$1"^^ . . . . . "http://genome.crg.es/datasets/abs2005/entries/$1.html"^^ . . "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s."^^ . . . . . "human" . "gallont" . "^r\\d+$"^^ . . "P00024"^^ . . . . "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information."^^ . . . . "^\\d{3}\\w(\\w|\\d_)\\d{4}X$"^^ . "^MMAR\\_\\d+$"^^ . . "biomedical science" . "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID="^^ . "Identifier of an entry from the AAindex database."^^ . "pubmed"^^ . "false"^^ . . . . . . . . "^B\\d+$"^^ . . . "label"^^ . . . . "obo" . . . . "false"^^ . . . "hesa" . . . . . "An identifier for a resource or metaresource." . "0000519"^^ . "^\\w+$"^^ . . . "false"^^ . . . "kegg.genes" . . . . . "asfis" . . . . . . . . . . . "false"^^ . "obo" . "false"^^ . . . "rna" . . . . "dron" . . "000064"^^ . . . . "pathguide" . . . . "genome" . "001"^^ . "co_366" . . . . . . . . . . "cognitive neuroscience" . . "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"^^ . "identifier for an academic research group issued by the CNRS"^^ . . . "Viral Bioinformatics Resource Center" . "Ascoli@gmu.edu" . . . . . . "^\\d{7}$"^^ . . "false"^^ . . . . "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility."^^ . . "developmental biology" . . . . . "microscopy" . . "go.rule" . . . . "Novus Biologicals" . "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"^^ . "https://www.nextprot.org/db/entry/$1"^^ . . "ClassyFire" . "bel" . . "http://purl.obolibrary.org/obo/WBbt_"^^ . . . . . "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"^^ . . "MimoDB" . _:N41f3ae9625fb413e8d7851b179f42388 . "Gert Vriend" . . . "biological sample" . . "dna" . . "false"^^ . . "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . "semantic web" . . "https://www.kegg.jp/entry/"^^ . . . . . . . "PhosphoSite Residue" . "false"^^ . . . . "MIRIAM Legacy Registry Identifier" . . "agriculture" . . . . . "The responsible person for a resource" . . "Ensembl Bacteria" . "pgxbs-kftva5zv"^^ . "WWF" . . "Call for paper topics in EasyChair"^^ . "The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another."^^ . "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer."^^ . . . . . . . . . "^\\d+$"^^ . "IRCT20080904001199N7"^^ . . . "http://purl.org/spar/pwo/$1"^^ . . . "subject agnostic" . . "ab275461"^^ . . . . "false"^^ . . . _:N0b947b7b473b4387b084765374d32e99 "helpdesk@cropontology-curationtool.org" . "agriculture" . . . . "relationships" . "Variants in dbVar."^^ . . "^\\w+$"^^ . . . "false"^^ . "false"^^ . "anatomy" . "false"^^ . . "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^ . "^[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}$"^^ . "EcoPortal" . . . . . "^\\d+$"^^ . . . . "RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project"^^ . . "^EB\\d+$"^^ . . . . "data management" . . . "^\\d+$"^^ . "https://data.oncomx.org/OMX_"^^ . . "Orientations of Proteins in Membranes Database" . "https://bioregistry.io/lgic:"^^ . . "PXD000500"^^ . "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NDFRT&code="^^ . "false"^^ . . . . "biomedical science" . "Integrated Genomic Resources of human Cell Lines for Identification" . "VFDB Genus" . "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records."^^ . "glycomics" . . . . . . . . "false"^^ . "http://www.case.edu/EpilepsyOntology.owl#"^^ . "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records."^^ . "3DMET is a database collecting three-dimensional structures of natural metabolites."^^ . "0000127"^^ . "^FCB\\d{3}$"^^ . . . "phenotype" . . . . . . . . . . . "obo" . "0001927"^^ . . . . "1664"^^ . . . . . . "false"^^ . . . "lgai.cede" . . . "^[0-9]+$"^^ . "The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved." . . . . . "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. "^^ . . . "http://purl.obolibrary.org/obo/OBA_$1"^^ . . . . . "ontology" . . "81944ba1-81d0-436e-8552-33d77a27834b"^^ . . "Biological Collections Ontology" . . "protein" . "0000019"^^ . . . "http://phenol-explorer.eu/foods/"^^ . "false"^^ . . . . "https://www.npmjs.com/package/"^^ . "https://cgap.nci.nih.gov/Pathways/BioCarta/$1"^^ . "birnlex" . "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard."^^ . . . . "Tetrahymena Stock Center" . . "report" . "BioMagResBank" . "Chen Yang" . . . . . . "false"^^ . . "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN)."^^ . . . . . "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan="^^ . . "Aceview Worm" . "^\\d+$"^^ . "domain" . . . . "51"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_func_"^^ . . . . . . . "assetConcepts"^^ . "Unified Phenotype Ontology" . . . . . . . "MIRBASE_FAMILY" . "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . "botany" . "sao" . . "reo" . . "false"^^ . "Cell line collections (Providers)"^^ . . . . . . "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . "quality" . . . . "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl."^^ . . "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks."^^ . "http://jaxmice.jax.org/strain/$1.html"^^ . . . "false"^^ . "biology" . "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"^^ . "NMRShiftDB" . "supply" . . . . . "^[A-Za-z_0-9]+$"^^ . "false"^^ . . . "300108/p3934_A-172"^^ . . "^\\d+$"^^ . "A database containing predicted viral miRNA candidate hairpins."^^ . . . "https://bioregistry.io/bykdb:"^^ . . "GLIDA GPCR" . "computational biology" . . . . . . "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available."^^ . . . . . "Uber-anatomy ontology" . "protein" . "systems biology" . "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert="^^ . . . . . . . "false"^^ . . "cas" . . "intact" . "archdb" . . . . . "http://purl.obolibrary.org/obo/FIDEO_"^^ . . . . "phenotype" . "false"^^ . . "false"^^ . "assay" . . "^\\d+$"^^ . "https://cropontology.org/rdf/CO_335:$1"^^ . . "embryonic stem cell" . "metatlas.metabolite" . . . "RiceNetDB Compound" . "preclinical studies" . "^DRKS\\d+$"^^ . "0004"^^ . "bibliography" . . "genes" . . . . "0000001"^^ . "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"^^ . "taxonomic classification" . . . . "false"^^ . . "AllSomeInterpretation"^^ . . . . . . . . "SMP0000219"^^ . "life science" . . . "ontology and terminology" . "FlyBrain Neuron Database" . . . . . . "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . . "anatomy" . "^\\d+$"^^ . . "false"^^ . . . "structure" . . _:Nee718a1169484f53b606356afc36575f "pierre.sprumont@unifr.ch" . "goldbook" . "^HGVPM\\d+$"^^ . "hilmar.lapp@duke.edu" . "DrugBank" . . "subject agnostic" . "Sabine.Oesterle@sib.swiss" . . . "false"^^ . "http://edamontology.org/operation_"^^ . . . . . . . "Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted."^^ . . "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid="^^ . "MLCommons Association artifacts, including benchmark results, datasets, and saved models."^^ . "developmental biology" . . "kegg.orthology" . "hathitrust" . "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein."^^ . . . . "Satya S. Sahoo" . . "https://bio.tools/$1"^^ . "annethessen@gmail.com" . . "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:"^^ . . . . . . "natural science" . "Pascale Gaudet" . "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."^^ . "jason.stajich@ucr.edu" . . . "Biological Imaging Methods Ontology" . . "drug" . . "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once."^^ . . . . "http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1"^^ . . . . "https://drugs.ncats.io/drug/$1"^^ . . "false"^^ . . . . "pharmacological family classification" . . . "ontology and terminology" . . . . "Cell line databases/resources"^^ . . "false"^^ . . . "citation" . "cdao" . "https://biopragmatics.github.io/providers/sdis/$1"^^ . "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name="^^ . . . . "Genomes Online Database" . "https://cgap.nci.nih.gov/Pathways/BioCarta/"^^ . . "false"^^ . . . . . . "metabolomics" . . . . . . . . "https://cn.dataone.org/cn/v2/resolve/{$1}"^^ . . . "^[a-zA-Z0-9\\-:#/\\.]+$"^^ . . . . "fairsharing.organization" . . . . "protclustdb" . "false"^^ . "http://reg.clinicalgenome.org/allele?hgvs=$1"^^ . . "true"^^ . . . . "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . "T30002"^^ . "gene expression" . "false"^^ . "false"^^ . . "Sugar Kelp trait ontology"^^ . . "http://purl.obolibrary.org/obo/DOID_"^^ . "true"^^ . . . "Joshua Orvis" . . . . "m4i" . "http://purl.obolibrary.org/obo/LABO_"^^ . . . . . "phylogenetics" . . "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . . . "Abcam" . "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters."^^ . "cellular components" . . . "false"^^ . "Yang Chai" . . "false"^^ . "^\\d+$"^^ . . . "miRNA Target Prediction at EMBL" . "false"^^ . "cardiology" . . . . . "eurofir" . . . "transcript" . "false"^^ . "David Osumi-Sutherland" . . "obo" . . . . . . "tetrahymena thermophila" . . . . . . . "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information."^^ . . . . "http://www.kegg.jp/entry/"^^ . . . . . "Babelon" . . _:N15f1101e5afe405f9d53181d2c5a6e24 "more.info@allotrope.org" . . . "true"^^ . . . "http://purl.org/spar/pro/"^^ . . "http://tuberculist.epfl.ch/quicksearch.php?gene+name="^^ . "medicine" . "GN_G03681DA"^^ . "^\\d{5}$"^^ . "https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1"^^ . . . "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^ . "https://integbio.jp/dbcatalog/en/record/$1" . "Dan Berrios" . . . . . . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code="^^ . "scientist" . "bioschema" . "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . "food" . "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId="^^ . . . "^C\\d{4}$"^^ . "supfam" . . "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."^^ . "I31.952"^^ . . "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/"^^ . "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design."^^ . "https://github.com/"^^ . . . . "0000011"^^ . . . . . "ito" . . . "bhalla@ncbs.res.in" . . . . "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls."^^ . . . . . "cheminformatics" . . _:N29cffc1ec179407e8925a065fa656ab4 . . . "RL3R1_HUMAN"^^ . "natural language processing" . . "http://purl.obolibrary.org/obo/FLOPO_"^^ . "288"^^ . "https://www.pombase.org/gene/$1"^^ . "^\\d{7}$"^^ . . . "http://purl.obolibrary.org/obo/OARCS_"^^ . . . "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid="^^ . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene."^^ . . . "glytoucan" . . . "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"^^ . . "ICEberg family" . . "vendor" . "latitude"^^ . . . "glycomics" . . . . "zea" . . "An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union."^^ . . . . "Joanne Kamens" . . . "jesper.friis@sintef.no" . "NDFI4Cat Collection" . . . . . "^\\d{1,9}$"^^ . . . . . "frim1"^^ . . . "https://glytoucan.org/Structures/Glycans/"^^ . . . "proteomics" . "false"^^ . . . . . . "tctr" . . "cghdb" . "^\\d{7,}$"^^ . . . . . . . "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID="^^ . . . "0000005"^^ . . . . "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1"^^ . "NCBITaxonomyID" . . . "SCTID_2010_1_31" . . . . "false"^^ . . "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/"^^ . . . . . "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . "environmental science" . . . "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated."^^ . "IUPHAR_LIGAND_ID" . . "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants."^^ . "http://purl.obolibrary.org/obo/ARO_$1"^^ . . . "true"^^ . . . . . "ramirez@macn.gov.ar" . . . "17254"^^ . . . . . . . . . . . . "https://scicrunch.org/resolver/RRID:AGSC_$1"^^ . . "dna structural variation" . "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . . . "The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI)."^^ . "Alliance of Genome Resources Knowledge Base" . "false"^^ . "aging" . . . "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016"^^ . "Neural ElectroMagnetic Ontology" . "1.1.1.1"^^ . "margaret.woodhouse@usda.gov" . "doco" . "subject agnostic" . "computer science" . . . "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability."^^ . "Philippe Le Mercier" . . . . . . . . . . . "biomedical science" . . . "UCR00513"^^ . "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples."^^ . "true"^^ . "https://fungidb.org/fungidb/app/record/gene/"^^ . . . . . . . "life science" . . "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^ . . . . . . . . . . . . "^PPR\\d+$"^^ . "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^ . . . . . . . . "metadata standardization" . . . . "ontology" . . . "omim.ps" . . . . . . "false"^^ . . "food" . "http://uri.neuinfo.org/nif/nifstd/sao"^^ . . . "phenotype" . "false"^^ . . "https://medical-data-models.org/forms/"^^ . "DBG2 Introns" . "^\\d{7}$"^^ . "david.sehnal@gmail.com" . "cheminf" . . "false"^^ . . . . . . . "http://sideeffects.embl.de/se/$1"^^ . . . . . . "metabolomics" . . "true"^^ . . . . "true"^^ . . . . . . . "^[1-9]\\d*$"^^ . . . . . . . "sabiork.compound" . "insertion" . "Sharkipedia Trait" . "http://rdfs.org/ns/void#"^^ . "Jennifer R Smith" . . . "http://purl.org/pav/$1"^^ . . . . "knowledge and information systems" . . "https://hdl.handle.net/hdl:20.500.12633/"^^ . . . . . "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases."^^ . . "genetic disorder" . . "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . "https://www.uniprot.org/tissues/"^^ . "0000586"^^ . . . . "false"^^ . . "institution" . . . . . . . "true"^^ . . . . . . "https://www.nextprot.org/term/FA-$1"^^ . . . "false"^^ . . . . . . . . . . "http://www.w3.org/ns/odrl/2/"^^ . . "https://uts.nlm.nih.gov/uts/umls/semantic-network/$1"^^ . "false"^^ . . "FAIRSharing" . . . . . "ontology" . . . . . . . . . "P10636"^^ . "obo" . . . "BAC045"^^ . . "http://purl.obolibrary.org/obo/MFMO_"^^ . . "false"^^ . . "^[a-z0-9\\-]+$"^^ . . . . . . "drug-drug interactions" . "events" . . . . "reecehart@gmail.com" . "cc" . . . . . "Universal Spectrum Identifier" . . "http://purl.obolibrary.org/obo/FLOPO_$1"^^ . . . . "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1"^^ . . . "nbo" . . "experimental animal" . . . . . . . . . . . . . "Yongqun Oliver He" . "haiiu@dtu.dk" . . . . . "protein" . . . . . . "false"^^ . . . . "Eric W. Sayers" . . "^\\w+$"^^ . . . . . . "pathwaycommons" . . . "^\\d+$"^^ . "citation" . . "EGAS00000000001"^^ . . . . "NCI" . . "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^ . "omics data analysis" . "^GCF_[0-9]{9}(\\.[0-9]+)?$"^^ . "Influenza Virus Database" . "ontology" . "0001350"^^ . . "^[A-Z]{2}\\d+$"^^ . "NLXBR" . "biochemistry" . . "An ontology for the description of Drosophila melanogaster phenotypes."^^ . "Work"^^ . . . . . . . . "protein" . "data analysis service" . . . . . . . "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE)."^^ . . . "false"^^ . . "https://www.ebi.ac.uk/interpro/set/pfam/$1"^^ . . "ontology" . "study design" . "false"^^ . . . . . . . "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"^^ . . . "genome" . "genetree" . . "false"^^ . . "false"^^ . . . . . "post-translational modification" . "false"^^ . "false"^^ . "0007133"^^ . . "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage)\nNote that the website uses a different identifier then the one reported in this semantic space."^^ . . "Zebrafish developmental stages ontology" . "cl" . "virology" . . "^\\d+$"^^ . . . "^\\d+$"^^ . . "NCBI Genome" . . . . . . . "genpept" . . . . . . "ontology" . . "ontology" . . "Causal_Graphical_Model"^^ . . . . "John Westbrook" . . . . . . . "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^ . . "0000504"^^ . "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas."^^ . . . . . . . . . "http://purl.obolibrary.org/obo/VBO_"^^ . . . . "false"^^ . . "http://emmo.info/emmo#EMMO_$1"^^ . . . "drks" . "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/"^^ . . "^\\w{2,4}\\d{5}$"^^ . . . "true"^^ . "O08709"^^ . . . "http://www.bioguo.org/AnimalTFDB/family.php?fam="^^ . "MGgn0008978"^^ . "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id="^^ . "false"^^ . . . . "ChEMBL database of bioactive drug-like small molecules - Cell lines section" . . . "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^ . . "Gene Expression Analysis Resource" . "https://biopragmatics.github.io/providers/scomp/$1"^^ . . "315.1"^^ . . . . "iobc" . . . "life science" . "http://purl.obolibrary.org/obo/FAO_"^^ . . "^\\d{8}$"^^ . "zinc" . . "0000026"^^ . . "traits" . . . . . "true"^^ . . . . "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . . "life science" . . "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$"^^ . "survey" . . "obo" . "obo" . . . "adult" . . . . . "DepMap Cell Lines" . "dg.4503" . "cell" . "http://phenol-explorer.eu/foods/$1"^^ . . "andreas.ruepp@helmholtz-muenchen.de" . "https://cropontology.org/rdf/CO_348:"^^ . "0000190"^^ . "clb" . . . . "https://bioregistry.io/nsrrc:"^^ . . . . . "https://shop.vbc.ac.at/vdrc_store/$1.html"^^ . . "molecular interaction" . . "pathogen" . . . "oslc" . . "^\\d+$"^^ . . "jgrethe@ucsd.edu" . "0001191"^^ . . . . . "false"^^ . "https://smid-db.org/smid/$1"^^ . "^[CN]*\\d{4,7}$"^^ . "animal organ development" . . "obo" . "https://datalab.rwth-aachen.de/MINDER/resource/"^^ . . . . . "bertram@helix.mgh.harvard.edu" . "00000011-a"^^ . . . "false"^^ . "Global Biodiversity Information Facility" . . . . . "biomedical science" . . . "^\\d{5}$"^^ . . . "https://lincs.hms.harvard.edu/db/sm/$1"^^ . . . "morpheus" . . . . "co_326" . . "ontology" . . . . . "0000546"^^ . "rmrich5@gmail.com" . . . "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . "oriental-cds@163.com" . "http://purl.obolibrary.org/obo/HP_$1"^^ . . "https://aftol.umn.edu/glossary?category="^^ . . . "germline" . . . . "mvx" . "http://swissregulon.unibas.ch/query/"^^ . "false"^^ . . . . "bioregistry.collection" . . "http://purl.obolibrary.org/obo/GO_$1"^^ . "oharb@pcbi.upenn.edu" . . "https://www.dsmz.de/collection/catalogue/details/culture/"^^ . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"^^ . . . . "https://www.kaggle.com/"^^ . . . "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession="^^ . . "Application ontology for entities related to insecticide resistance in mosquitos"^^ . . "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes."^^ . . . "protein" . . . . . . "mhb120@gmail.com" . "Panorama Public" . "biomedical science" . . "International Classification of Diseases, 10th Revision, Clinical Modification" . "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"^^ . "opmi" . . . . . "^[0-9]+(LR)?$"^^ . . "false"^^ . "Bernd Müller" . "nicolas.matentzoglu@gmail.com" . . . "swiss-model" . "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id="^^ . "Mass spectrometry ontology" . "MCDS_L_0000000001"^^ . . . . . "false"^^ . "health" . . "cell" . "structure" . "http://www.bioinfo.org/NONCODEv4/show_gene.php?id="^^ . . . . . . "65"^^ . . . "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . "health" . . "LOC_Os01g49190"^^ . . "InterPro" . . . "https://cropontology.org/rdf/CO_347:$1"^^ . "anatomy" . . . "Publication Provenance Prefixes" . . "Deepak Unni" . . . . "false"^^ . . "yperez@ebi.ac.uk" . . "SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as \"sssom:mapping_justification\" are defined in the sssom namespace."^^ . "pubchem.bioassay" . "https://purl.dataone.org/odo/SASAP_"^^ . . . . "biodiversity" . "false"^^ . . "gene" . . . . . . "false"^^ . . . "fabrice.legeai@rennes.inra.fr" . . "^\\d+$"^^ . . "bioinformatics" . . . . . . "Antibiotic Resistance Genes Database" . "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"^^ . . . . . . . "chemistry" . . . . . . . . . . "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser."^^ . "https://www.pombase.org/gene/"^^ . . . "citation" . . "protein" . . "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID="^^ . . "gene ontology enrichment" . . . . "FHIR External Terminologies" . . "unigene" . "ontology" . "electronic health record" . "EDAM Format" . . "life science" . . . "Node Package Manager" . "https://ssbd.riken.jp/database/dataset/"^^ . "life science" . "Stefanie Seltmann" . . . "hms.lincs.cell" . . "life science" . "dbvar.study" . . . . . . . . . "orphanet.ordo" . . "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology" . "neurobiology" . . "Gene Ontology Rules" . . "false"^^ . . "ecology" . "^(\\w+)?\\d+$"^^ . . . . . "http://senselab.med.yale.edu/ORDB/Data/"^^ . . . . "BioSystems" . . "obo" . . "false"^^ . "vjenkins@morgan.harvard.edu" . "ScerTF" . . . . "repository" . . "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling."^^ . . . . . . . . "cell" . . . . . . . "http://purl.obolibrary.org/obo/DRON_$1"^^ . "Metabolomics Standards Initiative Ontology" . . . . . . . . . . . . . . . "https://pb.apf.edu.au/phenbank/strain.html?id="^^ . . "Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog."^^ . . . . . . . . "food" . . "http://purl.obolibrary.org/obo/AAO_$1"^^ . "https://www.ebi.ac.uk/miriam/main/resources/"^^ . . "^\\d{7}$"^^ . . . "ILX" . . . . "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . . "UPISO" . . "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data."^^ . "ZINC1084"^^ . "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$"^^ . "pathway" . . "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/"^^ . . "Identifiers.org Registry" . "protein" . . . "Clinical measurement ontology" . "A repository of software packages written in Ruby."^^ . "plant phenotypes and traits" . . . . "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/"^^ . . "1"^^ . "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century."^^ . . "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"^^ . "false"^^ . . . "Health Data Research Innovation Gateway" . "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1"^^ . . "rnamods" . . . "Cell line collections (Providers)"^^ . "DECIPHER CNV Syndromes" . . . "051"^^ . . . "hasOpenAccessRating"^^ . "ORCID" . "C0001"^^ . "false"^^ . "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier."^^ . "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . . . . . . . . . . . "miaa" . "anatomy" . "DASHR expression" . . "GeneFarm" . . . . . . . "http://purl.obolibrary.org/obo/ARO_"^^ . "Zhiliang Hu" . "life science" . . "virgen" . . . "wikidata.property" . . "coriell" . "http://purl.obolibrary.org/obo/WBbt_$1"^^ . . . . "subject agnostic" . . "http://purl.obolibrary.org/obo/OMIABIS_"^^ . . . . "ATC_code" . . . . . . . . . "^\\d{9,9}$"^^ . "idpo" . . . . "epigenomics" . . "https://www.ebi.ac.uk/interpro/entry/InterPro/"^^ . . "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . . . . . "http://purl.obolibrary.org/obo/MC_"^^ . . "https://www.pesticideinfo.org/chemical/$1"^^ . . . "bernd.mueller@zbmed.de" . . . . . . "Five Stars of Online Research Articles Ontology" . "life science" . "^\\d{4}$"^^ . . . . "false"^^ . "119514"^^ . . "https://www.picb.ac.cn/limore/cellLines/single?para="^^ . . . . "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production."^^ . . "experimental condition" . . . . . "ovarian" . "S1"^^ . . "https://mediadive.dsmz.de/solutions/$1"^^ . . "true"^^ . "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_"^^ . . "Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system."^^ . . . "neuron" . . "mycobank" . "obo" . . "234"^^ . "100"^^ . . "Yi Zhao" . . "https://fairsharing.org/"^^ . "sh" . "true"^^ . . . "NONCODE v3" . . . . . . . . . "CAID" . "0000400"^^ . . "false"^^ . . . . "ICD-10" . "0001009"^^ . "drug" . . "botany" . . . . . . "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"^^ . . . "https://w3id.org/mixs/"^^ . . . "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"^^ . "strain" . . . "RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database."^^ . . "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways."^^ . "^\\d{7}$"^^ . "contributor"^^ . . . . "OTTHUMG00000169812"^^ . . "https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip"^^ . . . "44259"^^ . . . . . . . "life science" . . . "https://data.4dnucleome.org/experiment-set-replicates/$1"^^ . . "jeffvin.wong@utoronto.ca" . . "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source."^^ . . . . . "https://www.iedb.org/reference/$1"^^ . . . . . "ontology" . . "karel.berka@upol.cz" . . . . . "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names."^^ . . . . . "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist="^^ . "Terms from the source appear in the target resource" . . "https://vocab.org/vann/#$1"^^ . . . . "http://uri.neuinfo.org/nif/nifstd/"^^ . . . "mpid" . . . "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1"^^ . "false"^^ . . "CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazards—such as explosions or toxic fumes."^^ . . "^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . . "Information about the C57BL/6J. Includes genetic background and disease data."^^ . . . "GSTA1"^^ . "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^ . . . "phenotype" . . . . . . . "software engineering" . . . . . . . "https://www.swisslipids.org/#/entity/SLM:$1"^^ . . "ontology" . "pdro" . . "EAWAG Biocatalysis/Biodegradation Database" . "false"^^ . "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context."^^ . "plant breeding" . _:N1e6ec8430d304806b4538fc7137b9053 . "health science" . . . . . "00001234"^^ . . "https://pharmacome.github.io/conso/"^^ . . . "NXP" . "HomologyRelation"^^ . "interaction" . . "UniProt Variants" . "developmental biology" . . . "Beta Cell Genomics Ontology" . . . . . . . . "npm" . . . "enzo" . "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$"^^ . . . . . "true"^^ . "Paul David Neil Hebert" . "false"^^ . . . "true"^^ . . . "enzyme" . . . . . . . "https://run.biosimulations.org/simulations/$1"^^ . "ontology" . . "false"^^ . . . . "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42)."^^ . . . . "tissue" . "^\\w+(\\.)?\\w+(\\.)?\\w+$"^^ . . . . "PF3D7_1328700"^^ . . . . . "1"^^ . . . "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records."^^ . "http://purl.obolibrary.org/obo/SCDO_"^^ . . "polcaes@gmail.com" . . . . "proteomics" . . . . "molecules" . . . . "structure" . . "nihhesc" . . . "Selventa legacy complex namespace used with the Biological Expression Language"^^ . . . . . . "false"^^ . "mutant" . "chemistry" . . "haendel@ohsu.edu" . . "kupo" . "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information."^^ . "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest."^^ . . . . . "GPM32310002988"^^ . . . . "0000060"^^ . . . . . "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol."^^ . "^[A-Za-z0-9]+$"^^ . . . . _:N684dfaa5304e4af58860ef3f4a47b23a "William Klimke" . . "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid="^^ . . . "false"^^ . . "AOPWiki (Key Event)" . "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . "model" . "An ontology for description of concepts in the nutritional studies domain."^^ . . . "https://www.worldcat.org/oclc/"^^ . . . "^\\d+$"^^ . . "ontology" . . . . . . "Encyclopedia of DNA Elements" . . "Cooperative Patent Classification" . "^\\d+$"^^ . . . "prediction" . . . . . . "https://pdc.cancer.gov/pdc/study/"^^ . . . "http://qudt.org/schema/qudt#$1"^^ . . . . "General Enquiries" . . . . . . . . . . . "inhibitors" . "0000598"^^ . . "4776"^^ . "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers."^^ . . . . "http://oid-info.com/get/"^^ . "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"^^ . "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage."^^ . . . . . . . "The 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."^^ . . "genetics" . "false"^^ . "http://www-bionet.sscc.ru/sitex/index.php?siteid="^^ . "The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page)."^^ . . . . . . . "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics"^^ . "opm" . "rgd" . "protein" . . . "http://www.kegg.jp/entry/$1"^^ . . . "ontology" . . . . . . . "Susan Tweedie" . . "^\\d+$"^^ . "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^ . . . . . . "anatomy" . "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid="^^ . . "http://stitch.embl.de/interactions/"^^ . . . . "PhenX Toolkit" . . . . "biomedical science" . . . "10.1038/s41597-022-01807-3"^^ . . "Selventa legacy disease namespace used with the Biological Expression Language"^^ . . . . "https://www.checklistbank.org/dataset/$1"^^ . . . . "roman@ebi.ac.uk" . . "wormpep" . . "^P\\w+$"^^ . "molecular biology" . . "Jonathan Karr" . "27106865"^^ . . . _:Nfc145c4b3c9440d782e6e175eb21b434 "Plant Ontology Administrators" . . . . . "earth science" . . "1023371"^^ . . "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix. See examples [here](https://bioregistry.io/highlights/relations#canonical)." . "human" . . . . . "bbkg" . . . "NLXQUAL" . . . . "UPVAR" . . . . . . "storedb.dataset" . "^\\d{7}$"^^ . "dbprobe" . . . . . "Physico-chemical process" . _:N080da5f29fdd435f9aaec76ffbd54dbb "J.Bard@ed.ac.uk" . . "structure" . "2008-005144-16"^^ . . "^\\w{1,2}\\d{8,10}$"^^ . . . . "protein" . "Metabolites in drugbank"^^ . . . . . . . . "http://purl.obolibrary.org/obo/FBdv_$1"^^ . . . "false"^^ . . . . "0000983"^^ . . "false"^^ . "62"^^ . . . . . . . . . . . . "^SM\\d{5}$"^^ . . . "spar" . . "obo" . "ontology" . . "https://easychair.org/cfp/"^^ . . "http://purl.obolibrary.org/obo/MAO_"^^ . "splicenest" . "oridb.sacch" . . . . "obo" . . . . . "Anton I Petrov" . . . "0004828"^^ . . "0000005"^^ . . . "eukaryotic" . "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"^^ . . "biology" . "false"^^ . . "sewilson@lbl.gov" . . . . . . . . . . . . "https://www.geonames.org/recent-changes/featurecode/$1/"^^ . "taxonomic classification" . "metascience" . "RDF Schema" . "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1"^^ . . . . "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id="^^ . "^CPX-[0-9]+$"^^ . . . . . "NIF Standard Ontology: Organisms" . . "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1"^^ . . . . . . . . . . . . "EC number" . . "modeling and simulation" . . . . . . . . . "mcmelek@msn.com" . "^\\d{7}$"^^ . . . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . "^\\d+$"^^ . "protein" . . . "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more."^^ . "tbreddy@lbl.gov" . . "^\\w+(\\.)?(\\d+)?$"^^ . "cdt" . . "Simon Jupp" . . . . . . . _:N44200d5f561d43b5912b0d14cadae2a0 "Maria Herrero" . "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^ . . "imaging" . . . . . . . . . . . . . "ILMN_129894"^^ . . . "ontology" . . . . . "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . . . "geography" . . . . . . . . "drug" . . "agriculture" . "^[A-Z0-9]+$"^^ . . . "Xenbase" . . "hmsl_id" . "Aron Marchler-Bauer" . "Harry E. Pence" . "brain" . "embryonic stem cell" . _:N07c9995202684d52922d84b31e2f5ded . "biomedical science" . "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId="^^ . "bibliography" . . "^\\d+$"^^ . . "false"^^ . . . . . . . . . "http://purl.obolibrary.org/obo/DISDRIV_"^^ . . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_mol_"^^ . . . . "molecule" . "ontology" . . . . . . "ontology" . . "Vocabulary of Interlinked Datasets" . "false"^^ . . . . . "false"^^ . "hescriva@obs-banyuls.fr" . "false"^^ . . . . . "REPRODUCE-ME Ontology" . "https://labsyspharm.github.io/lspci/"^^ . . . . "false"^^ . . . "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1"^^ . . "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts © National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\"."^^ . "12345"^^ . "food" . . . "phenotype" . . "csv"^^ . . "genome" . "An organization" . . "mutation" . . . . . "false"^^ . "epigenetics" . . "Sandra Orchard" . . "false"^^ . "nextdb" . . . "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1"^^ . . . . "41455251.1"^^ . . "phylogenetics" . "^[1-9]\\d*$"^^ . . . . "biochemistry" . "life science" . . . . "^\\d{7}$"^^ . . . "http://purl.obolibrary.org/obo/PORO_$1"^^ . "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]"^^ . . "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." . . "false"^^ . . . . . . . . "Catalog of purchasable reagents and building blocks"^^ . . . "anatomy" . . "sio" . . . "CIViC gene" . "^C\\d+$"^^ . . . . . "Fungal Nomenclature and Species Bank" . . . . . . . "^\\d{6}$"^^ . . . . . . "http://purl.obolibrary.org/obo/PSDO_$1"^^ . "013681"^^ . . "kegg.enzyme" . . . . . "hybrid" . "E-cyanobacterium entity" . . . "marine ecology" . . . "life science" . . "Oat ontology" . . . "InterPro" . . "rs11603840"^^ . . . "disease process modeling" . . . _:N270077e13b3b43218f7bbeda7477b8a6 . "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards."^^ . . "false"^^ . "Life cycle stages for Platynereis dumerilii"^^ . "0000728"^^ . . . . "Higher-level classifications of COG Pathways"^^ . . . "false"^^ . "https://pmb-bordeaux.fr/maggot/metadata/$1"^^ . . . "Willy Wong" . . "^[1-9]\\d{3,7}$"^^ . . "^\\d+$"^^ . "false"^^ . "ontology" . . "O80725"^^ . . . . . . . "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . . "The bioRxiv is a preprint server for biology"^^ . "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"^^ . . . . . _:Na753bc128ae04b158307c2af391f4ddf "curator@inoh.org" . "https://bioregistry.io/treebase:"^^ . . . "ncats.bioplanet" . "^\\d+$"^^ . . "Egon Willighagen" . . . . "http://purl.obolibrary.org/obo/T4FS_$1"^^ . . . . . . "protein" . "measurement" . "protein" . . . "UPLOC" . . "0000061"^^ . . "http://purl.obolibrary.org/obo/VariO_$1"^^ . . "false"^^ . . "cell" . . "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . . . "conferences" . . . "epidemiology" . . "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id="^^ . . . "Zhang Zhang" . "^ACYPI\\d{6}(-RA)?$"^^ . "0000485"^^ . "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"^^ . "false"^^ . "Karen.Christie@jax.org" . "http://birdgenenames.org/cgnc/GeneReport?id="^^ . . . "https://biopragmatics.github.io/providers/pba/$1"^^ . . "^\\d+$"^^ . . . . "ontology" . . . . "biomedical science" . . . "pdbechem" . "obo" . _:Nb22dfd61607942bdbd6c144a3383a12a "Crop Ontology Helpdesk" . . "An application ontology for use with miRNA databases."^^ . . "TubercuList" . . "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . . . "false"^^ . . "classification" . "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-"^^ . "Daniel Schober" . . . "^\\d{7}$"^^ . . . . . . "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.\n\nThe original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]"^^ . "false"^^ . . . "vendor" . . . "false"^^ . . . "report" . "centrally registered identifier" . . "false"^^ . . . . . "UniProt Chain" . . . "classification" . "anatomy" . . . . . . "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/"^^ . . "https://www.ndexbio.org/viewer/networks/"^^ . "functional genomics" . . . "false"^^ . . . "^\\d+$"^^ . "BRENDA Ligand Group" . . _:N5fc61388a1f34b48a985d50eb5fef93d "Crop Ontology Helpdesk" . "http://icd9cm.chrisendres.com/index.php?action=search&srchtext="^^ . . . . . "ontology" . . . . . "UPI000000000A"^^ . "The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample."^^ . "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id="^^ . . "An ontology that enables the description of reviews of scientific articles and other scholarly resources."^^ . . . . "orthology assignment" . . . . "CRISP" . . "proteins" . "Simple Modular Architecture Research Tool" . . . "kisao" . "CRISP Thesaurus, 2006" . . . "neurovault.collection" . . . . . . "anatomy" . . "false"^^ . . "https://w3id.org/faircookbook/$1"^^ . "false"^^ . "life cycle stage" . "cjmungall@lbl.gov" . . "fortuna@ebd.csic.es" . . . . "^\\d+$"^^ . . "^\\d{7}$"^^ . . "00100005"^^ . "Ontology for simulation, modelling, and optimization" . . "ontology" . . "SNOMEDCT_US_2022_12_31" . . . . "http://opendata.inra.fr/ATOL/ATOL_$1"^^ . "Georgeta Bordea" . . "100E"^^ . . . . . . . "mdm" . "0000204"^^ . . "National Drug Code" . . "controlled term" . . "WBbt" . "cellular component" . "^\\d{7}$"^^ . "protein" . . . . "Vaccine Ontology" . . . . . . "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.pharmgkb.org/drug/$1"^^ . "Food Type identifiers, supporting codes and vocabularies based on the EFSA FoodEx2 (https://www.efsa.europa.eu/en/data/data-standardisation) that are being tested in the development of the FSA's code and data standards repository. These codes may be used within FSA data."^^ . . "FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements."^^ . . . "dna" . . "Maize ontology" . "biopragmatics/bioregistry"^^ . . . . . "protocol" . . "Jennifer C. Girón" . . . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id="^^ . "false"^^ . . "^\\d{7}$"^^ . "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/"^^ . . "https://bioregistry.io/metaregistry/go/"^^ . . . . "http://purl.obolibrary.org/obo/OMRSE_$1"^^ . . "ecology" . "fbql" . . . "https://www.ebi.ac.uk/ega/studies/$1"^^ . . . . "090801"^^ . "^[0-9]+$"^^ . . . . . "false"^^ . . "An additional Japanese clinical trial registry"^^ . . . . . . "^\\d+$"^^ . "0000001"^^ . . "Pierre Baldi" . . . . . "false"^^ . "https://pathbank.org/view/"^^ . . . "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships."^^ . . . "false"^^ . "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . . . . . . "090701"^^ . . "dsm-iv" . . "protein" . . "ftp://hgdownload.cse.ucsc.edu/goldenPath/"^^ . "^\\d+$"^^ . . . . . . . . "study design" . . . "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$"^^ . "dna" . . . . "ontology" . "Cell line collections (Providers)"^^ . "transcript" . . "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^ . . . "18125"^^ . "https://www.ncbi.nlm.nih.gov/bioproject/?term="^^ . . . "false"^^ . . "UM-BBD compound" . . . "^\\d{7}$"^^ . . . "polysaccharide" . . . "ontology" . . . . "An issue in any public repository on GitHub."^^ . "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]."^^ . . . "false"^^ . . . . . . "false"^^ . "Conference Ontology" . . "Melissa Haendel" . "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features."^^ . "http://bigg.ucsd.edu/models/universal/reactions/"^^ . "^\\d+$"^^ . "pancreatic islet function" . . . . "^\\d+$"^^ . . . "human genetics" . . "false"^^ . . "uniprot.taxonomy" . "https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn$1"^^ . . "false"^^ . "protein" . . "https://www.storedb.org/store_v3/download.jsp?fileId=$1"^^ . . "spp" . . . "worm" . . "obo" . . . "false"^^ . "robert.thacker@stonybrook.edu" . . "false"^^ . "https://www.fishbase.ca/summary/$1"^^ . "^\\d+$"^^ . . "^S\\d+$"^^ . . . "obo" . . "Protein Ensemble Database ensemble" . . . . "Brett G. Olivier" . "^\\d+$"^^ . . "ontology" . "tissue" . . . . "false"^^ . . . "Discourse Elements Ontology" . . . "^K[0-9]+$"^^ . "^\\w+$"^^ . . "false"^^ . . . . "KEGG LIGAND" . . . "^SAM[NED](\\w)?\\d+$"^^ . . . . "Metadata4Ing" . "snap" . "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . . "false"^^ . "ymdb" . . "biomedical science" . . . . . . . "http://purl.obolibrary.org/obo/DERMO_"^^ . . "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . . . "E13035"^^ . . "genetic analysis" . "sequence" . . . . "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^ . "Database of Macromolecular Interactions" . "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id="^^ . . "Sigma Aldrich is a life sciences supply vendor."^^ . . "false"^^ . "http://ciliate.org/index.php/feature/details/$1"^^ . "computer science" . "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs)."^^ . . . "^\\d+$"^^ . "helpdesk@cropontology-curationtool.org" . "false"^^ . . "https://vocab.org/vann/#"^^ . . . . "false"^^ . "pathway" . "ontology" . "http://drugcentral.org/drugcard/$1"^^ . . . . . "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . . . . . . . . . . . "protein" . . . . "7207"^^ . . . "2673500"^^ . . . . . . . "disease" . "SNOMEDCT_US_2023_09_01" . . "janna.hastings@gmail.com" . "structure" . "^\\w+$"^^ . "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . . "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur."^^ . "http://purl.uniprot.org/core/$1"^^ . "Categories in the AFTOL database"^^ . "https://www.datanator.info/metabolite/$1"^^ . "academy" . . . . "http://purl.obolibrary.org/obo/RXNO_"^^ . . . . "Ceri Van Slyke" . . . . . . . . "10531"^^ . . . . . . "SNOMEDCT_US_2022_07_31" . . . "Gerhard Mayer" . . "Daniel C. Berrios" . "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id="^^ . . . . "^ENST\\d{11}$"^^ . . "genome" . "omrse" . . "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases."^^ . "http://www.antweb.org/specimen.do?name="^^ . . . . . . . . "structure" . "Cell line collections (Providers)"^^ . . . . . . . . "beck@ncbi.nlm.nih.gov" . "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region."^^ . "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^ . "life science" . . . "https://cropontology.org/rdf/CO_366:$1"^^ . . . . "irefweb" . . "CIP - potato ontology - december 2018"^^ . . . . . . . . "https://bioregistry.io/ukprn:"^^ . "^\\d{7}$"^^ . . "https://www.ncbi.nlm.nih.gov/clinvar/variation/"^^ . . . . . . . . . "https://bioregistry.io/metaregistry/go/$1"^^ . "ISRCTN10175490"^^ . "http://purl.obolibrary.org/obo/NIF_CELL_$1"^^ . "PubChem Classification" . "^[a-z_A-Z0-9]+$"^^ . "GCST000035"^^ . . . "LBCTR2023015204"^^ . _:Nad2e205775ec4086893d6f8fac120366 . . . . "0000070"^^ . . "051"^^ . . "genome" . . . . "ATCC(dna)" . . . . . . . . "false"^^ . . . . "http://edamontology.org/format_$1"^^ . "https://cropontology.org/rdf/CO_370:$1"^^ . . "The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)"^^ . "false"^^ . "false"^^ . . "Molecular database for the identification of fungi" . "drug target" . . "https://bioregistry.io/jaxmice:"^^ . "Sciflection" . . . "anatomy" . . "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop="^^ . . . . . . . . "identifier for a chemical compound per EINECS or ELINCS"^^ . . "false"^^ . . "Biological Expression Language" . . . . . . . . . . . "ontology" . . "APID Interactomes" . "phenotype" . . "^\\w+(\\-|\\.|\\w)*$"^^ . "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases."^^ . . . . "pgdso" . . "http://purl.org/spar/doco/$1"^^ . "^ARBA\\d+$"^^ . "Documentation of the Phenoscape Curation Workflow"^^ . . . . . "https://bioregistry.io/dragondb.dna:"^^ . . "life science" . . . . . . "planp" . "false"^^ . "cgnc" . . "false"^^ . . . "3"^^ . . . . _:N1ec65468174440efa22fc2161b2bcbf1 . . "https://www.mavedb.org/#/experiments/urn:mavedb:"^^ . . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . . . . . "^\\d+(\\w+)?$"^^ . . . . "meteorology" . . "0000001"^^ . "http://purl.obolibrary.org/obo/OHPI_"^^ . "mirbase.mature" . . "https://www.ebi.ac.uk/chembl/compound/inspect/$1"^^ . "publishing" . . "https://coconut.naturalproducts.net/compound/coconut_id/$1"^^ . . . . "brendanx@uw.edu" . "biology" . . . "ECOCYC" . . "e.arnaud@cgiar.org" . "http://purl.obolibrary.org/obo/BSPO_"^^ . "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013."^^ . "Eric Sid" . . "david.wishart@ualberta.ca" . "has canonical prefix" . . "plant phenotypes and traits" . "molecular neuroscience" . . _:Nfbe0e8521e37434badd542c98d5cadea "Michelle Futornick" . . "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR)."^^ . . . "false"^^ . "molecular biology" . . "pdb" . "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"^^ . . . "IPR" . . . . "non-coding rna" . . . . . "http://lincsportal.ccs.miami.edu/datasets/#/view/"^^ . . . "false"^^ . . "epidemiology" . "It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]"^^ . . "http://purl.obolibrary.org/obo/DDPHENO_"^^ . "imgt.hla" . . . . "anatomy" . "false"^^ . "ontology" . . . "ontology" . "database" . . . "http://www.onto-med.de/ontologies/gfo.owl#$1"^^ . . "KEGG Reaction" . "4"^^ . . . . "false"^^ . . . . "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id="^^ . "OriDB Schizosaccharomyces" . "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales."^^ . . . . "The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system."^^ . . . "diagnosis" . . . "http://immunet.cn/bdb/index.php/mimoset/"^^ . . "false"^^ . . . . "KYinno cell lines" . "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . . . . . . "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . . "obo" . . . "http://topdb.enzim.hu/?m=show&id=$1"^^ . . . . . . "ecmdb" . . "imex" . . . . . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$"^^ . . "dso" . . . . . "https://cropontology.org/rdf/CO_358:"^^ . "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code="^^ . . . . "agricola" . "Leigh Carmody" . "278"^^ . . "false"^^ . "false"^^ . . "life science" . . . . "This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from )"^^ . . . . "0000001"^^ . . . "^\\d+$"^^ . "^\\d{6}$"^^ . . "MF_01400"^^ . "linguist" . . "https://www.uniprot.org/database/$1" . . . "protein" . . "EY223054.1"^^ . . . "Atsushi Yoshiki" . . . . . . . . . . . "certain"^^ . . . . "drug" . . . "https://www.mlcommons.org/mlc-id/$1"^^ . . . "articles" . . "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms."^^ . . . . . "Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]"^^ . . "false"^^ . . . . . "http://rest.bmrb.wisc.edu/bmrb/$1/html"^^ . . . . . . "RNACentral" . . . . "kegg.reaction" . . "false"^^ . . . . . "UM-BBD_reactionID" . . "Electrocardiogram Ontology" . "ATCC" . . "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . . . . . "https://lobid.org/gnd/$1"^^ . . . _:Nb6b37a7b77e34a5eb7eefc59be1db2d7 "julie@igbmc.u-strasbg.fr" . . . . "false"^^ . "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_"^^ . . "Cell line collections (Providers)"^^ . . . . . . . . "genetics" . . . . . "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)."^^ . . "https://www.gwascentral.org/phenotype/$1"^^ . . . "Gemeinsame Normdatei" . . . . . "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue."^^ . _:N9b7f1cbc7ff94c8baf5784763220d782 . . "^\\d+$"^^ . . . . "ontology" . "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."^^ . . . . . . . . . . . . "gene expression" . . "https://flybase.org/reports/FBrf$1"^^ . . . "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster="^^ . "aBq"^^ . . . . "SwissLipid" . . . . . "Rebuilding a Kidney" . "^\\d{7}$"^^ . "2c6s"^^ . "^\\w+(\\.\\d+)$"^^ . . . . "false"^^ . . . . . . "life sciences" . "Bgee stage" . . . . "false"^^ . . "life science" . "basic research" . . . . "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^ . . . . "^\\d+$"^^ . "true"^^ . . "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. "^^ . . . . . . "true"^^ . . "vbrc" . . . . . "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"^^ . . . . "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs."^^ . "kdurante@stanford.edu" . "false"^^ . "life science" . . "chemical" . "caps" . "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid="^^ . "http://purl.obolibrary.org/obo/SOPHARM_"^^ . "A database of fly neurons and pathways with an associated 3D viewer."^^ . . . . . "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1"^^ . "The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA."^^ . "Gs0000008"^^ . . "MAM01234c"^^ . . "nextProt" . . . . . . . "https://w3id.org/oc/oci/"^^ . . . "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019"^^ . . "Index Fungorum" . . . "http://www.wikigenes.org/e/gene/e/$1.html"^^ . . . . "1"^^ . . . "transcriptomics" . "http://www.hprd.org/protein/$1"^^ . . . "chemistry" . . . "http://www.knapsackfamily.com/knapsack_core/information.php?word="^^ . "microbial" . "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id="^^ . . "false"^^ . . . "https://repo.napdi.org/study/$1"^^ . "adrien.coulet@loria.fr" . "genomics" . . "CHEMBL3307800"^^ . "morphology" . . "http://sabiork.h-its.org/newSearch?q=$1"^^ . . "ai10e-kctd13b"^^ . . . "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id="^^ . "biomedical science" . . "hospital" . . . . . . . . "unii" . . . "MGD" . . "https://terminology.hl7.org/CodeSystem-v3-$1"^^ . . "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"^^ . . "chemistry" . "603903"^^ . . . . . . "1001"^^ . . "life science" . . . . . . . "transgene" . "^\\w+$"^^ . . . "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No="^^ . "human" . . . "life science" . . . . . "microbiology" . . "Antoine Danchin" . . . . . . "ribonucleic acid" . "false"^^ . . . . "qualities" . . "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."^^ . . . "false"^^ . . . . "schaefec@mail.nih.gov" . . "bibliometrics" . . . "obo" . . . . "false"^^ . . "Stemcell Knowledge and Information Portal" . "HL7 External Code Systems are stored within the greater OID system" . . . "emotion" . . "structure" . . . . . "lam87@cornell.edu" . . . . . "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."^^ . . . . . "gbif" . . "has alternative prefix" . "chemistry" . "bigg.model" . . . "NIF Standard Ontology: Cognitive Function" . . . "upheno" . . "BARC-013845-01256"^^ . "obo" . "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$"^^ . . . . . . . . "http://purl.obolibrary.org/obo/PLANA_"^^ . "000000001"^^ . . . . "false"^^ . . . "bioregistry"^^ . "false"^^ . . "Troy Pells" . . "Miguel A. Fortuna" . . . "1"^^ . "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"^^ . "joel.richardson@jax.org" . . "false"^^ . . "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . "^\\d+$"^^ . . "A database-specific registry supporting curation in the Gene Ontology"^^ . . . . "http://purl.obolibrary.org/obo/TAHE_"^^ . . "http://yeastrc.org/pdr/viewProtein.do?id=$1"^^ . "false"^^ . . . "reaction" . . "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations."^^ . . . . . . . "PSI-MOD" . . . . "William Hogan" . . . . "pharmacogenomics" . . . "https://www.cellbiolabs.com/search?keywords=$1"^^ . "dlxb" . . . . "https://bioregistry.io/schema/#"^^ . . . . "^(data|topic|operation|format)\\_\\d{4}$"^^ . . "Hepatitis C Virus Database Project" . . "dg.anv0" . "false"^^ . . . "structure" . "Zebrafish anatomy and development ontology" . "anatomy" . . . . "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant."^^ . . "false"^^ . . . . . . . . . . . . . . "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^ . "eukaryotic" . "^[A-Za-z0-9_-]+$"^^ . . "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools."^^ . . . "AT5G05330"^^ . . . . . . . . . . . . . . . . . . . "ucas" . "botany" . "^\\d+$"^^ . . . . . . . . . "t4fs" . . . "life science" . . "Raja Mazumder" . "identifierPattern"^^ . . . . "false"^^ . "http://www.ubio.org/browser/details.php?namebankID=$1"^^ . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models."^^ . . "DateTimeDescription"^^ . . "developmental biology" . . . "tao" . . . . . . "true"^^ . "biocuration" . "ipi" . . "false"^^ . "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information."^^ . . . "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information."^^ . . "biology" . . . . . . . . "^\\d{7}$"^^ . "microbiome" . . . . . "false"^^ . "http://purl.enanomapper.org/onto/ENM_"^^ . "bfo" . "mwitt@purdue.edu" . "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures."^^ . . . . . . "https://bioportal.bioontology.org/ontologies/$1" . "Osamu Ohara" . "life science" . "https://cropontology.org/rdf/CO_337:$1"^^ . "Bong Hyun Sung" . "International Standard Serial Number" . "false"^^ . "omo" . "Universal Natural Products Database" . "Sabine Oesterle" . . . . . "This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace. "^^ . . "neurophysiology" . "https://cryptodb.org/cryptodb/app/record/gene/"^^ . _:N3e7c81cd11fa492a82b3573ccfdc6237 "ncictcaehelp@mail.nih.gov" . "^\\d+$"^^ . "false"^^ . . "Barley ontology" . . "knowledge and information systems" . . . "https://hpscreg.eu/cell-line/$1"^^ . . . . "https://bioregistry.io/mesh.2013:"^^ . . . . "http://bigg.ucsd.edu/models/"^^ . . . _:N0a3b10f91bc9432d844ddbb98489eb84 . . . . . . . "European Paediatric Cardiac Codes" . "false"^^ . . . "false"^^ . . . . . . "life science" . "ontology" . "005012"^^ . "false"^^ . . "^RPCEC\\d+$"^^ . "life science" . . . . . "medical biotechnology" . "TS-0001"^^ . "^CCDS\\d+\\.\\d+$"^^ . "structure" . . "Kaggle" . . "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . "0000423"^^ . "0000000"^^ . . "drduke" . . . . "gene mapping" . "Identifiers for proposals/projects at the Joint Genome Institute"^^ . "civic.sid" . . "Ontology for Nutritional Studies" . "http://purl.obolibrary.org/obo/MOP_"^^ . . . . . "Neil McKenna" . "ontology" . "medicine" . . . "Uberon Property" . "2842"^^ . . "mutant" . . . . "A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces."^^ . . . "Ioannis Xenarios" . "sheeba.samuel@uni-jena.de" . "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1"^^ . "kyinno" . . . . . . . "^\\d+$"^^ . . . . . "geodesy" . "^nbdc\\d+$"^^ . . "obo" . . . "^([a-zA-Z]+-)?\\d+(\\.\\d)?$"^^ . "false"^^ . . . _:N865ae216243546ca96f93a846edbb7bc "helpdesk@cropontology-curationtool.org" . "0000001"^^ . "hpa" . . . . . . . "ncbidrs" . "^\\d{7}$"^^ . "^[0-9]+$"^^ . "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org"^^ . . . _:N9b7f1cbc7ff94c8baf5784763220d782 "First DataBank Customer Support" . . . "false"^^ . "https://gnomad.broadinstitute.org/variant/$1"^^ . "sequence" . . . "apweiler@ebi.ac.uk" . . . . . "false"^^ . "drug metabolism" . . . . . . . . . . "^10.\\d{2,9}/.*$"^^ . "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"^^ . . . . . . . "^[A-Za-z_0-9]+$"^^ . . . . . . . . . "^A_\\d+_.+$"^^ . "TDR" . "TP53-47"^^ . . "Rolf Apweiler" . "http://www.wikidata.org/entity/$1" . . "cog" . . . "^TCTR\\d+$"^^ . . "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . "https://biomedit.ch/rdf/sphn-ontology/sphn#"^^ . "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical."^^ . . "study design" . . . "scicrunch" . "structure" . . . "hgvs" . "chemical" . . "MINID Test" . "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"^^ . . "endocrinology" . . . "false"^^ . "identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829"^^ . . . . . "http://purl.obolibrary.org/obo/VT_"^^ . . . "10001-101"^^ . "life science" . . . "https://bioregistry.io/ligandexpo:"^^ . . . "multicellds" . "^.*?--%3E.*?$"^^ . . . "http://purl.obolibrary.org/obo/OHD_$1"^^ . . . . . . . . . "SR0000178"^^ . . . "Michael Riffle" . . "protein" . "biology" . . "Cell line collections (Providers)"^^ . . . . . "metacyc.compound" . . . . "50885"^^ . . "Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID]"^^ . . . . . . "ontology" . "Mathematical modeling ontology" . "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1"^^ . . "https://medlineplus.gov/genetics/condition/$1"^^ . . . . . . . "false"^^ . . . . . "René Ranzinger" . . . . "maxneal@gmail.com" . . . . . . . . . . . . . . . . . "cooperl@oregonstate.edu" . . . . . . . . . "54"^^ . . . "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA."^^ . . . . . . "https://proteinensemble.org/"^^ . . . "None"^^ . . "false"^^ . . . . . "^\\d{7}$"^^ . . "metascience" . "genetics" . "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^ . "cl3603"^^ . . . "A Knowledge Resource for Innate Immunity Interactions and Pathways" . "interaction" . "Development Data Object Service" . . . "Assembly" . . . . . "citation" . . . . . . . . . "NameRXN" . "http://bigg.ucsd.edu/compartments/"^^ . . . . . . . . . . "ontology" . . "false"^^ . . . . "AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms."^^ . . . . "true"^^ . "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."^^ . . . "PathoPlant®" . "http://purl.obolibrary.org/obo/VT_$1"^^ . . . . . . . "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . "biomedical science" . "https://amzn.com/$1"^^ . . . . "false"^^ . "221058"^^ . "health sciences" . . . . . . "ensembl.plant" . "cordis.article" . "mathematics" . _:N44ea25e78e4a4c21a4fc2751279240af . . "yoh@dartmouth.edu" . "https://www.gwascentral.org/study/$1"^^ . . . "alan.bridge@isb-sib.ch" . "https://www.probes-drugs.org/compound/"^^ . . . . . "60025709"^^ . . "proco" . . . . . "Alzheimer Gene Database" . "https://fcs-free.org/fcs-database?$1"^^ . "obo" . . . . . "http://www.case.edu/EpilepsyOntology.owl#$1"^^ . . "http://purl.bioontology.org/ontology/CSP/"^^ . "nbrc" . "^\\d+$"^^ . . . . . "nb2018006591"^^ . . . . . . "ontology" . "ga4ghdos" . _:Nad2f9fd8a95c45bf99bbdc790171afb0 "Usha Mahadevan" . "0000006"^^ . . "centrally registered identifier" . . "Units of measurement ontology" . . "afo" . . "ontology" . "Dataset"^^ . . . "Uniprot Core Ontology" . "Interlinking Ontology for Biological Concepts" . . "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"^^ . . "^[0-9]*\\.*[0-9]*$"^^ . . . . . "dna" . . . . . . . "life science" . "^[1-9]\\d{0,6}$"^^ . "European Genome-phenome Archive Dataset" . . "1398574"^^ . "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype."^^ . . "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models."^^ . . . . . . . . . "nif.dysfunction" . . "Homology Ontology" . "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals."^^ . . . . "animal genetics" . . . "drosophila" . . . . . . . . "false"^^ . "pathway" . . "fair" . . . . . . . . "EDAM Data" . "biomedical science" . . "^\\w{14}$"^^ . . "^KIAA\\d{4}$"^^ . . . . "chebi"^^ . "https://swissmodel.expasy.org/repository/uniprot/$1"^^ . "medicine" . "9"^^ . . "102l"^^ . . "^[A-Za-z0-9]+$"^^ . . . . . . . "false"^^ . "stato" . . . . "preclinical studies" . . "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/"^^ . . . . "DBLP author ID" . "parasite" . . "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . "nicolas.terrapon@univ-amu.fr" . . . "esldb" . . "genomics" . "http://uri.neuinfo.org/nif/nifstd/sao$1"^^ . . . . "false"^^ . . . . . "^\\d+$"^^ . "structure" . "Sigma Aldrich" . . "unpd" . . . "FuncBase Mouse" . . . . . "037727"^^ . . "Authorea author ID" . . "Schema for the export of the Bioregistry as RDF"^^ . "BioStudies database" . "ontology" . . . "false"^^ . . . . . "Os01t0883800-02"^^ . . . . "IntAct provides a freely available, open source database system and analysis tools for protein interaction data."^^ . . . . . . . . . "mediadive.medium" . . "https://signor.uniroma2.it/relation_result.php?id="^^ . . . . . "Adam Godzik" . "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry."^^ . . . . . _:Nb17ffaa62b3744119234c8e614e3fe61 "af8d@nih.gov" . . . "mf" . "people/11035"^^ . "http://arabidopsis.org/servlets/TairObject?accession=AASequence:"^^ . . . "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]"^^ . "^R\\d+$"^^ . "ARP-1513"^^ . "diet" . . . . "Ekaterina Chuprikova" . "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity."^^ . . "false"^^ . "nawrocke@ncbi.nlm.nih.gov" . "^M\\d+$"^^ . "subject agnostic" . "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene."^^ . "caro" . . . . . . "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research."^^ . . "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no="^^ . . . . "pathway" . "viralzone" . "1"^^ . "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"^^ . . . . . . "^TIGR\\d+$"^^ . _:N4abb5ec25bc84b7794aa116c6e227a95 "Chebi Administrators" . "http://purl.org/obo/owlEOL_$1"^^ . . "epo" . . "BEI_Resources" . . "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^ . . . . . "Chemical Methods Ontology" . "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]="^^ . . . . "fairsharing.user" . . . "http://www.pharmgkb.org/disease/$1"^^ . . "matrixdb.association" . "ISBN-10" . . "YMDB00001"^^ . . . . . . "dhowe@zfin.org" . "false"^^ . . . . . "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study."^^ . "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"^^ . "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$"^^ . . "https://horizondiscovery.com/en/search?searchterm="^^ . "^TA\\d+$"^^ . "https://europepmc.org/article/ppr/"^^ . "An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)"^^ . . . . . . . . . . "Robert Court" . . . "14"^^ . . . . . . . . "corrdb" . . . . . . . . . . . "https://www.biozol.de/en/product/$1"^^ . "agriculture" . . . . "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains."^^ . . "false"^^ . "http://www.pseudomonas.com/feature/show/?locus_tag="^^ . "^\\d+$"^^ . . . "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"^^ . . "Célia Michotey" . "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier."^^ . . "false"^^ . . . "obo" . . . . . "https://bioregistry.io/metaregistry/prefixcommons/"^^ . . . . . "MMP0523"^^ . . . . "OECD Harmonised Templates" . . . . . "Assembling the Fungal Tree of Life - Taxonomy" . "^oai\\:cwi\\.nl\\:\\d+$"^^ . . . . "false"^^ . "http://purl.obolibrary.org/obo/APOLLO_SV_$1"^^ . . . "LexicalMatching"^^ . . . . . . "false"^^ . . "^[A-Z_a-z]+$"^^ . . "https://dblp.org/pid/$1"^^ . . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_br_"^^ . . "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information."^^ . . . . "false"^^ . . . "smiles" . "microbiome" . . "faseb list" . . . "geographical location" . . . . . . . "https://github.com/biolink/biolink-model" . . "10343835"^^ . . "ambystoma" . "Jim Balhoff" . . . . . . "MAM01234c"^^ . "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles."^^ . "http://sweetontology.net/matrMineral/$1"^^ . . "life science" . "obo" . . . . "^\\d+$"^^ . "0000052"^^ . "data model" . "obo" . . . "mirbase.family" . "lcnafid" . "false"^^ . . . "henrich@embl.de" . "pocketome" . . "false"^^ . . "^\\d{7}$"^^ . . . . "Jingshan Huang" . . . . . . . . "obo" . . "infectious disease medicine" . . "http://purl.obolibrary.org/obo/OMRSE_"^^ . . . . "Disease Class" . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . "odc.sci" . "https://www.sharkipedia.org/traits/"^^ . "^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$"^^ . . "The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation."^^ . . "RiceNetDB Gene" . "760050"^^ . . "SED-ML model format" . . "LIPID MAPS" . . . . _:N99631d09d986422da1d50c116ee97530 . "TCTR20230429001"^^ . . . . . . . "jeetvora@gwmail.gwu.edu" . "agriculture" . . "http://antibodyregistry.org/AB_"^^ . "https://www.datanator.info/metabolite/"^^ . "0000001"^^ . . . _:N7f6fc0e00f37489aa7d35d8d331533dc "Frédérick Giasson" . . . "gene" . . . "reproduction" . . . . . . "Zazuko Prefix Server" . . "false"^^ . . "frbr" . "taxonomy" . "phenotype" . "life science" . . . . . "EcoLexicon" . . "Information for ligand groups (chemical classes)."^^ . "false"^^ . "0000049"^^ . "BOLD Systems taxon" . . "true"^^ . . . . "ecology" . . . . . . "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"^^ . "Sean May" . _:N41f3ae9625fb413e8d7851b179f42388 "helpdesk@cropontology-curationtool.org" . . "life science" . . . "^(MAM\\d{5}\\w)|(MAR\\d{5})$"^^ . "relations" . "http://purl.obolibrary.org/obo/YPO_"^^ . . . . . "botany" . . . . "genome" . "Kelly T. Hughes" . "Zenodo" . . . "imke.tammen@sydney.edu.au" . "landreshdz@gmail.com" . . "false"^^ . . "Vertebrate Taxonomy Ontology" . "Oryzabase Strain" . . "^(bmr|bmse|bmst)?[0-9]{1,6}$"^^ . . . "^\\w+$"^^ . "Collection" . "http://topdb.enzim.hu/?m=show&id="^^ . "diagnosis" . "biology" . "David Eisenberg" . . . . "http://purl.obolibrary.org/obo/COB_$1"^^ . "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world."^^ . "iresite" . "2022.07.08.499378"^^ . "NIF Gross Anatomy" . "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1"^^ . . _:N5fc61388a1f34b48a985d50eb5fef93d "helpdesk@cropontology-curationtool.org" . "glycomics" . "^\\d{7}$"^^ . "0000032"^^ . "A database-specific registry supporting curation in the Gene Ontology" . "NCBI_gi" . "dictyBase Expressed Sequence Tag" . . . "Curated Drug-Drug Interactions Database - Drug" . "medicine" . . . "false"^^ . . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID="^^ . "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules."^^ . . "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code="^^ . "https://go.drugbank.com/reactions/"^^ . "https://www.perkinelmer.com/searchresult?searchName=$1"^^ . . "^\\d{7}$"^^ . "omit" . . "http://purl.obolibrary.org/obo/OGI_$1"^^ . . "0000025"^^ . "rna" . "neurobiology" . "ontology" . . . . . . "iedb" . "http://purl.obolibrary.org/obo/ERO_"^^ . . . "GeoNames" . . . . "rare disease" . "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"^^ . . . . "NCITm" . "mao" . "Protein covalent bond" . "Vienna Drosophila Resource Center" . . . . . . . "229"^^ . . . . "0000187"^^ . . . "NeuroNames" . "^S\\d+$"^^ . . "PWY3O-214"^^ . "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da)."^^ . . . . . "taxonomic classification" . "http://www.begdb.com/index.php?action=oneMolecule&state=show&id="^^ . . "ogsf" . . . "life science" . . . "Beta Cell Biology Consortium" . "B00162"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_$1"^^ . "^\\d{5,6}$"^^ . "jt6@sanger.ac.uk" . . "http://viroligo.okstate.edu/main.php?vid="^^ . "supply" . . . . "Foundational Model of Anatomy" . "life science" . . "nihreporter.project" . . "life science" . . . . . . "goa" . . "metadata" . "PWY-1042"^^ . "http://www.w3.org/2003/01/geo/wgs84_pos#"^^ . "2200950"^^ . . . . "oai:cwi.nl:4725"^^ . . "pathway" . . "false"^^ . . . . . "0000001"^^ . . . "G-Rich Sequences Database" . . "false"^^ . "Open Digital Rights Language Ontology" . . . . "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^ . "false"^^ . "umbbd.reaction" . . . "https://www.ncbi.nlm.nih.gov/pubmed/"^^ . . "CNBG_0001"^^ . . . "Ontology for Biobanking" . . "false"^^ . . "REACT" . "Cell line collections (Providers)"^^ . . . "http://purl.obolibrary.org/obo/INO_$1"^^ . . . "^\\d+$"^^ . _:N1d19e00ba7954d99888290da420c49d2 "William Bug" . "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release."^^ . . . "plant genetics" . . "giant.plankton@gmail.com" . . . . "http://purl.org/spar/biro/$1"^^ . . "ontology" . . . . . . "chemistry" . "TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)"^^ . . . . . . . . . . "obo" . . "trichdb" . "apd" . "eff796f3-6195-11e5-8ac5-06603eb7f303"^^ . . . . "https://www.ebi.ac.uk/intact/interaction/$1"^^ . . "genomics" . "Chris Mungall" . "larvae" . . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"^^ . . "http://purl.obolibrary.org/obo/EHDAA_$1"^^ . "UniProt Resource" . "A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids."^^ . . . . _:N67bba369e0514790a627d10e8fd5af6d . . . . . "ontology" . . . . . . . . "https://dcmi.github.io/openwemi/ns#"^^ . "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"^^ . . "metabolomics" . "false"^^ . . . . "kcoyle@kcoyle.net" . "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:"^^ . . . "022586"^^ . . "mouse" . . . . . "Alejandra Gonzalez-Beltran" . . . . . . . . "Bio-MINDER Tissue Database" . . . "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1"^^ . . "^MTBLS\\d+$"^^ . . . "MobiDB is a database of protein disorder and mobility annotations."^^ . _:Nb22dfd61607942bdbd6c144a3383a12a "helpdesk@cropontology-curationtool.org" . . . "National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]"^^ . . . . "^MIMAT\\d{7}$"^^ . "^\\w+$"^^ . . "genomics" . . . . "false"^^ . . . . "ontology" . "68513255-fc44-4041-bc4b-4fd2fae7541d"^^ . . . . . . . "David Wishart" . . "gene" . . . . . . . "2GC4"^^ . "UTRdb" . "egon.willighagen@maastrichtuniversity.nl" . "Agilent Probe" . "http://purl.obolibrary.org/obo/DC_CL_$1"^^ . "0000108"^^ . . . . . . "53504"^^ . "false"^^ . . . . . "Regulation of Transcription"^^ . . . . . . . "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^ . "leen.vandepitte@vliz.be" . . "sequenced strain" . . "eukaryotic Subcellular Localization database" . . . . "SNOMEDCT_US_2023_03_01" . . . . "NIH Human Embryonic Stem Cell Registry" . . . . . . "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l="^^ . "Pharmacogene Variation Consortium" . . . "false"^^ . . . . . . "CUT"^^ . . . "true"^^ . . "ontology" . . . . . "^\\d+$"^^ . "miriam" . "false"^^ . . . "2244"^^ . . . . . "PXD000440"^^ . "http://purl.obolibrary.org/obo/$1"^^ . . . . . . . . . . "ftt" . "rat" . "2224"^^ . . "pharmgkb.disease" . . "genetic disorder" . . "TTHERM_00648910"^^ . . . . "biostudies" . . "^IHW\\d+$"^^ . "^[A-Z0-9*:]+$"^^ . "^\\d{7}$"^^ . . "false"^^ . . . . "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolites."^^ . . "genomics" . "Human ancestry ontology for the NHGRI GWAS Catalog"^^ . "Conferences in EasyChair"^^ . "poro" . . "false"^^ . . . "gene" . . "Molecular Modeling Database" . . . . "false"^^ . "false"^^ . . "false"^^ . . . . "^\\d+$"^^ . "nif.grossanatomy" . . "00100037"^^ . "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication."^^ . "^\\d{7}$"^^ . . "^\\d+$"^^ . "JWS Online" . . . . . . . . "iclc" . . . "false"^^ . . "small molecule" . . . "bcp47" . "^\\d+$"^^ . . . "fluticasone"^^ . "false"^^ . . . . . . . "1351341"^^ . . "false"^^ . "^IS\\w+(\\-\\d)?$"^^ . . . . "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language."^^ . . . . "ontology" . . . . . "40000617"^^ . . "cmecs" . . "^\\d+$"^^ . "Semantic Mapping Vocabulary" . . "Name Reaction Ontology" . "false"^^ . . "Sugar Kelp trait ontology" . "Animal TFDB Family" . . "genetics" . . . . "biodiversity" . . . "http://uri.neuinfo.org/nif/nifstd/nifext_$1"^^ . . . . . . "Human developmental anatomy, abstract" . "PS" . _:N452d5df5d4174c6ea0a4aed0f83019b6 "vladimir.n.mironov@gmail.com" . "A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum."^^ . "cell lines" . . . . . . . "app-d678n-tottori"^^ . . . "life science" . "nmpdr" . "false"^^ . "false"^^ . "metabolomics" . "false"^^ . . . . . . "https://biopragmatics.github.io/providers/sdis/"^^ . "^\\d+$"^^ . . . "kegg.module" . "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^ . "9008500"^^ . . "This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from )" . "KNApSAcK" . "c.dudek@tu-braunschweig.de" . . . . "life science" . . "rna" . "false"^^ . . . . . . "disease phenotype" . "wwpdb" . "6819"^^ . . . "confident.series" . . . . . "Vincent Robert" . . "http://purl.obolibrary.org/obo/EUPATH_$1"^^ . "Histopathology Ontology" . . "xmetdb" . . "Toxic Process Ontology" . . . "Human developmental anatomy, abstract version" . . "structure" . . . . "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds."^^ . "structure" . . "http://phylomedb.org/?seqid="^^ . . "genomics" . . . . . . "Fabian Schreiber" . "false"^^ . . . "mesh.2012" . . . . "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms."^^ . "rnajunction" . "2d-page" . . . . "10087"^^ . "mavedb" . "true"^^ . "0001157"^^ . . "The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF." . . . . . "long-finned-pilot-whale"^^ . . "maya.schuldiner@weizmann.ac.il" . "ArrayMap" . . "^\\d{7}$"^^ . . "false"^^ . . "false"^^ . . . "model organism" . . . . "bioinformatics" . "hoip" . . . . . . "ontology" . . . . "DataCollection"^^ . . . . "http://www.narcis.nl/publication/RecordID/"^^ . . . . . . . . . _:N23ddc6feb53a4e3faf299933d3451260 "bert.van.nuffelen@tenforce.com" . . "https://e-cyanobacterium.org/models/model/"^^ . . . "false"^^ . . . "00000"^^ . . . . "selventa" . "williams.antony@epa.gov" . "ontology" . . . . . "https://www.disprot.org/idpo/IDPO:$1"^^ . . . "http://www.xmetdb.org/xmetdb/protocol/"^^ . "lincs.protein" . "identifiers.namespace" . . "false"^^ . "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes."^^ . "nmrshiftdb2" . . . "Christine Pourcel" . "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^ . . "Fossilworks Taxon" . . . . . . . . "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols."^^ . "human geography" . "phylogenetics" . . . "data management" . . . . "vsmo" . . "henriette007@ebi.ac.uk" . . . . "11"^^ . . . . . . . . "3639"^^ . "knowledge and information systems" . "Entrez Gene" . . "PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains."^^ . "^(c|k)\\d{7}$"^^ . "https://entomology.ca.uky.edu/content/$1"^^ . . . "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^ . . . "emapa" . . "Drug Central" . . . . "^\\d{9}$"^^ . . . . . . "false"^^ . . . "0440"^^ . "^ACH-\\d+$"^^ . . . "false"^^ . . . "PF11_0344"^^ . . "AT1G01030.1"^^ . "https://go.drugbank.com/salts/"^^ . "molecular biology" . . . . "umbbd.enzyme" . "virology" . . . . . . . . . "methods" . _:N92e5ed142870468bac61f5ddc8c2e9ba "bgee@isb-sib.ch" . "health science" . . . "KEGG Drug" . "ohmi" . . . . . "modularmassactionprimer"^^ . . "^\\d{7}$"^^ . . "computer science" . "dna" . "genome" . "Rodent Unidentified Gene-Encoded Large Proteins" . . . . "anatomy" . "dna" . . . . "metadata" . "study design" . . "Fab.Schreiber@gmail.com" . . . "F45.21"^^ . . . . . "OBO Foundry" . . "asrp" . . . . "nif.std" . . . "E-MTAB-2037"^^ . "http://geneontology.org/docs/gene-product-information-gpi-format/#"^^ . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid="^^ . "http://lincsportal.ccs.miami.edu/cells/#/view/"^^ . . . . "ecyano.model" . . . . . "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules."^^ . . . "http://purl.obolibrary.org/obo/MICRO_"^^ . . . . "mmmp:biomaps" . "DrugBank Metabolite" . . "workflow" . . "Scopus affiliation ID" . "minid" . "false"^^ . . "immune system" . . . . . . "00000000"^^ . . . . . . "GenInfo Identifier" . . . . . . . . . "phenotype" . . "nucc.characteristic" . "SNOWMEDCT" . . "https://www.cellosaurus.org/CVCL_$1"^^ . . "idocovid19" . "genome" . "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive)."^^ . "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . "M1"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_cell_"^^ . . "http://purl.obolibrary.org/obo/RS_$1"^^ . "food" . . "false"^^ . . . . "fair" . "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."^^ . "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee."^^ . "decimal"^^ . "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies."^^ . . "https://cropontology.org/rdf/CO_341:"^^ . . . . "worldavatar.kin" . . . . . . . "false"^^ . . . . "false"^^ . . "ontology" . . . . "obo" . "genome" . "4DN" . . . . . . . "MAR11851"^^ . "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment."^^ . . . . . . "functional genomics" . . "false"^^ . . "K"^^ . "KEGG Genes" . . "igrhcellid" . . . . . "molecular interaction" . . . "http://purl.obolibrary.org/obo/UO_"^^ . . "forest management" . "jws" . . . . "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"^^ . "ontology" . . "Intelligence Task Ontology" . . "e999"^^ . . . . . . "http://uri.neuinfo.org/nif/nifstd/oen_$1"^^ . "Asiyah Yu Lin" . . "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^ . "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . "http://modelseed.org/biochem/reactions/"^^ . . "biodiversity" . "NHMRC Australian PhenomeBank" . . . . . . . "experimental measurement" . . . "http://purl.obolibrary.org/obo/kestrelo_"^^ . . . . . "ontology" . . "grid" . . "dbo" . . . . "bibliometrics" . . . "sequence" . . . "NP_003997.1:p.Trp24Cys"^^ . . . . . "disease" . "^\\d{7}$"^^ . . . "ontology" . "https://bioregistry.io/collection/$1"^^ . "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID="^^ . "FAIRsharing User" . . . "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . . . . . . "Steven E. Wilson" . "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$"^^ . "false"^^ . "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term="^^ . . "famplex" . . . "Agronomy Ontology" . "^\\d{6}$"^^ . "Xenopus Phenotype Ontology" . . . . . "jmg11@cam.ac.uk" . . . . "physical geography" . . . . "arXiv" . "biomedical science" . "SIDER Drug" . "Zebrafish Experimental Conditions Ontology" . "A10BA02"^^ . . . . "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^ . . . "https://tetrahymena.vet.cornell.edu/display.php?stockid="^^ . "^\\d{6}$"^^ . . "datacommons" . . "false"^^ . . . . . . . . . . . . . . . "https://www.grid.ac/institutes/$1"^^ . . . "chmo" . . . "false"^^ . "population dynamics" . . . . "HIP000030660"^^ . "false"^^ . . "https://w3id.org/oc/meta/"^^ . "false"^^ . . "gene prediction" . . "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively."^^ . "WoRMS-ID for taxa" . . . "phylogenomics" . . "electronic health record" . "An ontology to standardize research output of nutritional epidemiologic studies."^^ . . . . "AU124"^^ . _:Nb22dfd61607942bdbd6c144a3383a12a . "false"^^ . "http://purl.obolibrary.org/obo/PPO_"^^ . . . "clinical studies" . "The Bibliographic Ontology" . "http://www.fairsharing.org/ontology/subject/SRAO_"^^ . "https://cropontology.org/rdf/CO_323:$1"^^ . . . . "ontology" . "0000055"^^ . "false"^^ . . . . "Steven G. E. Marsh" . "ontology" . . . . . "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT="^^ . . . . . "http://purl.org/gc/"^^ . . "vw253@cam.ac.uk" . "http://www.jcvi.org/mpidb/experiment.php?interaction_id="^^ . . "true"^^ . . . . "PMID" . . . _:Nd34bbd7daf4e4f95b69eabbbfbb1663c "J.Bard@ed.ac.uk" . . "https://ensaiosclinicos.gov.br/rg/"^^ . "Gene Ontology Database references" . . . . . "98034"^^ . . . "cell regeneration" . "false"^^ . "https://omabrowser.org/oma/hog/HOG:"^^ . . . "^\\d+$"^^ . "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$"^^ . "false"^^ . . "genome" . . . "Ximbio" . "^\\d+$"^^ . "0000138"^^ . . . . "datanator.metabolite" . . "culture" . "Yeast Searching for Transcriptional Regulators and Consensus Tracking" . "PD10000"^^ . . . "https://civicdb.org/links/evidence/$1"^^ . . . "ontology" . . _:N675fee80caff42db81030ecf60b6eab2 "Pat Brooks" . "Ontology of Biological Attributes" . "Identifiers.org Terms" . . . . . "panther.node" . . "life science" . . "doi"^^ . "^\\w+$"^^ . . "http://isbndb.com/search-all.html?kw=$1"^^ . . . . . . . . . . "dommino" . . . "http://purl.obolibrary.org/obo/CIO_$1"^^ . . . "https://www.scopus.com/authid/detail.uri?authorId=$1"^^ . "^PRO_[0-9]{10}$"^^ . "Circular double stranded DNA sequences composed" . . . . "Golm Metabolome Database Profile" . . "Sabrina Toro" . "drug" . . "projects_to"^^ . . . . "false"^^ . . . "dna" . . . . . "jrsmith@mcw.edu" . . "http://ensembl.org/glossary/ENSGLOSSARY_$1"^^ . . "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team."^^ . . . . . . "0000003"^^ . . . . "KEGG DRUG" . "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . . . "subject agnostic" . . . . . "drug discovery" . "multicellds.collection" . . "https://neurovault.org/images/"^^ . . . . "ArchDB" . . "1-FEH+w3"^^ . . . . . . . . "life science" . . "https://portal.issn.org/resource/ISSN/$1"^^ . "http://purl.obolibrary.org/obo/BCO_"^^ . "false"^^ . "https://www.e-cyanobacterium.org/bcs/entity/$1"^^ . "ico" . "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$"^^ . "FR-FCM-ZYGW"^^ . "^[0-9]+$"^^ . . . . "false"^^ . "plant phenotypes and traits" . . . "CharProt" . . . . . "obo" . "bel" . . . . . . "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"^^ . . . . . . . "chemical entity" . . . . . . "Human Proteome Map Peptide" . "http://purl.obolibrary.org/obo/OGSF_"^^ . . . . "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$"^^ . . . . . . . . . . . . "Yaroslav Halchenko" . "Resources used in the semantic web, drawing from lists in [BioContext](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) and [LinkML](https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/linked_data.curated.yaml) as well as W3C recommendations." . "https://scicrunch.org/scicrunch/interlex/view/ilx_"^^ . "Veterinary Substances DataBase" . "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . . . . . . . . "false"^^ . "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_"^^ . . . "cytology" . "https://bioregistry.io/flybrain.ndb:"^^ . . . "http://purl.dataone.org/odo/SENSO_"^^ . "Terence D. Murphy" . . . . . . . . . "aspgd.locus" . . "gene expression" . . "The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members."^^ . "https://go.drugbank.com/metabolites/$1"^^ . . . . . "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data."^^ . . "false"^^ . . . "Philipp Bucher" . "HsapDO:0000004"^^ . "false"^^ . . . . . . "phenotype" . "genome" . "murine" . "^\\d+$"^^ . . . . . "pictar" . . . . . "PlasmoDB" . "RNA Modification Database" . . "lucas.leclere@obs-vlfr.fr" . "nucleotide" . . "matrixdb" . . . . "georgeta.bordea@u-bordeaux.fr" . . "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"^^ . . "https://uniresolver.io/#did:"^^ . "life science" . . . . _:Nc42a19a78be84c6a84585e4d75f98e29 "sschurer@med.miami.edu" . . . "hivreagentprogram" . . "iECABU_c1320"^^ . . "1.10.8.10"^^ . _:N02215f8b79c94205b423321cccd2c962 . . . . . "0000574"^^ . . . . "ontology" . . "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . . . "ontology" . "disease" . "https://w3id.org/babelon/$1"^^ . . . . . . "xao" . . . . "https://biopragmatics.github.io/providers/scomp/"^^ . . . . "mouse" . . . "false"^^ . "NCIT" . . "http://sabiork.h-its.org/newSearch?q=ecnumber:"^^ . . . . . . . . "^\\d+$"^^ . "Rat Genome Database" . "false"^^ . "http://purl.obolibrary.org/obo/PROCO_$1"^^ . "http://purl.obolibrary.org/obo/RoleO_$1"^^ . . "0107180"^^ . . "gold standard" . "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains."^^ . "https://rnacentral.org/rna/$1"^^ . . . "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^ . "CCLE_867"^^ . "http://w3id.org/nkos/$1"^^ . . "false"^^ . . . . . . . "ontology" . . "Pathogen Host Interaction Phenotype Ontology" . . "genomics" . "YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references."^^ . . "^[a-z0-9\\_]+$"^^ . . "fma" . . "http://purl.obolibrary.org/obo/RBO_$1"^^ . . . "virology" . . "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . . . . . . . "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"^^ . . "https://bioregistry.io/skm:"^^ . "Andreas Ruepp" . "^\\d{4}$"^^ . . . . "http://www.kegg.jp/entry/"^^ . "false"^^ . . "164750"^^ . . "bioinformatics" . "00000001"^^ . "false"^^ . . . "false"^^ . . "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID="^^ . . . "http://purl.obolibrary.org/obo/CDNO_"^^ . "false"^^ . . . . . . "genome" . "developmental biology" . "sedml.format" . . . "ontology" . "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$"^^ . "^\\d+$"^^ . "https://cropontology.org/rdf/CO_320:"^^ . "https://www.nextprot.org/term/FA-"^^ . . . . . . . . . . . . "https://www.wikidata.org" . . "Germplasm Resources Information Network" . . . . . "agsd" . "ontology" . "https://www.ebi.ac.uk/ega/studies/"^^ . . . . . . . . "HS000015122"^^ . . . . "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO="^^ . . . . "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$"^^ . . "http://purl.org/ontology/bibo/"^^ . "0400109"^^ . "false"^^ . . . . . . . "^[a-f0-9]+$"^^ . . . ""^^ . "ega.dataset" . . . . . . . . "Soybean ontology" . . . . . . . "^ISRCTN\\d+$"^^ . "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities."^^ . . . . . "life science" . . . . "protein" . . "ontology" . . . . . "http://purl.org/cerif/frapo/$1"^^ . . "^[0-9]+$"^^ . _:Nc8116353cdbb47418cccd7d79b6ca2a2 "slarson@ncmir.ucsd.edu" . "structure" . "obo" . . . _:Nfc145c4b3c9440d782e6e175eb21b434 . "citation" . . . "^\\d{7}$"^^ . . . . . . . . . _:N99631d09d986422da1d50c116ee97530 "Pierre Sprumont" . . . "agriculture" . . . . . "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"^^ . . . . . "mlc" . "SRS086444"^^ . "Arctic Data Center Academic Disciplines Ontology" . "bioinformatics" . "https://cropontology.org/rdf/CO_340:"^^ . "obo" . "maglott@ncbi.nlm.nih.gov" . "^\\d+$"^^ . . . "A database for Triticeae and Avena gene symbols."^^ . "ettensohn@cmu.edu" . . . . . . . "dna" . . "phenxtoolkit" . . "http://www.scopus.com/record/display.url?origin=inward&eid="^^ . . "span" . "obo" . . . "global health" . . . . . . "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$"^^ . . . . . "uniref" . "image" . "PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored."^^ . . . . . . . . . . . "kegg.glycan" . "00000014"^^ . . "https://goldbook.iupac.org/terms/view/$1"^^ . "false"^^ . . . . . "ons" . "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels."^^ . "ncithesaurus" . . . "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^ . . "molecular neuroanatomy resource" . "PhosphoSite Site Group" . . "Represents chemical kinetic reaction mechanisms."^^ . . . "ontology" . . . "life science" . . "crisprdb" . . "https://bioregistry.io/odor:"^^ . "https://www.checklistbank.org/dataset/3LR/taxon/$1"^^ . "Biolink Model Registry" . . . "http://search.sisuproject.fi/#/variant/$1"^^ . "https://bioregistry.io/hivreagentprogram:"^^ . . . . "Coronavirus Infectious Disease Ontology" . "medicine" . "https://www.ncbi.nlm.nih.gov/gene/"^^ . . . . . . . "^\\d{7}$"^^ . . . . "genome" . "dc.elements" . . "false"^^ . . "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location."^^ . . . _:N80f4a0195df04675932685e7c74132f3 "willisj@mail.nlm.nih.gov" . . "anatomy" . . . . "https://cells.ebisc.org/"^^ . . . "http://purl.obolibrary.org/obo/MAO_$1"^^ . "sasap" . "http://purl.obolibrary.org/obo/XCO_"^^ . "36010371"^^ . "http://www.w3.org/ns/odrl/2/$1"^^ . . . . "AY109603"^^ . . . "^\\d+$"^^ . "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^ . . . . "Regulation of Gene Expression Ontology" . . . "Janna Hastings" . . . . . . . "mathematical model" . . "protein interaction" . "biodiversity" . . . "ontology" . . "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands."^^ . . . . . . "Drivers of human diseases including environmental, maternal and social exposures."^^ . "health science" . . "cell" . "prodom" . . . . . . . "nlx.cell" . . . "preclinical studies" . . "blast" . "https://depmap.org/portal/cell_line/"^^ . . "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id="^^ . . "ProGlycProt" . . . "google.book" . "rbo" . . "High-quality Automated and Manual Annotation of microbial Proteomes" . . _:Nb442475fa3224b19bb8053380c939eec . . . "FDA Submission Tracking Number" . . "^CHEMBL\\d+$"^^ . . "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . "https://www.ncbi.nlm.nih.gov/nucest/"^^ . . "gear" . "dinto" . "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^ . "earth science" . . "obo" . "Human Developmental Stages" . . "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki."^^ . "DrugBank Target v4" . . "obo" . "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions."^^ . . . . . "4349895"^^ . "biology" . . . "http://purl.obolibrary.org/obo/UPHENO_"^^ . . "false"^^ . . "PTHR12345"^^ . "drug name" . . . . . . . . "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse."^^ . "false"^^ . . . "life science" . "ICEberg integrative and conjugative element" . "genome" . . . . . "25011"^^ . . . . . . . . "false"^^ . "rnamod" . . . . "obib" . . . . . "Richard Boyce" . . . "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. \"Inheritance\" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method × object of research."^^ . . . . "https://data.oncomx.org/OMX_$1"^^ . . . . . "cazy" . . . . . "luana.licata@gmail.com" . . . . . . "A comprehensive compendium of human long non-coding RNAs"^^ . . . . . "interaction" . . . . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME"^^ . "false"^^ . . . . . . . . . "chemical entity" . . "true"^^ . . . "https://omim.org/MIM:PS$1"^^ . . "Genetic Testing Registry" . "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence."^^ . "11303"^^ . "^\\d{7}$"^^ . "MULT_4_VAR1_bovine"^^ . . . "MNXR101574"^^ . . . "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome."^^ . . . "Australian New Zealand Clinical Trials Registry" . "cito" . . "Alberto Traverso" . . . "MJoachimiak@lbl.gov" . . "frbr" . "_space_group_symop.operation_xyz"^^ . . . . "false"^^ . . "obo" . . "HMDB" . "xsd" . . . "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry."^^ . "Paul Schofield" . . . . . "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite."^^ . "empiar" . . "https://biopragmatics.github.io/providers/diseaseclass/"^^ . _:Ne1468601788e47eca2b22312b36a1bba "data@food.gov.uk" . . . . "Mechanism, Annotation and Classification in Enzymes" . "biomedical science" . . . . "ucsc" . "ctcae" . . "antibodies" . . . . . . . . . "life science" . . . "ontology" . "drugs" . . . "obo" . "alzheimer's disease" . "gene" . . "clustering" . "2"^^ . "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"^^ . . . "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^ . . . "storedb.file" . . . . "true"^^ . . "IMGT/PRIMER-DB" . . "Sam Griffiths-Jones" . . "ICD9CM_2006" . "ontology" . . "^\\w+$"^^ . "Interaction Network Ontology" . . . "false"^^ . . "life science" . "kcris" . . . . "VMH Gene" . "false"^^ . "ontology" . "https://bioregistry.io/resolve/github/issue/"^^ . . . . . . . . . . . . "false"^^ . . "false"^^ . "false"^^ . . . "health monitoring" . . . "j.harry.caufield@gmail.com" . . "biochemistry" . "environmental science" . "toby.gibson@embl.de" . "http://purl.obolibrary.org/obo/IDOMAL_$1"^^ . "ontology" . "^\\w{4}$"^^ . "genome" . "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^ . "0000512"^^ . "drug" . . "CRISPRdb" . "false"^^ . . . "phs000768.v2.p1"^^ . . . . . . "https://www.thermofisher.com/antibody/product/$1"^^ . . "^.+$"^^ . . "taxid" . . . . . . "false"^^ . . . . "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information."^^ . "0000000"^^ . . "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information."^^ . "National Library of Medicine Catalog" . . "false"^^ . . . "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^ . . . . . "090201"^^ . . . . . . . . . . "MolBase" . "Alzforum Mutations" . "obo" . "Heather Piwowar" . . . "langual" . . . . . . "false"^^ . . "taxonomy" . . "ontology" . "foster@uchicago.edu" . . . . . . . . . . . . "py.vandenbussche@gmail.com" . . . . . . "http://purl.obolibrary.org/obo/MI_"^^ . . . "health science" . . "chromatography" . . . . . "http://purl.obolibrary.org/obo/LIPRO_$1"^^ . . "false"^^ . . "false"^^ . . . "paul.fabry@usherbrooke.ca" . "TP53"^^ . . . . . "T01B6.1"^^ . . . "Apollo Structured Vocabulary" . . . . "protein" . "false"^^ . . "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1"^^ . . _:N865ae216243546ca96f93a846edbb7bc "Crop Ontology Helpdesk" . . . "gaog@mail.cbi.pku.edu.cn" . . . . . . . . . "https://icd.who.int/browse10/2019/en#/"^^ . . . . . "chemistry" . . . . "molecular biology" . . "chemistry" . . "false"^^ . . "rna" . . . . _:Na97d430be7184cf8b6ff1a06628e1cb0 . . "natural product" . . . . . "experimentally determined" . . "^\\d{7}$"^^ . . . . . "David S. Wishart" . "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^ . "Sharkipedia Species" . "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$"^^ . "ontology" . "https://civicdb.org/links/assertions/$1"^^ . . . . "genatlas" . . "biomedical science" . "^\\d+$"^^ . . . . . . . . . "cio" . . "false"^^ . . . . . . . . . . "ViralZone" . "Linear double stranded DNA sequences" . "ttd.drug" . . "false"^^ . . "AffyProbeset"^^ . . . . . . "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. "^^ . . . "The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan."^^ . "http://bioinfo.lifl.fr/norine/result.jsp?ID="^^ . . . "http://www.cellsignal.com/reference/pathway/$1.html"^^ . . . . . . . "351"^^ . "obo" . . . "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"^^ . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"^^ . "false"^^ . . "K00973"^^ . . "nanotechnology" . "farming systems research" . . . "^\\d+$"^^ . . "identifier of an author or reviewer, in Semion"^^ . . "ENSFM00500000270089"^^ . . . . . . "ontology" . . . "snornabase" . . "NCBI Taxonomy" . . "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification."^^ . . . . "humanities" . "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . "come" . "cthoyt@gmail.com" . . . . . . . . "http://www.genome.jp/dbget-bin/www_bget?ec:"^^ . "MMP743597.11"^^ . . "https://registry.identifiers.org/registry/$1"^^ . . . . . . . . . "ASTD" . "^\\d{7}$"^^ . "false"^^ . "zenodo" . . . . "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. "^^ . . . "^\\d+$"^^ . "transposon family" . "unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)"^^ . . "Alex Bateman" . "https://pharmacome.github.io/conso/$1"^^ . . . . . "https://molmedb.upol.cz/mol/"^^ . . . . . . "radlex" . "https://biopragmatics.github.io/providers/icepo/$1"^^ . . "^[0-9a-z]{24,24}$"^^ . "refseq" . "Frederic Bastian" . . . "CADAFLAT00006211"^^ . . . "http://metlin.scripps.edu/metabo_info.php?molid="^^ . "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.\n\nNote that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D."^^ . . "^\\w+$"^^ . . "life science" . "0000138"^^ . . "https://www.gtexportal.org/home/gene/"^^ . . _:N448b82cbd59945169b3836f32e3eefba "mike.adams@bbsrc.ac.uk" . . "mbrochhausen@gmail.com" . "100010"^^ . . . . . . . . . "Odor Molecules DataBase" . "botany" . . . . . . . . "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/"^^ . . . . . . "^\\w+$"^^ . . . "life science" . "Relation Ontology" . . . . "https://ror.org/"^^ . "epidemiology" . "rateRule"^^ . . "NCBI Gene Expression Omnibus" . "SEQF1003"^^ . . "datasubs@ebi.ac.uk" . . . . . "false"^^ . . "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest."^^ . . "Genotype-Tissue Expression" . . "biosimulations" . "https://www.ebi.ac.uk/ega/datasets/"^^ . . "https://www.kazusa.or.jp/rouge/gfpage/"^^ . . "http://purl.obolibrary.org/obo/PR_"^^ . . "https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code=$1"^^ . "^\\d{5}$"^^ . . . . "Akt_PKB"^^ . . "MAMpol005339"^^ . "jrct" . "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . . . "SUBSET_SIREN" . . "gene" . . . . "medical microbiology" . "lipro" . "genomics" . . . . "social media" . "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."^^ . "https://biofactoid.org/document/$1"^^ . . . "ontology" . "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId="^^ . . . "false"^^ . . "metascience" . "1455"^^ . "host" . . . . "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName="^^ . . . . . "https://www.ebi.ac.uk/miriam/main/"^^ . . . . . "medical informatics" . "VirOligo" . "false"^^ . . . . . . . . . "obo" . "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^ . "flu" . "epidemiology" . . "molecular entity" . "false"^^ . . . . . . . . "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1"^^ . . . . . . . . . . "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA)."^^ . . "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . "An ontology designed to support the semantic annotation of epidemiology resources"^^ . "HIX0004394"^^ . . . "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB)."^^ . "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database."^^ . "fbol" . . . . . "^\\w{3}\\d+$"^^ . . . _:N15429ae11b764183a9987e206494294c . "daniel.gautheret@u-psud.fr" . . . "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1" . _:N15429ae11b764183a9987e206494294c "mejino@u.washington.edu" . . "^\\d{7}$"^^ . . . . . . . . "https://uniresolver.io/#did:$1"^^ . . . . . . . . "edam.topic" . "MycoBrowser smegmatis" . "ontology" . . . . . . "^UP\\d{9}$"^^ . . . "glasner@svm.vetmed.wisc.edu" . . . . . "developmental biology" . . "http://purl.obolibrary.org/obo/AEON_$1"^^ . "structure" . "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/"^^ . . . . "pathway" . "The Statistical Methods Ontology" . . . . . . . . "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^ . "dorloff@ncmir.ucsd.edu" . "cath.superfamily" . . . "environmental science" . . . "obo" . . . . . . "1668761"^^ . . "false"^^ . . . . . . . . . "false"^^ . "business administration" . "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . . "biochemistry" . "https://eol.org/pages/$1"^^ . . "variation" . "ismail.fliss@fsaa.ulaval.ca" . "https://omia.org/OMIA$1"^^ . "PharmGKB" . . "http://www.w3.org/2006/time#"^^ . . "disease" . . "dna" . . . . . . "preclinical studies" . . "sequence" . "true"^^ . . . "molecular" . . . . . . . "ontology" . "cell biology" . . "Cell line collections (Providers)"^^ . "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release)."^^ . . . "disease" . . . . . . . "European Genome-phenome Archive Study" . . . . . "ontology" . . . . . . "druzinsk@uic.edu" . . "genetics" . "The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners."^^ . "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)."^^ . . . . . "A formal represention for drug-drug interactions knowledge."^^ . . . . . "Ali Syed" . "NIF Standard Ontology: Chemical" . "Medical Data Models" . "Dublin Core Metadata Initiative Terms" . "Gene Expression Ontology"^^ . . "http://purl.obolibrary.org/obo/OMP_"^^ . "drug report" . "developmental biology" . . "http://purl.obolibrary.org/obo/OGSF_$1"^^ . . . . . . . "https://github.com/semanticchemistry/semanticchemistry" . . "http://purl.obolibrary.org/obo/TADS_"^^ . . "BN000065"^^ . . "GPST000024"^^ . . . "dietary restriction" . . "false"^^ . . . . "https://prosite.expasy.org/"^^ . . . . "https://lincs.hms.harvard.edu/db/antibodies/$1"^^ . . . "miriam.collection" . . . "^\\d+$"^^ . . . . . . "https://drks.de/search/en/trial/"^^ . . . "false"^^ . . "0000001"^^ . . "false"^^ . . . "computational biology" . "ontology" . "false"^^ . . . "http://purl.obolibrary.org/obo/DRON_"^^ . . . "NCIThesaurus" . "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$"^^ . "organ" . . "jwest@rcsb.rutgers.edu" . . . . . . . . "OASIS Open Services for Lifecycle Collaboration Core Vocabulary" . . . . . . . . "interaction" . . "false"^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1"^^ . . . "gene" . "jcsd" . . . . . . . . "Cell line collections (Providers)"^^ . "2200934"^^ . "^\\d+$"^^ . . . "http://purl.obolibrary.org/obo/MIRO_"^^ . "277.9"^^ . "ontology" . "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^ . . . "The International Harmonization of Nomenclature and Diagnostic criteria" . "ontology" . "bibliography" . . . "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"^^ . "FB00000917"^^ . "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available."^^ . . "false"^^ . "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies."^^ . . "ECOLI:CYT-D-UBIOX-CPLX"^^ . _:N3b58243ab27745cdb371ab0bc0d041b0 . "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra."^^ . . "classification" . "^CA\\d+$"^^ . "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . . . . "^[0-9]+:[0-9]+$"^^ . . . . . . . . . "https://www.ebi.ac.uk/ena/data/view/$1"^^ . . "http://purl.org/sig/ont/fma/fma$1"^^ . "Chemical Component Dictionary" . . "Arun Prasad Pandurangan" . . . "4"^^ . "Gene Ontology Registry" . . . . "^URS[0-9A-F]{10}(\\_\\d+)?$"^^ . . "^XB\\-\\w+\\-\\d+$"^^ . . . "epidemiology" . . . . . . . . . . "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"^^ . "false"^^ . . "https://bioregistry.io/dragondb.allele:"^^ . "http://hpc-bioinformatics.cineca.it/fusion/cell_line/"^^ . . . . "organelle" . "UMLS CUI" . . . "Donny Winston" . . . . . "http://purl.obolibrary.org/obo/AMPHX_$1"^^ . . . . . . . "ontology" . "life science" . "false"^^ . . . . . "Apple Ontology" . . . "false"^^ . . . . . . . . "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data."^^ . . "^\\d+$"^^ . . . . "classification" . . . . . "pr" . . "life science" . . "pathology" . . . . "data model" . . . "0187632"^^ . "civic.variantgroup" . . . "genomics" . "ERM00000044"^^ . "organ" . "https://entomology.ca.uky.edu/content/"^^ . "botany" . "true"^^ . . . . . . _:Ne2eb2958e37a46608ca817d8e0d9ba50 "Tim Vandermeersch" . . . . . . "lipidmaps" . "guiderdoni@cirad.fr" . "life science" . "uniprot.keyword" . . . . . . "rna" . "http://aber-owl.net" . "rvita@liai.org" . . "http://purl.obolibrary.org/obo/NOMEN_"^^ . . . . . . . . . . "cst.ab" . . . . . . . "obo" . . . . . . . . . . "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences."^^ . . "prefixcommons" . . . . . . "1kfv"^^ . . . . . . . . . . "http://www.humanproteomemap.org/spectrum.php?pep_id="^^ . . . "MultiCellDS" . . . _:N41f3ae9625fb413e8d7851b179f42388 "Crop Ontology Helpdesk" . . . . "rs" . . . . "ucum" . . . . . . . . "pharmacology" . "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data."^^ . . "imaging" . "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes."^^ . "100000001"^^ . "^MCDS_C_[a-zA-Z0-9]{1,10}$"^^ . . . "planttfdb" . "NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4 includes robust protein predictions (NemPep4), and protein families for 63 nematode species, over 600,000 ESTs and over 250,000 proteins."^^ . "OrthoDB" . . . . "PTN000000026"^^ . . . "Basic Register of Thesauri, Ontologies & Classifications" . "life cycle stage" . . . . . . "David.Linke@catalysis.de" . "https://progenetix.org/services/ids/$1"^^ . . "ShiBASE" . "Joao Pedro de Magalhaes" . . "G. Thomas Hayman" . . . . "eol" . . . . . . "ADH1"^^ . "1374"^^ . "https://www.discoverx.com/?post_type=product&s="^^ . "http://www.signaling-gateway.org/molecule/query?afcsid="^^ . . "^\\d{7}$"^^ . . "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."^^ . . . . . . . . "Rutger Vos" . . . . "ontology" . . . . . . "CLO" . . "0000000"^^ . . "false"^^ . . . . _:Nc42a19a78be84c6a84585e4d75f98e29 "Stephan Schurer" . "sequence" . "false"^^ . "Horizon Discovery cell line collection" . . "gene expression" . . "^\\d{7}$"^^ . . . "https://metacyc.org/compound?orgid=META&id="^^ . . "http://www.w3.org/ns/rdfa#$1"^^ . . "true"^^ . "2404"^^ . "^\\d{7}$"^^ . . . . "https://w3id.org/oc/oci/$1"^^ . . "https://cropontology.org/rdf/CO_346:$1"^^ . "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"^^ . . "https://civicdb.org/links/gene/$1"^^ . "intenz" . . . . "Amazon Standard Identification Number" . . . . . "expression" . "https://bitbucket.org/"^^ . . "https://www.ncbi.nlm.nih.gov/sra/$1"^^ . . "translation_language"^^ . "xl" . "obo" . "NASC code" . . . "wormbase" . "false"^^ . . . "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id="^^ . . . . . . . . "Tanja Bekhuis" . . . . "NIA Mouse cDNA Project" . . . . . . . "Comprehensive Resource of Mammalian protein complexes" . . . . . _:N270077e13b3b43218f7bbeda7477b8a6 "Plant Ontology Administrators" . . . "obo" . "0000339"^^ . . . "https://cropontology.org/rdf/CO_321:$1"^^ . "00000180"^^ . "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . "MI0026471"^^ . "ConfIDent Event" . . . . . "false"^^ . . "false"^^ . . . . . . . . "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"^^ . "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature."^^ . "false"^^ . . "https://hl7.org/fhir/us/$1"^^ . "obo" . "tissue" . . "gro" . "https://easychair.org/cfp/topic.cgi?tid=$1"^^ . . . "statistics" . . . . "^\\d+$"^^ . . . "ontology" . . "false"^^ . "oba" . . "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^ . "biomodels.kisao" . "Molecular Signatures Database" . "https://civicdb.org/links/sources/$1"^^ . "^\\w+$"^^ . . "drug" . . "false"^^ . "phenotypes" . . . . . "obo" . . . . "ERP004492"^^ . "protein" . . "ygyingli@ncsu.edu" . . . "nsrrc" . "http://purl.obolibrary.org/obo/PO_$1"^^ . . "lang"^^ . . . . _:N560c1b9b384a4f05be40aadc76ea025d "Allen Institute for Brain Science" . "fly lines" . . . "C. elegans ORFeome cloning project" . "false"^^ . "Dylan McGagh" . "18466622"^^ . . . . . "ACM1_HUMAN"^^ . "Jeet Vora" . . "graingenes.symbol" . "knowledge and information systems" . . . . . . "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database."^^ . . "Lindsay.Cowell@utsouthwestern.edu" . "Creative Commons Rights Expression Language" . "systems biology" . "social science" . . . "ontology" . "knockout" . . . "cgd" . . . . . . . "ensemblglossary" . . . . . "false"^^ . "ontology" . . . . "https://n2t.net/$1:"^^ . . . "^\\d{7}$"^^ . . . . . . "obstetrics" . . "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1"^^ . . . . "http://cellimagelibrary.org/images/"^^ . "Lipid"^^ . . "false"^^ . . . "https://sed-ml.org/urns.html#format:$1"^^ . . . "ontology" . . . . . . . . "https://packagist.org/packages/$1"^^ . "https://repeatsdb.org/protein/$1"^^ . . "false"^^ . "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=$1"^^ . . "gene functional annotation" . "subject agnostic" . . "A public place to process, interpret and share GC/MS metabolomics datasets."^^ . "co_359" . "Neuroscience Multi-Omic BRAIN Initiative Data" . "^(HOM)?\\d{7}$"^^ . "Cell Signaling Technology Antibody" . "nucleotide" . . . . "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases."^^ . "sickle cell disease" . . "tanja.bekhuis@tcbinfosci.com" . . "https://w3id.org/nmdc/$1"^^ . "expression" . "molecular biology" . . . . "Bob Thacker" . . . "life science" . . "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al."^^ . "https://giardiadb.org/giardiadb/app/record/gene/$1"^^ . . "Paula Duek Roggli" . . . "false"^^ . . "pseudogene" . . . . . . . "Unified Medical Language System Concept Unique Identifier" . "^\\d+$"^^ . . "bibliography" . . . . . . "https://bioregistry.io/cazy:"^^ . . . "^\\d+$"^^ . "false"^^ . . . . . . . . "^\\d+$"^^ . "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails."^^ . "false"^^ . . . "https://pypi.org/project/$1"^^ . "dna" . . . . . . "gene" . . "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . . . "phenotype" . . . "hsa-mir-200a"^^ . . "161671"^^ . . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . . . "http://modelseed.org/biochem/compounds/"^^ . . . "primary health care" . . "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO)."^^ . . . . . "http://www.ebi.ac.uk/astd/geneview.html?acc=$1"^^ . . . . "Fabrice Legeai" . . . . . . "https://ensaiosclinicos.gov.br/rg/$1"^^ . . . . . . . "life cycle stage" . "kegg.ligand" . . "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . . . "pkarp@ai.sri.com" . "2023"^^ . "minid.test" . . . . "clinvar" . . . . . . . . "selventa" . . . . "subject agnostic" . . . . "^\\d+$"^^ . "obo" . . . . . . . "The cBioPortal for Cancer Genomics" . . "http://scicrunch.org/resolver/SCR_"^^ . . "SNOMECT" . . "Ramona Walls" . . "Richard John Roberts" . . . _:N3b58243ab27745cdb371ab0bc0d041b0 "American Medical Association" . . "obo" . . "Mosquito insecticide resistance" . . . . . . . . "sssom" . "Software Heritage" . "vaccine" . . . . . "genome" . . . "phenotype" . "Addgene Plasmid Repository" . . . . . . . . . "GOLD genome" . "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"^^ . . . "0000253"^^ . "Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)"^^ . . "false"^^ . . . . . . . "https://cropontology.org/rdf/CO_366:"^^ . "grouping" . "The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)"^^ . "http://purl.obolibrary.org/obo/GO_"^^ . "Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . . . . . . . . . . . . "Marie-Angélique Laporte" . "0002533"^^ . . . "cheminformatics" . "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved."^^ . . . "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns."^^ . . . "cancer" . . . . . "umbbd.compound" . . . . "biomaterial supply resource" . "http://purl.obolibrary.org/obo/PRIDE_$1"^^ . . . . "eukaryotic" . . "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome."^^ . . "co_356" . . . . . . "^WBRNAi\\d{8}$"^^ . . "protein" . . . . . "0058"^^ . . "SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome."^^ . "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."^^ . . "Edison Ong" . "classification" . . . . . "^T[A-Z]\\d{7}$"^^ . . . . . . "HBB"^^ . . . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information."^^ . "life science" . . . . . . . . "dna" . . . "kegg.drug" . "0000003"^^ . "^[1-9]\\d{5}$"^^ . . "A0014"^^ . "subject agnostic" . . . . . "MarDB includes all sequenced marine microbial genomes regardless of level of completeness."^^ . "https://www.rrrc.us/Strain/?x="^^ . "FBcv" . "structure" . "ontology" . . . . "The pattern for expanded URIs in the given resource" . . . . . . . . "inaturalist.place" . "Hugh.Shanahan@rhul.ac.uk" . . "https://bioregistry.io/vsdb:"^^ . . . "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1"^^ . . "^\\d+$"^^ . . . . . . . . . . . . "Johannes B. Goll" . . . . "Human Pluripotent Stem Cell Registry" . "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA="^^ . "http://www.t3db.org/toxins/$1"^^ . "false"^^ . . "ohd" . "false"^^ . "genetic interaction" . "2004-2820"^^ . . . . . . . "multicellds.cell_line" . . . . "^C\\d+$"^^ . . "https://dandiarchive.org/dandiset/$1"^^ . . . . . . . "uniprot.core" . . "phenotype" . "Cellosaurus identifeirs for publications, like Pubmed"^^ . . "http://purl.uniprot.org/uniprot/"^^ . "Broad Fungal Genome Initiative" . "ontology" . "http://ddinter.scbdd.com/ddinter/interact/$1"^^ . . "false"^^ . "CAS_RN" . . . "Alvis Brazma" . . . "subject agnostic" . "life science" . . "HEPRO is an ontology of informational entities and processes related to health procedures and health activities."^^ . "Werner Müller" . . "nlx.oen" . . . "http://edamontology.org/data_"^^ . . . "ontology" . . "PPR103739"^^ . "pass2" . . "false"^^ . "mbrochhausen@uams.edu" . . "dna" . . "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . . "Tiffany J. Callahan" . "false"^^ . . "Bioregistry" . . "https://www.obofoundry.org/ontology/$1" . . "foodon" . "alistair.miles@linacre.ox.ac.uk" . . . . . . "https://depmap.org/portal/cell_line/$1"^^ . . "The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)"^^ . . . "000912"^^ . . . . "mutations" . . . "life science" . . "gene" . "G8944"^^ . . "antweb" . "https://biopragmatics.github.io/providers/icepo/"^^ . "The LifeWatch ERIC repository of semantic resources for the ecological domain." . . . . "drug" . "life cycle stage" . "enzyme" . "nckyrpides@lbl.gov" . "^\\d{7}$"^^ . . . . . "01001"^^ . . "research" . . "true"^^ . "^\\d{7}$"^^ . "Stephen Randal Voss" . . "biomedical science" . . . . . . _:N1ec65468174440efa22fc2161b2bcbf1 "MedDRA MSSO" . "NIF Standard Ontology: External" . . . . . "http://purl.obolibrary.org/obo/MRO_"^^ . . _:N8e7200565e95498cbc33e59130e8e542 "J.Bard@ed.ac.uk" . "EOL Secretariat" . "false"^^ . . . "589462"^^ . . "Maximilian Haeussler" . . . . . "Bacterial Tyrosine Kinase Database" . "AP011135"^^ . . . "SwissRegulon" . . . . "one" . . . . . "leafsnap" . . . . "life science" . . . "virsirna" . . "alzheimer's disease" . _:N448b82cbd59945169b3836f32e3eefba . "life science" . . "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^ . "H-InvDb Transcript" . . . "eagle-i resource ontology" . . "nasc" . "^[a-zA-Z0-9\\-:#\\.]+$"^^ . . . "genome" . "ENST00000407236"^^ . "http://vocabularies.bridgedb.org/ops#"^^ . . . "ocid" . "false"^^ . "Person"^^ . . "D0001"^^ . "cmpo" . . "biology" . . "Wikidata Property" . "Dawood B. Dudekula" . "biomedical science" . . "Arabidopsis Small RNA Project" . . "^\\d+$"^^ . "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . . . _:N1699cf1ea2754508a32e555023a392e4 . . . "^PTHR\\d{5}(\\:SF\\d{1,3})?$"^^ . . . "https://cropontology.org/rdf/CO_359:$1"^^ . . . "ESi007-A"^^ . "software engineering" . . . . _:N3f1124850c29450a9be0c635dfd41a59 . . . . . "kwsm@dbcls.rois.ac.jp" . . . "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA."^^ . . . . . . . . . . "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download."^^ . . "Ilene Karsch-Mizrachi" . . . "ArrayExpress" . "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF)."^^ . . . . . . . "false"^^ . . . . . . . "animal" . . "agriculture" . "false"^^ . . "0001290"^^ . . . "false"^^ . . . . . "Metabolic Atlas Reaction" . "github" . . "^\\d+$"^^ . "0000001"^^ . "co_360" . "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information."^^ . "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1"^^ . . "ECCODE" . . . "Progenetix" . . "colao" . . . . "pathogen" . "microbiology" . . "^FB\\w{2}\\d{7}$"^^ . . "gene" . "kegg.metagenome" . "NLXCHEM" . . . "http://www.ebi.ac.uk/efo/EFO_$1"^^ . . "true"^^ . . "146421"^^ . "67"^^ . "http://classyfire.wishartlab.com/tax_nodes/C"^^ . . . . "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . . . . . . . . . . "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"^^ . "insdc.sra" . "string" . "blood" . "^virsi\\d+$"^^ . . "https://www-is.biotoul.fr/scripts/ficheIS.php?name="^^ . "http://purl.obolibrary.org/obo/OMIT_$1"^^ . . "ontology" . "protocol" . "false"^^ . . . . . . "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_"^^ . . "experimental measurement" . "genomics" . "https://ontology.iedb.org/ontology/ONTIE_"^^ . "structure" . "false"^^ . . "imotdb" . . "^\\d+$"^^ . "ontology" . . "N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a"^^ . . . "curies"^^ . . . "https://registry.identifiers.org/registry/$1" . . . . "alberto.traverso@maastro.nl" . . . "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data."^^ . . "^\\w.+$"^^ . . "^\\w+$"^^ . . . . "https://www.ncbi.nlm.nih.gov/protein/"^^ . . . . "resource metadata" . "gramene.taxonomy" . . . . . . . "https://aopwiki.org/events/$1"^^ . "Codon Usage Tabulated from GenBank" . "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . . . . . "false"^^ . . . . . "mfoem" . . . . "c elegans" . "http://hawaii.eagle-i.net/i/$1"^^ . . "http://purl.obolibrary.org/obo/MPATH_$1"^^ . "A controlled vocabulary to support the study of transcription in the developing human brain"^^ . . . . . . . . . "http://purl.uniprot.org/annotation/VAR_"^^ . . . . . . "sourceDateStart"^^ . . . . . . . . . . . . . . . . . . . . "sed-ml.level-1.version-1"^^ . . "obo" . "^\\d+$"^^ . . . . . . . . . "Human Endogenous Retrovirus Database" . "structure" . . "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . . "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . "vandf" . . "BioCyc collection of metabolic pathway databases" . . "^\\w\\d{4}\\w\\d{2}(\\-[35])?$"^^ . . . . . . "LIPID MAPS" . . . . . . "false"^^ . . . . . "Ontology Lookup Service" . . . . "fbsp" . "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1"^^ . "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO)."^^ . . . . . . "mass spectrometry assay" . . "phenotype" . . "handle" . . "http://purl.obolibrary.org/obo/PCO_"^^ . "Gianni Cesareni" . . "MLCommons Association" . . "http://www.imgt.org/ligmdb/view?id=$1"^^ . "false"^^ . . . . . . "Zebrafish Phenotype Ontology" . "foodb.compound" . . . "215"^^ . . . . . . "FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge."^^ . "subtilist" . . "ggplot2"^^ . . . . "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds."^^ . "63250"^^ . . . . . . "apo" . . . . "https://www.uniprot.org/database/"^^ . . . . "person" . "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram."^^ . . . . . "molecular chemistry" . "false"^^ . . "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^ . "glycomedb" . . "gold.genome" . "Terminologia Embryologica" . . . . "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi."^^ . . "MMP3312982.2"^^ . . . "phenotype" . "Person" . . . "^\\d+$"^^ . . "gwascentral.marker" . "https://omim.org/MIM:"^^ . "phenomics" . . . . . . "Database of Spatially Interacting Motifs in Proteins" . "zmp@ebi.ac.uk" . . . "ICD9_2005" . . "embryo" . . . . . . "upper-level ontology" . . "David Brodbelt" . . "TreeFam" . . . . "biology" . "^[0-9a-zA-Z\\.\\-\\_]+$"^^ . "clinical studies" . "TF101014"^^ . . "ascl" . "Gene Location" . . "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory."^^ . . . "genotyping" . . . "^TTDS\\d+$"^^ . "DI" . "hoganwr@gmail.com" . . "GO Relations" . . "https://www.kerafast.com/Search?SearchTerm="$1""^^ . . "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^ . "reaction" . . "plant" . "domain" . "PhosphoPoint Phosphoprotein" . . . . "genotype" . "genome" . . . "http://www.genomesize.com/result_species.php?id=$1"^^ . "https://www.wwpdb.org/pdb?id=$1"^^ . "https://www.fisheries.noaa.gov/species/$1"^^ . . . "Rv1908c"^^ . . "developmental biology" . . "enzymatic reaction" . . "STUDY1040"^^ . "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . . "https://bioregistry.io/polbase:"^^ . . "hc.trial" . . . . . "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes."^^ . . . . "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^ . . . "^\\d{7}$"^^ . . . . "genome-wide association study" . . "fish" . . . "http://www.treefam.org/family/"^^ . "genome" . . "General Standard for Food Additives Online Database" . . . "Toshiaki Katayama" . "DEF"^^ . . _:N44200d5f561d43b5912b0d14cadae2a0 "maria.herrero@kcl.ac.uk" . "authorList"^^ . "protein" . . "https://w3id.org/oc/corpus/$1"^^ . . . "credit" . "PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant® also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment."^^ . . . . "ontology" . "https://ssbd.riken.jp/database/project/$1"^^ . "genomics" . "Studies in dbVar."^^ . "Contains information about cells and data sheets related to transfection."^^ . . . . . . "^\\d+$"^^ . . . "Minimal Anatomical Terminology" . "The RNA Modification Database" . . . "biomedical science" . . . "1755"^^ . "galen" . . . "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^ . "http://purl.obolibrary.org/obo/TAXRANK_"^^ . "unichem" . . . . . . . "Terminology of Anatomy of Human Embryology" . . "Scopus Publication" . . . . . . . . . "false"^^ . . . "Núria Queralt Rosinach" . . . . "molecular structure" . "Daniel N. Wilson" . . . . . . . "P3DB Site" . "https://proteinensemble.org/$1"^^ . . . "00073"^^ . "false"^^ . "obo" . . . . . . . . . . "classification" . "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl="^^ . "KEGG_DRUG_GROUP" . . . "integbio" . . "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML."^^ . . . . . . . . . . . . "^\\d+$"^^ . "9-1-1 Complex"^^ . . . "^GR\\:\\d+$"^^ . . . "https://www.gbif.org/species/"^^ . . . . . "cido" . "http://purl.obolibrary.org/obo/OPMI_$1"^^ . _:N3e69e1e263a943b3837d9bf1b0810d0d . . "expression" . "dragondb.allele" . "https://www.mlcommons.org/mlc-id/"^^ . "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^ . "Lucas Leclere" . . . . . . . . "^\\d{7}$"^^ . "structure" . . . . "https://biopragmatics.github.io/providers/cvx/$1"^^ . . "false"^^ . . "col" . "true"^^ . "xml" . . . . . . . "SNCTP000005580"^^ . "iao" . . . . "0000081"^^ . . . "deustp01@med.nyu.edu" . . "Vertebrate Breed Ontology" . "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements."^^ . "241"^^ . . "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^ . . . . "^PRJ[DEN][A-Z]\\d+$"^^ . . . _:N80f4a0195df04675932685e7c74132f3 "Jan Willis, NLM" . "false"^^ . "http://www.w3.org/XML/1998/namespace#$1"^^ . "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . "computational chemistry" . . "false"^^ . . . . _:Nd34bbd7daf4e4f95b69eabbbfbb1663c . "obo" . "https://mediadive.dsmz.de/medium/$1"^^ . "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#"^^ . "Wyeth W. Wasserman" . . . . "^\\d+$"^^ . . "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors."^^ . . "https://www.kazusa.or.jp/rouge/gfpage/$1"^^ . . . . "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . . . "taxonomic classification" . . "ximbio" . . "https://archive.gramene.org/db/ontology/search?id=GR_tax:"^^ . . "false"^^ . "lei" . "gene" . . "phenomics" . "National Microbial Pathogen Data Resource" . . "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories."^^ . "The Echinoderm Anatomy and Development Ontology" . . "Mammalian Phenotype Ontology" . "obo" . "CTCAE" . "disease" . . . . "https://purl.dataone.org/odo/MOSAIC_"^^ . . . . . . "human" . . "cellopub" . . "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology."^^ . "^DBCAT\\d+$"^^ . . . "m4i" . "ValidatorDB" . "Randi Vita" . . "265912"^^ . "false"^^ . . "^\\d{7}$"^^ . "allyson.lister@oerc.ox.ac.uk" . "https://arxiv.org/abs/$1"^^ . . . . . . "NLXCELL" . . . "0002927"^^ . . "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments."^^ . . . . "false"^^ . . . "frederic.bastian@unil.ch" . "https://pubchem.ncbi.nlm.nih.gov/cell/$1"^^ . . . "false"^^ . . . "biomaterial manufacture" . . . "false"^^ . . "GeneAnnot: Microarray Gene Annotation" . "Salk Institute for Biological Studies" . "false"^^ . . . . "nembase" . . . . "re3data" . "ontology" . "false"^^ . . . . . "http://www.gramene.org/db/protein/protein_search?protein_id="^^ . . "^\\d+$"^^ . . . "millipore" . . "Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021"^^ . . . "http://arabidopsis.info/StockInfo?NASC_id="^^ . "Cell line databases/resources"^^ . . . . . "ontology" . "Protein Affinity Reagents" . . "MEROPS Entry" . . . "anatomy" . "f665230-5267"^^ . "Database portal containing replicate experiments of different assays and samples"^^ . . "berman@rcsb.rutgers.edu" . . . "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."^^ . . "http://genomics.senescence.info/genes/details.php?id="^^ . "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform."^^ . . . . . "lncipedia" . . . "https://web.www.healthdatagateway.org/dataset/$1"^^ . . . "omics" . . . "49"^^ . . "gene" . "LGCEDe-S-000002244"^^ . . "http://purl.obolibrary.org/obo/XAO_"^^ . . "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs."^^ . . . . . . "https://fungi.ensembl.org/id/"^^ . "false"^^ . . "000059"^^ . "PKDB00198"^^ . . "plant phenotypes and traits" . . . . "13GS"^^ . "easychair.topic" . . . . . . . "nif.cell" . "An ontology to represent genomics cohort attributes."^^ . . "false"^^ . "structural biology" . . . "wmk@amu.edu.pl" . . "genome" . . . . "personalized medicine" . "^\\d+$"^^ . . "0000590"^^ . . "Sequence Read Archive" . . "interaction" . "academy" . . "^\\d+$"^^ . . "MMSL_CODE" . . . "phenotype" . . . . "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level."^^ . . "false"^^ . . . . . "^MMP\\d+.\\d+$"^^ . . . . . "rna" . "ecg" . . . . "Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present."^^ . "biomedical science" . . . . "http://purl.obolibrary.org/obo/PLO_"^^ . . . . "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element."^^ . . "DBPedia Ontology" . . . . . . . "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state."^^ . "ontology" . . . "ontology" . . . . . "genome" . . . . . . . "false"^^ . . "true"^^ . "^\\d{5}$"^^ . "scop" . . . "false"^^ . . . "schemaorg" . . . . "ontology" . "^\\d+$"^^ . "^\\d{6}$"^^ . . "https://fairsharing.org/users/"^^ . . . "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories)."^^ . "mouse strain" . "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources."^^ . "false"^^ . . "http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid="^^ . . "^[\\w\\-:,]{3,64}$"^^ . "https://togoid.dbcls.jp/#$1" . . "false"^^ . . . . . . . . . . . . "http://purl.obolibrary.org/obo/APO_$1"^^ . . . . . . "ST000900"^^ . "false"^^ . "lynn.schriml@gmail.com" . . . "functional genomics" . . . "http://www.drugtargetontology.org/dto/DTO_$1"^^ . . "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_"^^ . "false"^^ . . . . . "ontology" . "Peter Midford" . . "http://purl.org/spar/cito/$1"^^ . "subject agnostic" . "^\\d{7}$"^^ . "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#"^^ . . . . . "Leafsnap" . . . . . . . . "false"^^ . . . "false"^^ . . . "MycoBrowser leprae" . . "tobias.schulze@ufz.de" . . "Uniprot ID" . . "^\\d+$"^^ . . . . . . "false"^^ . . . . . "interaction" . . . . "Leigh.Carmody@jax.org" . . "natural science" . . . "^\\w+$"^^ . "KEGG Disease" . . "https://sumlineknowledgebase.com/?page_id=$1"^^ . . "kushida@biosciencedbc.jp" . . . . . . "false"^^ . . "preclinical studies" . . . "pathway" . "rr@uga.edu" . "false"^^ . . . "^\\d{7}$"^^ . "structural biology" . . "https://dataguids.org/ga4gh/dos/v1/dataobjects/"^^ . "spbase" . "https://viperdb.org/Info_Page.php?VDB="^^ . . . "^\\w+$"^^ . . "organic chemistry" . "biology" . "^\\d+$"^^ . . . "A database of GlycoMaps containing 2585 conformational maps."^^ . "binding" . . . "^FOOD\\d+$"^^ . "ribonucleic acid" . . . "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions."^^ . . . "false"^^ . "false"^^ . "phylogeny" . . . "http://qudt.org/schema/qudt#"^^ . . . "The Mammalia Polymorphism Database is a secondary database designed to provide a collection of all the existing polymorphic sequences in the MammaliaOnline query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches)."^^ . "Environment Ontology" . . "104674"^^ . . "chromosome" . . "Li7"^^ . . "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats."^^ . . "NIH RePORTER" . . "jgraybeal@stanford.edu" . "false"^^ . . "publishing" . . . "^PACTR\\d+$"^^ . "Genotype Ontology" . . . . "false"^^ . "eukaryota" . "Topology Data Bank of Transmembrane Proteins" . "https://hdl.handle.net/hdl:20.500.12633/$1"^^ . . . "https://biopragmatics.github.io/providers/bs/$1"^^ . "ontology" . "UniProt journal" . "ontology" . . "Omar S. Harb" . . . . "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations."^^ . . . "false"^^ . . . . . . "https://cryptodb.org/cryptodb/app/record/gene/$1"^^ . . "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases"^^ . "false"^^ . . . . . . . "^\\d+$"^^ . . "Manufacturers of Vaccines" . . . . . "false"^^ . . "meddra" . "false"^^ . . . . . "http://tolweb.org/$1"^^ . . . "PubChem_Compound_CID" . "Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations"^^ . "^[A-Z]+[0-9]+(\\.\\d+)?$"^^ . "seinet" . . . . . . "protein" . "false"^^ . "http://www.co-ode.org/ontologies/galen#"^^ . . . "bpdb" . . . "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation."^^ . . "soybase" . . "ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea."^^ . . . "drug" . . "KEGG Enzyme" . . "false"^^ . "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.\n"^^ . "genomics" . "HL7 V2 Code Systems" . "environmental science" . "^LBCTR\\d+$"^^ . "Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science."^^ . . "false"^^ . "assay" . "https://go.drugbank.com/bio_entities/$1"^^ . "life cycle stage" . . "gene expression" . . . . . . . "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily."^^ . . "Plant Gall Ontology" . . . "ontology" . . . . "pandura@mrc-lmb.cam.ac.uk" . . . "life science" . "Doug Howe" . . "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . "http://www.drugbank.ca/drugs/$1"^^ . . "https://data.4dnucleome.org/experiment-set-replicates/"^^ . . . . . . . "KEGG.COMPOUND" . . "developmental biology" . "swisslipids@isb-sib.ch" . . "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"^^ . "CTRI/2023/04/052053"^^ . "geoinformatics" . . "^[A-Za-z0-9]+$"^^ . "centrally registered identifier" . . "https://www.devtox.org/nomenclature/ml_manus.php?mno="^^ . . . . "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . . "ontology" . . . "protein" . . "datanator.reaction" . . . "image" . . "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . . . . . . "dna" . "sprint" . . . . "Allotrope Merged Ontology Suite" . "protein" . . . "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. "^^ . . "stem cell" . "https://bionumbers.hms.harvard.edu/bionumber.aspx?id="^^ . . "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms."^^ . . "biomedical science" . . "ontology" . . . . "phylogenetics" . "https://sorgerlab.github.io/famplex/$1"^^ . . "false"^^ . "cp" . "false"^^ . . "Gemma L. Holliday" . "https://repeatsdb.org/protein/"^^ . "derivatives%2Fthiocyclam%20hydrochloride"^^ . . . . . . . . . . "colonatlas" . "RAP-DB Locus" . "jiezheng@pennmedicine.upenn.edu" . "ATCC(in host)" . . "ngbo" . . "genetics" . . "^\\d+\\-\\d+\\-\\d+$"^^ . . "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name="^^ . . "umbbd.pathway" . . "small molecule" . "CGH Data Base" . . "http://purl.obolibrary.org/obo/CL_$1"^^ . . _:Na8edbc95dc9943cead4287a28ea4f5dc . . . . "Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle"^^ . . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . . . _:Na498744430974b0f965343f882a62ba4 "J.Bard@ed.ac.uk" . . . "^ITMCTR\\d+$"^^ . . . "Tatsuya Kushida" . . . "NCBI Protein" . . . . . . . . . "https://europepmc.org/article/CBA/"^^ . "http://purl.uniprot.org/isoforms/$1"^^ . . "geonames.feature" . "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders"^^ . . . . "Pavel Hobza" . "^[A-Za-z0-9]+$"^^ . . . . . "bsu:BSU01340"^^ . . . "http://www.yeastract.com/view.php?existing=locus&orfname="^^ . "false"^^ . . "http://bigg.ucsd.edu/models/$1"^^ . . . "false"^^ . . "philippe.rocca-serra@oerc.ox.ac.uk" . "Coriell Institute for Medical Research" . . "life sciences" . . "false"^^ . "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^ . "http://purl.obolibrary.org/obo/EHDA_$1"^^ . "elm" . . "http://www.jstor.org/stable/$1"^^ . "Endogenous Regulatory OligoPeptide knowledgebase-Moscow" . "epso" . . "Guide to Pharmacology Target" . . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID="^^ . . . . . . . . . "^\\w+\\d+$"^^ . . "false"^^ . "http://exac.broadinstitute.org/gene/$1"^^ . . . . . . "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models."^^ . . . "Pathway ontology" . . . "TOKU-E Cell-culture Database" . . . . . . "botany" . . . "false"^^ . . . . "ontology" . . "0000008"^^ . . . "david.gloriam@sund.ku.dk" . "EBI-2307691"^^ . "col.taiwan" . "^[A-Za-z0-9]+$"^^ . . "false"^^ . . . . . "medicine" . . "gthayman@mcw.edu" . "BioGRID Interactions" . "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID="^^ . "false"^^ . . . . . . . . . . . . . . "life science" . "edam.format" . . "0000069"^^ . . "mota@i.nagoya-u.ac.jp" . . . . "citation" . "pancreatic islet development" . . . . "Contains entries for various database identifiers" . "false"^^ . . . . . . . . "http://www.nematodes.org/nembase4/cluster.php?cluster=$1"^^ . . . "classification-model"^^ . "^\\w+$"^^ . . . "structure" . "research" . . . . "^[A-Z-a-z0-9]+$"^^ . "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val="^^ . "synapse" . "life science" . . "mirnest" . . "^\\d{7}$"^^ . "https://swissmodel.expasy.org/repository/uniprot/"^^ . . . "food" . "small molecule" . "2555646"^^ . "false"^^ . . . . . . . "diagnosis" . "http://www.peptideatlas.org/PASS/$1"^^ . . . . . . . "stock" . . . . "http://purl.obolibrary.org/obo/EUPATH_"^^ . "P3DB Protein" . . . . . . "http://www.ymdb.ca/compounds/"^^ . . . . "station.6051b2f8b9142a5b8c676342"^^ . . "runbiosimulations" . . . "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"^^ . . "false"^^ . "http://physics.nist.gov/cgi-bin/cuu/Value?"^^ . "false"^^ . "http://www.kegg.jp/entry/"^^ . . "https://nsrrc.missouri.edu/nsrrc$1info/"^^ . "http://purl.obolibrary.org/obo/OGI_"^^ . . . "http://purl.obolibrary.org/obo/OMO_"^^ . . . "false"^^ . . . . . . . . . "identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)"^^ . "dgrc" . . . "resource metadata" . . "DB14938"^^ . "biochemistry" . . . . . . "pathway" . "controlled vocabularies" . "microsporidia" . . . "ontology" . "https://publons.com/researcher/$1"^^ . "mp" . . . . . "edeutsch@systemsbiology.org" . "Search Tool for Interactions of Chemicals" . . "anatomy" . . "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . "biomedical" . . . . . . . "bibliography" . "http://purl.obolibrary.org/obo/RS_"^^ . "pathway" . "http://nava.liacs.nl/cgi-bin/nava.py?id=$1"^^ . "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . . . "small molecule" . . "00001"^^ . . . . "carlo.ravagli@novartis.com" . . . . "The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are:\n\n- [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.)\n- [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC)\n- [GENCODE](https://www.gencodegenes.org/) (uses GenBank)\n- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc)\n- [STRING](https://string-db.org/) (uses UniProt)" . . "688"^^ . . . . . . "geography" . . . . . . . . . . "frapo" . . "bioinformatics" . . "00056"^^ . "Oryzabase Reference" . . . . "^\\d{7}$"^^ . . "medicine" . . . . . . . "https://e-cyanobacterium.org/models/model/$1"^^ . . "Pierre-Yves Vandenbussche" . . . . . . . "molmedb" . . . . "15567"^^ . . . . "data model" . "false"^^ . . "odor" . . "false"^^ . . . . . "SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.)."^^ . "Natural Product-Drug Interaction Research Data Repository" . "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . . . . "hagr.genage" . . . . . . . . "uo" . . "obo" . . . . "mass spectrum" . "https://cropontology.org/rdf/CO_325:$1"^^ . "protein" . "100000000000001"^^ . . . . "scopus.work" . . . "obo" . "https://www.storedb.org/?$1"^^ . . "enzymatic reaction" . . "human" . . . . . . . . . "sigmaaldrich" . . . . . "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae."^^ . "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors."^^ . . . . . "vendor" . . "hms.lincs.antibody" . . . . "DrugBank Reaction" . . . . . "assays" . . . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes."^^ . . "https://www.clinicaltrialsregister.eu/ctr-search/search?query="^^ . "genome" . . . . "spar" . . . "http://purl.obolibrary.org/obo/OBIB_$1"^^ . . . . "false"^^ . . . . . "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object="^^ . "false"^^ . "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^ . . "46"^^ . "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs)."^^ . . "^\\d+$"^^ . "protein" . . _:Nb442475fa3224b19bb8053380c939eec "willisj@mail.nlm.nih.gov" . . . "paralogous" . "biomedical science" . . . "co_350" . . "agriculture" . . . . . . "https://books.google.com/books?id=$1"^^ . . "false"^^ . "bioschemas" . "mondo" . . . "genetics" . . "owl" . "5.1"^^ . "^\\d{7}$"^^ . . . . . . "https://cropontology.org/rdf/CO_345:"^^ . . . . "life science" . "^M\\d{5}$"^^ . . . . . . . . . "FlyBase Qualifiers" . . "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^ . "obo" . . . . "https://molmedb.upol.cz/mol/$1"^^ . . . "morphology" . . "ontology" . "immunology" . . "0000046"^^ . "citation" . . "glycoepitope" . . "taxonomy" . . "Sequencing Initiative Suomi" . . . . . _:N9e47917e61904b6ca52093f043990cdc "info@who.int" . "false"^^ . . . . . . . . . "^\\d{7}$"^^ . . . "http://www.signaling-gateway.org/molecule/query?afcsid=$1"^^ . "device" . . . . . "experimental measurement" . . . . . "false"^^ . . "ncbigi" . . "3SBPLMKKVEVR"^^ . . . . . . "Ontology of Zebrafish Experimental Conditions"^^ . . "^\\d+$"^^ . "VIRsiRNA" . . . . . . . "456789"^^ . "http://purl.obolibrary.org/obo/BFO_"^^ . . "structure" . "false"^^ . . "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . . . "obo" . . . . "PdumDv" . . . . . . . "https://bioregistry.io/metaregistry/ncbi/$1"^^ . . "false"^^ . . . "life science" . . . "Plant Genome Network" . . "These are the terms that are improted for FOVT to describe vertebrate traits."^^ . "http://neuromorpho.org/neuron_info.jsp?neuron_name="^^ . . . "disease" . . . . . . . . . . "^\\d{7}$"^^ . . . . . . . "disease process modeling" . "37af84f2-bfd7-4653-b608-eaff44febba6"^^ . "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1"^^ . "http://www.genomesize.com/result_species.php?id="^^ . "154022"^^ . . . "^\\d+$"^^ . . . . "anatomy" . "protein" . . . . "0000004"^^ . . . . . . "false"^^ . . . "ontology" . "http://multicellds.org/MultiCellDB/$1"^^ . . . . "neuroscience" . . "imaging" . "http://www.orpha.net/ORDO/Orphanet_"^^ . "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"^^ . "cellosaurus" . "Observation"^^ . "false"^^ . "data integration" . . . . . "genome" . . . "http://www.gramene.org/db/genes/search_gene?acc=$1"^^ . "dna" . . . . . . . "false"^^ . "https://trialsearch.who.int/Trial2.aspx?TrialID="^^ . "diagnosis" . "Evan E Bolton" . . "973a9333-fec7-46dd-8eb5-25738f06ee54"^^ . . . . . "false"^^ . . . "http://www.bind.ca/Action?identifier=bindid&idsearch=$1"^^ . "comparative neurobiology" . . "humIGHV025"^^ . . . . . . . "genewiki" . "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . . "biochemistry" . . . . . . . . . . "ev" . . "https://bioregistry.io/gard:"^^ . "^[0-9]*$"^^ . . "life science" . . . . "^\\d+$"^^ . "0000044"^^ . . . . . . "https://biopragmatics.github.io/providers/dhba/$1"^^ . . . . . . . . . . . . "false"^^ . . . . . . . . . "mammalian" . "Evgeny M Zdobnov" . "false"^^ . . "^\\d{6}$"^^ . "geo" . _:N615b517125c946639821d2766320e103 "The World Health Organization" . "GrainGenes" . "MetaNetX reaction" . "Karen Eilbeck" . . "wujm@bjmu.edu.cn" . "post-translational modification" . "http://purl.obolibrary.org/obo/GALLONT_"^^ . . . "dblp.author" . . "report" . . . "https://prefix.cc/" . . . "image" . . . "social science" . "Golm Metabolome Database" . . . "TreeBASE" . . . . "chemistry" . "genomics" . . . "^rx[0-9]{5}$"^^ . "The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page)\nNote that the web page that resolves this trial does not correspond to the semantic space"^^ . . "centrally registered identifier" . "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1"^^ . "00042"^^ . . . "http://purl.org/spar/c4o/"^^ . . . . . . "http://erop.inbi.ras.ru/result2.php?PepName="^^ . "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO."^^ . "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances."^^ . "omics" . "Mouse gross anatomy and development, timed" . "^T3D\\d+$"^^ . . "pathway" . . . . . "phenolexplorer" . "RNAloops" . . . "https://chem.nlm.nih.gov/chemidplus/rn/"^^ . "^CLPUB\\d+$"^^ . . . . . . . "proteomics" . "https://rism.online/"^^ . . . "dermo" . "Vaccine Adjuvant Compendium" . . . "SNOMEDCT" . . "gene expression" . "rubygems" . . . "Vertebrate trait ontology" . . . "DataCite Ontology" . . . . "false"^^ . . . "false"^^ . "uniprot/swiss-prot" . . "genome" . . . "9606"^^ . . . . "00026f50-858a-446b-8ed9-b0e3ecd7b20e"^^ . "ontology" . . . . . . "^[0-9]{15}[0-9X]{1}$"^^ . "identifier for species classified under the New Zealand Threat Classification System"^^ . . "326705068"^^ . . "false"^^ . . . "1537"^^ . . "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name="^^ . . . . "UniRule" . "https://omim.org/MIM:$1"^^ . . . "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration."^^ . . "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . "^\\d+$"^^ . . . . . "sam.griffiths-jones@manchester.ac.uk" . . . . . . "Maria Gould" . . "virology" . . . . . "false"^^ . "Salmon Ontology" . . . . . . "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies."^^ . . "https://bioregistry.io/dashr.expression:"^^ . . "epcc" . . "unipathway.reaction" . . "International Protein Index" . . . . "mamo" . . "peptideatlas" . . "The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)"^^ . . "https://crates.io/crates/$1"^^ . . "MGYA00002270"^^ . "0000066"^^ . . . . "PANTHER Node" . . . . "OMIM Phenotypic Series" . . "^OSR\\d{4}$"^^ . "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species="^^ . "KG09531"^^ . "citation" . "life science" . . . . . "David Craik" . "pathway" . "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons."^^ . . . . . "protein-containing complex" . . . . . "sopharm" . . . "protocol" . . "bigg.compartment" . "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . . "xeni.kechagioglou@lifewatch.eu" . . "Amphibian gross anatomy" . "https://prosite.expasy.org/$1"^^ . . "MESH" . . "^\\d+$"^^ . "jcrb" . "http://purl.bioontology.org/ontology/HCPCS/"^^ . "gene" . . "http://hdl.handle.net/$1"^^ . . . "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use."^^ . "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease."^^ . "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family="^^ . . . "protein" . "genome" . . . "rna" . . . "https://www.ebi.ac.uk/chembl/compound/inspect/"^^ . . . . . . . "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."^^ . . . . . "Publons publication" . . "Association-Rule-Based Annotator" . . . "https://www.uniprot.org/locations/"^^ . . . "cheminformatics" . . . "International Classification of Functioning, Disability and Health" . . "1047874"^^ . . "Jianjiong Gao" . . "David Linke" . . . "andreas.ledl1@fhnw.ch" . "false"^^ . "http://www.alanwood.net/pesticides/$1.html"^^ . "^\\d{7}$"^^ . . "Chris Stoeckert" . "false"^^ . . "ensembl.fungi" . . "A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number."^^ . . . . "protein"^^ . . . . . "Genatlas" . . . . "odam" . . . . "https://mmp.sfb.uit.no/databases/marcat/#/records/"^^ . "ChEBI Data Sources" . . "^MSV\\d+$"^^ . . "true"^^ . . . . . "http://www.crop2ml.org/cropmdb/"^^ . . . "lotus" . _:Na02fc64581ae4e3a98fdb9896d829d8f . . . . "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . "genome" . "false"^^ . . . . . "false"^^ . "false"^^ . "N1899"^^ . "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . . . "false"^^ . . . . "^\\d+$"^^ . "biomedical science" . . "2639"^^ . . "Minimal set of terms for anatomy"^^ . "^\\d{7}$"^^ . "false"^^ . "CALIPHO Group Ontology of Human Anatomy" . . . "false"^^ . "LINCS Data" . . "dna" . . . . . . . "ontology" . "structural biology" . "ML0224"^^ . . . "protein" . . "https://n2t.net" . "false"^^ . "te" . "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting" . . . . "false"^^ . "deletion" . . . . . . . "^\\d+$"^^ . "https://www.glycoepitope.jp/epitopes/"^^ . "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/"^^ . . . . "https://www.confident-conference.org/index.php/Event_Series:$1"^^ . . "NX_O00165"^^ . "http://rdfs.org/ns/void#$1"^^ . . . . . . . . . . "Gazetteer" . . "Nucleic Acids Phylogenetic Profiling" . . "spike00001"^^ . "repeatsdb.protein" . "http://purl.obolibrary.org/obo/FLU_"^^ . . "ncbi.gi" . "yuki.yamagata@riken.jp" . "http://purl.obolibrary.org/obo/MSIO_"^^ . "https://cropontology.org/rdf/CO_357:$1"^^ . . . "anatomy" . . "0000080"^^ . "AmoebaDB" . "https://togoid.dbcls.jp/#$1"^^ . . . . . . . . "^e\\d+$"^^ . . . "Sebastien Moretti" . . "https://www.ebi.ac.uk/metabolights/$1"^^ . "http://purl.obolibrary.org/obo/FBcv_"^^ . . "reactions" . "Sylvie Ricard-Blum" . . . "Tb927.8.620"^^ . . . "disease" . "false"^^ . "^D\\d+$"^^ . . . "environmental science" . . "http://purl.obolibrary.org/obo/HANCESTRO_"^^ . . . "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally."^^ . "false"^^ . . . "limore" . . . . "http://purl.obolibrary.org/obo/CIDO_$1"^^ . . . . . "Biological Magnetic Resonance Data Bank" . . . . "^\\d+\\w?$"^^ . "http://terminology.hl7.org/CodeSystem/v2-"^^ . . "https://urgi.versailles.inra.fr/gnpis/#result/term="^^ . "isacorreia@tecnico.ulisboa.pt" . . "https://www.genedb.org/gene/"^^ . . "ontology" . "molecular entity" . "Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets."^^ . . "https://smpdb.ca/view/"^^ . "taxonomy" . "life science" . . . "pathobiochemistry" . . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id="^^ . . "preclinical studies" . . . "elisa-kits" . . "https://biopragmatics.github.io/providers/peff/$1"^^ . . . . "https://bioregistry.io/metaregistry/ncbi/"^^ . "false"^^ . . "mmsinc" . "ivdb" . "true"^^ . "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information."^^ . "protein" . . . . . "plant anatomy" . . . . . . . . "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities."^^ . . . "Coleoptera Anatomy Ontology" . . "false"^^ . "life science" . . . . . . . . . "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other."^^ . "ontology" . . . . . "gnps.task" . "The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format."^^ . . "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^ . "chemistry" . "Anvil" . "http://exac.broadinstitute.org/transcript/$1"^^ . . . . "marine biology" . . "Tudor Oprea" . . "Gregory Landrum" . . . "^\\d+$"^^ . . . "obo" . "Gramene Reference" . . . "mieg@ncbi.nlm.nih.gov" . . "Rice annotation Project database" . . "http://gmd.mpimp-golm.mpg.de/Analytes/$1"^^ . "14"^^ . "MESHD" . "http://zfin.org/"^^ . . "rna" . "http://www.pharmgkb.org/disease/"^^ . "ontology" . . "violinID" . . "animal husbandry" . . "^\\d{7}$"^^ . . "bioinformatics" . . "B2067"^^ . . "occupational medicine" . . . "vocabularies" . "^[0-9a-zA-Z]{8}$"^^ . . "https://bioportal.bioontology.org/" . . "^\\d{7}$"^^ . . . . "http://eugenes.org:7072/.bin/fbidq.html?"^^ . "https://glycopost.glycosmos.org/entry/$1"^^ . "false"^^ . "LOC_Os02g13300"^^ . . "molecular biology" . "pibase" . . . "^\\d+$"^^ . "life science" . . "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^ . . . . . . "endocrinology" . . . "https://www.inaturalist.org/taxa/$1"^^ . . "BioLegend is a life sciences supply vendor."^^ . . . . . "obo" . "chemistry" . "false"^^ . "MetaboLights Compound" . . . . . . . . . . "genetics" . . . . "70"^^ . . . "silvio.tosatto@unipd.it" . . . . . . . . "ribocentre" . . "phenotype" . . . "Christopher Mull" . "comparative genomics" . . . "^\\d+$"^^ . . . "0000121"^^ . . "puro" . "SNOMEDCT_US_2019_09_01" . "rgd.strain" . "development" . . "http://en.wikipedia.org/wiki/"^^ . . . "https://www.ebi.ac.uk/ols4/ontologies/$1" . . . "report" . "Functional Requirements for Bibliographic Records Entity-Relationship Model" . . . . . . . . "kegg.rclass" . . . . "Ribocentre is designed to contain comprehensive information of all natural ribozymes."^^ . . . "ecyano.experiment" . . "https://www.storedb.org/store_v3/study.jsp?studyId=$1"^^ . . . . "American Type Culture Collection" . . "https://cropontology.org/rdf/CO_336:"^^ . "animal husbandry" . "false"^^ . "expression" . . "^\\w+:[\\w\\d\\.-]*$"^^ . "clao" . "Ontology"^^ . "natural science" . "http://www.w3.org/ns/shex#"^^ . . "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions."^^ . "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'."^^ . . "npo" . "CHEBI" . . . . "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier."^^ . "false"^^ . . "34"^^ . . . . . . "cellosaurus.resource" . "c0001"^^ . . "Psychology Ontology" . _:Nae36e2aebfee4e58acbcb8a52f217512 "helpdesk@cropontology-curationtool.org" . . . . . . "Paul D Thomas" . "http://wodaklab.org/iRefWeb/interaction/show/$1"^^ . . "taxonomic classification" . "http://www.cathdb.info/cathnode/$1"^^ . . "The Ecosystem Ontology" . . . . . . . . . . . "ALA"^^ . . . "ForwardStrandPosition"^^ . . "Ensembl Protists" . . . . . "biomedical science" . . . "1829126"^^ . . "metadata standardization" . "UniProt Proteomes" . "Metabolites in the Xenobiotics Metabolism Database."^^ . . "Annika Jahnke-Bornemann" . . "disease" . . . . "NBK331"^^ . . "https://modeldb.science/"^^ . . "https://rism.online/$1"^^ . "false"^^ . . "Costal and Marine Ecological Classification Standard" . . . . . "bioregistry.registry" . "est" . "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"^^ . "Research Resource Identifiers" . "Ontology of Physics for Biology" . "http://uri.neuinfo.org/nif/nifstd/nlx_chem_"^^ . . "movie" . . . "ontology" . . . . "IC9CM" . . . "https://caninecommons.cancer.gov/#/study/$1"^^ . . "false"^^ . "Pierre-Yves LeBail" . . "ligandbox" . . . "171"^^ . . . "Health Surveillance Ontology" . "50018"^^ . . . "http://ecmdb.ca/compounds/"^^ . "false"^^ . . "https://pmb-bordeaux.fr/maggot/metadata/"^^ . . . . . "exposure" . . . . "https://www.eionet.europa.eu/gemet/en/concept/$1"^^ . . "obo" . . . . . "false"^^ . . "reagent" . . . . . "isbn" . "^\\d+$"^^ . . . . . "https://prefix.zazuko.com/" . . . "https://w3id.org/oc/corpus/"^^ . "false"^^ . . "bhsung@kribb.re.kr" . . . . . . . . . . "^\\d+$"^^ . . . . . . "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form="^^ . . . "^(R)?PXD\\d{6}$"^^ . "http://purl.obolibrary.org/obo/BOOTSTREP_"^^ . . "SCTID" . . "ontology" . "^Os\\S+t\\d{7}-\\d{2}$"^^ . . "myco.lepra" . "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"^^ . . "https://www.encodeproject.org/$1"^^ . "https://sparontologies.github.io/fabio/current/fabio.html#"^^ . . "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature."^^ . . . . . . . . . . "civic.eid" . . "topalis@imbb.forth.gr" . . . "shex" . "biomedical science" . . . . . "false"^^ . . . "hasPrimaryUriPattern"^^ . "Jack R Harkema" . . . . . "false"^^ . . "repository" . . "https://cellmodelpassports.sanger.ac.uk/passports/$1"^^ . "^\\d+$"^^ . . . "transcription factor" . "Edgar Wingender" . . . . . . . . "life science" . "bioregistry.schema" . . . . "^\\d{7}$"^^ . . "hcpcs" . "miRNEST" . . "Yam ontology" . . "P53350"^^ . "dna" . . . . . "phenotype" . "scr" . . . . . "genes" . . . "oclc" . . "https://umgear.org/p?id=$1"^^ . "false"^^ . . . "http://purl.obolibrary.org/obo/VTO_"^^ . . . . . . "^\\d+$"^^ . . "false"^^ . "^\\d+$"^^ . . . . "horizon_discovery" . . . . . "snomedct" . "ordo.orphanet@inserm.fr" . . . . "https://bioregistry.io/wicell:"^^ . . "gnpis" . "chemical" . "^\\d{7}$"^^ . . . . . . . "http://purl.obolibrary.org/obo/WBPhenotype_"^^ . . . . . . "^\\d{7}$"^^ . . . . "Web of Science ID (work)" . "chemspider" . "micro" . . "ontology" . . . . . . . "https://www.thaiclinicaltrials.org/show/"^^ . "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id="^^ . . "false"^^ . "data retrieval" . "mutant strain" . "YBR125c"^^ . . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . . "rs17852708"^^ . "https://bioregistry.io/prints:"^^ . . . . "Jeffrey Wong" . . "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . . . . . "1242"^^ . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information."^^ . . . "dg.f82a1a" . . . . . . . . . . . . . . "BugBase Expt" . . . . . . . . "drugbank.condition" . . . . . "gene" . . "NIST/CODATA ID" . . . . . . . "false"^^ . . . . . "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q="^^ . . . . "false"^^ . . . "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis."^^ . . "false"^^ . . . "8"^^ . . "sharesAuthorInstitutionWith"^^ . . . "0000062"^^ . "protein" . . . . . . . . . . "biomedical science" . . "0000079"^^ . "false"^^ . . . "false"^^ . "co_343" . "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"^^ . . . "report" . "ligandbook" . "Metabolic Network Exchange Database" . "^\\d+$"^^ . "true"^^ . "francesco.vitali@ibba.cnr.it" . "genomics" . . "EHDAA:2185"^^ . . _:Nc5649c0b3ba24647bf32bddea5052c76 "helpdesk@eionet.europa.eu" . "nmr" . . . . . "^(\\d|\\w)+-\\d$"^^ . "false"^^ . . . . . . "has local unique identifier pattern" . . "systems biology" . . . . "Livestock Product Trait Ontology" . . "false"^^ . "false"^^ . . . . "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources." . . . . "ontology" . "https://w3id.org/biolink/vocab/$1"^^ . . . . . . "false"^^ . "false"^^ . . . . . "HMS-LINCS" . "MIMIC III Database" . "chemical biology" . "^\\w{2,3}(-\\w+)?$"^^ . "false"^^ . . "CNP0171505"^^ . . . "https://www.vmh.life/#gene/$1"^^ . "classification" . "^\\d+$"^^ . . . . "genome" . . . . "pseudomonas" . . "neurobiology" . "https://www.encodeproject.org/"^^ . "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$"^^ . . "gary.bader@utoronto.ca" . . . "false"^^ . "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC)."^^ . "FMAID" . "chemistry" . "ontology" . . . . "database" . . . . . "false"^^ . "MEDIGUE Claudine" . "biomedical science" . "https://protists.ensembl.org/id/$1"^^ . . . . "botany" . "MSV000082131"^^ . . "0000685"^^ . . . "^[AEP]-\\w{4}-\\d+$"^^ . . "neurobiology" . "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . "https://www.ebi.ac.uk/metagenomics/projects/"^^ . "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . "small molecule" . . "Multum MediSource Lexicon" . "95-0166C6"^^ . . . . . "parasitology" . . "simon.harding@ed.ac.uk" . . . . . "bandrow@gmail.com" . "neurobiology" . "wikidata" . . "enrique.blanco@crg.eu" . . . . "swisslipid" . . . . "false"^^ . "Lars Holm Nielsen" . "Tanya Barrett" . "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology."^^ . "false"^^ . . "transcriptomics" . "false"^^ . "phenotype" . . "botany" . . . "chemical" . . "https://chem.nlm.nih.gov/chemidplus/rn/$1"^^ . "phenotype" . . "molmovdb" . . . . "^\\d+$"^^ . . . . . . "false"^^ . . "https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1"^^ . . . . "Amos Bairoch" . . "life science" . "false"^^ . "violinId" . . . . "^\\d+$"^^ . "anatomy" . . . . . "Animal Trait Ontology for Livestock" . . . . "https://www.worldcat.org/oclc/$1"^^ . "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^ . . "VCell Published Models" . "MeSH 2012" . "data retrieval" . "life science" . . . . "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"^^ . . . "fionamcc@arizona.edu" . . "reagents" . . . . . "protein" . "false"^^ . "International Standard Book Number" . . . "pathogen" . "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies"^^ . . . . . . . . . . . "Danielle Welter" . "false"^^ . "society" . "Mike Cherry" . . . "Wojciech M. Karlowski" . . . . . . "The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class ‘dietary nutritional component’ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe ‘analytical methods’ for quantification, ‘physical properties’ or ‘dietary function’. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the ‘nutritional component concentration’ class may be used to represent quantification of components described in the ‘dietary nutritional component’ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) ‘Food product by organism’, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum."^^ . . "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^ . . . "nucc.taxonomy" . . . "COSMIC Gene" . "rna" . . . "false"^^ . . . . . . . . "ontology" . "peteremidford@yahoo.com" . . . "^\\d+$"^^ . "false"^^ . . "false"^^ . . . . . "PDB Structure" . "phenotype" . "true"^^ . . . . . "Human Cell Atlas Ontology" . . . . . . . . . "https://bioregistry.io/lrg:"^^ . "NCit" . "Homologous Vertebrate Genes Database" . . "https://cropontology.org/rdf/CO_327:$1"^^ . . "DICOM Controlled Terminology" . "codelink" . . . "19333"^^ . . . . . "Imanis Life Sciences cell line products" . "https://medical-data-models.org/forms/$1"^^ . "MarFun" . . . . "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . "alayne.cuzick@rothamsted.ac.uk" . . "pictar-vert" . "false"^^ . . "http://purl.obolibrary.org/obo/COLAO_"^^ . "NMR Restraints Grid" . . . "reaxys" . "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community."^^ . . . . "0000001"^^ . "The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure."^^ . . . "david@mbi.ucla.edu" . . . "ontology" . . "377369"^^ . "protein" . . "Michael Witt" . . "proteomics" . . "PRIDE Project" . . . "ontology" . . . "Benjamin M. Gyori" . . "https://www.gwascentral.org/study/"^^ . . "^rs\\d+$"^^ . . . . "fly" . . . . . "interaction" . "Semion author ID" . . "registry" . . . . "centrally registered identifier" . "Cuban Registry of Clinical Trials" . . "Nicolas Terrapon" . . . "78073"^^ . "https://identifiers.org" . . . . "^[0-9]*$"^^ . "jgi.proposal" . "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"^^ . . . "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . . . . . . "biochemistry" . "https://www.wormbase.org/get?name=$1"^^ . . . . . "https://bioregistry.io/vdrc:"^^ . . "PGOHUM00000289843"^^ . . "^\\d+$"^^ . "obo" . . . "Ath_AT1G01030.1"^^ . "cell lines" . "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research."^^ . "https://www.uniprot.org/locations/$1"^^ . . "http://purl.obolibrary.org/obo/OHPI_$1"^^ . "Rat Genome Database qTL" . . . . "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines."^^ . . . "germplasma" . . . . . "unipathway.pathway" . . "gene name" . . . "Jeff Beck" . . "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . "https://world-2dpage.expasy.org/repository/"^^ . "inxight-drugs" . . . . . "NCT00222573"^^ . . "Chemical Information Ontology" . "http://pepbank.mgh.harvard.edu/interactions/details/$1"^^ . . "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described."^^ . "SSF57615"^^ . . "iuphar.family" . . "ontology" . . "ontology" . "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam="^^ . "obo" . . "The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]"^^ . . . "https://portal.gdc.cancer.gov/cases/"^^ . . . . . "^[A-Z0-9]+$"^^ . . . . . . . . . . "vrandecic@gmail.com" . . "INN_ID" . "brenda.ligandgroup" . . . . . . . . . "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1"^^ . "^ZDB\\-\\w+\\-\\d+\\-\\d+$"^^ . . . "^\\d+$"^^ . . . . . "0001885"^^ . . "BeAn 70563"^^ . . "Funding, Research Administration and Projects Ontology" . . "https://www.sharkipedia.org/species/$1"^^ . . "^UPC\\d{5}$"^^ . . "http://www.noncode.org/NONCODERv3/ncrna.php?ncid="^^ . "^\\d{7}$"^^ . . "^\\d{7}$"^^ . . "EB0170"^^ . . "subject agnostic" . "2023-503698-40-00"^^ . "immunology" . . "false"^^ . . . . . "Confidence Information Ontology" . "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^ . . "Metabolomics Workbench Study" . "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections."^^ . . . "obo" . . . "0000199"^^ . . . "validatordb" . "NA06985"^^ . . . . . . . . . . . . . "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?"^^ . . "Pigeonpea ontology" . . "fix" . . "gramene.protein" . . . "http://purl.obolibrary.org/obo/SO_$1"^^ . . "false"^^ . _:N14aec72fb9624574a7835e3cbcbfd5e9 "zimmerly@ucalgary.ca" . "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier."^^ . "http://purl.obolibrary.org/obo/OBA_"^^ . "s_mart_db" . . "false"^^ . . . "^\\d+$"^^ . "ontology" . . . . . "false"^^ . "aro" . . . . . . "drugbankv4.target" . . . . "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3"^^ . . . "COL3A1"^^ . . "^\\w+$"^^ . "European Nucleotide Archive" . . . "mgnify.proj" . . "Daniel Himmelstein" . . . "http://purl.obolibrary.org/obo/NOMEN_$1"^^ . "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products."^^ . . "huang@southalabama.edu" . "http://purl.obolibrary.org/obo/LPT_"^^ . "experimental measurement" . . . . . "ontology" . . . . . . . . "life science" . "Glenn King" . "anatomical therapeutic chemical code" . . . . . . "mutant mouse strain" . . "Crystallographic Information Framework" . . . . . "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease."^^ . "occ" . . . . . . . . . "false"^^ . . "birgit.kersten@thuenen.de" . "http://www.geneontology.org/formats/oboInOwl#$1"^^ . . . . . . "developmental biology" . . . . "http://purl.obolibrary.org/obo/MOP_$1"^^ . . . . . "disease" . . "3851"^^ . "Stefan Kuhn" . "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs)."^^ . "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^ . . "false"^^ . "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^ . . "adriano.mari@allergome.org" . . . . . . . . "Sensitive Data Ontology" . . . . "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$"^^ . . "phenotype" . . . . . . . . "life science" . . . "https://bioregistry.io/dragondb.protein:"^^ . . . . . "ontology" . . . "phenotype" . "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115="^^ . . . . . "reactome" . . . . . . . . . . . . . . "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"^^ . . . . . . "Marijane White" . . . "publons.publication" . "^\\d{8}$"^^ . "metabolomics" . "pig" . . . . . . "genome" . "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank."^^ . . . "1"^^ . . . . "https://fcs-free.org/fcs-database?"^^ . . "teri.klein@stanford.edu" . . "Higher order grouping of Pfam families"^^ . "dpv" . "agriculture" . "biology" . . . . . "keilbeck@genetics.utah.edu" . . "http://purl.obolibrary.org/obo/AGRO_"^^ . . . . "cubedb" . . . "false"^^ . _:Nb5cf4dffbb9545e5b5258205b63dabd6 "heinrich.herre@imise.uni-leipzig.de" . . "gene" . . . . . . . _:N2b9b6b3f37684d34bdfa4f00edbd153e "vlee@ebi.ac.uk" . . . "^PA\\d+$"^^ . . . . . . "agriculture" . . . "Gene Regulation Ontology" . "biology" . "protein" . . "https://www.kegg.jp/entry/$1"^^ . "false"^^ . . "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field."^^ . . "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world."^^ . . . . . . "1251"^^ . "sdis" . . . . . . "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . "http://www.chemspider.com/inchikey=$1"^^ . . . . "dna" . "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"^^ . "false"^^ . "obo" . "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web."^^ . "ontology and terminology" . . "co_345" . . . "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1"^^ . "false"^^ . . . . "immunology" . "false"^^ . "food" . . . "dna" . "ADA"^^ . . . . "rna" . "A web-developer centric archive of prefixes and URI prefixes" . . "Core Ontology for Biology and Biomedicine" . "orthology" . "http://oid-info.com/get/$1" . . . "false"^^ . . . . . _:N66cf499252324c29a5fea5f7bf331f08 "Stephan Schurer" . . . . . . "genome" . "http://database.deepsolar.space:18080/dbs/nlfff/$1"^^ . "flopo" . . . "dctypes" . "Environmental Molecular Sciences Laboratory Project" . "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . "domain" . . "genome" . . "0000030"^^ . "norine" . . "DP00086r013"^^ . . . . "clinical veterinary medicine" . . . "https://proteinensemble.org/$1"^^ . . . . . . . . . . "false"^^ . "gene" . "https://www.metanetx.org/comp_info/"^^ . . . . "^KW-\\d{4}$"^^ . . . _:N554742b5d5ea45529b998c824a4e7c6a "Jonathan Bard" . . "^\\d+$"^^ . . . . . . "botany" . "0100010"^^ . "morbidity" . . . . "epidemiology" . . . "TB2:S1000"^^ . "http://www.obofoundry.org/" . "life science" . "unirule" . . . . "sequence" . . . . . . . . . . "DrugBank Salts" . "https://reactome.org/content/detail/$1"^^ . . . . . . . "false"^^ . "wikipathways.vocab" . "life science" . . . "PR" . . "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^ . . . . "http://purl.obolibrary.org/obo/PdumDv_$1"^^ . . . . "^\\d{7}$"^^ . . "genomics" . . "RO_proposed_relation" . . . "http://purl.obolibrary.org/obo/OOSTT_"^^ . "Ontologized MIABIS" . . "ontology" . "http://solgenomics.net/phenome/locus_display.pl?locus_id="^^ . . "^\\d{7}$"^^ . "http://modelseed.org/biochem/reactions/$1"^^ . . . . . . . . "40565"^^ . "false"^^ . . "C138986"^^ . . . "N0000001662"^^ . "^\\d{7}$"^^ . . "false"^^ . "Pan African Clinical Trials Registry" . . . . . . . "https://models.physiomeproject.org/exposure/"^^ . "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id="^^ . . "ontology" . . "https://gnss-metadata.eu/MOID/"^^ . . . . . "Groundnut ontology" . "Terminology of Anatomy of Human Histology" . "small molecule" . . "10153"^^ . . . . "SABIO Reaction Kinetics" . . "http://cellimagelibrary.org/images/$1"^^ . "^\\d{7}$"^^ . "https://portal.issn.org/resource/ISSN/"^^ . "false"^^ . . "GC06M052656"^^ . . . . . . "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI."^^ . "SED-ML data format" . . . . . "ontology" . . . . "data model" . . . "https://biopragmatics.github.io/providers/diseaseclass/$1"^^ . "cell replacement" . "COB brings together key terms from a wide range of OBO projects to improve interoperability."^^ . "^GCST\\d{6}\\d*$"^^ . "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^ . . "ontology" . "pathway" . . . . "transcriptomics" . "http://opendata.inra.fr/ATOL/ATOL_"^^ . "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"^^ . . . . _:Nc5649c0b3ba24647bf32bddea5052c76 "Eionet Helpdesk" . . . . "ontology" . . . . . . . . . "enzyme" . . "rna" . . "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells."^^ . "mingxun.wang@cs.ucr.edu" . . "Tick Cell Biobank" . . "biology" . "http://purl.obolibrary.org/obo/BSPO_$1"^^ . . . . "ABC"^^ . . . "SNOMEDCT_US_2018_03_01" . . . . . . . . "dna" . "biomedical science" . . "Enzo Life Sciences" . . "ontology" . . . "2526"^^ . "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research."^^ . "biomedical science" . . "National Center for Biotechnology Information Registry" . . . . . . "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."^^ . "disease" . "00023232"^^ . . "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles."^^ . "An ontology of phenotypes covering microbes"^^ . . "SpliceNest" . "http://uri.neuinfo.org/nif/nifstd/nlx_organ_"^^ . "DailyMed" . . . "https://w3id.org/faircookbook/"^^ . . "labo" . "ontology" . "obo" . "identifier for an educational organization issued by the UK Register of Learning Providers"^^ . . . . . . . . . . "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1"^^ . . . . . . . . "Genetic Code" . "Sorghum TDv5 - Oct 2019"^^ . . "https://jjj.bio.vu.nl/models/$1"^^ . "health science" . . . . . . . . "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . . . "A pull request in any public repository on GitHub."^^ . . . . . . . "^\\d{7}$"^^ . . "http://oid-info.com/get/$1"^^ . . . . "^\\d{3}$"^^ . "https://polbase.neb.com/polymerases/$1#sequences"^^ . . "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data."^^ . . "chemical entity" . . . . . . "functional genomics" . . . "https://www.ncbi.nlm.nih.gov/clinvar/submitters/"^^ . "0101963"^^ . . "http://purl.obolibrary.org/obo/PD_ST_"^^ . "gsfa" . . . "^\\d+$"^^ . . "https://run.biosimulations.org/simulations/"^^ . . "gfo" . . . "false"^^ . "false"^^ . . "has URI pattern" . . . . . . "https://bioschemas.org/profiles/"^^ . . "https://assets.nemoarchive.org/"^^ . "56"^^ . . "false"^^ . . . . "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$"^^ . "An anatomical and developmental ontology for ctenophores (Comb Jellies)"^^ . . "life cycle stage" . "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby."^^ . . . "data management" . . "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways."^^ . "false"^^ . . . . . . "fly" . "chenyangnutrition@gmail.com" . "health science" . . . "chris.overall@ubc.ca" . "^[0-9]+$"^^ . . . . . . . . "https://bioregistry.io/iceberg.ime:"^^ . "owlstar" . "rrid" . . . . "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . "gene" . . . "0000890"^^ . . "health_care_quality_assessment"^^ . . . . . . . . . . "^LTS\\d{7}$"^^ . "Influenza Ontology" . . . . "Radiation Biology Ontology" . . . . "medicine" . . . . . "SABIO-RK Compound" . . . "rwinslow@jhu.edu" . . . . . . . . "umls.cui" . . . . . "Open Data Commons for Spinal Cord Injury" . "SIDER Side Effect" . . . "PANTHER Family" . . . . "false"^^ . . . . "false"^^ . . . . "^\\d{7}$"^^ . . . "flowrepository" . . . "^\\d+$"^^ . . "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"^^ . . "ontology" . . . . "5282"^^ . . . . . . "genome" . "repository" . . . . . . . "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId="^^ . "false"^^ . "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"^^ . "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary"^^ . "false"^^ . . . "4.2.78"^^ . . "56586"^^ . . . "^\\d+$"^^ . "yrcpdr" . . . . . . . "Pierre-Alain Binz" . . "Cell Line Ontology [derivative]" . . . "taxonomic classification" . . . "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"^^ . . . . "metagenomics" . . . . "gtr" . . "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . . . "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1"^^ . "life science" . "genetics" . . "img.taxon" . . "false"^^ . . . . "The coding sequence or protein identifiers as maintained in INSDC."^^ . . "https://www.inaturalist.org/observations/$1"^^ . . . "webelements" . . . "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1"^^ . . "false"^^ . . . "fig|306254.1.peg.183"^^ . "false"^^ . . "david.lynn@flinders.edu.au" . . "hospital" . . "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#"^^ . "heart" . "gard" . "^FDB\\d+$"^^ . . . . . . . . . . "Pankaj Jaiswal" . "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L"^^ . . . . . . "burkesquires@gmail.com" . . "obo" . . "obo" . "life science" . "exac.transcript" . . "Software Heritage is the universal archive of software source code."^^ . . . . . . "http://purl.obolibrary.org/obo/AISM_"^^ . "http://purl.obolibrary.org/obo/OPL_"^^ . . . . . . "biomedical science" . . . . . "ngl" . "http://www.w3.org/2003/11/swrl#$1"^^ . "^\\d+$"^^ . . . . . . "false"^^ . "ontology" . . . . . . . . . . "functional genomics" . "FBbi" . . . "http://purl.obolibrary.org/obo/ONS_$1"^^ . . . . . . . . "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice="^^ . . "genomics" . . . . "eaglei" . . . "zoology" . . . "enzyme" . . . . _:N5901e4409121428e9e75b3699ed6053b . . . "^\\d+$"^^ . . . . . . . "000177759000002"^^ . . "mw.project" . . "taxonomy" . . . . "obo" . _:Nbde6269f4f6443d69a8fb868ba8954f9 "chebi-help@ebi.ac.uk" . . "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession)." . . . . "918902"^^ . . . "vhog" . "resid" . . . "hoelzel" . . "virushostdb" . . . "ChEMBL" . . . . . . "umbbd.rule" . "structure" . "angiology" . "Gerald Guala" . . . . . "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line="^^ . . . . . "false"^^ . . . "^\\d{8}$"^^ . . . . "false"^^ . . . . . . "Ontology of RNA Sequencing" . . . "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^ . . "BioContext" . "false"^^ . . . . . . . . . . . "metacyc.pathway" . . . . . . "citation" . . . "obo" . . . . "^\\d+$"^^ . . "046-19"^^ . "ogi" . "https://cropontology.org/rdf/CO_326:"^^ . . . . "Ronald C. Beavis (Ron Beavis)" . . . "agriculture" . "Cube db" . . "false"^^ . "Paul Fabry" . . "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$"^^ . "https://www.ncbi.nlm.nih.gov/nucleotide/"^^ . "https://www.ncbi.nlm.nih.gov/research/cog/pathway/"^^ . "false"^^ . "ontology" . "false"^^ . . . . . . . . . . . "funcbase.fly" . "semion" . . . "false"^^ . . "Milton H. Saier, Jr." . "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_"^^ . . "MGnify Project" . . . . . . . "sider.drug" . . "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . . "^\\d+$"^^ . . . "https://bioregistry.io/cldb:"^^ . "Plant Experimental Conditions Ontology" . . "obo" . . . "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."^^ . . . . . "cryopreserved" . . "paxdb.organism" . . . "safisher@upenn.edu" . . . . . . "metaproteomics" . "ontology" . "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"^^ . . . . . . . . . "https://www.jax.org/strain/$1"^^ . . "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC."^^ . "http://www.pharmgkb.org/gene/$1"^^ . "genomics" . . . . "ICD10" . "Ruben Abagyan" . . . . "https://ximbio.com/reagent/$1"^^ . "radiology" . . . . . "false"^^ . . "http://www.whocc.no/atcvet/atcvet_index/?code="^^ . "nihgeneid" . . "obo" . "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures."^^ . "regulation of gene expression" . . . . "false"^^ . . "https://ligandbook.org/package/$1"^^ . . . . "obo" . "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . . "obo" . . . . . . "structure" . . . . . "KCT0008394"^^ . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$"^^ . "http://purl.obolibrary.org/obo/ONS_"^^ . "^\\d{7}$"^^ . . "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^ . "stacia@stanford.edu" . "cabri" . . . . . . . "784"^^ . "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . _:N4abb5ec25bc84b7794aa116c6e227a95 . "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID="^^ . "1a05"^^ . "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . . . . . "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."^^ . . . "true"^^ . . . . . . "0002502"^^ . "1915"^^ . "Peter D. Karp" . . . . . . . . "648028003"^^ . . "false"^^ . . . . . "false"^^ . . . . "http://www.jcvi.org/charprotdb/index.cgi/view/$1"^^ . . "spdx" . "life science" . "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG"^^ . "biomedical science" . . . "https://civicdb.org/links/assertions/"^^ . "https://bioregistry.io" . "Snapshot" . . "17186"^^ . . . . "dragondb.locus" . "modeldb.concept" . "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect"^^ . "biochemistry" . . . "^\\d{7}$"^^ . . . . "Jianmin Wu" . "128011350"^^ . . . . . . "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource"^^ . . _:N639b47a900af489b96783cabd2d49df1 "pbrooks@hcfa.gov" . "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information."^^ . . . "http://sweetontology.net/matrMineral/"^^ . "false"^^ . . . . "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^ . . . "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$"^^ . . . . . . . "3000045"^^ . . . . "metascience" . . . . "Gene Ontology Registry" . "inaturalist.user" . . . . . . . . . . "NCBI Bookshelf" . . . "https://www.sigmaaldrich.com/US/en/product/sigma/"^^ . . "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information."^^ . . "^(\\d+)|(\\w+)$"^^ . "mat" . . "https://dcmi.github.io/openwemi/ns#$1"^^ . . "en-GB"^^ . "bgee@sib.swiss" . "https://bioregistry.io/cst:"^^ . . "Gm00047"^^ . . "annotation" . . "adw" . . . "https://neurovault.org/collections/$1"^^ . "gianni.cesareni@torvergata.it" . "Open Tree of Life" . "^PASS\\d{5}$"^^ . . "The pattern for identifiers in the given resource" . . . . "false"^^ . . "Christophe Dunand" . . . . "biogrid" . . "comparative genomics" . . "^\\d{7}$"^^ . . . . . "true"^^ . . . "1044544"^^ . "itmctr" . "Database of Quantitative Cellular Signaling: Pathway" . . . . "insecticide resistance" . . "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene="^^ . . "jupp@ebi.ac.uk" . "^IID\\d+$"^^ . . "genetics" . "Mihail Anton" . . . . . . "nist.codata" . "https://n2t.net/$1:$2" . . . "mosaic" . . . . "nutritional science" . "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^ . . "fibroblast" . "pennsieve" . . . "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="^^ . "http://purl.obolibrary.org/obo/SOPHARM_$1"^^ . "http://purl.obolibrary.org/obo/OHD_"^^ . "false"^^ . . "emdb" . . . . "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies."^^ . "RepeatsDB Structure" . . "IRD Segment Sequence" . . "aging" . . . . . "^2\\d{4}$"^^ . "ontology" . "animal genetics" . . . . . "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid="^^ . . "https://www.affymetrix.com/LinkServlet?probeset="^^ . . . "kclb" . . "^[A-Z0-9]{4}$"^^ . "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported."^^ . "miriam"^^ . "72ff6ff882ec447f12df018e6183de59"^^ . . . . . . . "epigenetics" . "reagent" . "^G\\d+$"^^ . . . "https://cells.ebisc.org/$1"^^ . "nlx.mol" . . . . . . "https://www.signalingpathways.org/datasets/dataset.jsf?doi="^^ . . . . "fsnp" . "plant" . . . "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac="^^ . . . . . "AD834"^^ . "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information."^^ . . . "165a"^^ . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^ . . . "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1"^^ . . "Common Science and Technology Resources" . . . . . "cell lines" . "false"^^ . . "KEGG_PATHWAY" . . . "classification" . . . . . . . "daniel.c.berrios@nasa.gov" . . "ontology" . "inchi" . "false"^^ . "bigg.metabolite" . "fd8d0743-344a-4758-bb97-f8ad84a37357"^^ . . . "http://clipserve.clip.ubc.ca/topfind/proteins/"^^ . . . . "bioinformatics" . "molecular infection biology" . "life science" . "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"^^ . . . . . "Mingxun Wang" . . . "ontology" . "co_321" . . . . . . "gene" . . . "life science" . . "MSH" . . . . . "201022999"^^ . . "phenotype" . . "http://func.mshri.on.ca/yeast/genes/list_functional_scores/"^^ . . . . "false"^^ . "false"^^ . . "0000054"^^ . . "https://www.devtox.org/nomenclature/ml_manus.php?mno=$1"^^ . "SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes."^^ . . . . "phosphosite.residue" . . . . . "^\\d+$"^^ . . . . . "David Clunie" . . . "00000001"^^ . . "false"^^ . . . . . . . . . "antibody" . "gene" . . . . "false"^^ . . . . . "false"^^ . . . . . "ontology" . "https://www.ebi.ac.uk/pdbsum/"^^ . . . "miR-1"^^ . . "citation" . . . . . . . . . . "http://www.pseudomonas.com/feature/show/?locus_tag=$1"^^ . . "genome" . "Sue Bello" . "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions."^^ . . "cell reprogramming" . "neuroscience" . . . . . . . . . . "life science" . "pharmacogenomics" . "0000858"^^ . . "miRBase mature miRNA" . . "genetic strain" . . . . . . . . "disease" . "mirnao" . . "https://giardiadb.org/giardiadb/app/record/gene/"^^ . "false"^^ . "false"^^ . . . . . . . . . . . . "U49845"^^ . "plant phenotypes and traits" . "https://www.re3data.org" . . . "https://orcid.org/"^^ . . . . . "metadata" . . . . . . . . . . . . "ruili.huang@nih.gov" . . "interpro" . "eric.sid@nih.gov" . . "false"^^ . . . . "https://glycopost.glycosmos.org/entry/"^^ . . "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_"^^ . . "knockout" . . . "Anatomical Therapeutic Chemical Vetinary" . . "NMR-instrument specific component of metabolomics investigations" . "ComplexPortal" . . "unimod" . . "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"^^ . . . "genetic engineering" . . . . "pmr.workspace" . . "life science" . . . "vendor" . . . . . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . . "life science" . . "https://bioregistry.io/metaregistry/scholia/$1"^^ . . . "4007166"^^ . . "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^ . "https://mmp.sfb.uit.no/databases/marref/#/records/$1"^^ . . . . . . "conso" . . . . "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"^^ . . "RBR-6qvdftm"^^ . . "^\\d{7}$"^^ . "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id="^^ . "JCOIN" . . . "http://crdd.osdd.net/servers/virsirnadb/record.php?details="^^ . . "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events"^^ . "bcio" . . . "epidemiology" . . . . . . . . . . . . . . "GnpIS" . "false"^^ . . . . . . . . . . . . . "cell line" . . "uniprot.disease" . . "gene" . "false"^^ . . . "tropicalis" . "false"^^ . "CIViC Assertion" . "http://eugenes.org:7072/.bin/fbidq.html?$1"^^ . . . . "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^ . . . . . . "true"^^ . . . . . . "true"^^ . . . "https://bioregistry.io/metaregistry/cellosaurus/"^^ . . "https://bioregistry.io/cst.ab:"^^ . . . "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . . "myco.marinum" . . "https://europepmc.org/article/CTX/"^^ . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode="^^ . "phenotype" . . . "ontology" . . "ontology" . . "obo" . "https://www.ebi.ac.uk/arrayexpress/experiments/$1"^^ . . . "false"^^ . . . "10595"^^ . . "Pathguide" . . . . . . . . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/PLANP_$1"^^ . . "pathway" . . "P00747__P07355"^^ . . . . . "qafeQTWIWmcC"^^ . . . "genomics" . . "https://bioregistry.io/smiles:"^^ . "deoxyribonucleic acid" . . . "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1"^^ . . "info@casrai.org" . . "wikidata" . "harukin@protein.osaka-u.ac.jp" . . . . . . "vfdb.genus" . "life science" . . . "conference" . . "AB1925000"^^ . . . "https://www.kew.org/data/grasses-db/www/$1"^^ . . "http://purl.bioontology.org/ontology/IDODEN_$1"^^ . . . "Gene Product Information Schema" . "anatomy" . . . "ontology" . . . . . . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"^^ . . . . "civic.disease" . "http://ctdbase.org/detail.go?type=chem&acc="^^ . . . . . "obo" . . . . "has local unique identifier example" . "biocatalogue.service" . "https://www.sharkipedia.org/species/"^^ . "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"^^ . . "genome" . "https://www.kegg.jp/entry/$1"^^ . . "earth science" . . "false"^^ . . . . "data integration" . . "medicinal chemistry" . "http://www.cellresource.cn/cellsearch.aspx?sc=1&where="^^ . . . "Lepidoptera Anatomy Ontology" . "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR."^^ . . . . . "usageNote"^^ . . . . . "Cell line collections (Providers)"^^ . "ontology" . "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1"^^ . . "small molecule" . "tair.gene" . . "false"^^ . "European Collection of Authenticated Cell Culture" . . . . . . . . . . "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."^^ . . "expression data" . . "https://www.ncbi.nlm.nih.gov/probe/?term=$1"^^ . . . . . . "gerhard.mayer@rub.de" . "GR:0080039"^^ . "Maya Schuldiner" . "^\\d{7}$"^^ . . . . . . . . "Store DB" . "mmp.ref" . . "The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/)."^^ . . . "botany" . _:N5901e4409121428e9e75b3699ed6053b "HL7 Support" . . "true"^^ . "obo" . "false"^^ . "protein" . . . . . "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . . "microbiology" . "https://www.ebi.ac.uk/gxa/genes/"^^ . "Ontology for vector surveillance and management" . . . . . "preclinical studies" . . . "200282"^^ . . . "false"^^ . "classification" . "true"^^ . . . . . . "https://tools.ietf.org/rfc/rfc$1"^^ . . . . . . "The ALlele FREquency Database" . . . . "^PD\\d+$"^^ . . . . . "true"^^ . . "bkc640"^^ . "Geonamaes" . "true"^^ . . . . . "Eukaryotic Linear Motif Resource" . . . . . "http://purl.obolibrary.org/obo/CVDO_$1"^^ . . "silvio.peroni@unibo.it" . "100101"^^ . "PANTHER Pathway" . . . "https://www.ncbi.nlm.nih.gov/biosystems/$1"^^ . . . . . "data visualization" . "H-InvDb Protein" . "^\\d{7}$"^^ . . . "200-003-9"^^ . "https://fungi.ensembl.org/id/$1"^^ . "false"^^ . . . . . "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine."^^ . . "lgic" . . . "^\\d{7}$"^^ . _:Ndfc62fb6799e46b0be4ddad6be24c69c "Albert Goldfain" . . . "infection" . . . "^[A-Za-z_0-9]+$"^^ . . "https://scicrunch.org/resolver/RRID:IMSR_TAC_"^^ . . . . . . . _:N6f930f1da65341b9bb1888984de2ebb0 "helpdesk@cropontology-curationtool.org" . . . . . "FlyBase" . . . . . "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers."^^ . . "ChEMBL" . . . "false"^^ . "false"^^ . . . . . "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q="^^ . "biomedical science" . . . "oceanography" . . . "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . . "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012"^^ . "Luana Licata" . "https://odc-sci.org/data/"^^ . . . . . . . . . "chembl.compound" . "protein" . . . . "assay" . "false"^^ . . . . . . . . "Rat Genome Database strain" . . "PIR Superfamily Classification System" . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"^^ . "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts."^^ . . . . . . . . . "634515043"^^ . . . . . "fyler" . "protein" . "iNaturalist User" . . "3"^^ . "Hölzel Diagnostika" . . "knowledge and information systems" . . "46977"^^ . . "Philippe.Lemercier@sib.swiss" . . . . . "75"^^ . "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id="^^ . . . . . "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" . . . "life science" . . . . . . "0000062"^^ . "^[0-9]+$"^^ . . "biocompute" . . "PomBase" . . . . "DisProt" . "life science" . . . . "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1"^^ . "PhosphoPoint Kinase" . . . . "kestrelo" . "Ontology of Organizational Structures of Trauma centers and Trauma systems" . . . "DragonDB Protein" . . . "http://www.vbase2.org/vgene.php?id=$1"^^ . _:N35b9ad34ce8c47dd8af00d082157e04c "loinc@regenstrief.org" . "false"^^ . . . . . . "ontology" . . "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."^^ . . "63"^^ . "Damian Smedley" . "false"^^ . "Publishing Roles Ontology" . . . . . "chemical biology" . . . . . . . . . "Susan J. Brown" . . . . . . . . . . "http://www.humanproteomemap.org/protein.php?hpm_id="^^ . . "false"^^ . "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis."^^ . "http://purl.obolibrary.org/obo/AGRO_$1"^^ . . "aop.relationships" . . . . "RXN-14904"^^ . "true"^^ . . . "protein" . "false"^^ . "trait" . . . . . "wikipedia" . . . . . . . "762"^^ . "https://www.eionet.europa.eu/gemet/en/concept/"^^ . . . . "^MF_\\d+$"^^ . . . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1="^^ . "diseases" . "SKIP001214"^^ . . "Allotrope Merged Ontology Suite"^^ . "oarcs" . . . "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . . . . . . "citation" . "interaction" . . "https://www.thaiclinicaltrials.org/show/$1"^^ . "metadata" . "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id="^^ . . . . . . . . "genedb" . . "0024"^^ . . . "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information."^^ . . . . . "ptm site prediction" . . . "study design" . "http://www.w3.org/ns/adms#$1"^^ . . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . . "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID="^^ . . "false"^^ . "https://bioregistry.io/n2t:"^^ . . . . "http://substrate.burnham.org/protein/annotation/$1/html"^^ . "https://www.ncbi.nlm.nih.gov/research/cog/cog/"^^ . . "https://www.ebi.ac.uk/biosamples/sample/"^^ . . . "http://w3id.org/nkos/"^^ . "EJH014"^^ . "dna" . "true"^^ . . . "human" . . . "6000122"^^ . . "deo" . . . "John Graybeal" . "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier."^^ . . . . "http://www.hmdb.ca/metabolites/$1"^^ . . "developmental biology" . "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^ . . . . . . "Vilma Hualla Mamani" . . "The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations."^^ . "0005067"^^ . . . "phenotype" . "http://data.europa.eu/89h/"^^ . . "Cell line databases/resources"^^ . . "pfr" . "rnacentral" . "https://flybase.org/reports/FBrf"^^ . "A controlled vocabulary to describe phenotypic traits in plants."^^ . . "subject agnostic" . . . . . . . . . . "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating."^^ . . "^GPST[0-9]{6}$"^^ . "0003"^^ . . "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM="^^ . . . . . . . . . . "life science" . "19"^^ . . "life science" . "http://www.pharmgkb.org/gene/"^^ . . . "Nicolas Le Novère" . . "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results."^^ . "evan@epatters.org" . "https://plants.ensembl.org/id/$1"^^ . "molecule" . "GARD" . "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^ . . . "ontology" . "http://purl.obolibrary.org/obo/OPL_$1"^^ . "8497"^^ . "https://bioregistry.io/metaregistry/$1"^^ . . . . "DBCOND0066902"^^ . "SNOWMEDCT_US" . . "https://www.inaturalist.org/observations/"^^ . . "emmo.cif" . "MarFun is manually curated database for marine fungi which is a part of the MAR databases."^^ . "biology" . . "3355"^^ . . "botany" . . . "omid" . . . . "true"^^ . "AB0"^^ . . . "0000411"^^ . . . . . "NIST" . "OBO in OWL" . . . "false"^^ . . . . "1868"^^ . "https://www.nextprot.org/db/entry/"^^ . . "false"^^ . . . . . . . "obo" . . "false"^^ . . . "CID" . "vaccine" . . . . . . "0000066"^^ . . "^\\d+$"^^ . . . "phenotype" . . . "protein" . "Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment."^^ . . . "0000712_1"^^ . . "srao" . "Stephen Fisher" . "International repository of Adverse Outcome Pathways."^^ . "true"^^ . . . "Ana Rath" . . "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$"^^ . . . . . . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id="^^ . . "PDB_CHEM_ID" . . . . . "Vertebrate skeletal anatomy ontology."^^ . . . "https://biopragmatics.github.io/providers/sfam/$1"^^ . . . . "drug metabolism" . "Molecular Interactions Controlled Vocabulary" . . . . . "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . . . "obo" . . . "OBO Metadata Ontology" . . "Alan Bridge" . . "false"^^ . . . . "https://fairsharing.org/users/$1"^^ . "00030692-0FE1-4A1B-955E-A2E55D659267"^^ . . . "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^ . . . . . "dna" . . . . . . . . . . . "RepeatsDB Protein" . . . . . . . . "^\\d+$"^^ . . . "false"^^ . "90000018"^^ . "PharmGKB Gene" . . "ChEMBL target" . "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://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"^^ . . "^\\w+$"^^ . . . . . . . . . "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym="^^ . . . . "oboinowl" . "caripark@iastate.edu" . _:N0b8e586b4b274c769184d4708ff70754 "Crop Ontology Helpdesk" . . . "genetic disorder" . . "Pearl millet ontology" . "^\\d{7}$"^^ . . . . . . "ontology" . . . "true"^^ . . . "false"^^ . . . "false"^^ . "false"^^ . "Dr Paul Schofield" . . "goccid" . . "https://www.ncbi.nlm.nih.gov/nucest/"^^ . "rbk" . . "http://ecmdb.ca/compounds/$1"^^ . . "http://purl.obolibrary.org/obo/OBI_$1"^^ . "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites)."^^ . . . . . "rebec" . . . . . . . . . . . . . "Emotion Ontology" . . . "https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1"^^ . "false"^^ . "http://purl.obolibrary.org/obo/CHIRO_$1"^^ . "^[a-z0-9\\-_]+$"^^ . "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."^^ . "false"^^ . . _:N4bb080adea3244668a33721fe25e6ef1 . "chemical" . . . . . . "https://www.disprot.org/$1"^^ . . . "Search the world's most comprehensive index of full-text books."^^ . "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions."^^ . . . "Paleobiology Database" . . "0000435"^^ . "ontology" . . . . . . . . . . . . "WBGene00000001"^^ . "Mark Engelstad" . . "^DBMET\\d+$"^^ . . . . "dna" . . . "http://www.peptideatlas.org/PASS/"^^ . . . "35742"^^ . . . . "nanoparticle" . . . . . . "M0001"^^ . . . . . "L000001"^^ . . "PED00017e001"^^ . . "Cell line collections (Providers)"^^ . . . . . "^\\w+$"^^ . . "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . . . . . "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1"^^ . "protein" . . . . . "atmospheric science" . . "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology."^^ . . . . . . . . . "March 2017 version "^^ . . "chemistry" . "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699."^^ . "17:41223048"^^ . . "sequence" . "false"^^ . . . . . . "https://www.fao.org/fishery/en/species/$1"^^ . . . . . "^[A-Za-z_0-9]+$"^^ . "James C. Hu" . . . . . "^\\d{7}$"^^ . "http://purl.org/spar/pro/$1"^^ . . "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid="^^ . "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."^^ . "Potato ontology" . . . . "edgar.wingender@edgar-wingender.de" . . . . "0807.4956v1"^^ . "TVAG_386080"^^ . "environmental science" . . . . . . . . . . "https://glytoucan.org/Structures/Glycans/$1"^^ . . . . . . . "^\\w+$"^^ . "false"^^ . "gene" . . "clo" . "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources)."^^ . . . . . . . . . "false"^^ . . . . "txpo" . "FHIR United States Implementation Guides" . "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^ . "bmeldal@ebi.ac.uk" . "statistics" . "WiCell Research Institute Cell Collection" . . . "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_"^^ . "oboformat" . . . "preprints" . "false"^^ . . "food" . "nlx.func" . . . . . . . . . "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^ . . . . "false"^^ . "Aromatic"^^ . "glycosylation" . "http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1"^^ . "^TTHERM\\_\\d+$"^^ . . . . . "food" . "KESTREL Ontology" . . "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . "ypo" . . . . _:N0b8e586b4b274c769184d4708ff70754 . . . . . . "http://aber-owl.net/ontology/$1" . . . . "00000000"^^ . "enzyme" . . . "cellular neuroscience" . "^RCV\\d+(\\.\\d+)?$"^^ . "Compluyeast-2D-DB" . . . . "taxonomy" . "regulation" . "gene expression" . "ontology" . "https://data.bloodpac.org/ga4gh/drs/v1/objects/"^^ . . "ontology" . . "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc."^^ . . "https://w3id.org/mixs/$1"^^ . "Asset"^^ . "clinical studies" . . "obo" . . . . "life science" . "http://purl.obolibrary.org/obo/SYMP_$1"^^ . "report" . . . . "false"^^ . . "Insertion sequence elements database" . . . . "SEED Reactions" . . . . . . "electron microscopy" . "small molecule" . . "false"^^ . "Quinoa Ontology" . "earth science" . "Inge Jonassen" . . . "lreha@ualberta.ca" . . . "Disease Drivers Ontology" . . . . . "University hospital Medical Information Network Clinical Trial Registry" . . . . "false"^^ . "http://pombe.oridb.org/details.php?id="^^ . . "false"^^ . . "nemo" . "ICDCM_2005" . . . "CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains."^^ . . . . . "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^ . "biomedical science" . . . . . . "Gary Bader" . "evidence" . "schoch2@ncbi.nlm.nih.gov" . "^EP\\d{4}$"^^ . . . "false"^^ . "registry" . . "https://mediadive.dsmz.de/ingredients/"^^ . . . "biology" . . . . "NCI_Thesaurus" . . . "false"^^ . . . . . . . . . "false"^^ . "http://bigg.ucsd.edu/compartments/$1"^^ . . "1004" . . "Phenotype And Trait Ontology" . "biomedical science" . "BioContext contains modular JSON-LD contexts for bioinformatics data." . "http://www.cathdb.info/cathnode/"^^ . . . "lspci" . "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . "obo" . "protocol" . "MTBLS1"^^ . "isrctn" . . . . . "LigandBox" . "repec" . "dsm5" . "https://cropontology.org/rdf/CO_348:$1"^^ . "homologous" . . . . "functional genomics" . . . . "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id="^^ . "UMLS Semantic Types Ontology" . . . "http://purl.obolibrary.org/obo/PCO_$1"^^ . . "false"^^ . . "plant phenotypes and traits" . "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1"^^ . "false"^^ . . . . . . . . "casspc" . _:Nfa653585832f480d92bb1b122af31629 "evoc@sanbi.ac.za" . . "ontology" . . . . "^\\d+$"^^ . . . "https://grch38.togovar.org/variant/$1"^^ . "ontology" . _:N92e5ed142870468bac61f5ddc8c2e9ba "Bgee team" . . . . "obo" . . . "1"^^ . "Rice ontology" . "^\\d{7}$"^^ . . . . "disease" . . . . . . . . . . . . "issn" . "http://purl.obolibrary.org/obo/MPIO_"^^ . "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . . . . . "http://purl.obolibrary.org/obo/ENVO_$1"^^ . . "https://fairsharing.org/organisations/"^^ . . . . "donny@polyneme.xyz" . . "^\\d{7}$"^^ . "GlycoPOST" . . . "subject agnostic" . . "molecular biology" . . "hello@vivekkrish.com" . "methods" . . "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology."^^ . . . . . "The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains."^^ . . . . . . "Metabolomics Workbench Project" . . "The COVID-19 Infectious Disease Ontology" . "37"^^ . . . "^\\w+$"^^ . . "proteins" . . . "Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions"^^ . "M58335"^^ . "phenotype" . "EC-CODE" . "ASRP1423"^^ . "true"^^ . "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"^^ . . "Dietmar Schomburg" . "genetics" . . "rdfa" . . "http://purl.obolibrary.org/obo/OARCS_$1"^^ . . . "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements."^^ . . "Cell line databases/resources"^^ . . "E-cyanobacterium Experimental Data" . . . . . . . . . . . "http://purl.obolibrary.org/obo/DOID_$1"^^ . . . . . "Protein modification" . "Minimum Anformation About a Phylogenetic Analysis Ontology" . "data management" . . "ontology" . "gene" . "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^ . "false"^^ . . "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level)."^^ . . . . . . . . "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins."^^ . . . . . . . . "Matthias König" . . . . . "CCDS13573.1"^^ . . . "0471491039"^^ . . "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^ . . . . . . "gene" . . . . . "GXA Gene" . . "false"^^ . . . . . "74"^^ . . "false"^^ . . . . "http://www.allergome.org/script/dettaglio.php?id_molecule="^^ . "funderregistry" . . "https://www.geonames.org/$1"^^ . . . . . . . . . . "^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\\.[0-9]+(-[0-9]{3}\\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$"^^ . . . "^\\d+$"^^ . "false"^^ . . . . . . . . . . . . "genome" . "ontology" . "goeco" . "Matthias Samwald" . . "c"^^ . . "26"^^ . "http://www.phosphosite.org/proteinAction.do?id=$1"^^ . . . "https://bioregistry.io/dragondb.locus:"^^ . . "report" . . "false"^^ . . "ontology" . _:N3e7c81cd11fa492a82b3573ccfdc6237 . . . . . "structure" . "RGD" . . . . "^\\d+$"^^ . "biomedical science" . . "false"^^ . . . . . . . "false"^^ . "maude.pupin@univ-lille.fr" . . . . . . "life science" . "Allyson Lister" . . . . . "Enrique Blanco" . "0000690"^^ . "Lentil ontology" . . . . . "PS00001"^^ . . . . . . . . . . "^rs\\d+$"^^ . . "false"^^ . "sébastien Aubourg" . "https://cropontology.org/rdf/CO_365:$1"^^ . "PaxDb Organism" . "0000004"^^ . "structure" . "subject agnostic" . "anatomy" . . . . "^\\d{7}$"^^ . "Glycan Naming and Subsumption Ontology" . "baoym@big.ac.cn" . . "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1"^^ . . "http://purl.obolibrary.org/obo/HOM_"^^ . . . . . . . "CAS Registry Number" . "obo" . . "true"^^ . . "http://purl.org/spar/pwo/"^^ . . . "hpm.peptide" . "health science" . "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013."^^ . . . . . . "^EGAS\\d{11}$"^^ . . "http://purl.bioontology.org/ontology/IDODEN_"^^ . . . . "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene."^^ . . . . . . . . . "dal.alghamdi92@gmail.com" . "htn" . . . "Japan Chemical Substance Dictionary" . "Monique Zahn" . . . . . . . . "Olfactory Receptor Database" . . "Open Data Commons for Traumatic Brain Injury" . . . "civic.did" . . . . . "Vaccine administered code set" . "molecular interaction" . . . "fisheries science" . "small molecule" . "^\\d{7}$"^^ . . . . "ontology" . . "Echinobase" . . . . . . "EntrezGene" . "Jennifer C. Giron" . . . . "IPP900099"^^ . . "biolegend" . "biozy@ict.ac.cn" . . "biogrid.interaction" . . "0000632"^^ . "imedvedeva@celgene.com" . "FuncBase Yeast" . "Pseudomonas Genome Database" . . . . . . "false"^^ . . "Henriette Harmse" . "959"^^ . "false"^^ . . . . "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$"^^ . . . . . . . . . . . . . . . "https://thebiogrid.org/interaction/"^^ . . "obo" . "metadata standardization" . "^AT\\d+$"^^ . . "rna" . "An alternative or synonymous prefix" . "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"^^ . . . "Erik van Nimwegen" . "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"^^ . "protein" . "DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects."^^ . . "molecular dynamics" . "101775319"^^ . . "SpBase" . . . . . . . "https://morpheus.gitlab.io/models/"^^ . . . . . . . . . . . . "Feature Type Thesaurus" . _:Naa56318ac26547a6b2bc62f503f794a6 "psidev-gps-dev@lists.sourceforge.net" . . . . . . "^[-A-Za-z0-9\\_]*$"^^ . . "false"^^ . "spar" . "The Dietary Restriction Gene Database" . . "regulation" . . . "https://bacteria.ensembl.org/id/$1"^^ . . . "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1"^^ . . "glycosciences.db" . . . "biological regulation" . . "false"^^ . . "false"^^ . . . . "true"^^ . . . . . . "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code."^^ . . . "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . . "ENVO" . . . . . . "NLXOEN" . . . . "http://physics.nist.gov/cgi-bin/cuu/Value?$1"^^ . "bpeters@lji.org" . . . "false"^^ . . . "ontology" . . "life science" . . . . . "bibliography" . . . . . . . . . . . "chemical structure" . . . "clinical studies" . "analytical chemistry" . . "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites."^^ . . . "KEGG" . "Frederique Lisacek" . "https://mediadive.dsmz.de/solutions/"^^ . "false"^^ . "http://purl.obolibrary.org/obo/CMF_"^^ . . "Hector Escriva" . . "pathway" . "PF" . . "UK Provider Reference Number" . . "ctgov" . . . "BG11523"^^ . "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence."^^ . . . "data model" . . . "ontology" . "447860"^^ . "knowledge and information systems" . "biomedical science" . "health science" . . . . . . "rcb" . . . . . . . "genome" . "IMGT/HLA human major histocompatibility complex sequence database" . "Guy Cochrane" . . "nsf.award" . . "classification" . . "http://purl.obolibrary.org/obo/ONTOAVIDA_$1"^^ . "bila" . "eccode" . "mro" . . . . . . "subject agnostic" . . "dna" . . . . . "Lentil Trait Dictionary in template v5 - ICARDA - July 2015"^^ . . "https://www.genome.jp/virushostdb/"^^ . . . "Blue Brain Project Knowledge Graph" . "ctri" . . . . . . . . . . "http://purl.obolibrary.org/obo/GENEPIO_$1"^^ . . . . "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic."^^ . . "Ensembl Gene" . "Daniel Sonenshine" . . "Epidemiology Ontology" . . "false"^^ . "Selventa Chemicals" . . . . "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . . "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^ . . "http://purl.uniprot.org/annotation/VAR_$1"^^ . "carole.goble@manchester.ac.uk" . . . "^\\d{7}$"^^ . . "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically."^^ . "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information."^^ . . . . . "KEGG Metagenome" . . . _:N684dfaa5304e4af58860ef3f4a47b23a "klimke@ncbi.nlm.nih.gov" . . . . . . . . . "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . "biological regulation" . _:N8567bba41b474a04adf4491efb98c660 "Jim Amsden" . . . . . "hinv.transcript" . . . . . . "http://leafsnap.com/species/$1/"^^ . . . . "false"^^ . . . . "strain" . . . "false"^^ . . . "http://www.ebi.ac.uk/astd/geneview.html?acc="^^ . "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker."^^ . . . . . . . "nomen" . . . . . . . . "false"^^ . "https://www.ebi.ac.uk/pride/archive/projects/"^^ . . "adam@burnham.org" . "ncbiprotein" . "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc."^^ . "medicine" . . . . "http://stormo.wustl.edu/ScerTF/details/"^^ . . . . "orthologous" . . . . "https://www.ebi.ac.uk/arrayexpress/arrays/"^^ . "obo" . "sibo" . "false"^^ . "classification" . . "false"^^ . "617102"^^ . "habronattus" . "http://www.whocc.no/atc_ddd_index/?code="^^ . "An application ontology built for beta cell genomics studies."^^ . . "^\\d{7}$"^^ . . . . . . "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO)."^^ . "13"^^ . "openwemi" . . . "^\\d{7}$"^^ . "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data."^^ . . . . "microbial" . . "physiology" . . . . . . . _:Ne38cefa1b7b748d98dc227b75908f096 "rafael.goncalves@stanford.edu" . "^M[0-9]{4,}$"^^ . . . . . . . . "clinical decision support systems" . . . . "w3c rec" . . "Drosophila development" . . . "90801"^^ . . . "LinJ.20.0070"^^ . . "bel" . . . "bgee.stage" . . "http://gmd.mpimp-golm.mpg.de/Analytes/"^^ . "VIPERdb" . "https://www.genenames.org/data/genegroup/#!/group/$1"^^ . . . "anatomy" . . "ClinVar Submission" . "veterinary medicine" . "ontology and terminology" . . . "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name="^^ . . . . . "false"^^ . "human" . . . "statistics" . "Bgee organ" . . "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"^^ . . "http://purl.obolibrary.org/obo/MFOMD_$1"^^ . "http://dictybase.org/gene/$1"^^ . "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases"^^ . . . . "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies."^^ . . "^\\d+$"^^ . "Pathguide contains information about 325 biological related resources and molecular interaction related resources."^^ . . "gmelin" . "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."^^ . . "false"^^ . "Reaxys eMolecules" . . "assay" . . . . . . . . "Curation of Neurodegeneration Supporting Ontology" . "obo" . "03yrm5c26"^^ . . "true"^^ . . . . . . "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"^^ . "https://lincs.hms.harvard.edu/db/antibodies/"^^ . . . "obo" . . . . . . . "PF11779"^^ . . "^\\d+$"^^ . . . . . . . "Valerie Wood" . . . "Signaling Network Open Resource" . . _:Ndfc62fb6799e46b0be4ddad6be24c69c . "Protein Model Database" . . . . "DrugBank Condition" . . . . "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^ . . "false"^^ . "HL7 V2 Code Systems" . "https://datacommons.org/browser/"^^ . . . . "pubchem.assay" . . . "NeuroMorpho" . . "^SCV\\d+(\\.\\d+)?$"^^ . . "Reference"^^ . . . . . "degradome" . . . "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments."^^ . "rdb20@pitt.edu" . . . "ontology" . "false"^^ . . "false"^^ . "false"^^ . . . . "http://scicrunch.org/resolver/SCR_$1"^^ . . "interaction" . . . . . . "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier."^^ . "^[A-Za-z0-9]+$"^^ . "life science" . "taxonomy" . "aquaculture" . "false"^^ . . . . "anatomy" . . . . . "Adnan Malik" . "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . . . . . "LOC_Os01g49190.1"^^ . . . . "^\\d+$"^^ . . . . "^\\S+$"^^ . . "00000022"^^ . "allergen" . "Tom Gillespie" . . . "bibliography" . . . "https://data.4dnucleome.org/biosources/$1"^^ . "smp-m3w9hbe"^^ . . "experimental condition" . "hrehm@mgh.harvard.edu" . . "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/"^^ . . "mouse" . "metabolomics" . . . "kegg.genome" . . . . "International repository of Adverse Outcome Pathways."^^ . "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA."^^ . . . . . . . . "ontology" . . _:N39ed82037cb5445ab076272c9b940c48 "cozzone@ibcp.fr" . . . . . "http://www.w3.org/2001/XMLSchema#"^^ . . . . . "https://vcell.org/biomodel-"^^ . . . "https://www.uniprot.org/database/" . . "cell_model_passport" . . . "ontology" . "The allele registry provides and maintains identifiers for genetic variants"^^ . . . "protein" . "phenomics" . . . . . . "ontology" . "genome" . . . "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1"^^ . . . "https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_$1"^^ . . . . "illumina.probe" . . . "appears in" . "Lars Eisen" . . . . . . . . "fdb8a927-45c3-48b7-9743-cbb5e16837fa"^^ . . . . . . . . . . . "http://purl.obolibrary.org/obo/ATO_"^^ . "co_337" . . "BioModels Database" . . . . "developmental biology" . . "biomedical science" . . . "drug" . . . . . "h_aktPathway"^^ . . . "uc001rvw.5"^^ . "sfam" . . . . . . . "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID="^^ . . "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^ . "plant phenotypes and traits" . "http://purl.obolibrary.org/obo/"^^ . "version control" . . . "false"^^ . . . . "https://gen3.theanvil.io/ga4gh/drs/v1/objects/"^^ . . . "orchard@ebi.ac.uk" . . "NPC139585"^^ . "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library."^^ . . . "Healthcare Organizations and Services Ontology" . "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"^^ . . . "Space Life Sciences Ontology" . . "MIRBASEM" . . . . "mutation" . "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology."^^ . "taxonomic classification" . . "https://www.flymine.org/come/entry?gn=$1"^^ . . "aao" . "Anne Morgat" . . . . "http://purl.obolibrary.org/obo/HSO_"^^ . . . "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein="^^ . . . . . . . . "Gene Wiki" . . "Bioregistry Collections" . "structure" . "Michael Hucka" . . . "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information."^^ . "http://purl.obolibrary.org/obo/HOM_$1"^^ . "Assembling the Fungal Tree of Life - Category" . . . . "^\\d{6}$"^^ . _:Nd45bb82a739d443a9a81f0bffd8efefc . . . . "Porifera Ontology" . "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis="^^ . . . . . . . . . "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . . . . . "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population."^^ . . . . . "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"^^ . . "support@bel.bio" . . "chemistry" . . "https://www.kew.org/data/grasses-db/www/"^^ . . . "molecular chemistry" . . . . . "https://gitlab.com/"^^ . . . "https://biopragmatics.github.io/providers/peff/"^^ . . . . . . . . . "https://glytoucan.org/Structures/Glycans/$1"^^ . . . "Donna R. Maglott" . . "Process Chemistry Ontology" . "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data."^^ . . "http://purl.obolibrary.org/obo/NBO_$1"^^ . "piroplasma" . "eupath" . "cryoem" . . . "physical samples" . "^[A-Z]+[0-9]+$"^^ . . "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." . . . "true"^^ . "VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host."^^ . "Activity Streams" . . "protein" . . . "life science" . . . . "obo" . "snoRNABase" . "Fernanda Farinelli" . . . "false"^^ . . . "^[A-Za-z0-9+_.%-:]+$"^^ . . . "^\\d{7}$"^^ . "1915"^^ . . "Mental Disease Ontology" . . . . . "taxonomy" . . . . "0000001"^^ . . . _:N39ab7487df2d480a9cb36e248b317eea . "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n"^^ . "MatrixDB Association" . . "The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model."^^ . "https://bioregistry.io/panorama:"^^ . . "^DDInter\\d+$"^^ . . . . _:N4bb080adea3244668a33721fe25e6ef1 "Gregg Kellogg" . "^[0-9]+\\.[0-9]+$"^^ . . . "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available."^^ . "LCSCCPN"^^ . . . "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . . . . "DeBiO" . . . "^DTXSID\\d+$"^^ . "computational biology" . "983"^^ . "synthetic biology" . "false"^^ . . "https://biocomputeobject.org/BCO_$1"^^ . . "PK-DB" . "false"^^ . . "academy" . . "SWISS-MODEL Repository" . . "tahh" . "^\\d+$"^^ . . "pato" . . "International Medical Device Regulators Forum" . . "merops.inhibitor" . "false"^^ . "pride.project" . "food" . . . . . "PiroplasmaDB" . . . . . . "unique academic work identifier assigned in Scopus bibliographic database"^^ . . "61467"^^ . . "false"^^ . "false"^^ . . . . "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"^^ . "^\\d+$"^^ . . . . . "study design" . . "biology" . . "false"^^ . . "http://purl.obolibrary.org/obo/PDRO_$1"^^ . "Data Object Service" . . "datf" . . "EMD-1001"^^ . . . . . "Medical Dictionary for Regulatory Activities Terminology" . . "^\\d+$"^^ . . . "https://omabrowser.org/oma/hog/HOG:$1"^^ . . "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."^^ . "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms."^^ . . "MMsINC" . "gpcrnava" . . . . "false"^^ . "42840"^^ . . . "life science" . "https://bioschemas.org/profiles/$1"^^ . . . "false"^^ . . . . "ICD9CM" . . "^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$"^^ . "^\\d+$"^^ . "https://www.merckmillipore.com/catalogue/item/$1"^^ . . "ontology" . . "Simple Knowledge Organization System" . . . "subject agnostic" . . "false"^^ . . "false"^^ . . . . "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$"^^ . . . . "viroligo" . . . . . . . . "^[a-z0-9-]+$"^^ . _:Nbbc79547cdff4e5c9df18bd7c99700af "Michael Lincoln" . . . . . . "false"^^ . . . . . . . . . "development" . . "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes."^^ . "obo" . "life science" . . . . "chemistry" . "agriculture" . "false"^^ . "antibodyregistry" . "genome" . "ontology" . . . . "^G(PL|SM|SE|DS)\\d+$"^^ . . . . "NIF Standard Ontology: Molecules" . . . . "carrine.blank@umontana.edu" . "irgsp" . . "data model" . . "biology" . "obo" . . . "Software ontology" . "^[0-9\\-_]+$"^^ . "disease" . "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . . "http://www.co-ode.org/ontologies/galen#$1"^^ . . "http://purl.obolibrary.org/obo/PAO_$1"^^ . . . "Cell line collections (Providers)"^^ . "oral surgery" . . . "DAP000773"^^ . . . "vgnc" . . . . "0001021"^^ . . . . "Ryan Brinkman" . . "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"^^ . . . . "botany" . "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . "nlx.res" . . . . "Thorsten Henrich" . "Japan Registry of Clinical Trials" . . . . . . "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^ . . . . "A vocabulary for the catalysis disciplines" . . "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1"^^ . . . "Margaret R. Woodhouse" . "Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID]"^^ . "life science" . "Semantic Web for Earth and Environment Technology Ontology" . . "report" . . . "has identifier space owner" . . . . . . . . "https://www.nsf.gov/awardsearch/showAward?AWD_ID="^^ . . . . "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . . . . . . . . . . . . . . . . . "http://bigg.ucsd.edu/models/universal/metabolites/"^^ . "tngb" . . . . . . . . "The SEED;" . . . "dce" . "false"^^ . . . . "false"^^ . . "false"^^ . . . "^\\d+$"^^ . "glycosciencesdb" . . "Reagent Ontology" . . . . "symp" . . "https://neurovault.org/collections/"^^ . "SCOP(e) concise classification string" . "National Science Foundation Award" . . . "Christian-Alexander Dudek" . . . . . "GLIDA Ligand" . "protein" . "MGI" . . . "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$"^^ . . "^\\d{7}$"^^ . "false"^^ . "morphology" . . . . "obo" . . . "http://purl.obolibrary.org/obo/FYPO_"^^ . . . "^\\d{7}$"^^ . "https://genelab-data.ndc.nasa.gov/genelab/accession/"^^ . . "https://biosimulators.org/simulators/$1"^^ . . . . . "Tick Anatomy Ontology" . "CHEMBL3467"^^ . "j.detras@cgiar.org" . "ktk@netlabs.org" . . "spider" . "^DB-\\d{4}$"^^ . "eagle-i" . . "http://purl.obolibrary.org/obo/IDO_"^^ . . . . . "A manually curated resource for the representation and annotation of metabolic pathways"^^ . . . . . . . . . "environmental material" . "allergome" . . . "Datanator Metabolite" . "https://www.osti.gov/biblio/"^^ . "Taxonomic rank vocabulary" . . . "http://string.embl.de/interactions/"^^ . . "^\\d{7}$"^^ . . . . . . . . . . . . . "ontology" . "Legacy disease classes that later became MONDO"^^ . "^RCB\\d+$"^^ . . . "infectious disease medicine" . . . . "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . "false"^^ . "health science" . . "genomics" . . . "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."^^ . "Jens Klump" . "Human Plasma Membrane Receptome Families" . . . "https://lov.linkeddata.es/dataset/lov/vocabs/$1" . . "grouping" . . "sharkipedia.species" . "http://purl.obolibrary.org/obo/MIAPA_$1"^^ . "medicine" . . . "cheminformatics" . . . "chemistry" . . "chembank" . . . "false"^^ . . "Transport Systems Tracker" . "obo" . "topics" . . . . . . . "345201101230312003"^^ . . . . . . "Flybase Cell Line" . "^\\d{8}$"^^ . "agrkb" . "NIF Standard Ontology: Cell Types" . . "neurobiology" . "gxa.gene" . "biomedical science" . . "protein" . "^\\d{7}$"^^ . . _:N8567bba41b474a04adf4491efb98c660 . "http://www.probonto.org/ontology#PROB_$1"^^ . . _:Ndf8772f8d5b14f2a81291b8a225d1742 "pbrooks@hcfa.gov" . . "Mathias Uhlen" . . "data identity and mapping" . "^\\d+$"^^ . . . "development" . . . . "1000001"^^ . . "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks."^^ . "https://www.arraymap.org/pgx:$1"^^ . "^\\d+$"^^ . "false"^^ . . . "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^ . "false"^^ . . . "Sequence-Structural Templates of Single-member Superfamilies" . . . " The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies.\n\nIn 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)"^^ . "awalker@apa.org" . "0002350"^^ . "orcid" . "inaturalist.taxon" . "dev.ga4ghdos" . "^\\d+$"^^ . . "mediadive.ingredient" . . . . "biocyc" . "false"^^ . "UK Higher Education Statistics Agency" . "health science" . "TogoID" . . "^\\d+$"^^ . "electrocardiography" . "^HIP\\d{9}(\\.\\d+)?$"^^ . "12dgr161"^^ . . "protein" . . . . . . "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure"^^ . "^NONHSAT\\d{6}$"^^ . . "ChEBI" . . "eroshkin@burnham.org" . . "botany" . "https://www.re3data.org/repository/$1" . . "http://metnetonline.org/browse_pathway2.php?pthID="^^ . . "cryopreservation" . . "https://gold.jgi.doe.gov/resolver?id="^^ . . "false"^^ . . . . "http://genomics.senescence.info/diet/details.php?id=$1"^^ . "obo" . . "bibliography" . . . . "spectrometry" . "^\\d+$"^^ . . "dna" . "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"^^ . . "anatomy" . . . . . "true"^^ . "microscope" . "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations."^^ . "obo" . . . . "https://purl.dataone.org/odo/ADCAD_"^^ . . . "cran" . "classification" . . . . . "protein" . . . "SCC111"^^ . . "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^ . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1"^^ . "https://browser.planteome.org/amigo/term/PECO:"^^ . "SUPERFAMILY" . . "comparative genomics" . . "1731"^^ . "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan."^^ . . . . . "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u"^^ . . . . . . . . "false"^^ . . . . "Accession number of an entry from the BIND database."^^ . "uBio NameBank" . . . . "OpenCitations Meta Identifier" . "structure" . "nutritional science" . "drugs" . . . "mirEX" . "genecards" . "https://pharmacodb.ca/cell_lines/$1"^^ . . "Intrinsically Disordered proteins with Extensive Annotations and Literature" . . "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics."^^ . . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"^^ . "Chemical Entity Materials and Reactions Ontological Framework" . "snp2tfbs" . "chemical entity" . . . "NCI Data Commons Framework Services" . . . "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks."^^ . "Electron Microscopy Data Bank" . . . "ihw" . . . "^\\d{7}$"^^ . . . "gene name" . . . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1"^^ . . . "614"^^ . . . . . . . "Q-2958"^^ . . . . . "phylogenetics" . . . . . . . "https://www.vmh.life/#gene/"^^ . "Chinese Clinical Trial Registry" . "VEGA" . . . . . . . "https://purl.dataone.org/odo/SALMON_"^^ . . . "https://www.uniprot.org/keywords/$1"^^ . "addexbio" . "false"^^ . . . "electronic health record" . . "^\\d+$"^^ . . "Shorthand representations of languages and their subtypes"^^ . "^\\d{7}$"^^ . . "F11903"^^ . "icd9" . . "PSI-MI" . "developmental biology" . . "true"^^ . . "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"^^ . . . . . . . . . . "https://sed-ml.org/urns.html#format:"^^ . . . "ero" . "ontology" . . "Loggerhead nesting" . . . . "wd" . "http://purl.org/spar/c4o/$1"^^ . "false"^^ . . . "https://cropontology.org/rdf/CO_360:"^^ . "organ" . . . . "TAX" . "phenomics" . "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . "NLXMOL" . "binding site" . . . "^UDB\\d{6}$"^^ . "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata."^^ . . "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^ . "ontology" . . . "0000255"^^ . . "National Repository of Fish Cell Lines" . "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"^^ . . . . . "^\\d{7}$"^^ . . . . . . "pathogen" . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"^^ . "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . . . "genetics" . "Life cycle stages for Medaka"^^ . . . "mapping_justification"^^ . . . . . . "MeDRA" . "false"^^ . . "125768"^^ . "^AB\\d+$"^^ . . . . . "NONCODE v4 Transcript" . . "computer science" . . . "ccrid" . "Surjeet Kumar Arya" . . "Barry Smith" . "^\\w\\d+$"^^ . . . . . "genome" . "biokc" . . . "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^ . . . "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . . "bioproject" . "SubstrateDB" . . "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays."^^ . . "https://bioregistry.io/wikigenes:"^^ . . "gobp" . . "http://purl.obolibrary.org/obo/GNO_"^^ . "false"^^ . "ASKEM Epidemiology Prefixes" . . . . . "false"^^ . . "false"^^ . . . "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures."^^ . "false"^^ . . . . . . . . . . "false"^^ . "Jörg Stülke" . . "false"^^ . . . . . "civic.mpid" . . . . . "regulation" . "cls" . . "Molecular Process Ontology" . . . "^\\d+$"^^ . "Conserved Domain Database at NCBI" . . . . . . "wbls" . . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1"^^ . . . . . . . "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships."^^ . . . . . . "false"^^ . . "abandrowski@ncmir.ucsd.edu" . . "Raymond Lee" . . . . . . "https://bioregistry.io/genpept:"^^ . . . "anatomy" . . . "https://www.pirbright.ac.uk/node/"^^ . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . "Drosophila RNAi Screening Center" . . . "false"^^ . "A0TMC"^^ . . . . . . "^[0-9a-zA-Z]+$"^^ . . . "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . . . . . "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps."^^ . . . "Ligand-Gated Ion Channel database" . "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language."^^ . . "https://ssbd.riken.jp/database/project/"^^ . . . . "Laurel Cooper" . "https://mednet-communities.net/inn/db/ViewINN.aspx?i="^^ . "Jeffrey Grethe" . "life cycle" . "^EBI\\-[0-9]+$"^^ . . . . . . . . . . . . . . . . "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations."^^ . "http://purl.obolibrary.org/obo/PD_ST_$1"^^ . "omics" . . "AC119"^^ . "https://cropontology.org/rdf/CO_334:"^^ . . . . . . . . "sjbrown@ksu.edu" . "computational biology" . . . "ontology" . . . . . . . "obo" . . "Citation Typing Ontology" . . . . . . . . "statistics" . . . . "243002_at"^^ . . "Cell Ontology" . . . . . "biomedical science" . . "NeuroVault Image" . . . . . . . . "false"^^ . "KEGG Orthology" . . "sequence" . . . "cath.domain" . "false"^^ . "ontology" . "GO Evidence Code" . "false"^^ . . "false"^^ . . . "https://dbpedia.org/ontology/$1"^^ . "tahe" . "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID="^^ . . "uniprot.resource" . . "biology" . . . . "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."^^ . "Elvira Mitraka" . "earth science" . . . . . "true"^^ . . . "false"^^ . "OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources."^^ . . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . . . . "Ecological terms"^^ . . . "http://purl.obolibrary.org/obo/FOBI_"^^ . . . . . . "Healthcare Common Procedure Coding System" . "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . . "CryptoDB" . . . . . "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^ . . "chiro" . . . "GenProp0699"^^ . . "true"^^ . . . "vbo" . "https://bioregistry.io/abs:"^^ . "https://www.metanetx.org/equa_info/$1"^^ . . "https://www.ebi.ac.uk/interpro/entry/pfam/$1"^^ . . . . . "NUI" . "^\\d{7}$"^^ . "http://www.wikidata.org/entity/$1"^^ . . . "^SIGNOR\\-[A-Z]+\\d+$"^^ . "biomedical science" . . "faldo" . "obo" . . . . "Oryzabase Gene" . "ontology" . . . . "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"^^ . . . . . . "genome" . . . "functional genomics" . . . . . . . . "hinv.locus" . . . "https://www.ebi.ac.uk/QuickGO/GProtein?ac="^^ . "salk" . . . . . . . "inn" . . "4390079"^^ . . . . "http://snomed.info/id/"^^ . . "Ontology of Host Pathogen Interactions" . "http://purl.org/pav/"^^ . . . "Datanator Gene" . "https://pubchem.ncbi.nlm.nih.gov/classification/#hid="^^ . "ontology" . "Networked Knowledge Organization Systems/Services/Structures" . "false"^^ . . . "vario" . "tissue" . . . . . "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^ . . "^\\d+$"^^ . . . "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^ . . . "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1"^^ . . . . . . "biomedical science" . . "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . "An ontology for dengue fever."^^ . . "NIHhESC-10-0083"^^ . . "gregory.landrum@phys.chem.ethz.ch" . . . . . _:N833306e1b1f5424d97974ffc4ab537e9 . . . "false"^^ . . . . . "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE."^^ . . "^PR\\d{5}$"^^ . . "biology" . . . "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences."^^ . . . . "oct 2016"^^ . "ac" . . . . "false"^^ . . "Matthew Brush" . "0000057"^^ . "cpd15380"^^ . . . "https://www.biozol.de/en/product/"^^ . "false"^^ . . "ontology" . "AOPWiki (Stressor)" . "^\\d+$"^^ . . . "307"^^ . "false"^^ . . . "^\\d+$"^^ . "dashr.expression" . . . "earth science" . . . "false"^^ . . "false"^^ . . . . . "false"^^ . . "pathway" . "^\\d+$"^^ . "0020"^^ . . . "protein" . . . . . . . "http://purl.obolibrary.org/obo/GENEPIO_"^^ . . . "ontology" . . . . . . . . . "NIFEXT" . "2gc4"^^ . . "RubyGems" . "http://purl.obolibrary.org/obo/GECKO_"^^ . "rsankar@iitk.ac.in" . . . "https://pubchem.ncbi.nlm.nih.gov/cell/"^^ . "covid-19" . . . . "http://purl.org/oban/"^^ . "false"^^ . . . . . . "oryzabase.mutant" . . . . . "Alice Allen" . "tred" . "biomedical science" . "compulyeast" . "SM0000020"^^ . . . "http://sideeffects.embl.de/se/"^^ . "VMH reaction" . . . . . "27267"^^ . . . . . . "small molecule" . "false"^^ . . . "inbred rat strain" . . . . . "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^ . . . . "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"^^ . . . "false"^^ . . . . . . . . "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"^^ . . "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. "^^ . "Cancer Data Standards Registry and Repository" . "http://purl.obolibrary.org/obo/CLO_$1"^^ . "NLXRES" . "elvira@imbb.forth.gr" . . . . "http://scop.berkeley.edu/sid=$1"^^ . "https://www.uniprot.org/diseases/"^^ . . "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$"^^ . . . . . . . . "FCB005"^^ . . . . . . "physiology" . "false"^^ . . . . . . . . "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1"^^ . . . . . . "ontoavida" . . "version 2019 - pvs"^^ . "insdc" . . . . "http://purl.org/spar/datacite/$1"^^ . . . . "bioresource" . "murphyte@ncbi.nlm.nih.gov" . . . . "4D Nucleome Data Portal Experiment Replicate" . . "fish" . "0000029"^^ . "protein" . . . "VMH metabolite" . "IntellectualContribution"^^ . "Sustainable Development Goals Interface Ontology" . . . "^\\w+$"^^ . "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community."^^ . "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?"^^ . . . "molecular entity" . . . "https://repo.napdi.org/study/"^^ . "https://cropontology.org/rdf/CO_331:$1"^^ . . "https://bioregistry.io/ccdc:"^^ . . . "https://www.genedb.org/gene/$1"^^ . . . . . "false"^^ . . . . "metatlas" . "^000\\d{5}$"^^ . "false"^^ . . "biology" . "https://nztcs.org.nz/nztcs-species/"^^ . "Pierre.Cosson@unige.ch" . . . "HGNC gene symbol" . . . "genome" . . . . . . . "Clytia hemisphaerica Development and Anatomy Ontology" . "live mouse" . . . "jstor" . . . . . . "0000404"^^ . "false"^^ . . "plant phenotypes and traits" . "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata."^^ . . "https://fairsharing.org/organisations/$1"^^ . "tccd" . . "Dorothea Iglezakis" . . "^\\d{7}$"^^ . . . . . "^[A-Z-_0-9]+$"^^ . . . . "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay."^^ . "NeuroVault Collection" . "http://purl.obolibrary.org/obo/MONDO_"^^ . . "nanoparticle" . "0000139"^^ . "metabolomics" . "false"^^ . . . . "false"^^ . "geography" . "SBML RDF Vocabulary" . . . "false"^^ . . . "ontology" . . . . . . . . . . "pathway" . "Polygenic Score Catalog" . "^\\d{7}$"^^ . . . . . "Virus' miRNA target" . "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact."^^ . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules."^^ . "http://scop.berkeley.edu/sunid="^^ . "ontology" . . "^\\d+$"^^ . . "SNOMEDCT_US_2021_03_01" . . . . "The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]"^^ . . "false"^^ . . "^\\d+$"^^ . . . . . . "false"^^ . . . "Comparative Data Analysis Ontology" . "Data Science Ontology" . . . . . . . "uniprot.ptm" . . "true"^^ . "Chemistry resources"^^ . "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases."^^ . . . . . . "confident.event" . . "metabolite" . "domain" . "^\\d{7}$"^^ . "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"^^ . "https://cropontology.org/ontology/$1" . "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . "ontology" . "Fyler" . . "foaf" . . . . . . "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^ . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . . . . "nucleotide" . "https://publons.com/publon/"^^ . . . . . . "false"^^ . . "Christopher M. Overall" . "https://www.brenda-enzymes.org/php/result_flat.php4?ecno="^^ . . . . "biomedical science" . . "https://gpcrdb.org/protein/"^^ . "spike.map" . . "bionumbers" . . "iso.3166" . . . . . . . "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"^^ . . . . "https://bioregistry.io/kerafast:"^^ . . . . "protein" . "plant" . "baeverma@jcvi.org" . . . . . . . . . . "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins."^^ . . "The Drug Ontology" . "plasmid" . . . . "pharmacology" . "fcsfree" . "iceo" . . . . "genome" . . . "http://purl.obolibrary.org/obo/PO_"^^ . . . "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster="^^ . "gomfid" . . . "chemistry" . . . . "The Amphioxus Development and Anatomy Ontology" . "structure" . "taxonomy" . "amino acid sequence" . "ontology" . . "http://www.icd9data.com/getICD9Code.ashx?icd9="^^ . "classification" . "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . "Dictyostelium discoideum phenotype ontology" . . . _:Nc8116353cdbb47418cccd7d79b6ca2a2 "Stephen Larson" . . . "false"^^ . "DIP-743N"^^ . . . "An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix)."^^ . . . . "https://books.google.com/books?id="^^ . "https://lov.linkeddata.es" . . "91792"^^ . "http://standards.iso.org/iso/15926/part14/$1"^^ . . "false"^^ . . "scop.sid" . . . "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off"^^ . "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"^^ . . . . . . "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth."^^ . "biobank" . . "mass spectrum" . "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1"^^ . . "NIH HIV Reagent Program" . "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"^^ . . "cosmic.cell" . . . . . . . "Cellosaurus Publication" . . . . "OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . "true"^^ . . "organ" . "https://doi.org/$1"^^ . . . "maize" . . "0005250"^^ . "https://cropontology.org/rdf/CO_337:"^^ . . . . . "ovae" . "obo" . . . "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . . . "PerkinElmer cell line collection" . . "UniChem compound" . . "false"^^ . . "Research Organization Registry" . . "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)"^^ . . . "SoyBase" . . . "feolo@ncbi.nlm.nih.gov" . . "InterLex" . "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." . . "^\\d+$"^^ . _:N648de9a3c9414188aeff24d0e23085c4 "kate.rose@noaa.gov" . "digital curation" . "^\\d{7}$"^^ . "health science" . . "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"^^ . . "http://vocabularies.bridgedb.org/ops#$1"^^ . . "rpillich@ucsd.edu" . . "Cell Lines in PubChem"^^ . . . "0000001"^^ . "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"^^ . "rna secondary structure" . "slm" . "life science" . "bibliography" . "These resources represent software repositories" . . "vertebrate" . . "https://web.expasy.org/cellosaurus/cellopub/"^^ . . . "gene" . . . . . . . . . . . . . . . . . . . . . . "UM-BBD_pathwayID" . . . . "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code="^^ . . . . . . . . "ebisc" . . . . "false"^^ . "viaf" . . . "https://aopwiki.org/relationships/$1"^^ . . "frim1"^^ . "false"^^ . . . "stitch" . . "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"^^ . "KC-0979"^^ . . . . "Matt Yoder" . . . "Carbohydrate Active EnZYmes" . . . . "behavior" . "Clair Kronk" . . "life science" . . . "gxa.expt" . "http://genomics.senescence.info/diet/details.php?id="^^ . "protein" . "false"^^ . . "ndr@ebi.ac.uk" . . . . "ontology and terminology" . "sasbdb" . . "false"^^ . "life science" . . . "vipr" . . . "26753"^^ . . . "pactr" . . "dna" . . . . . . . "vmhgene" . . "^\\d+$"^^ . . "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . . . . . . . . . . . . . . . . . . "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID="^^ . "^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$"^^ . . . "pharmacogenomics" . "Gary L Andersen" . . . . "enzyme commission number" . . . . . . _:N35b9ad34ce8c47dd8af00d082157e04c . "TTD Target" . . . . . . . . . _:Nb442475fa3224b19bb8053380c939eec "Jan Willis, NLM" . . . "chemrof" . . . "ontology" . . . . . . "unique identifiers" . . . . . . . . . "^\\d+$"^^ . . . "Elspeth Bruford" . . "87"^^ . . "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did="^^ . . "^[1-9]\\d{0,11}$"^^ . "false"^^ . "nmr" . . . . "fplx" . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"^^ . . "https://bioregistry.io/bmrb:"^^ . . . . . . . "Identifiers.org Ontology" . . "civic.tid" . . "AOPWiki" . "https://www.ncbi.nlm.nih.gov/biosystems/"^^ . . . . . . . . . . "http://purl.obolibrary.org/obo/EHDAA2_"^^ . . . . . . "An expanded example URL for a resource or metaresource." . "^\\d{7}$"^^ . . . . "Bacillus subtilis genome sequencing project" . . . . "Cellosaurus" . . . "http://www-snorna.biotoul.fr/plus.php?id="^^ . . . . . . . "http://purl.obolibrary.org/obo/PATO_$1"^^ . . . "ebf69ca24298b28b2361e7d43eb52d6c"^^ . . . . . "microbiology" . . . . . . "^[A-Za-z-0-9]+$"^^ . "iso15926" . . "sdap" . . "vcell" . . . . . . "The reviewer of a prefix" . . "protein" . . "cob" . . . "bioinformatics" . . . "medical informatics" . "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information."^^ . "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo"^^ . . "nucleotide" . "john.garavelli@ebi.ac.uk" . "https://crates.io/crates/"^^ . . . "molecular physical chemistry" . "f.grieder@nih.gov" . . . "1868"^^ . . . . . "CIViC Variant Group" . . . "DRUGBANK_ID" . . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena."^^ . . . . . . "false"^^ . . . "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)"^^ . . . "biology" . . . "BacMap Map" . "BP100000"^^ . "biomedical science" . . . "^\\d+$"^^ . . "go.model" . . . . "Catalogue of Life in Taiwan" . "adverse reaction" . "https://arxiv.org/abs/"^^ . . "Patricia Siguier" . . "98346"^^ . . _:N7f6fc0e00f37489aa7d35d8d331533dc . "https://bioregistry.io/mirex:"^^ . "ontology" . "fyeco" . . "http://purl.obolibrary.org/obo/WBls_$1"^^ . . . "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project."^^ . . "life science" . . . "^GLDS-\\d+$"^^ . . "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id="^^ . . . . . "true"^^ . . "http://purl.obolibrary.org/obo/TTO_$1"^^ . . . "https://www.imanislife.com/?s="^^ . . "project management" . "HD+118-001"^^ . . . "Maria Taboada" . . "^\\d+$"^^ . . . . . "tissue" . . . "http://cgsc.biology.yale.edu/Site.php?ID=$1"^^ . "regulation" . . "BIOMD0000000048"^^ . . "false"^^ . "biodiversity" . . . "egon.willighagen@gmail.com" . "http://bigg.ucsd.edu/models/universal/metabolites/$1"^^ . "https://biopragmatics.github.io/providers/dhba/"^^ . "gateway" . "DG00301"^^ . . "http://repository.topdownproteomics.org/proteoforms/$1"^^ . "genomics" . "mouse" . "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information."^^ . . . "Intrinsically Disordered Proteins Ontology" . . . "true"^^ . . "GOLD metadata" . "microRNA Ontology" . . . . "ontology" . . "Identifier for a place in iNaturalist"^^ . "fbbi" . . "Models developed with the Virtual Cell (VCell) software prorgam."^^ . . . . "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^ . . . "http://fossilworks.org/?a=taxonInfo&taxon_no="^^ . . "^\\d{7}$"^^ . "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1"^^ . "0000189"^^ . . . "6978836"^^ . . "http://www.w3.org/2002/07/owl#"^^ . . . . . "protein" . . . . . . "mmp.cat" . "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."^^ . . . "mediadive.solution" . . . "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^ . "data model" . . "genome" . . . . "false"^^ . "sepio" . . . . . . . . . . "Reference Sequence Collection" . . "viperdb" . . "hsa-let-7a"^^ . . . "TripleExpression"^^ . "d1id" . . . . "MmusDv" . . . . "^\\d+$"^^ . "ontology" . "false"^^ . "oryzabase.strain" . . . "http://purl.obolibrary.org/obo/CMF_$1"^^ . . . . . . "phosphorylation" . . . . . . . "FMA_RETIRED" . . . . . . "cba" . "http://purl.obolibrary.org/obo/EMAP_"^^ . . "pathway model" . "false"^^ . "An ontology describing the anatomical structures and characteristics of Porifera (sponges)"^^ . "false"^^ . "ontology" . . "false"^^ . "http://www.alzgene.org/geneoverview.asp?geneid=$1"^^ . "GlycomeDB" . . "agilent.probe" . . "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies."^^ . . . . . "HGVPM623"^^ . . "^B\\d{5}$"^^ . . "genetic engineering" . . . . "gene" . . . . "ontology" . . . . . . . "^\\d{7}(_\\d)?$"^^ . . . "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ="^^ . . "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"^^ . . "false"^^ . "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^ . . . . . "pathways" . . . "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.\n\n**Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3))."^^ . . . "false"^^ . . "embryo" . . . "https://go.drugbank.com/indications/$1"^^ . . . . . . "http://www.informatics.jax.org/accession/MGI:"^^ . . . . "The Artificial Intelligence Ontology" . . "organism supplier" . "^2-s2\\.0-\\d+$"^^ . . "FlowRepository" . . . . "http://purl.obolibrary.org/obo/kestrelo_$1"^^ . . . "obo" . "19803"^^ . "https://www.glycoepitope.jp/epitopes/$1"^^ . . . . . "life science" . . "obcs" . . "bel" . . . . "MassBank" . . . . . "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . . . "http://purl.obolibrary.org/obo/SEP_$1"^^ . "^[0-9]*$"^^ . . . . . . . . . "6VDC956"^^ . . "life science" . . "C0017565"^^ . . . . . . . . . "SIGNOR-C41"^^ . "plant phenotypes and traits" . . "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . "kegg" . . . "551115"^^ . . . "embryonic stem cell line" . "false"^^ . . "ABL1"^^ . . . . . . "life science" . "KEGG.DRUG" . . . . . "false"^^ . . "plant phenotypes and traits" . "3771877"^^ . . . "imgt.primerdb" . "^DBCOND\\d+$"^^ . . . "ontology" . "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"^^ . "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . "21393"^^ . . "mmmp.biomaps" . "http://purl.obolibrary.org/obo/LIPRO_"^^ . . . "https://bioregistry.io/rebase:"^^ . . . . . "true"^^ . . . "https://cropontology.org/rdf/CO_321:"^^ . "bioinformatics" . "mark@gersteinlab.org" . "http://purl.obolibrary.org/obo/ZECO_$1"^^ . . . . "Friend of a Friend" . "nucleic acid sequence" . . "^[EL]D[SG]-\\d+$"^^ . . "phenotype" . . . "google.patent" . "Drug Target Ontology" . . . . "0000254"^^ . "omics" . . "Protein Interaction Network Analysis" . "PomBase" . "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"^^ . . "http://www.wikipathways.org/instance/"^^ . . "agaedigk@cmh.edu" . "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"^^ . . . "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples."^^ . "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors."^^ . "^\\d+$"^^ . . . "abs" . . . . . "false"^^ . "GeneCards" . . . . . "1948"^^ . . "https://lincs.hms.harvard.edu/db/proteins/"^^ . . "https://cropontology.org/rdf/CO_343:$1"^^ . "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests."^^ . . . "Drosophila Genomics Resource Center" . . . . "^\\d{7}$"^^ . . "asin" . . . "ontology" . "^[A-Z\\-]+$"^^ . "immunogenetics" . "117145750"^^ . "Tuan Amith" . . "^\\d{7}$"^^ . "ontology" . . . . "false"^^ . "CVCL" . . . . "life science" . . . . "r3d100010772"^^ . . . . . . . "obo" . "J0705A10"^^ . . . . . . "https://gpcrdb.org/protein/$1"^^ . . . "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id="^^ . . . . . . . . "epidemiology" . . . . "agb@ebi.ac.uk" . . "^\\d+$"^^ . "0000072"^^ . . "SNHG3"^^ . . . . "^\\d+$"^^ . "ttd.target" . . . . . . "subtiwiki" . . . . . "pesticideinfo" . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . "http://purl.obolibrary.org/obo/FOVT_$1"^^ . . "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed."^^ . . . "entrez gene/locuslink" . . "http://www.receptors.org/nucleardb/proteins/"^^ . . . "false"^^ . . . "neuroscience" . "true"^^ . "genome" . "bibliography" . "Publons Researcher" . . . . "http://aps.unmc.edu/AP/database/query_output.php?ID="^^ . "http://purl.obolibrary.org/obo/HABRONATTUS_"^^ . "http://xmlns.com/foaf/0.1/"^^ . . "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . . "^\\d{7}$"^^ . "NIF Standard Ontology: Neurolex" . "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . . "ssbd.dataset" . . "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?"^^ . "https://spdx.org/licenses/"^^ . "computer science" . . "cellular component" . "^\\d{7}$"^^ . . . . . "^(\\w+)?\\d+$"^^ . . . . . . . "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."^^ . "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements."^^ . "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=$1"^^ . . "AntiBodies Chemically Defined database" . . . "LTS0004651"^^ . "false"^^ . . . "SMP0000219"^^ . "life science" . "008893080"^^ . . . . "emaps" . . "Microbial Conditions Ontology" . "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . . . . "NIF Standard Ontology: Brain Regions" . . "life science" . "http://purl.obolibrary.org/obo/SWO_$1"^^ . . . . . . "biomedical science" . . . . . "SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops."^^ . "23159291"^^ . . "151022"^^ . . "obo" . . . "https://smpdb.ca/view/$1"^^ . . "ajacobs@cas.org" . "pascale.gaudet@isb-sib.ch" . . "https://dgrc.bio.indiana.edu/product/View?product=$1"^^ . . . "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease"^^ . "proteomicsdb.peptide" . "dmba" . . . . . . . "https://go.drugbank.com/metabolites/"^^ . "neuroscience" . . . . "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$"^^ . "probesanddrugs" . . . . "Next Generation Biobanking Ontology" . . "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . "todd@wormbase.org" . . . "ddc" . . . . "This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]"^^ . . "Registry of Toxic Effects of Chemical Substances" . . "obo" . "^[0-9]+$"^^ . "https://medlineplus.gov/genetics/condition/"^^ . . "slkbase" . . . . . "National Uniform Claim Committee Taxonomy" . "ontology" . . . "covid19" . . . "metadata" . "false"^^ . "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1"^^ . "false"^^ . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id="^^ . "biomedical science" . "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . . . . . . "ganesh.swaminathan@sanger.ac.uk" . . . "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . "Cell Lines Service" . . "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . "^\\d{6}$"^^ . . "T0599"^^ . . . . . "RID1"^^ . . "The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . . "wb" . "http://purl.obolibrary.org/obo/SEPIO_"^^ . . . "^[A-Za-z0-9-]+$"^^ . . . . "Sri Lanka Clinical Trials Registry" . . "doi" . "grid.225360.0"^^ . "false"^^ . . . . . "ontology" . . . . "http://purl.obolibrary.org/obo/ADO_$1"^^ . "^\\d+$"^^ . "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis."^^ . "https://goldbook.iupac.org/terms/view/"^^ . . . "study design" . . . . . "false"^^ . . . . . . . . "PTM" . . . . . . . "C063233"^^ . "http://purl.obolibrary.org/obo/PSO_"^^ . "kegg_genome" . "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . . . . "http://purl.obolibrary.org/obo/ECTO_$1"^^ . . . . . "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$"^^ . . . "^DP\\d{5}r\\d{3}$"^^ . "ised" . . "Antony Williams" . . "w.simpson@orcid.org" . "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information."^^ . "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . "biomedical science" . . . "^\\d+$"^^ . "disease" . "https://discover.pennsieve.io/package/$1"^^ . "16941567"^^ . . . "false"^^ . "Simon Cox" . . _:N0e9622e07aba42a0b14922d6456e5c09 . . "1"^^ . . "Terminologia Histologica" . . . . "enzymatic reaction" . "false"^^ . . . "false"^^ . . . . . "phosphosite.sitegroup" . "false"^^ . . . "http://purl.obolibrary.org/obo/MFO_"^^ . . "^\\d+$"^^ . . . . . "Yeast Metabolome Database" . "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources"^^ . . . . "emmo" . . . . . "HMDB00001"^^ . "^IRCT\\d+N\\d+$"^^ . . "genetic disorder" . . . "diagnosis" . . "^[A-Z_0-9]+$"^^ . "experimental measurement" . "https://bioregistry.io/metaregistry/scholia/"^^ . . . "rna" . "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."^^ . . . . "0000006"^^ . . . . . "brazma@ebi.ac.uk" . "https://www.pharmvar.org/gene/"^^ . . . . . "disprot" . . "EHDAA2_RETIRED" . "worms" . "https://www.clinicaltrials.gov/study/"^^ . . . . . . "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO."^^ . "false"^^ . "http://purl.obolibrary.org/obo/MS_"^^ . "proteomics" . "P01116"^^ . . . . . . . . "false"^^ . "^\\d+$"^^ . . "Anita Bandrowski" . . . . "0002233"^^ . . . "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^ . . "https://www.ebi.ac.uk/complexportal/complex/$1"^^ . "true"^^ . . "File inside StoreDB"^^ . . . . . "27223"^^ . "ontology" . . . . . . "molecular biology" . . "false"^^ . "biology" . . . "638309541"^^ . "Lipid Ontology" . . "http://www.kegg.jp/entry/$1"^^ . "addgene" . "ecogene" . "http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2" . "Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research."^^ . "zachll@umich.edu" . "food" . . . . "Arabidopsis Information Portal" . "alignedWith"^^ . . "http://purl.obolibrary.org/obo/CLAO_$1"^^ . . . . "ontology" . . . "https://biopragmatics.github.io/providers/goche/$1"^^ . "gene" . . "^CHEMBL\\d+$"^^ . _:N92e5ed142870468bac61f5ddc8c2e9ba . "National Experimental Cell Resource Sharing Platform" . . . . . . . . "Carrine Blank" . "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds."^^ . "https://cropontology.org/rdf/CO_330:$1"^^ . . . "The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes."^^ . . "dcat" . "false"^^ . . "interlex" . "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."^^ . . . . . . . "embryo" . . . . . "nextprot" . "false"^^ . . . . "Mouse Tumor Biology Database" . "http://www.bindingdb.org/compact/"^^ . "biosimulators" . . . . "https://www.sharkipedia.org/trends/$1"^^ . . "Philippe Rocca-Serra" . "http://purl.obolibrary.org/obo/APO_"^^ . . . . . "brettolivier@gmail.com" . . . . "support@ccdc.cam.ac.uk" . . . "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature."^^ . "false"^^ . "http://unite.ut.ee/bl_forw.php?nimi="^^ . . "false"^^ . . . . "Carl F. Schaefer" . "0000001"^^ . "microbial" . . . . . . "faseb list" . . "https://www.inaturalist.org/taxa/"^^ . . . . . "03307879"^^ . . "ontology" . . "African Population Ontology" . . . . "biological sample" . "life science" . "mutant mouse strain" . . . . "COG_Cluster" . "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent."^^ . "false"^^ . . "4145692"^^ . . . "n.lenovere@gmail.com" . . . . . . "prosite" . . . . . . . . "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it."^^ . . "estdab" . . . . . . "Ctenophore Ontology" . . . "false"^^ . . . . . . . . "proteomicsdb.protein" . . . "hpo" . "^[0-9a-z_:\\.-]+$"^^ . . "AnVIL DRS" . "comparative genomics" . . . . . "^\\d+$"^^ . "00007294"^^ . . "Yeast Genome Order Browser" . . . "VSAO_RETIRED" . . . . . . "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)"^^ . "kanehisa@kuicr.kyoto-u.ac.jp" . . . . . . "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities."^^ . "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"^^ . "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties."^^ . . . "https://bbp.epfl.ch/nexus/web/studios/public/"^^ . "http://www.chemspider.com/$1"^^ . . . . . . . . . . "ontology" . . _:N3f1124850c29450a9be0c635dfd41a59 "Michael J. Lincoln MD" . "SNOMEDCT_2005_07_31" . . . "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"^^ . . . . . . . "MO000027"^^ . "https://www.ribocentre.org/docs/$1"^^ . . . "http://edamontology.org/format_"^^ . "57-27-2"^^ . . . . . . . "false"^^ . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . . . . . . . "CASRAI Contributor Roles Taxonomy" . . "ToxoDB" . . . . "https://biomedit.ch/rdf/sphn-ontology/sphn#$1"^^ . . "http://xmlns.com/foaf/0.1/$1"^^ . . "oostt" . . "^S\\w+(\\.)?\\w+(\\.)?$"^^ . "life science" . . . . . "false"^^ . . "protein" . . "scopus" . . . "Google Patents" . "http://purl.obolibrary.org/obo/EO_$1"^^ . . . "^\\d{8}$"^^ . . . "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"^^ . _:Na02fc64581ae4e3a98fdb9896d829d8f "WikiData Support" . . "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$"^^ . . "AP00378"^^ . "insdc.cds" . "false"^^ . . . "bioinformatics" . "false"^^ . . . "ontology" . "psychiatry" . . "false"^^ . . . "dna" . "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . "https://idr.openmicroscopy.org/search/?query=Name:idr$1"^^ . . . "life science" . . "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools."^^ . "skosxl" . "curated information" . "https://purl.dataone.org/odo/SASAP_$1"^^ . . . "obo" . "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."^^ . . . . "AAindex" . . . "Thermo Fisher Scientific" . "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1"^^ . . "ECU03_0820i"^^ . . . "^\\S+$"^^ . . "zoology" . "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties."^^ . "jimhu@tamu.edu" . . "https://flybase.org/reports/FBtc"^^ . "function" . . . . . . "obo" . . . . . . . . . . . . "anatomy" . "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"^^ . "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"^^ . . . "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments."^^ . "European Searchable Tumour Line Database" . "ontology" . . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . . . . "^\\d{7}$"^^ . . . "Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years."^^ . . . "false"^^ . "A controlled vocabulary to support the study of transcription in the mouse brain"^^ . "Environmental conditions, treatments and exposures ontology" . . "david.c.blackburn@gmail.com" . . . . "scop.sunid" . . "^[A-Za-z_0-9]+$"^^ . . "intact.molecule" . . "0010039"^^ . . "Ontology about the gross anatomy of the C. elegans"^^ . . "10015919"^^ . . "false"^^ . . . . . "ctd.gene" . "organic molecular chemistry" . . "http://scipion.i2pc.es/ontology/CRYOEM_$1"^^ . . . . . "Redistributor of bilogics and biomedical supplies"^^ . "false"^^ . "https://www.ebi.ac.uk/metagenomics/analyses/"^^ . "obo" . "International Traditional Medicine Clinical Trial Registry" . "https://civicdb.org/links/gene/"^^ . . "biomedical science" . . "false"^^ . . "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump"^^ . . "obo" . "http://opm.phar.umich.edu/protein.php?pdbid=$1"^^ . . "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information."^^ . "drug interaction" . . . . "false"^^ . . . . . "Genome assembly database - INSDC accessions" . . . "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents."^^ . "genome" . "rexo" . . "https://www.ncbi.nlm.nih.gov/nlmcatalog/"^^ . . . "pathogen" . "taxrank" . . . . . _:Nee718a1169484f53b606356afc36575f . "edam" . . . . . . "Livestock Breed Ontology" . . "anatomy" . "Adriano Mari" . . . "cmedigue@genoscope.cns.fr" . . "life science" . . . . . . . "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)."^^ . . . . . . "SLCTR/2023/010"^^ . . "^\\d+$"^^ . "drug" . . "http://scop.berkeley.edu/sid="^^ . . "metagenomics" . . "TBK Reddy" . "^[1-9]\\d{0,5}$"^^ . . . . "false"^^ . . . . . . . . "Gemina Symptom Ontology" . "neurobiology" . . "^\\d+$"^^ . . . . . . . "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012."^^ . . "false"^^ . . "^\\w+$"^^ . . "ICD9CM_2005" . "PseudoGene" . . . "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"^^ . . . "cas_id" . . . "^PF\\d{5}$"^^ . . . "https://www.uniprot.org/journals/"^^ . "NCIt" . . . "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/"^^ . "genomics" . . . . . . . "false"^^ . "cryptodb" . "false"^^ . . "false"^^ . . "sylvie.ricard-blum@univ-lyon1.fr" . . "Food Classification and Description System (from FSA Food Type identifiers)" . . "Human Protein Atlas tissue profile information" . "false"^^ . "neurovault.image" . . "https://orcid.org/$1"^^ . "depod@embl.de" . . . . "Neuro Behavior Ontology" . . . . . . "lipid" . . "pepbank" . . "2966"^^ . "mutation" . . "dna" . . "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum"^^ . . "biodiversity" . "medical informatics" . "PubMed Central" . . "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^ . . . . "false"^^ . . . . "disorder" . . . . . . "infection" . "false"^^ . "ccf" . . . . "Yeast Phenotype Ontology" . . . . "http://data.food.gov.uk/codes/foodtype/id/"^^ . "SNP to Transcription Factor Binding Sites" . "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$"^^ . "false"^^ . . . . "regulation of gene expression" . . "false"^^ . "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"^^ . . . . . . "Vernon Putz-Anderson" . . . . . . . "^[WAICV]\\d{2,}$"^^ . "false"^^ . . . "^[0-9][A-Za-z0-9]{3}$"^^ . . . . "uniprot.keyword" . . "Petra Fey" . . "false"^^ . . . "hdr" . "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources."^^ . . . . . "Sickle Cell Disease Ontology" . "sebastien.aubourg@inrae.fr" . "Global LEI Index" . . . . "Supplier of mice for research purposes. [from RRID]"^^ . . . . . "Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses."^^ . . "population genetics" . . "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype."^^ . . . . . . "Molecule role (INOH Protein name/family name ontology)" . "ontology" . "^\\d+$"^^ . "Ontology for Modeling and Representation of Social Entities" . . . . . . _:N39ed82037cb5445ab076272c9b940c48 . "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . "pharmacogenomics" . "rfam" . "^[a-zA-Z0-9-]+$"^^ . . . "panther.pthcmp" . . "hgnc.symbol" . "ISO 3166-1 Country Code" . . "knowledge and information systems" . . _:N615b517125c946639821d2766320e103 . "protein" . . "interaction" . . . "3618"^^ . . . "institution" . . . . "http://www.wikipathways.org/instance/$1"^^ . . "false"^^ . "false"^^ . . . . . "gramene.reference" . . . . "emap" . . . "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information."^^ . "Oryzabase Stage" . . . "hsa00190"^^ . . . "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding."^^ . "Jean-Luc Jannink" . "population genetics" . . "spider" . . . . "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^ . . . . . . "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information."^^ . . . "^\\d+$"^^ . . . "nucleotide" . . . "http://www.w3.org/ns/activitystreams#$1"^^ . . . . . "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1"^^ . . "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment."^^ . . . . "http://stormo.wustl.edu/ScerTF/details/$1"^^ . . . "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records."^^ . . "0000000"^^ . "expressed sequence tag" . . "16"^^ . . "Animal Genome Cattle QTL" . . "transcriptomics" . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information."^^ . . . . . . . . . "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . "The 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."^^ . . . . . . "vbase2" . . "sayers@ncbi.nlm.nih.gov" . "Mouse pathology ontology" . . . . "hp" . . "Simple Knowledge Organization System eXtension for Labels" . "wormbase" . . "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions."^^ . . "genes" . "^\\d+$"^^ . . . "drug discovery" . . . . . . . "https://vectorbase.org/gene/"^^ . . "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide)."^^ . "Veterans Health Administration (VHA) unique identifier" . . "data transformation" . . . "biology" . . . . "http://id.who.int/icd/entity/$1"^^ . "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/"^^ . . . . "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id="^^ . "^\\d{5}$"^^ . . . "John-Marc Chandonia" . . . "neurophysiology" . . . "false"^^ . "The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species."^^ . . "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1"^^ . "cro" . "Chinese Biological Abstracts" . . "ricenetdb.compound" . "http://www.radiomics.org/RO/$1"^^ . "false"^^ . "Online Mendelian Inheritance in Man" . . "https://cropontology.org/rdf/CO_336:$1"^^ . "molecular" . . "vertebrate" . . . "did" . . "false"^^ . . . . . "life science" . . . . . . . . "http://purl.obolibrary.org/obo/OMIT_"^^ . . "computational chemistry" . . . . "gwascentral.study" . . "REBASE Enzyme Number" . . . . "^CHEMBL\\d+$"^^ . . "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$"^^ . "biomodels.kisao" . "^NCT\\d{8}$"^^ . . "ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc."^^ . . "0000ffeb-36e0-4a29-b21d-84423bda979d"^^ . "false"^^ . . "http://www-snorna.biotoul.fr/plus.php?id=$1"^^ . "msig" . . . . . "http://ctdbase.org/detail.go?type=gene&acc=$1"^^ . "0000-0003-4423-4370"^^ . "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors."^^ . . . . "Office of Scientific and Technical Information (OSTI)" . . "TC010103"^^ . . . "disease" . "VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences."^^ . "Maize gross anatomy" . "aclame" . "http://purl.obolibrary.org/obo/VHOG_$1"^^ . "laml_tcga_pub"^^ . . . "19-T4"^^ . . "325.4"^^ . "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"^^ . "aftol.taxonomy" . . . "aftol.category" . "obo" . . . . "cell" . "false"^^ . "https://www.ebi.ac.uk/intact/search?query="^^ . "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"^^ . "GeneDB" . "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer"^^ . "^[a-z_A-Z0-9]+$"^^ . . "^[1-9]\\d*$"^^ . . . . . . . "INSDC CDS" . "^\\d{7}$"^^ . "false"^^ . "ontology" . . "false"^^ . "http://zinc15.docking.org/substances/$1"^^ . . . "computer science" . "^[0-9]{10}$"^^ . . . _:Nc42a19a78be84c6a84585e4d75f98e29 . "descriptor" . "An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains"^^ . . . . "OMA HOGs" . . . . . . "Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications."^^ . "0000013"^^ . . . "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="^^ . . "Nanbyo Disease Ontology" . . "GenBank" . . "Philip Strömert" . . . "gmd.gcms" . . "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community."^^ . . . "ASZ"^^ . . . "cldb" . . . "false"^^ . . "iNaturalist Observation" . "https://registry.bio2kg.org" . "^[a-zA-Z0-9]+\\.[a-f0-9]{24}$"^^ . . . . . "^CE\\d{5}$"^^ . . . "http://data.europa.eu/89h/$1"^^ . . . . . . "^\\d+$"^^ . . _:Nb210a71e511f4cbfa454a654c89797e8 "Crop Ontology Helpdesk" . "digital curation" . . "https://www.ebi.ac.uk/ega/datasets/$1"^^ . . "Plant Trait Ontology" . . "http://purl.obolibrary.org/obo/CRO_$1"^^ . . . . "DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use."^^ . . . . "ClinGen Allele Registry" . . . . "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways."^^ . "^\\d{7}$"^^ . "Genome Aggregation Database" . . "false"^^ . . "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^ . . "1000000"^^ . . . . "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"^^ . _:Nf2777a2942e4414f95db524e51c78f67 "Kota Ninomiya" . "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"^^ . . . " Hendrik Borgelt" . . . "12"^^ . "protein" . . . . . . . . "preclinical studies" . "YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes."^^ . . . . . "https://bioregistry.io/dbd:"^^ . "SPCC13B11.01"^^ . "RGD Disease Ontology" . "Performance Summary Display Ontology" . . . . "UniPathway Reaction" . "bioinformatics" . "chemistry" . "http://purl.obolibrary.org/obo/SBO_$1"^^ . . "apdavis3@ncsu.edu" . . . . . . . "j.huerta@csic.es" . . "Gwen Frishkoff" . . "protein" . . . . "https://www.ebi.ac.uk/arrayexpress/arrays/$1"^^ . . "http://www.weizmann.ac.il/molgen/loqate/gene/view/"^^ . "false"^^ . "0000078"^^ . "0000004"^^ . . "false"^^ . . . "nlx.org" . "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . . . . "consulting" . . . "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"^^ . "DragonDB Locus" . . . . . . "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends)."^^ . "^\\d+$"^^ . . "^([A-Z]+)?\\d+(\\.\\d+)?$"^^ . "Hilmar Lapp" . "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^ . . . "^\\d{7}$"^^ . . . . "TGN is a structured vocabulary currently containing around 1,106,000 names and other information about places. Names for a place may include names in the vernacular language, English, other languages, historical names, names and in natural order and inverted order. Among these names, one is flagged as the preferred name. TGN is a thesaurus, compliant with ISO and NISO standards for thesaurus construction; it contains hierarchical, equivalence, and associative relationships. Note that TGN is not a GIS (Geographic Information System). While many records in TGN include coordinates, these coordinates are approximate and are intended for reference only. The focus of each TGN record is a place. There are around 912,000 places in the TGN. In the database, each place record (also called a subject) is identified by a unique numeric ID. Linked to the record for the place are names, the place's parent or position in the hierarchy, other relationships, geographic coordinates, notes, sources for the data, and place types, which are terms describing the role of the place (e.g., inhabited place and state capital). The temporal coverage of the TGN ranges from prehistory to the present and the scope is global. The TGN is a hierarchical database; its trees branch from a root called Top of the TGN hierarchies (Subject_ID: 1000000). Currently there are two TGN facets, World and Extraterrestrial Places. Under the facet World, places are arranged in hierarchies generally representing the current political and physical world, although some historical nations and empires are also included. There may be multiple broader contexts, making the TGN polyhierarchical. The primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public."^^ . . . "w3c rec" . "agronomy" . . . . "medicine" . "false"^^ . . "gsherloc@stanford.edu" . . "cell culture" . . . "http://purl.obolibrary.org/obo/BCO_$1"^^ . . . . "https://biopragmatics.github.io/providers/goche/"^^ . . "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" . . "ev:E00032"^^ . . . . "concentration" . . . . . "medicine" . . "hepro" . . . "https://www.kazusa.or.jp/huge/gfpage/$1"^^ . . "wb.rnai" . . . "rxn00001"^^ . . . . _:N80f4a0195df04675932685e7c74132f3 . . . "structure" . . "tritrypdb" . . . . . . "ecocore" . "AHR"^^ . . . "Marc Ciriello" . "Nematode Expression Pattern DataBase" . . . "qb" . "Ian Foster" . . . . . "https://www.cellbiolabs.com/search?keywords="^^ . "http://clipserve.clip.ubc.ca/topfind/proteins/$1"^^ . . . . . "http://purl.obolibrary.org/obo/CLYH_"^^ . . "major histocompatibility complex" . . "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$"^^ . . "depends on" . . "genomics" . . . . "false"^^ . . . "^\\d{7}$"^^ . . . "^CL\\d+$"^^ . . . . "tgv139393198"^^ . . _:Nbe62732905da46fa8b5b42f91dc55de9 . . . . . . . . . "false"^^ . . . . "subject agnostic" . . "DDB0016567"^^ . . . . "expression" . "Antibiotic Resistance Ontology" . "http://purl.obolibrary.org/obo/PSDO_"^^ . . . . "obo" . . . . . . . . . "Teri E Klein" . . "gexo" . "false"^^ . . . . "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output."^^ . . "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable."^^ . . . . . . . . . . "model organism" . "pathway" . "1"^^ . . "SNOMEDCT_US_2022_09_01" . "bioinformatics" . . . "The COVID-19 epidemiology and monitoring ontology" . "Issaku Yamada" . . . "civic.molecularprofile" . "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:"^^ . "https://www.kegg.jp/entry/"^^ . "Digital archive of scholarly articles" . "^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$"^^ . . . "pathogen" . . "admin@envipath.org" . . . "obo" . . . . . "NIF Standard Ontology: Investigations" . . . . . . . "jkissing@uga.edu" . "fideo" . . "rouge" . . . "MGnify Sample" . "preclinical studies" . . . "worm" . . "botany" . "subject" . "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor."^^ . . "Vir-Mir db" . . . . "gene feature" . . . . . "FuncBase Fly" . . . "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1"^^ . . . . "^\\d{7}$"^^ . "genetic material" . . . . "http://purl.obolibrary.org/obo/COVIDO_$1"^^ . . . . . "https://bioregistry.io/cghdb:"^^ . "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources."^^ . . "AICARTRANSIMPCYCLO-CPLX"^^ . . . "Computational Chemistry Ontology" . "^C\\d+$"^^ . "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID="^^ . _:Nf670dc591a464c0e95466a2df952cb59 "helpdesk@cropontology-curationtool.org" . "159787"^^ . . . . . "https://creativecommons.org/ns#"^^ . . "subject agnostic" . "ontology" . . . "Carlo Ravagli" . . . "Brendan MacLean" . . . "life science" . . . . "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"^^ . . . . . "EAWAG Biocatalysis/Biodegradation Database" . . "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence."^^ . "identifier for chemicals linked to information on occurrence in plants"^^ . . . "MarCat" . . "https://sumlineknowledgebase.com/?page_id="^^ . . . "https://prefix.cc/$1" . "https://www.arraymap.org/pgx:"^^ . "https://bioregistry.io/bpdb:"^^ . . . . "International Traditional Medicine Clinical Trial Registry" . . "FB" . . "https://umgear.org/p?id="^^ . . . . . "http://www.ymdb.ca/compounds/$1"^^ . "life science" . . "ThermoFisher is a life sciences supply vendor."^^ . . . . . "ghr" . . "ontology" . "vaccination" . "1200"^^ . . . . . . "obo" . . "https://bartoc.org/" . . . "false"^^ . "obo" . . _:Nc4693202043b456eaa44488266112b67 . . . "0000156"^^ . . "preclinical studies" . . . "ontology" . . . . . . . . "uminctr" . . "^\\d{7}$"^^ . . . . . "20090303"^^ . "http://purl.obolibrary.org/obo/RBO_"^^ . . . "Amanda Hicks" . "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."^^ . "Global Proteome Machine Database" . . . . . "false"^^ . . . "resource metadata" . . "physics" . . . "ontology" . . . . . . "false"^^ . "http://www.cazy.org/$1.html"^^ . . "https://units-of-measurement.org/"^^ . . "lrg" . . . . . . . . . . . . . . . . "data model" . . . . . "1"^^ . . "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"^^ . . "PA146123006"^^ . "PepBank Peptide Database" . . "taxonomy" . "ecto" . . "Aquatic Sciences and Fisheries Information System" . "biomedical science" . . . . "https://www.vmh.life/#metabolite/$1"^^ . . . "w3c rec" . . "00000001"^^ . . . . . . . . . . . . . "SNOWMEDCT_US_2018_03_01" . . . . . "0019030"^^ . "Study inside StoreDB"^^ . . . "genecards.geneloc" . "pier.buttigieg@awi.de" . . "http://arabidopsis.info/StockInfo?NASC_id=$1"^^ . "12345"^^ . "Open Biomedical Annotations" . . . . . . "roberts@neb.com" . "http://www.scopus.com/record/display.url?origin=inward&eid=$1"^^ . "https://www.uniprot.org/arba/$1"^^ . . "ontology" . . . . "http://purl.obolibrary.org/obo/VSMO_$1"^^ . "^SLCTR/\\d{4}/\\d+$"^^ . . . . . . . "patient care" . "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1"^^ . . . . . "obo" . . "fernanda.dorea@sva.se" . "obo" . "http://senselab.med.yale.edu/ORDB/Data/$1"^^ . "false"^^ . . . . . . . "CORDIS Article" . . . "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum="^^ . "cell" . "3000887619"^^ . . . . . . . . . "dto" . . "repeatsdb.structure" . . "http://purl.uniprot.org/isoforms/"^^ . . "ZDB-GENE-041118-11"^^ . "mpidb" . "International Classifications of Diseases" . . "The main contact person for a registry" . . . . . . "0000210"^^ . . "pathway" . . . "ontology" . "FaceBase Data Repository" . . . . "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^ . . "false"^^ . . "AT1402"^^ . . "https://cropontology.org/rdf/CO_320:$1"^^ . . . "apollosv" . . . . . "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/"^^ . "NOAA Fisheries Species Directory" . "botany" . . . "botany" . . . . . . "regulation" . . . . "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . . "mouse" . . . . . . . "true"^^ . "voss@gbv.de" . "^\\d+$"^^ . . . . "goche" . "https://biosimulations.org/projects/"^^ . . . "ontology" . . . . "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical" . . . "false"^^ . "false"^^ . . . . "false"^^ . . . . . . . . . . "Obstetric and Neonatal Ontology" . . . . "myco.tuber" . . "Daniel Gautheret" . "false"^^ . . . . . . "Genome assembly database - RefSeq accessions" . . . . . . . . "The Ageing Gene Database" . . . . . . . . . . "false"^^ . . . . . . . . "protein" . . . . . . . "https://neurovault.org/images/$1"^^ . "eco" . . "http://purl.obolibrary.org/obo/INO_"^^ . "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"^^ . . . "agriculture" . . . . "false"^^ . "3305"^^ . . . "false"^^ . "Database of protein-protein complexes" . . "Cell line databases/resources"^^ . "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid="^^ . . . . . . . . . . . . . . "false"^^ . "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex)."^^ . . . . "hagr.gendr" . . . . "informatics" . . . . "cvx" . . . . "Google Books" . "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"^^ . . . "http://purl.obolibrary.org/obo/STATO_$1"^^ . "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . . . . "MEDLINE" . "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . "ppo" . "https://biopragmatics.github.io/providers/mba/"^^ . . . "D00001"^^ . . . "Allan Peter Davis" . . . . "interaction" . "false"^^ . "https://www.metanetx.org/chem_info/$1"^^ . . "https://pubchem.ncbi.nlm.nih.gov/element/"^^ . "http://champ-project.org/images/ontology/cao.owl#CAO_"^^ . . . "gene" . . . "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^ . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . . . "genome" . . "Ontology of units of Measure" . "ontology" . . . . . . "iRefWeb" . . "comparative genomics" . . . . "RHEA" . . . . . "Medical Dictionary for Regulatory Activities" . . . "life science" . "cath" . "spradling@ciwemb.edu" . . . "https://world-2dpage.expasy.org/repository/$1"^^ . . "^M\\d{4}$"^^ . . . . "mgiglio@som.umaryland.edu" . . . "0000547"^^ . . . . "https://reaxys.emolecules.com/cgi-bin/more?vid="^^ . "reagent" . . . . . . . . . . . . "fisheries science" . . . . "phenotype" . . . . . . "life sciences" . . "Compositional Dietary Nutrition Ontology" . "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"^^ . "^\\d{4,}((_[asx])?_at)$"^^ . . . . . "https://www.ebi.ac.uk/gwas/studies/$1"^^ . . "Chris Grove" . "false"^^ . . . . . "phenology" . . "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia."^^ . . . . . . . . "bioinformatics" . . "icdo" . "http://bioportal.bioontology.org/ontologies/"^^ . . "The cell line vocabulary inside FlyBase"^^ . . "false"^^ . . . . "biology" . . "false"^^ . "andreadega/systems-biology-compiler"^^ . . . "matt@tislab.org" . "functional genomics" . "structure" . . . . "NCI Pathway Interaction Database: Pathway" . "pharmacy" . . "genefarm" . . . . . . . "^\\w+$"^^ . "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms."^^ . "ProteomeXchange" . "6038"^^ . . . "swrl" . . "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^ . . . . "developmental biology" . . "GE86325"^^ . . . . . "0000050"^^ . . . . . "3447"^^ . . . "pierre.grenon@ifomis.uni-saarland.de" . "Thai Clinical Trials Registry" . "http://purl.obolibrary.org/obo/OlatDv_$1"^^ . "dawood@helix.nih.gov" . . . . . "NanoParticle Ontology" . "cell line" . . "life science" . . . "false"^^ . "false"^^ . . . "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . "ribonucleic acid" . "0000183"^^ . . "Golm Metabolome Database Reference Substance" . . . . . . "P12345"^^ . . . . . . . . "^\\w+(\\-)?\\w+(\\-)?\\w+$"^^ . . "genomics" . . . . . . "MicrobeamManipulation"^^ . . . . "uniprot" . . . "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." . . . . "^\\d+$"^^ . . . . . "DSSTox_Generic_SID" . . "tsc" . "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers."^^ . . . "^\\d+$"^^ . . . "debio" . "Shapes Constraint Language" . . "3517823"^^ . . . "marine biology" . "http://purl.uniprot.org/annotation/"^^ . . "PED00037"^^ . . "Plant Ontology" . . "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . . . . . "^MMP\\d+.\\d+$"^^ . "population genetics" . . "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec="^^ . . "http://purl.obolibrary.org/obo/EPO_$1"^^ . . . "Marilyn Safran" . "structural biology" . . . . . "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . "Robert Hoehndorf" . "A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . . . "biology" . "bliemsl@xs4all.nl" . . . . . . . . "Developing Mouse Brain Atlas" . "arrayexpress" . . . . "biochemistry" . "data model" . . "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id="^^ . . . . . "false"^^ . "false"^^ . "ird.segment" . . . . . . . . . . . "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"^^ . "ontology" . "false"^^ . . "false"^^ . . "false"^^ . "00573"^^ . "Planarian Phenotype Ontology" . . . . "^\\d+$"^^ . . . . . "life science" . "Antimicrobial Peptide Database" . "life science" . "http://purl.obolibrary.org/obo/PRIDE_"^^ . . . "https://www.ncbi.nlm.nih.gov/dbvar/studies/"^^ . "002368"^^ . "mutant mouse repository" . . . . . "false"^^ . . . . . . . . . . . . "life science" . . . "https://bioregistry.io/resolve/github/pull/$1"^^ . . . . "neurondb" . "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes)."^^ . "classification" . . "http://purl.obolibrary.org/obo/OMO_$1"^^ . "ChemBank" . . . . . . "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays."^^ . . . . . . . . "https://zenodo.org/record/$1"^^ . . "obo" . "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information."^^ . . . . . . "COSMIC Cell Lines" . "Soybean Trait Dictionary in template v5 - IITA - July 2015"^^ . . "false"^^ . "24801"^^ . "nucleardb" . . . . "004435"^^ . . . . . "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information."^^ . "http://purl.obolibrary.org/obo/HSO_$1"^^ . "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder."^^ . "https://biopragmatics.github.io/providers/cemo/"^^ . . . . . . _:Nbf80f06127494db5b73251968072335a . . . "development" . . "Pathguide contains information about 702 biological pathway related resources and molecular interaction related resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated. (from homepage)" . . . . . . "Montana Smith" . . "ontology" . . . . . . "BLL"^^ . . "AKR"^^ . . "BQJCRHHNABKAKU"^^ . . "http://vocab.getty.edu/page/tgn/$1"^^ . . . . . . "smr@stowers.org" . "A-GEOD-50"^^ . "90062901"^^ . "Provisional Cell Ontology" . . "http://purl.obolibrary.org/obo/FBbt_$1"^^ . . . "https://aopwiki.org/stressors/"^^ . . . . . . . "ATCC number" . . "false"^^ . "Simon Douglas Harding" . . . "false"^^ . . "louis@imbb.forth.gr" . "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^ . . . . . . . . . . . . "ontology" . . . . . . . "0002058"^^ . "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . . "ydpm" . . "dsmz" . . . . "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . . "268"^^ . "mo" . "Conrad L Schoch" . "vaccines" . . . . "resource metadata" . . . . "diagnosis" . . . . . "http://purl.obolibrary.org/obo/ECOCORE_"^^ . . . . "immunology" . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . "1250"^^ . . . . . "g.gkoutos@bham.ac.uk" . . . . "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems."^^ . . "general & upper" . . . . "faseb list" . "dct" . "https://bioregistry.io/ecoliwiki:"^^ . . "HMS Library of Integrated Network-based Cellular Signatures Datasets" . "mutation" . . . . . . . . . . . "Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance"^^ . . . . . . . . . "false"^^ . . "SECONDARY_CAS_RN" . . . "NIF Dysfunction" . "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf"^^ . . . "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively."^^ . . . "https://bdsc.indiana.edu/stocks/"^^ . . . . . . "md.tyers@umontreal.ca" . "single nucleotide polymorphism" . "false"^^ . . . . . . "diagnosis" . . . . . "false"^^ . "National Swine Resource and Research Center" . "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"^^ . . . "Al Kikhney" . . . . "false"^^ . _:N586e7aba53ab4b68932778362bfd0f96 . . . "https://cran.r-project.org/web/packages/"^^ . . . . "^[1-9]\\d{0,5}$"^^ . . . "nrfc" . "obo" . "genome" . . . . "1017"^^ . "Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a"^^ . "structural biology" . "http://purl.obolibrary.org/obo/EMAPA_"^^ . "Non-Coding RNA Ontology" . "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts."^^ . "1100107"^^ . . . . "https://scicrunch.org/resolver/RRID:IMSR_TAC_$1"^^ . . . . "^\\d+$"^^ . "protein" . . . . "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature."^^ . "00620027"^^ . . . . _:N1ec65468174440efa22fc2161b2bcbf1 "mssohelp@meddra.org" . "stewart.cole@epfl.ch" . . "http://europepmc.org/articles/$1"^^ . . "https://www.wikidata.org/wiki/Property:$1"^^ . . . "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" . "1200031"^^ . . . . "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view."^^ . . . _:N2b9b6b3f37684d34bdfa4f00edbd153e "Vivian Lee" . . . "biomedical science" . . "false"^^ . . . . "dna" . . . . . "comparative genomics" . . . "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID="^^ . . . . . . . "obo" . "https://mediadive.dsmz.de/ingredients/$1"^^ . . "obo" . . . . "Mungbean ontology" . . . . "VB.Ob.3736.GRSM125"^^ . . . . . . . . "computational neuroscience" . . "morbidity" . . . "0000001"^^ . . . . _:N13aaee59b0414bc887f8a768b19c3f7d "Vivian Lee" . . . . "http://drugcentral.org/drugcard/"^^ . . . . . . "sheriff@ebi.ac.uk" . "Structural Database of Allergenic Proteins" . "2381/12775"^^ . "^[A-Za-z_]+$"^^ . . . . _:N8e7200565e95498cbc33e59130e8e542 "Jonathan Bard" . "botany" . . "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId="^^ . "C. elegans Gross Anatomy Ontology" . . "TarBase" . "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1"^^ . . "duret@biomserv.univ-lyon1.fr" . . . . . . "false"^^ . . "obo" . . . "nucleotide" . . . . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID="^^ . . . . "false"^^ . . . . . "0000460"^^ . . "vectorbase" . "functional genomics" . "PyPI" . . . "doqcs.model" . . . . . . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/"^^ . . . . . "Alvin Walker" . "arraymap" . . "obo" . . . "https://e-cyanobacterium.org/bcs/rule/"^^ . . . . "^\\w+$"^^ . . . . "tol" . . "data model" . "iro" . . . "life science" . . "Database of homology-derived secondary structure of proteins" . . "ontology" . . "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id="^^ . . "PubChem Substance ID (SID)" . . . "^\\d+$"^^ . . . . "The set of prefixes used in the Cellosaurus resource" . . . . "hammer"^^ . . . "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^ . . . "http://purl.obolibrary.org/obo/ICO_"^^ . . . "^\\d+$"^^ . "Lindsey N. Anderson" . "Kim Durante" . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . . . "ukprns" . . "true"^^ . "Kinetic Simulation Algorithm Ontology" . . . "AY321118"^^ . . . "obo" . . . . . . . "0000000"^^ . "0000400"^^ . . . "GrassBase" . "0011124"^^ . . "https://www.pgscatalog.org/pgs/"^^ . "civic.gid" . . " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB."^^ . . "https://bioregistry.io/kyinno:"^^ . . "false"^^ . "biomodels.db" . "subject agnostic" . . . . . . "Satoshi Fukuchi" . "life science" . . . . "false"^^ . . . . . . "nasa/kepler-exoplanet-search-results"^^ . . . "dna" . . . "https://www.proteomicsdb.org/#human/proteinDetails/"^^ . . . "false"^^ . "Madeline Iseminger" . . . "false"^^ . . . . "false"^^ . "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . . . . . . . "protocol" . "^\\w+\\_\\d+(\\.\\d+)?$"^^ . "YOR172W_571.0"^^ . "th" . . . . "biodiversity" . . . . "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"^^ . "Manually curated collections of resources stored in the bioregistry"^^ . . "https://civicdb.org/links/diseases/"^^ . . "virsi1909"^^ . "http://www.gramene.org/db/ontology/search?id=GRO:"^^ . "Represent chemical entities having particular CHEBI roles"^^ . . "obo" . . . . "pharmacogenomics" . "c0000005"^^ . . . "proteomics" . "diseaseclass" . . . . . "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query="^^ . . "CAA71118.1"^^ . _:Na97d430be7184cf8b6ff1a06628e1cb0 "helpdesk@cropontology-curationtool.org" . . "https://stemcells.nindsgenetics.org?line=$1"^^ . . . . "Integrated Microbial Genomes Taxon" . "small molecule" . "Jacqueline Campbell" . "sequence" . . "data quality" . . . . . . . . "Clinical Trials Ontology" . . . . "0001417"^^ . "http://purl.obolibrary.org/obo/PSO_$1"^^ . . "^P\\d{5}$"^^ . . . "Mike Tyers" . . "drug" . . . "rna" . . "http://purl.obolibrary.org/obo/NCBITaxon_$1"^^ . . "chemistry" . . . "false"^^ . . . . . . "uniprot.tissue" . . . . . . "https://euclinicaltrials.eu/app/#/view/$1"^^ . . . "http://purl.obolibrary.org/obo/PATO_"^^ . "DB-0174"^^ . "kelly.hughes@utah.edu" . . . . . . . "virology" . "0278"^^ . "computational biology" . "cosmic" . . "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$"^^ . . "obo" . . . . "obo" . . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . "disorders" . . . "false"^^ . . . . "https://meshb.nlm.nih.gov/record/ui?ui="^^ . "Glyma0021s00410"^^ . "plant breeding" . "https://vocab.lternet.edu/vocab/vocab/index.php?tema="^^ . . . . "^\\d+$"^^ . . "mipmod" . . "^\\d{7}$"^^ . . "gene" . "OMIMPS" . . "9001411"^^ . "biomedical science" . . "false"^^ . . . "obo" . "https://bioregistry.io/abcam:"^^ . . . "false"^^ . "false"^^ . "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^ . "false"^^ . "false"^^ . "mgnify.samp" . . . "PharmacoDB Datasets" . . "false"^^ . . . . . . . . . . . . "fr" . . . . . "eNanoMapper ontology" . . "phenotype" . "false"^^ . . . . . . . . "Peer Bork" . "AN0097748"^^ . . . "transcriptomics" . . "pharmacology" . "metascience" . "Bgee family" . "HGVM15354"^^ . . . . "drugcentral" . . "The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources."^^ . "http://pombe.oridb.org/details.php?id=$1"^^ . . . . . "false"^^ . . "ontology" . . "https://scicrunch.org/resolver/RRID:BCBC_"^^ . . . . . "^\\d+$"^^ . "false"^^ . . . . . "http://thebiogrid.org/"^^ . "^[A-Za-z0-9+_.%-:]+$"^^ . "false"^^ . . . "true"^^ . . . . "genome" . . "Simple Standard for Sharing Ontological Mappings" . . . . . "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing."^^ . . "perry.miller@yale.edu" . . . . "The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community (from https://gnomad.broadinstitute.org)."^^ . . . "https://civicdb.org/links/drugs/"^^ . "THE1B"^^ . "Scientific Information Retrieval and Exchange Network" . . . . . . . . . "Encyclopedia of Life" . "^(MNXM\\d+|BIOMASS|WATER)$"^^ . . "Virus-HostDB" . . . . . "maria.gould@ucop.edu" . . . . . "^\\S+$"^^ . . "false"^^ . . . "statistics" . . . "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"^^ . "https://drks.de/search/en/trial/$1"^^ . . "https://w3id.org/seo#"^^ . . . "The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections."^^ . . . . "hgnc.genegroup" . . . . "false"^^ . "suzia@stanford.edu" . "hipsci" . "0000564"^^ . . "subject agnostic" . . . . . . "dna" . . . . . . . . . . "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature="^^ . "begdb" . "botany" . "Rachael P. Huntley" . "life science" . "S-EPMC6266652"^^ . . "life science" . . . . "biomedical science" . . . "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps."^^ . "bdgp.est" . . . . . . "Literature references in Gramene"^^ . "false"^^ . . . . . . "Tetrahymena Genome Database" . . . . . . . . . . "mazumder@gwu.edu" . . . . "ontology" . "metadata standardization" . . "117"^^ . . "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning."^^ . . "GitHub Issue" . "go" . . "mihail.anton@chalmers.se" . . . . . . . . "http://www.w3.org/ns/adms#"^^ . . . . . . . "false"^^ . . "Bioregistry Schema" . "10046"^^ . . . . . "rna" . "bolton@ncbi.nlm.nih.gov" . . "^\\d{7}$"^^ . . "false"^^ . "false"^^ . . "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^ . . . "https://civicdb.org/links/evidence/"^^ . . "genome" . . "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule="^^ . . . . "zeco" . "breeding" . "ontology" . . . "http://uri.neuinfo.org/nif/nifstd/oen_"^^ . . "agriculture" . "MMP02954345.1"^^ . "protein" . "Abdomen"^^ . . . . . . "This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures)."^^ . . "molecular microbiology" . . . . . "false"^^ . . . . . . . . . "http://purl.obolibrary.org/obo/GOREL_"^^ . "life science" . . . . . . . "biomedical science" . "Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models."^^ . . . . . "false"^^ . . "Paolo Romano" . . "info@hoelzel.de" . . . . . "false"^^ . "genome" . . "obo" . . . . . . . "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^ . . "https://www.uniprot.org/journals/$1"^^ . . . "1"^^ . "811"^^ . "AphidBase Transcript" . "322"^^ . . "http://www.ontobee.org/ontology/$1" . . "Global Biodata Coalition - Global Core Biodata Resources" . . "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:"^^ . . . . "YeTFasCo" . "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^ . . "lipid" . . . . . . . . . . . . "http://biomodels.net/rdf/vocabulary.rdf#$1"^^ . "classification" . _:N121f99ad90c846da8913ff92b247ea48 . . "Bjoern Peters" . . . "false"^^ . . . "pathway" . . "protein" . "licebase" . "https://ligandbook.org/package/"^^ . . . "https://www.ncbi.nlm.nih.gov/books/"^^ . . . . . "regulation" . . "co_357" . . . "Amphibian taxonomy" . . . "false"^^ . . . "protein" . . . . "Andrea Gaedigk" . . "protein" . "WB_REF" . . "http://ascl.net/"^^ . . . "The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]"^^ . . . "^HGVM\\d+$"^^ . "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^ . "false"^^ . "devtox" . . "structural biology" . . "ontology" . . "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . . . "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"^^ . . . "taxonomy" . "HBG284870"^^ . . . . . . . "disease" . "expression data" . "glycomics" . . . . . . "vriend@cmbi.ru.nl" . "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1"^^ . . . "http://wodaklab.org/iRefWeb/interaction/show/"^^ . . . "anatomy" . . . . "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/"^^ . . . . "http://purl.obolibrary.org/obo/LABO_$1"^^ . "CL0192"^^ . "^\\d+$"^^ . . "hpiwowar@gmail.com" . "^\\d+$"^^ . . "drugbank.target" . . "pesticides" . . . . . . "false"^^ . . "jstuelk@gwdg.de" . "0002902"^^ . "rhea" . "^\\d+$"^^ . . . . "animal husbandry" . "false"^^ . . . "life science" . "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1"^^ . . . "pmc" . "Teleost taxonomy ontology" . "nstd102"^^ . . . "https://www.google.com/patents/"^^ . . . "Open Citation Identifier" . . . . . . . . . . . "ontology" . "BiGG Metabolite" . . "^\\d(\\d|\\w)$"^^ . "obo" . "ontology" . . . . "BioLegend" . . . "https://registry.identifiers.org/registry?query=MIR:$1"^^ . . _:N1e6ec8430d304806b4538fc7137b9053 "Hajo Rijgersberg" . . . "disease" . . "New Zealand Threat Classification System" . "interactive portal" . . . . . "Terry Hayamizu" . "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm="^^ . . . "life science" . _:N0a3b10f91bc9432d844ddbb98489eb84 "whocc@fhi.no" . "000000021"^^ . . . . "https://www.novusbio.com/products/"^^ . "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs."^^ . . . "disease process modeling" . . "https://proteininformationresource.org/cgi-bin/resid?id="^^ . . . . . . "genome" . "BAMSC981"^^ . "edennis@ucsd.edu" . . . "https://rubygems.org/gems/"^^ . "https://www.affymetrix.com/LinkServlet?probeset=$1"^^ . . . . . . . "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref"^^ . . "Alayne Cuzick" . . "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"^^ . . "expression" . . "Beet Ontology ontology" . . . "dna" . . "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"^^ . . . "biomedical science" . . "dna" . . . . . . . "Reactome" . . . . "microbiology" . "anatomy" . . . . . . "ACHN"^^ . . . "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology."^^ . . "GO Chemicals" . "STOREDB at University of Cambridge" . . . "0000027"^^ . "proteomics" . . . "biomedical science" . . . . . "http://bcrj.org.br/celula/"^^ . "https://bioregistry.io/phosphopoint.protein:"^^ . "gene expression" . "false"^^ . . . "https://civicdb.org/links/variant/$1"^^ . . . . . . . "Carole Goble" . . "UR000124451"^^ . . . . "BindingDB" . . . . . . . . "https://eol.org/pages/"^^ . "Harshad Hegde" . "rna" . . "curated information" . "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp="^^ . . . . . . . . . . . "false"^^ . "MESHPP" . . "phenotype" . "http://www.w3.org/ns/dcat#$1"^^ . "hsapdv" . . "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . "181" . "false"^^ . "gocc" . . "OriDB Saccharomyces" . . . . . . . . "https://www.kegg.jp/entry/"^^ . . . . "false"^^ . . "Open Researcher and Contributor" . . . . "geographical location" . "^[A-Za-z-0-9_]+(\\@)?$"^^ . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"^^ . . "research" . . _:Nb17ffaa62b3744119234c8e614e3fe61 . "bridgedb" . "laevis" . "xenopus" . "evgeny.zdobnov@unige.ch" . . "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"^^ . "ontology" . "biomedical science" . "Pieter Mestdagh" . "life science" . "protein" . "0000001"^^ . . . "https://gnomad.broadinstitute.org/variant/"^^ . "comparative genomics" . . "^\\d{7}$"^^ . "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . . . "FBgn0000015"^^ . . "Melanie Courtot" . "food chemistry" . . "https://www.uniprot.org/unirule/"^^ . "Probability Distribution Ontology" . "metabolomics" . "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments."^^ . . . . "^[0-9]+$"^^ . "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways."^^ . "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . "SAMEA2397676"^^ . . . "false"^^ . . . . . "http://purl.obolibrary.org/obo/MIAPA_"^^ . "ModelDB concept" . . "gene" . . . . . "uberon" . "MultiCellDS Digital Cell Line" . "false"^^ . "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default"^^ . . . "SMID-DB" . "UniProtKB-SubCell" . "clinicaltrial" . "ICD10CM" . . . . . "pathology" . "nucleotide" . . . . . "interaction" . . . "life science" . "expression data" . . "http://mirbase.org/cgi-bin/mature.pl?mature_acc="^^ . . "seed" . . . . "protein" . . . . . . . . . "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."^^ . . . . . "obo" . "The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage)"^^ . . . . . "Ontology Concept Identifiers" . "anatomy" . "http://www.humanproteomemap.org/protein.php?hpm_id=$1"^^ . . . . "false"^^ . . . "An ontology representation of the LIPIDMAPS nomenclature classification."^^ . . . . . "http://purl.obolibrary.org/obo/CHMO_$1"^^ . _:Nb210a71e511f4cbfa454a654c89797e8 "helpdesk@cropontology-curationtool.org" . . . . "classification" . . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"^^ . . "true"^^ . "small molecule" . "http://www.w3.org/ns/prov#$1"^^ . "sjwang@mcw.edu" . . . "https://www.ebi.ac.uk/miriam/main/resources/$1"^^ . . "Decentralized Identifier" . "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . . . . . . "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1"^^ . "https://n2t.net/$1:" . "systems biology" . . . . "treebase" . "ontology" . . "https://www.proteomicsdb.org/#human/proteinDetails/$1"^^ . . . . . "false"^^ . . . "0001000"^^ . "health science" . . "UniProt Archive" . . "obo" . . "genetics" . "cattleqtldb" . . . . . . . "arrayexpress.platform" . "rsk00410"^^ . . . . "http://www.tcdb.org/search/result.php?tc=$1"^^ . "nmdc" . . . "http://purl.uniprot.org/annotation/$1"^^ . . . "life science" . "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases."^^ . . . . . . . "small molecule" . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . . "genome" . . . . . . "A controlled vocabulary to support the study of transcription in the human brain"^^ . . . "forest management" . . "batchelorc@rsc.org" . . . "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$"^^ . "emsl.project" . . "genotype" . "https://www.datascienceontology.org/concept/"^^ . . . . . . . . "^\\d+$"^^ . . "rgap" . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID="^^ . "GeoNames Feature Code" . . . . . "31"^^ . "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1"^^ . . . . "E00002"^^ . "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"^^ . . "pubchem.classification" . . "false"^^ . . "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . . . . "phenotype" . . "co_365" . . _:Nf2777a2942e4414f95db524e51c78f67 . . "chemical entity" . . . . "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^ . . . . . . "false"^^ . . . "biologics" . . "danbri@w3.org" . . "0000780"^^ . . . . . . "491187"^^ . . . . . . "http://www.ebi.ac.uk/cmpo/CMPO_"^^ . "http://string.embl.de/interactions/$1"^^ . . . . . . . "Shur-Jen Wang" . . "Web Ontology Language" . "^\\d{7}$"^^ . . . . . . . . . . "Christos Louis" . . "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1"^^ . . . . "Agricultural Online Access" . . "http://purl.obolibrary.org/obo/EMAPA_$1"^^ . "r.court@ed.ac.uk" . "https://mips.helmholtz-muenchen.de/corum/?id=$1"^^ . "life science" . . "0000101"^^ . . . "SD00043"^^ . . . . . "P29894"^^ . "ccdc" . "http://www.interfil.org/details.php?id="^^ . "NLXCELL conatins cell types with a focus on neuron types."^^ . . . . . "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation."^^ . . . . . . "Database of Interacting Proteins" . "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."^^ . . . "plant phenotypes and traits" . "gene" . . . "http://sideeffects.embl.de/drugs/$1"^^ . . . . "^\\d{7}$"^^ . . "remote sensing" . . . "ISO Object Identifier" . "http://purl.obolibrary.org/obo/CIO_"^^ . "https://schema.org/$1"^^ . "jcottrell@matrixscience.com" . "life science" . . . "^\\d{7}$"^^ . "false"^^ . . "hölzel" . . . . . . "false"^^ . . "biomedical science" . "DBrodbelt@RVC.AC.UK" . "https://www.arabidopsis.org/servlets/TairObject?type=locus&name="^^ . "vrobert@unistra.fr" . "CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC."^^ . "CCDC Number" . "pd_st" . "IPI"^^ . . . "^C?\\d+$"^^ . . . . . "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1"^^ . . "flicek@ebi.ac.uk" . "dolce" . "CATH domain" . . . . "agriculture" . "fhir.implementation" . "toxicology" . . . . . "transcriptomics" . "http://purl.org/dc/terms/"^^ . "^\\d+$"^^ . . "knowledge and information systems" . . "life sciences" . . . . . "CAA71118.1"^^ . "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived."^^ . "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$"^^ . "false"^^ . "genomics" . . "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"^^ . "ecocyc" . . "unists" . . . . "ontology and terminology" . . . . "Phenol-Explorer" . "false"^^ . "N21"^^ . . . _:Nad2e205775ec4086893d6f8fac120366 "helpdesk@cropontology-curationtool.org" . . . . . . "https://www.webelements.com/"^^ . . . "DP00003"^^ . . . . . "genomics" . . . . . . . . . . . . . . . "^[A-Za-z0-9]+$"^^ . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"^^ . "obo" . . . . "data coordination" . . "false"^^ . . . . "CHEMBL4303805"^^ . . . . . . . . . . "nbdc01071" . "^rxn\\d+$"^^ . . . "gene expression" . . . "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^ . . . . "https://knowledge.lonza.com/cell?id="^^ . "false"^^ . . . "CO_325" . . . "https://bioregistry.io/p3db.site:"^^ . . . . "https://fairsharing.org/$1" . "Clement Jonquet" . . . "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4."^^ . . . . . "imgt.ligm" . "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components."^^ . "life science" . . "https://europepmc.org/article/ppr/$1"^^ . "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences."^^ . . "biomedical science" . . . . . . "http://pax-db.org/#!protein/$1"^^ . . "creeas@gmail.com" . . . . "false"^^ . _:Nad2f9fd8a95c45bf99bbdc790171afb0 . . "Chemical Analysis Ontology" . . . . . . "experimental measurement" . . "arachnoserver" . . . . . "dna" . "has download URL" . "ontology and terminology" . "sharkipedia.trend" . "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . . . . . "false"^^ . . . . . "false"^^ . . . . . . . . . . "annotation" . "https://modeldb.science/$1"^^ . . "16S rRNA gene database" . . . . . . . . . . . . _:N999a3379cbec462b80acdd3f8d0a25df "gb-admin@ncbi.nlm.nih.gov" . "atsushi.yoshiki@riken.jp" . "obo" . "This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes."^^ . . . . . . . "FishBase" . . . "markley@nmrfam.wisc.edu" . _:Ne69efea612ad4b3ba46ab98730596773 . "pathways" . . "http://purl.obolibrary.org/obo/GAZ_$1"^^ . "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1"^^ . . . "http://purl.obolibrary.org/obo/KISAO_$1"^^ . . . . . . "Vitis ontology" . . . "life science" . "Andrew I Su" . "false"^^ . . . . . . "life science" . . . . . "0002066"^^ . . "immunology" . . . "David N. Orloff" . "Human Disease Ontology" . . . "http://purl.obolibrary.org/obo/DISDRIV_$1"^^ . . "life science" . . "https://www.cbioportal.org/study/summary?id=$1"^^ . . . . "phenotype" . "https://www.ebi.ac.uk/ena/data/view/"^^ . "false"^^ . . . "rdo" . "biomodels.teddy" . . "19210-3"^^ . "Identifiers.org namespace" . . . "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe."^^ . . "^\\d{7}$"^^ . "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym="^^ . . . "01N50ZZ"^^ . "0000006"^^ . . . . "experiment" . . . "false"^^ . . . . "National Bibliography Number" . . . "http://www.w3.org/ns/rdfa#"^^ . . . "http://www.pharmgkb.org/pathway/"^^ . "Yaroslava G Yingling" . . "agriculture" . "gene" . . . . "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession="^^ . . "gene" . . . . . . . "small molecule" . . "anatomy" . . . . . . . "https://icd.codes/icd10cm/"^^ . . . . "https://bioregistry.io/iceberg.cime:"^^ . "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . . . . . . . "duo" . "https://licebase.org/?q="^^ . . "http://purl.obolibrary.org/obo/PDRO_"^^ . . . . . . "life cycle stage" . . . . "https://bioregistry.io/registry/"^^ . . . . "http://purl.obolibrary.org/obo/CLO_"^^ . . . "^CTRI/\\d{4}/\\d{2}/\\d+$"^^ . . . . "Human Gene Mutation Database" . . "http://www.ecogene.org/gene/"^^ . . . "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc."^^ . . . . "disease phenotype" . "http://purl.obolibrary.org/obo/MSIO_$1"^^ . . . "https://bioregistry.io/cubedb:"^^ . "http://purl.obolibrary.org/obo/HAO_"^^ . . . "epidemiology" . . . . "false"^^ . . . "life science" . . "http://purl.obolibrary.org/obo/OGMS_$1"^^ . "ChemSpider" . . . . "false"^^ . . "Scientific Evidence and Provenance Information Ontology" . . . "https://biopragmatics.github.io/providers/schem/"^^ . "report" . . "true"^^ . . . . "^SIGNOR-\\d+$"^^ . "cao" . . "zebrafish" . "3dmet" . . "obo" . . . . . . . . "false"^^ . . . . "epigenetics" . "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^ . "gtex" . . . . . . . "http://wheat.pw.usda.gov/report?class=gene;name="^^ . . . "Ontology about C. elegans and other nematode phenotypes"^^ . "rare disease" . "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"^^ . . . . . . . . . . "AcknowledgementCondition"^^ . "Sol Genomics Network" . . "w3c rec" . . . . "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID="^^ . "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/"^^ . "mmdb" . . . . "http://purl.bioontology.org/ontology/CSP/$1"^^ . "ontology" . . "6472"^^ . . "false"^^ . . . . . . . . . . "support@bioontology.org" . "moid" . "florianv/swap"^^ . "dr.sebastian.koehler@gmail.com" . . . "casent0106247"^^ . . "Emmanuel Guiderdoni" . . "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1"^^ . "https://www.iedb.org/reference/"^^ . "https://rubygems.org/gems/$1"^^ . . "false"^^ . "false"^^ . "botany" . "img.gene" . . . "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"^^ . . "iNaturalist Place" . "^[A-Z0-9]{5}\\d+$"^^ . "life science" . . . . . "BridgeDb Vocabulary" . . . "https://www.webofscience.com/wos/author/record/"^^ . _:Nf670dc591a464c0e95466a2df952cb59 "Crop Ontology Helpdesk" . . . . . . . "has URI prefix" . . . . . . . . "SP_SL" . . . "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"^^ . . "obo" . . . . . "https://cropontology.org/rdf/CO_346:"^^ . "Epilepsy and Seizure Ontology" . "false"^^ . "evm" . . "false"^^ . "AspGD Protein" . . "gene" . . "^SD\\d+$"^^ . "https://bioregistry.io/diseasesdb:"^^ . "^BG\\d+$"^^ . "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"^^ . . . "Aspergillus Genome Database" . . "recombinase" . . . . . . . . "false"^^ . "true"^^ . . "chris@sanderlab.org" . . "Protein Ensemble Database" . "reactions" . . . . . "pombase" . "PDBsum; at-a-glance overview of macromolecular structures" . "obo" . . "co_340" . "protein" . . . "^\\d{5}$"^^ . . . . . . "bykdb" . . . "tricdb" . . "3G6A5W338E"^^ . "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."^^ . "binding site" . . . "0000038"^^ . . . "genome" . "GDS1234"^^ . . . . . "life science" . . "isfinder" . . "nutritional science" . . "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"^^ . "^GCA_[0-9]{9}(\\.[0-9]+)?$"^^ . . . . . . . . "phenotype" . . . . . . . "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data."^^ . "experimental measurement" . . . . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions."^^ . . "ontology" . "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc."^^ . . . . . "4195"^^ . "^\\d{7}$"^^ . . . . "proteomics" . . "https://www.uniprot.org/database/$1"^^ . . . "obo" . "^(SMP|PW)\\d+$"^^ . "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed."^^ . "https://biopragmatics.github.io/providers/msigdb/$1"^^ . . "^\\d{7}$"^^ . "biochemistry" . "transcript" . "ddinter.drug" . . "^TS-\\d+$"^^ . . . . . . . . . "https://biopragmatics.github.io/providers/uniprot.ptm/$1"^^ . . . . "IPI00000001"^^ . "false"^^ . . "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"^^ . "https://pubchem.ncbi.nlm.nih.gov/compound/"^^ . "http://addgene.org/"^^ . "0004486"^^ . . . . "^\\d{3}$"^^ . . . . . "https://athena.ohdsi.org/search-terms/terms/$1"^^ . "false"^^ . "fairsharing" . . . . . . "IntAct Molecule" . . "false"^^ . . . "ontology" . . . "biomedical science" . "true"^^ . . "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"^^ . . . "https://drugs.ncats.io/drug/"^^ . . . "FxnI151FMs"^^ . . _:N9dbce4005f294750b1a88391f8505532 . . . . . "epidemiology" . "http://scop.berkeley.edu/sccs=$1"^^ . "M00002"^^ . . . . "http://purl.obolibrary.org/obo/ONTONEO_$1"^^ . . "life cycle" . "Medical Action Ontology" . . . "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"^^ . . "biodiversity" . . . "false"^^ . "evolution" . . . . . "15000"^^ . . "Xenopus Anatomy Ontology" . "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1"^^ . . . . "http://vegbank.org/cite/"^^ . . "life science" . . "pmap.substratedb" . . . . . . . . "transcriptomics" . "https://www.ncbi.nlm.nih.gov/genome/"^^ . . . "hydrogeology" . . "human" . . . "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^ . . "sharkipedia.trait" . "000017"^^ . "beetlebase" . . . _:N5fc61388a1f34b48a985d50eb5fef93d . . "pwo" . . . . . . "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId="^^ . . "knockout" . . . . "false"^^ . . . . . . . . . . . "^MMP\\d+.\\d+$"^^ . "false"^^ . . . "^\\d+$"^^ . . . . "life science" . . "csp" . . "^\\d{7}$"^^ . . "biomedical science" . . "https://www.kaggle.com/$1"^^ . . "International Geo Sample Number" . "taxon" . "http://purl.obolibrary.org/obo/CDAO_"^^ . "UniProt Cross-ref database" . "https://go.drugbank.com/bio_entities/"^^ . . "^\\d+$"^^ . "small molecule" . . "oborel" . . "false"^^ . . "http://purl.org/obo/owlEOL_"^^ . . . "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium."^^ . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid="^^ . _:N648de9a3c9414188aeff24d0e23085c4 "Kate Rose" . . . . . . . . . . "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1"^^ . "false"^^ . "International Nucleotide Sequence Database Collaboration (INSDC) Run" . "12300"^^ . . . "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . . . "cell_biolabs" . . . "false"^^ . . "PGS000018"^^ . "phytozome.locus" . . "A representation of the variety of methods used to make clinical and phenotype measurements."^^ . "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community."^^ . . . "^\\d+$"^^ . "ontology" . . "0000127"^^ . . "00000101"^^ . . . . "ligandexpo" . "ontology" . . "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. \nDelivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts \nand humanities, Scopus features smart tools to track, analyze and visualize research."^^ . . "0000140"^^ . "http://tolweb.org/"^^ . "Database of the dielectric properties of biological tissues."^^ . "CRW_00469"^^ . . . . . . . "massive" . "samuel.friedman@cammlab.org" . . "Dalia Alghamdi" . . . "^[0-9]{1,7}$"^^ . . . . "AT1G73965"^^ . "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^ . "gno" . . . "1058367"^^ . . "biomedical science" . "http://scipion.i2pc.es/ontology/CRYOEM_"^^ . "gabdank@stanford.edu" . . "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . . . "National Drug Data File" . . . . . . . "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . "Alexey M. Eroshkin" . . . "https://biopragmatics.github.io/debio/"^^ . "biology" . . "Informed Consent Ontology" . "Cancer cell LInes GEne fusions portAl" . . . "https://viralzone.expasy.org/"^^ . . "bibliometrics" . . . . "BRENDA Tissue Ontology" . "alejandra.gonzalez.beltran@gmail.com" . "false"^^ . "morbidity" . . . . . "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . . "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data."^^ . "Ontology for General Medical Science" . "false"^^ . . . . . "frbrer" . . . . "gene" . . . . "^\\d+$"^^ . . "0000041"^^ . "http://ddinter.scbdd.com/ddinter/drug-detail/$1"^^ . . . . . "ontology" . . "false"^^ . . . "^[AMCST][0-9x][0-9]$"^^ . "J55.713G"^^ . "drug discovery" . . . "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools" . . . "HMS LINCS Compound" . . "Cassava ontology" . . . . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1"^^ . "false"^^ . . "genome" . "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . . . "false"^^ . . . "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life."^^ . "^\\d{7,8}$"^^ . . "false"^^ . . . . . "yetfasco" . "http://purl.obolibrary.org/obo/HANCESTRO_$1"^^ . "false"^^ . . "^HBG\\d+$"^^ . . "imanis" . . "false"^^ . "false"^^ . . "morbidity" . . "SABIO-RK EC Record" . . . . . . "gene expression" . . "http://emmo.info/emmo/cif-core#$1"^^ . . . . "^\\d+$"^^ . "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . . "0000111"^^ . . . "http://purl.obolibrary.org/obo/TTO_"^^ . . "nmr" . . "martin.pospisek@natur.cuni.cz" . . . "genome" . . . . "lars.eisen@colostate.edu" . "false"^^ . . "species-environment interaction" . "http://sabiork.h-its.org/reacdetails.jsp?reactid="^^ . . . . . "false"^^ . "gene" . "structure" . . . . . "gene" . "obo" . . . . "^\\d+$"^^ . . . . . . . . "protein" . . . . . . "registry" . . . . . "^\\d+$"^^ . . . "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources"^^ . . . "rupert.kellner@item.fraunhofer.de" . . . "http://purl.obolibrary.org/obo/MAT_$1"^^ . . "false"^^ . . . . . "00000008"^^ . . . "KEGG-path" . . "https://bitbucket.org/$1"^^ . . . . . . "genome" . . "metabolomics" . . "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures."^^ . "Idan Gabdank" . . "0000095"^^ . . . . "ortholog" . . "BUNA790102"^^ . "https://www.wormbase.org/species/c_elegans/rnai/"^^ . "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome."^^ . . . "74"^^ . "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . "true"^^ . . . . "ricecyc" . . . "KEGG COMPOUND" . . "https://glyconavi.org/hub/?id="^^ . "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . . . "false"^^ . . "ontology" . "Karen Coyle" . "60141"^^ . "ontology" . . . "jp@senescence.info" . . . . . "Vertebrate Homologous Organ Group Ontology" . . . _:Ndf8772f8d5b14f2a81291b8a225d1742 "Patricia Brooks" . . "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/"^^ . "^RF\\d{5}$"^^ . . _:Nd78e386571634ea5a7085ad29e0607bf . . . . . "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains."^^ . . . . . . "AutDB" . . . _:Na02fc64581ae4e3a98fdb9896d829d8f "info@wikidata.org" . "https://www.internationalgenome.org/data-portal/sample/$1"^^ . "sfukuchi@maebashi-it.ac.jp" . . . "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . . "OMIT" . . . "0000040"^^ . . "^\\d{7}$"^^ . . . . . . "proteomics" . "gnome" . . "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible."^^ . . "ontology" . . "8000221"^^ . . . . . . . "The set of prefixes used in the Cellosaurus resource"^^ . "social science" . . . "slime-mould" . "biopragmatics/bioregistry/416"^^ . . . . . "b97957"^^ . "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^ . "Patrice Buche" . "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . . "botany" . _:Naa56318ac26547a6b2bc62f503f794a6 . . "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."^^ . . . . . . . . . "eukaryotic" . . "community care" . . "Bibliometric Data Ontology" . . " http://edamontology.org" . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/FIDEO_$1"^^ . "TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)" . . . . "Hong-Yu Ou" . . . "caloha" . "biomedical science" . "insdc.gca" . "https://www.metanetx.org/comp_info/$1"^^ . "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^ . "false"^^ . "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . "kinetics" . . . "cell biology" . . . "genetics" . "signor.relation" . "PhylomeDB" . "UniProt Isoform" . . . "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network."^^ . . . "Genitourinary Development Molecular Anatomy Project" . . "http://purl.obolibrary.org/obo/PHIPO_$1"^^ . . . "Banana ontology" . "Isabel Sá-Correia" . . "false"^^ . "chemistry" . "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification."^^ . "6200"^^ . "Henning Hermjakob" . "LL379-9"^^ . . . "402558626"^^ . "https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_"^^ . . "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$"^^ . . "secretariat@eol.org" . . . . . . . . . . . . "KEGG_RCLASS" . "structure" . "depmap" . "01027931310-01022252312"^^ . "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . . . . "https://bioregistry.io/geonames.feature:"^^ . . . . "cdd" . . . . . . "^\\d+$"^^ . "https://www.ebi.ac.uk/biostudies/studies/"^^ . . _:Nda1926f0128c406c8ef98fc6a27a0fc7 . . . . . . . . . . "^\\d+\\-\\d+\\-\\d+$"^^ . . . "Todd W Harris" . . . . "false"^^ . "false"^^ . . . . "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name="^^ . . . "developmental biology" . . . "CHEBI" . . "protein" . . "ado" . "false"^^ . . . . . . "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . . "Rat Strain Ontology" . . . . . . . . . "false"^^ . . "co_334" . . "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^ . . . . "ontology" . . "false"^^ . "ontology" . . "structure" . . "Rat Resource and Research Center" . "Database of Escherichia coli Sequence and Function" . . "methylation" . . . "ontie" . . . . . . "the FAIR Cookbook" . . . . . . . . . . . . "gene" . . "zhu@iastate.edu" . . . "wos" . . . . . . . "HGVST1828"^^ . "Online Mendelian Inheritance in Animals" . "Prefix Commons" . . . . . _:Nd1e9b7f7d97d4a2a83127f2390a8ce15 . "0000091"^^ . "invertebrate" . "^\\d+$"^^ . . . . . "life science" . "Ontology for MicroRNA Target" . . . "http://data.food.gov.uk/codes/foodtype/id/$1"^^ . . . . "Homeodomain Research" . "rnaloops" . . "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions."^^ . . . . . "mgnify.analysis" . "http://purl.obolibrary.org/obo/CHEMINF_"^^ . . . . . . "sciflection" . "Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond."^^ . . . . . "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1"^^ . "https://www.ensembl.org/id/$1"^^ . . . "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound="^^ . . "https://bioregistry.io/$1:$2" . . "http://antibodyregistry.org/AB_$1"^^ . "^[a-z][a-z]/[0-9]+$"^^ . "https://repeatsdb.org/structure/$1"^^ . . . . . . . . "ISO 15926-14" . . . . . "http://www.receptors.org/nucleardb/proteins/$1"^^ . . . . . "neurobiology" . . . "obo" . . . . "http://www.pantherdb.org/panther/family.do?clsAccession="^^ . "ontology" . . . "Systems Biology Ontology" . "biology" . . "rfc" . "0000002"^^ . . . "SDY2614"^^ . "ontology" . . "ICEberg cis-integrative and mobilizable element" . . . . "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public."^^ . . "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG"^^ . . . "teddy" . . "046"^^ . . "http://darcsite.genzentrum.lmu.de/darc/view.php?id="^^ . "chemistry" . "Canadian Drug Product Database" . . . "true"^^ . . . "afpo" . . . . "The Ontology of Genes and Genomes" . . . . . "lpt" . . "eugenes@iubio.bio.indiana.edu" . . "ktym@dbcls.jp" . . . . . . . . . "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0="^^ . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id="^^ . "citation" . "An anatomical and developmental ontology for cephalopods"^^ . . "^(ZINC)?\\d+$"^^ . . . "^YMDB\\d+$"^^ . . . "biomedical science" . . . . . "ontology" . "25512"^^ . . "^\\d+\\.\\d+$"^^ . . "^PR[0-9]{6}$"^^ . "SP_VAR" . "computational biology" . . "https://www.kegg.jp/entry/$1"^^ . . "false"^^ . . . . "Support Email" . . "TrichDB" . . . "protein" . "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion."^^ . " A 7-character sid consists of \"d\" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('_' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1."^^ . "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information."^^ . . "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . "Jennifer Smith" . . "cell biology" . "msio" . "false"^^ . . "1001"^^ . "http://purl.obolibrary.org/obo/FBdv_"^^ . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/"^^ . . . "classification" . . . . . . "hinv.protein" . . "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines."^^ . . "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br"^^ . "https://bioregistry.io/csd:"^^ . . . . . . . "https://cropontology.org/term/$1:$2" . . . . "174"^^ . "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions."^^ . "metagenomics" . . "Jörg Overmann" . "https://www.aapc.com/codes/cpt-codes/"^^ . "modeling and simulation" . "0000111"^^ . . "report" . . . "RNA Virus Database" . "obo" . "mmp.db" . . "false"^^ . . . . "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . "ACC-1"^^ . . "SIGNOR" . . "pharmacodb.dataset" . . . "machine learning" . . . . "http://www.hgmd.cf.ac.uk/ac/gene.php?gene="^^ . "A Semantic Web Rule Language Combining OWL and RuleML" . . "subject agnostic" . . . . . "mauno.vihinen@med.lu.se" . . . . . . . "taxonomy" . . . "ontology" . . "disease" . . . . "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt="^^ . . . "medical imaging" . "false"^^ . . "A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc."^^ . "http://purl.obolibrary.org/obo/ECO_"^^ . "http://www.innatedb.ca/getGeneCard.do?id=$1"^^ . . "allele" . . "biology" . "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1"^^ . . . "gainesville.core" . "https://cropontology.org/rdf/CO_331:"^^ . . . . . . . . . "imdrf" . . . "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."^^ . . "bido" . "biosamples" . . "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"^^ . "https://doulix.com/constructs/"^^ . "fly" . "biomedical science" . . . . . . . "0000984"^^ . . "false"^^ . "^\\d+$"^^ . . "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$"^^ . "^\\d{7}$"^^ . . . . "^\\d+$"^^ . "function" . . . . "genome" . . . "proteomics" . "http://purl.jp/bio/4/id/"^^ . "database" . . . . "Resource" . . . "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"^^ . . "^PGS[0-9]{6}$"^^ . . "https://www.abmgood.com/search?query=$1"^^ . . "small molecule" . . . . . . "bioinformatics" . . . . "Molbase" . "false"^^ . . . "oryzabase.reference" . "px" . . . . . "Fetal Calf Serum-Free Database" . . "oncology" . . . "WikiPathways Ontology" . . . "ogms" . . "aging" . . . . "cnrs" . . . . . . . "hms.lincs.compound" . . . . . "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$"^^ . . . . . "false"^^ . . "http://purl.obolibrary.org/obo/XAO_$1"^^ . . . . "dc" . . . . "961"^^ . . "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id="^^ . "ontology" . . . . . . . . . . . "^\\d{6}$"^^ . . "Michelle Giglio" . "The Food Ontology" . . . "^AA\\d{4}$"^^ . . . "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid="^^ . . . . . "^\\d{7}$"^^ . "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information."^^ . . . . . . "Primate Brain Atlas" . . . . . . . . . "^\\w+$"^^ . "life science" . "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . . . "sequence annotation" . . . . . . . "lschriml@som.umaryland.edu" . . . "An ontology of Drosophila melanogaster developmental stages."^^ . . . "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable."^^ . . . . "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch."^^ . "ontology" . "^\\d{7}$"^^ . "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information."^^ . . "^\\d+$"^^ . . . "molecular entity" . . . . . . . . "false"^^ . . . . . . "Transcriptional Regulatory Element Database" . "^\\d+$"^^ . . . "UMLS_CUI" . . . . . . . . "https://www.yeastgenome.org/locus/"^^ . . . . . "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages."^^ . . . "Ontology of Biological and Clinical Statistics" . . . . . . "bcrc" . _:Nfc145c4b3c9440d782e6e175eb21b434 "po-discuss@plantontology.org" . . "DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases"^^ . "exposure" . . . "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"^^ . . "nlx.anat" . . . "http://purl.obolibrary.org/obo/MF_$1"^^ . . "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NDFRT&code=$1"^^ . . . "molecular entity" . . "http://n2t.net/ark:$1"^^ . "^\\d{7}$"^^ . . . . . . . "reaction" . "taxonomy" . "obo" . "false"^^ . "cpga" . . . "life science" . "EDAM Ontology" . . . "diapriid@gmail.com" . . . . . "medgen.gtr" . "https://www.webofscience.com/wos/author/record/$1"^^ . "false"^^ . . "ArrayGroup"^^ . . "microbiology" . . . "http://purl.obolibrary.org/obo/AISM_$1"^^ . "LMPR0102010012"^^ . "^\\S+$"^^ . . "true"^^ . . "http://www.chemspider.com/inchikey="^^ . . . . _:N3e69e1e263a943b3837d9bf1b0810d0d "PhenX Admin" . "ontology" . . . "http://phylomedb.org/?seqid=$1"^^ . . . . . . . . . . . . . "^[A-Z0-9]+$"^^ . . . . "^\\d{4}$"^^ . "pns12@hermes.cam.ac.uk" . . . . . . "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^ . . . "National Xenopus Resource" . . . "^\\d{7}$"^^ . . "091005"^^ . . . . . . . "^\\d+$"^^ . . "protein" . . "enm" . . "http://emmo.info/emmo#EMMO_"^^ . . "data mining" . "http://purl.obolibrary.org/obo/FLU_$1"^^ . . "ecology" . . "food" . "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1"^^ . "http://purl.obolibrary.org/obo/RNAO_$1"^^ . . "Ligand Expo" . . "false"^^ . "structure" . "bdsc" . . "dna" . . "Physiome Model Repository workspace" . . "https://scicrunch.org/resolver/RRID:AGSC_"^^ . . . . . . . "DI-04240"^^ . "http://getentry.ddbj.nig.ac.jp/getentry/dad/"^^ . . . "false"^^ . "A_24_P98555"^^ . . . . . . . "https://cordis.europa.eu/article/id/$1"^^ . "protein" . "obo" . "cdna" . . "neurophysiology" . "drug" . "rrrc" . . . . . . . . . _:Nbde6269f4f6443d69a8fb868ba8954f9 "chEBI" . "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . . "false"^^ . . . "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \r\nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon."^^ . "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1"^^ . . . . . . . . . . . "taxonomy" . . . . "dna" . . . "Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]"^^ . "https://cran.r-project.org/web/packages/$1"^^ . "PRI10"^^ . . . . "ontology" . "https://www.ebi.ac.uk/ols4" . "false"^^ . . . "^\\d{4}$"^^ . . . . "dr.shorthair@pm.me" . "A Database of Human Hemoglobin Variants and Thalassemias" . . . "false"^^ . . . "Amelanchier laevis"^^ . "Gramene protein" . "Cell line collections"^^ . "subject agnostic" . . "false"^^ . "http://www.pantherdb.org/panther/family.do?clsAccession=$1"^^ . "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees."^^ . "Medical Subject Headings Vocabulary" . "upper-level ontology" . . . "dunand@lrsv.ups-tlse.fr" . . . "false"^^ . "Cu.me.I1"^^ . "data model" . "^\\d{7}$"^^ . . "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID="^^ . "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"^^ . . . . "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide"^^ . . "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^ . "https://www.kegg.jp/entry/$1"^^ . . . . . . . . . "nemo2" . . . . "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"^^ . "https://www.hipsci.org/lines/#/lines/"^^ . . "drosophilidae" . "http://lipidbank.jp/cgi-bin/detail.cgi?id="^^ . . . "http://purl.uniprot.org/uniprot/$1"^^ . "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments."^^ . . . "http://purl.obolibrary.org/obo/OBCS_"^^ . . "taxonomy" . "host" . . "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"^^ . . . "ontology" . . . "BacDive" . "PR00001"^^ . . . "phenotype" . . "ontology" . "^Os\\S+g\\d{7}$"^^ . . "http://www.radiomics.org/RO/"^^ . "International Classification of Diseases, 11th Revision" . "141"^^ . . . "tair.protein" . . . "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^ . . . . . "https://grch38.togovar.org/variant/"^^ . . . . "https://hdl.handle.net/hdl:20.500.12582/$1"^^ . "A gazetteer constructed on ontological principles. The countries are actively maintained."^^ . . . "Q-2958"^^ . "http://purl.org/cerif/frapo/"^^ . . . "stock" . . . . . . . . . . . "peff" . "duplication" . . . . . "http://usefulinc.com/ns/doap#"^^ . "false"^^ . . . "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^ . "false"^^ . . "cherry@genome.stanford.edu" . _:N270077e13b3b43218f7bbeda7477b8a6 "po-discuss@plantontology.org" . . "https://chemkg.github.io/chemrof/"^^ . . . "d4e2515"^^ . "http://ascl.net/$1"^^ . . "Database of Macromolecular Movements" . . . . . . "6"^^ . . "bigg.reaction" . "http://www.bindingdb.org/compact/$1"^^ . . . . . . . "dna" . "^[0-9]+$"^^ . . . . "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information."^^ . "https://integbio.jp/en/" . . . . . . . "hogenom" . "human" . . . "rism" . . . . . "false"^^ . "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"^^ . . "https://www.novusbio.com/products/$1"^^ . "cgrove@caltech.edu" . "http://purl.obolibrary.org/obo/ExO_"^^ . . . . "https://precision.fda.gov/uniisearch/srs/unii/"^^ . . . . . "FAO/WHO_standards" . . "^\\d{7}$"^^ . . . "obo" . "17503"^^ . . . "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . . . . . . "drug interaction" . "false"^^ . . "https://www.confident-conference.org/index.php/Event:"^^ . . "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease."^^ . . "false"^^ . . . . . "subject" . . . "genetic disorder" . "http://purl.obolibrary.org/obo/MCO_$1"^^ . "environmental science" . . "^\\d+$"^^ . . . . "bioactivities" . "false"^^ . "false"^^ . "^\\d+$"^^ . "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank."^^ . "aisling.doyle9@gmail.com" . . "adriano.rutz@ik.me" . "storedb" . . . "false"^^ . "anatomy" . . "5"^^ . "intervention design" . . "achcar11"^^ . . "asu@scripps.edu" . "^\\d+$"^^ . "https://sed-ml.org/urns.html#language:$1"^^ . . . . . "co_333" . . "true"^^ . "^\\d+$"^^ . . . . "preclinical studies" . . . "cell lines" . "MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data.\n\nMetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)]. The majority of pathways occurring in it are from microorganisms and plants. MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number"^^ . . "https://www.gwascentral.org/marker/"^^ . . "lincs.data" . . . "gene" . . . . . . . . . . "^\\w{1,3}$"^^ . . "comparative genomics" . . . . "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^ . "TopFind" . "metabolite" . "Ivan Herman" . "http://purl.obolibrary.org/obo/LOGGERHEAD_"^^ . . . "clement.jonquet@inrae.fr" . . . "75121530"^^ . "rat" . "false"^^ . . . "Gene Regulation Ontology" . . . "Identifier (name code) for a taxon in the catalogue of life in taiwan"^^ . "protein" . "dsm4" . . "gobpid" . . "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^ . "cd00400"^^ . "MassIVE" . "violinnet" . "^\\S+$"^^ . . "pco" . . "https://biopragmatics.github.io/providers/hba/$1"^^ . "echinobase" . "chemistry" . "MC" . "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#"^^ . "mcarthua@mcmaster.ca" . "NLXFUNC covers terms for cognitive function."^^ . . . . "pharmacology" . "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . "adcad" . . . "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^ . . . . "has responsible" . . . . "genomic" . . . . . . . "^\\d{7}$"^^ . . "osa-miR446"^^ . . . . . "vendor" . . "ligea" . . . . "1199"^^ . . . . "https://www.abmgood.com/search?query="^^ . . . . "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies."^^ . "drugbank.bioentity" . . "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma."^^ . . "https://omim.org/MIM:PS"^^ . . . . "false"^^ . "https://www.uniprot.org/uniref/"^^ . . . . . "gold standard" . . "^[a-z]+/[0-9]+$"^^ . . . . "false"^^ . "metascience" . . . "taxonomic classification" . . . . . . . "data model" . "Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website]"^^ . "obo" . "biochemistry" . . "hpscreg" . "Cryo Electron Microscopy ontology" . . "S7000002168151102"^^ . "obo" . . _:Nbe62732905da46fa8b5b42f91dc55de9 "edd@usefulinc.com" . . . "3771992"^^ . "phenotype" . . . "SM_UB-81"^^ . . . . "Common Core Ontologies" . . "false"^^ . . "fivestars" . "bioinformatics" . "Rudolf T. Pillich" . . "NCBI Probe database Public registry of nucleic acid reagents" . "gold standard" . . "false"^^ . . . . . . . . "icd10cm" . . . "false"^^ . . . "ATTC" . . "agrovoc" . . . . . . "siqian.he@nih.gov" . . . "genome" . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . . . . . . . . . "classification" . . "ontology" . "graingenes.reference" . . . . "Alexander Diehl" . . . . . "https://hamap.expasy.org/unirule/$1"^^ . . "0000288"^^ . "ontology" . . "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours."^^ . . . . . . . . "isni" . . "balhoff@renci.org" . "John Beverly" . . . . . . . . . . . "gene" . . "21552"^^ . "biomedical science" . . "false"^^ . . "false"^^ . . "true"^^ . "functional genomics" . "image collection" . . . . . "^\\d{7}$"^^ . . . . . "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"^^ . . "1010"^^ . . . "^C\\d+$"^^ . "^\\d+$"^^ . . "ChEMBL-Cells" . . . "^\\w+$"^^ . "Span" . . "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$"^^ . . . . . . "An organization in FAIRsharing, including universities, labs, etc."^^ . "Uber Anatomy Ontology" . "nkos" . . . "128796-39-4"^^ . . "microbiome" . . "do" . . "false"^^ . . "gpcrdb" . . "false"^^ . "TogoID Ontology" . . "https://w3id.org/linkml/$1"^^ . "hpm.protein" . . "https://www.webofscience.com/wos/woscc/full-record/WOS:"^^ . "true"^^ . "Foods in FooDB"^^ . "proteomics" . "cog.pathway" . . . "natural language processing" . "false"^^ . . . "https://rpcec.sld.cu/en/trials/"^^ . . "https://rnaloops.cs.put.poznan.pl/search/details/$1"^^ . "http://www.molbase.com/en/index.php?app=search&search_keyword="^^ . . . "E5.11.2.0.0.0.4"^^ . _:N1e6ec8430d304806b4538fc7137b9053 "hajo.rijgersberg@wur.nl" . "ecn" . "http://isbndb.com/search-all.html?kw="^^ . "metabolite" . . "schober@imbi.uni-freiburg.de" . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/DERMO_$1"^^ . "The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns."^^ . . . "dna" . "false"^^ . . "14362"^^ . . "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?"^^ . "protein" . "URS0000759CF4"^^ . "Database of Complete Genome Homologous Genes Families" . "life science" . "co_367" . . . . . "data management" . . "Shape Expression Vocabulary" . "anatomy" . . . . . "lbo" . "mzspec" . "https://models.physiomeproject.org/workspace/"^^ . "http://www.ifomis.org/bfo/1.1/snap#"^^ . . . . "false"^^ . "biochemistry" . "SNOMEDCT_US_2015_03_01" . "http://tables.pseudogene.org/[?species_name]/"^^ . "true"^^ . "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating."^^ . "plant genetics" . . "dna" . "^\\d+$"^^ . . "obo" . "metascience" . . . . . . . . "^\\d+$"^^ . . . . . "https://www.uniprot.org/unirule/$1"^^ . . "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . "life cycle" . . "https://www.ebi.ac.uk/chembl/target/inspect/"^^ . . . "Fababean ontology" . "false"^^ . "BRENDA Ligand" . . . "gene" . "TriTrypDB" . . "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"^^ . . . . "001000"^^ . "kinetic model" . "The Bioinorganic Motif Database" . "http://purl.obolibrary.org/obo/FOODON_$1"^^ . "obo" . . "false"^^ . "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database."^^ . "PTPN1"^^ . . . . "translational medicine" . "Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases."^^ . . . . . . . . . "fao.asfis" . . "SCC111"^^ . . . "^(STUDY|FILE|DATASET)\\d+$"^^ . . . _:N5901e4409121428e9e75b3699ed6053b "hq@HL7.org" . "true"^^ . "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances"^^ . . . "false"^^ . "Metabolic Atlas Metabolite" . . "https://licebase.org/?q=$1"^^ . "http://purl.obolibrary.org/obo/ONTOAVIDA_"^^ . "non-coding rna" . . "helpdesk@cropontology-curationtool.org" . "^\\d{7}$"^^ . "http://www.lipidmaps.org/data/LMSDRecord.php?LMID="^^ . . "MCDS_S_0000000001"^^ . . "bakerc@unb.ca" . . . . . "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . . . "https://www.pgscatalog.org/pgs/$1"^^ . "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . . . "false"^^ . . "protein" . "ontology" . "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"^^ . "DBCAT000600"^^ . . . . . "ORPHA" . . . . . . "http://purl.obolibrary.org/obo/PW_$1"^^ . . . "0000066"^^ . . . "http://ensembl.org/glossary/ENSGLOSSARY_"^^ . . "PeptideAtlas Dataset" . . "protonet.cluster" . . "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^ . "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"^^ . . . "ChEBI Integrated Role Ontology" . "life science" . "molecular entity" . "pathway" . . . . . . . . "FAIRsharing Subject Ontology" . . "annotation" . "4623"^^ . "http://purl.obolibrary.org/obo/FBcv_$1"^^ . "comptox" . . . . . . "https://www.ebi.ac.uk/chembl/entity/$1"^^ . "false"^^ . "zp" . "gro-cpga" . . "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:"^^ . . . . . . . . . "false"^^ . . . . "false"^^ . . . "true"^^ . "Dewey Decimal Classification" . . . . . . "agriculture" . . . "false"^^ . "http://purl.dataone.org/odo/ECSO_$1"^^ . . . "false"^^ . . "life science" . "https://ecocyc.org/gene?id="^^ . . . . . . . "experimental plant" . . . . . . "agriculture" . "ontology" . . . . . . . "https://biopragmatics.github.io/debio/$1"^^ . "^\\d+$"^^ . . "Oral Health and Disease Ontology" . "protein" . . "https://pharmacodb.ca/tissues/$1"^^ . "neuroscience" . . "Grant"^^ . "false"^^ . . . . "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites."^^ . "anatomy" . . . . "nanosafety" . . "chebi" . . . . . "nb100-56351"^^ . . "false"^^ . "data science" . . . . "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases."^^ . . "https://lincs.hms.harvard.edu/db/cells/$1"^^ . . . . "Global Natural Products Social Molecular Networking Task" . . "GR_QTL" . "kinetic model" . "^\\d{7}$"^^ . "http://www.proglycprot.org/detail.aspx?ProId=$1"^^ . . "dc_cl" . "3075966"^^ . . . "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase."^^ . "Brassica ontology" . "obo" . "michel.dumontier@gmail.com" . "http://purl.org/gc/$1"^^ . "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links."^^ . . "cell biology" . . "plant anatomy" . "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases."^^ . "CategorialBibliometricData"^^ . "false"^^ . "antibodies" . . . . . "disease model" . "true"^^ . . . "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1"^^ . "dna" . . . . "unipathway.compound" . . . "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="^^ . . "BioGRID" . "http://purl.obolibrary.org/obo/FBbt_"^^ . "life science" . "false"^^ . . . . "bko" . "bams" . "http://edamontology.org/topic_"^^ . "bioinformatics" . "signaling" . . . . . . "Reece Hart" . "urn:nbn:fi:tkk-004781"^^ . . . . . . . . "http://purl.obolibrary.org/obo/ZP_$1"^^ . . . . "002678"^^ . "pathway" . . "small molecule" . "epidemiology" . "br/0601"^^ . "Tim Robertson" . . "embryology" . . "article" . . "https://amoebadb.org/amoeba/app/record/gene/"^^ . "37232"^^ . . "Cell line databases/resources"^^ . . . . . . "ceph" . . . . . . . . . "ontologies" . . "pubchem.compound" . . "http://purl.org/dc/elements/1.1/"^^ . . . . "ontology" . . . "https://www.grid.ac/institutes/"^^ . . "http://purl.obolibrary.org/obo/KISAO_"^^ . "https://www.probes-drugs.org/compound/$1"^^ . . . "An ontology of minimum information regarding potential drug-drug interaction information."^^ . . "nddf" . . . "Ioannis.Xenarios@unil.ch" . . . . . "cpt" . . "structure" . . "https://permalink.obvsg.at/$1"^^ . . . . . . . . "http://www.hmdb.ca/metabolites/"^^ . . "obo" . . . . "false"^^ . . . . "ReviewVersion"^^ . . . . . "Suggested Ontology for Pharmacogenomics" . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene."^^ . "http://www.geneontology.org/formats/oboInOwl#"^^ . "false"^^ . . "SEED Compound" . "The international standard for identifying health measurements, observations, and documents."^^ . "interaction" . . "false"^^ . . . . "^\\d+$"^^ . . "https://w3id.org/BCI-ontology#$1"^^ . . "jaiswalp@science.oregonstate.edu" . "Human Dermatological Disease Ontology" . . . . "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^ . . . "false"^^ . . . "GlycoMapsDB" . . "false"^^ . . . . "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . "FamPlex" . "zhengj2007@gmail.com" . . . . "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam="^^ . "^\\d+$"^^ . . "environmental science" . "life science" . "Nucleotide" . "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1"^^ . . "identifier for an author on the Authorea writing service"^^ . "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr="^^ . . "meteorology" . . "PeptideAtlas" . "bgee.family" . "The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada."^^ . . "false"^^ . "http://www.candidagenome.org/cgi-bin/locus.pl?dbid="^^ . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . "C. elegans Small Molecule Identifier Database" . . "http://purl.obolibrary.org/obo/OCCO_$1"^^ . "mim" . "http://w3id.org/owlstar/$1"^^ . "bibliography" . . . "OMIM" . . "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management."^^ . "John Kunze" . . . . "genetics" . "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs."^^ . "taxonomic classification" . _:N675fee80caff42db81030ecf60b6eab2 "patricia.brooks2@cms.hhs.gov" . . "^\\d{7}$"^^ . . "false"^^ . . "1"^^ . "tk2@ebi.ac.uk" . "glygen" . "jcm" . "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians."^^ . "Jesualdo Tomás Fernández-Breis" . "^001\\d{5}$"^^ . . . "https://www.ebi.ac.uk/metagenomics/projects/$1"^^ . . "^[8-9]\\d{3}(/[0-3])?$"^^ . . . . "physiology" . . . . "https://www.cameo3d.org/sp/targets/target/"^^ . . "genomics" . "IID00001"^^ . "software engineering" . "electronic health record" . . "Terry.Hayamizu@jax.org" . . "Karel Berka" . . "chemistry" . "https://covid19.sfb.uit.no/api/records/$1"^^ . . . . . . . . . "FunderRegistry" . . . . . . "^\\d+$"^^ . . . . . "molecules" . "^\\d{7}$"^^ . . . . . . . . . "https://pharmacodb.ca/cell_lines/"^^ . "frbr" . "medicine" . . . "obo" . . . "http://degradome.uniovi.es/cgi-bin/protease/"^^ . . "https://biopragmatics.github.io/providers/hog/$1"^^ . . "Rice Genome Annotation Project" . . "Yeast Intron Database v4.3" . "Network Data Exchange" . . "genomic sequence" . . . "anatomy" . . "Drosophila gross anatomy" . . . "Gene"^^ . . "Quality"^^ . . "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . . _:N639b47a900af489b96783cabd2d49df1 "Patricia Brooks" . "Small Molecule Pathway Database" . . "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."^^ . "miseming@sfu.ca" . "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1"^^ . "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems."^^ . . "molecular biology" . . . . . . . . . . . . . . . . . "0002989"^^ . . . . "^[A-Za-z0-9]+$"^^ . "^CNP\\d{7}$"^^ . . . . . . . . . . . . . . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/CLYH_$1"^^ . . . "dna" . . "false"^^ . "11478"^^ . . . "A vocabulary and ontology repository for agronomy and related domains." . "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies."^^ . . . "https://bioregistry.io/metaregistry/biocontext/$1" . "pid.pathway" . . . . . . "doid" . . "Federica Quaglia" . "ordo" . "ecology" . "vep1@cdc.gov" . . . . . "^\\d{7}$"^^ . . "http://www.pantree.org/node/annotationNode.jsp?id="^^ . . . . . . . . . "^\\w+$"^^ . . "A set of guides on implementing various processes within hospitals or healthcare systems."^^ . "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB."^^ . . "00000268"^^ . "https://commonchemistry.cas.org/detail?cas_rn=$1"^^ . "0000124"^^ . "histology" . . . . . "UMIN000049383"^^ . "animal breeding" . "ec-code" . "life cycle stage" . . "436605"^^ . . . "MMAR_2462"^^ . . _:Ne1468601788e47eca2b22312b36a1bba . . . "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species."^^ . . . "aap-1"^^ . . . . "bacmap.biog" . . "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM="^^ . . . . . "58788"^^ . "Jennifer L Harrow" . "MetaNetX compartment" . "alternative splicing" . "gene" . . . . . . . . . . . "sitex" . . . . "0000194"^^ . "^AS\\d{6}$"^^ . . . . . . "d.smedley@qmul.ac.uk" . "NCITt" . "proteomics" . . . "health science" . "Melanoma Molecular Map Project Biomaps" . "0000031"^^ . . "protein" . . . . . "https://www.nextprot.org/term/"^^ . "false"^^ . . . . "DataNode"^^ . "github.pull" . . . . . . . . . "evidence" . . . . . . "protein" . "matus.kalas@uib.no" . "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."^^ . "^[a-zA-Z0-9_\\.]+$"^^ . . . . . . . . "http://www.kegg.jp/entry/$1"^^ . "PjrpzUIAAAAJ"^^ . . . . . "http://sabiork.h-its.org/newSearch?q="^^ . "https://purl.dataone.org/odo/ADCAD_$1"^^ . "Spencer L. Liem" . . . "http://purl.obolibrary.org/obo/DC_CL_"^^ . . "Human Reference Atlas Common Coordinate Framework Ontology" . . "http://reg.clinicalgenome.org/allele?hgvs="^^ . . . . "adrienrougny@gmail.com" . . . . "https://lincs.hms.harvard.edu/db/cells/"^^ . . . "pcl" . . . "itis" . "http://viroligo.okstate.edu/main.php?vid=$1"^^ . . . . "virology" . . . "^\\w+$"^^ . . . "http://purl.obolibrary.org/obo/SWO_"^^ . "^EDI_\\d+$"^^ . . . . "880798137"^^ . . . _:N9dbce4005f294750b1a88391f8505532 "Kristin D. Kasschau" . "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1"^^ . "microbiology" . . . "Maxwell L. Neal" . . . "rbrinkman@bccrc.ca" . . "Cotton ontology" . . "false"^^ . . . "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term="^^ . "obo" . . "C0026339"^^ . "^[A-Z][a-z][0-9]+$"^^ . "false"^^ . "sabiork.ec" . . . . . . . . . . "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^ . . "evolution" . . . . "HPA000698"^^ . . . . . . . . . . . . . . . "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^ . "hsa-let-7a-2-3p"^^ . "http://www.ontologyrepository.com/CommonCoreOntologies/"^^ . . "The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits."^^ . . . . . . "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"^^ . "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information."^^ . . "https://biopragmatics.github.io/providers/mba/$1"^^ . . . . "annika.jahnke-bornemann@uni-hamburg.de" . . "0002999"^^ . . "A comprehensive proteomics data and process provenance ontology."^^ . "MicrosporidiaDB" . "false"^^ . "false"^^ . "conoserver" . "^[A-Z0-9]+$"^^ . "Experimental Factor Ontology" . "molecule" . . . "physiology" . . . . . . . "structure" . . . "Erik.Segerdell@cchmc.org" . . "https://ocid.ontochem.com/prefname?ocid=$1"^^ . "citation" . . "http://purl.bioontology.org/ontology/NDDF/"^^ . . . "http://sugarbind.expasy.org/$1"^^ . "Bitbucket" . . . "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters."^^ . . . . . "Database of Genomic Structural Variation - Study" . . . . . . "http://www.treefam.org/family/$1"^^ . "genetics" . "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^ . . . . . . . . . "Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)"^^ . . . . . . . . "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data."^^ . . . . "https://www.ncbi.nlm.nih.gov/books/$1"^^ . "gene" . . "Animal Genome Chicken QTL" . "Database of structurally defined protein interfaces" . "Dimension"^^ . . "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . . "metanetx.chemical" . . . . "SUM Breast Cancer Cell Line Knowledge Base" . . . . . "microarray" . "regulation" . . . "obo" . . "ontology" . . . "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . "obo" . "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)."^^ . . . "Genetics Home Reference" . "miRBase pre-miRNA" . . . . "developmental biology" . "Name-to-Thing" . "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"^^ . . "^E\\d+$"^^ . . . . . "false"^^ . . . . . . . . . . . . . . . . "http://multicellds.org/MultiCellDB/"^^ . . "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB."^^ . . . . . "pathway" . . "erm" . . "protein" . . . "^jRCT\\w?\\d+$"^^ . "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments."^^ . . . "ENSG00000026508"^^ . . . . . . . "ClinVar Record" . _:N44200d5f561d43b5912b0d14cadae2a0 . . "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$"^^ . "beta cell" . "https://www.inaturalist.org/users/"^^ . . "^([a-z]{3,5}_)?M\\d{5}$"^^ . "https://cropontology.org/rdf/CO_367:"^^ . "mmsl" . . "http://purl.bioontology.org/ontology/npo#NPO_$1"^^ . . "false"^^ . . . . . . "^[A-Z0-9]+$"^^ . "^[A-Z]+$"^^ . . . "https://www.cellrepo.com/repositories/"^^ . . . . . . . . . "https://bioregistry.io/p3db.protein:"^^ . "small molecule" . "ConoServer" . . "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 )."^^ . . "bibliography" . "false"^^ . . . "false"^^ . . . "Gavin H. Thomas" . . . . "false"^^ . "ena.embl" . . "mampol" . "data model" . "^\\d+$"^^ . "false"^^ . . "Computer Retrieval of Information on Science Projects Thesaurus" . "research project" . . . "chemistry" . "R. Burke Squires" . "^\\d+$"^^ . "https://nanbyodata.jp/disease/NANDO:"^^ . "UP000005640"^^ . "EDAM Operation" . . . "nmrcv" . . "obo" . . . "congenic rat" . . "genome" . . . "Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format."^^ . . "aio" . "isDocumentRelatedTo"^^ . . . "false"^^ . . . "https://radlex.org/RID/"^^ . . . . . . . "false"^^ . . "0002005"^^ . . "Data Commons" . . "Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity."^^ . . . . . . . . "ecology" . "^\\d+$"^^ . "diagnosis" . . . . "knowledge representation" . . . . "phenotype" . . . . . "false"^^ . . "false"^^ . . "^CONSO\\d{5}$"^^ . . . "https://sed-ml.org/urns.html#language:"^^ . . "true"^^ . _:N4c3dffe6e39b4106a71dd32df9563225 "adw_geeks@umich.edu" . . "https://mmp.sfb.uit.no/databases/mardb/#/records/"^^ . . . . . . . "protein" . . . . . "^(MNXR\\d+|EMPTY)$"^^ . "KEGG_REACTION_CLASS" . . . "false"^^ . . "Agronomy Vocabulary" . . . . "https://aftol.umn.edu/glossary?category=$1"^^ . . . . "MediaDive Medium" . "bioactivities" . . "E. coli Metabolite Database" . "sequence motif" . . . . "Peruvian Clinical Trial Registry" . "false"^^ . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_"^^ . . . . "phenx" . "owl" . . . "chemidplus" . . . . . "^\\d+$"^^ . . . . . . "Lorenz Reimer" . . . . . . . . . . . "^[SCTAGMNUI]\\d{2}\\.([AB]\\d{2}|\\d{3})$"^^ . "immunology" . . . . . . . . . . . . . "epd" . . "https://cordis.europa.eu/article/id/"^^ . . "adverse reaction" . "zenodo.record" . . . . . . "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1"^^ . "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref="^^ . "The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data."^^ . . "life science" . "pathway" . "IPR016380"^^ . . . . . "https://cellmodelpassports.sanger.ac.uk/passports/"^^ . . . . . . . . . "fobi" . "000001"^^ . . "Joint Genome Institute Proposals" . . "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . . . . . . . "Minimal Information About Anatomy ontology" . . . . "false"^^ . "http://www.fairsharing.org/ontology/subject/SRAO_$1"^^ . . "http://www.bioassayontology.org/bao#BAO_$1"^^ . . . . . "false"^^ . "^\\d{7}$"^^ . . "linguistics" . . "Human Unidentified Gene-Encoded" . . . "554"^^ . "https://bdsc.indiana.edu/stocks/$1"^^ . . "http://purl.obolibrary.org/obo/MS_$1"^^ . . . . . "https://cropontology.org/rdf/CO_339:$1"^^ . . . "VEuPathDB ontology" . "hprd" . "data_1664"^^ . . "http://purl.obolibrary.org/obo/FBcv_"^^ . "^HGVST\\d+$"^^ . . . "anatomy" . "life science" . "life science" . "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1"^^ . . . "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . . "gene" . . . . "false"^^ . . . "medicine" . _:Ne38cefa1b7b748d98dc227b75908f096 "Rafael Gonçalves" . . "ontology" . . "http://purl.obolibrary.org/obo/NCBITaxon_"^^ . . "^\\d{7}$"^^ . "kegg.brite" . . . . . "mKIAA4200"^^ . . "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value="^^ . . "true"^^ . . . "classification" . . "HWUPKR0MPOU8FGXBT394"^^ . "false"^^ . "false"^^ . . "Justin Whorton" . . . . . . "openalex" . . . . "ontology" . . "biomedical science" . . . "dbvar.studies" . "https://w3id.org/BCI-ontology#"^^ . . . . . . . . . "40592-R001-100"^^ . . . . . "Kids First" . . . . "false"^^ . "gene" . "Leif Oxburgh" . . . . . . "iuphar.ligand" . "ontology" . . . "^C\\d+$"^^ . "false"^^ . . "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"^^ . . . "disease" . . . "Carsten Linder" . . . . "human" . "publication" . "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"^^ . . "proteomics" . . . "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species."^^ . . . "Assists in resolving data across cloud resources."^^ . . "http://purl.obolibrary.org/obo/OBI_"^^ . . . "giardiadb" . . . . "classification" . . . . . . . . . . . "kinetics" . . . "OMA Protein" . "^[A-Z0-9]{6,7}$"^^ . . . . . . . . "A*01:01:01:01"^^ . . . . . _:Nd5000726c51a442e95b8c79d186a8132 "bioportal" . . . . . "false"^^ . "http://www.proteinmodelportal.org/query/uniprot/"^^ . . . . "OSR00185W"^^ . . "obo" . . . . . . "annotation" . . . "helpdesk@cropontology-curationtool.org" . . "https://w3id.org/linkml/"^^ . . "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes."^^ . . . . . . . . "satyasahoo@ieee.org" . "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . . . . . "dictyBase" . . . . _:Na8edbc95dc9943cead4287a28ea4f5dc "Julian Seidenberg" . . "Jade Hotchkiss" . . . "^\\d{7}$"^^ . . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments."^^ . "^\\d{7}$"^^ . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"^^ . . . . . "false"^^ . . "Yuki Yamagata" . . . . . . "https://web.www.healthdatagateway.org/dataset/"^^ . "life cycle stage" . "NLXINV" . . . "marine metagenome" . . "false"^^ . . "101"^^ . . "false"^^ . . . . "pylebail@rennes.inra.fr" . "insdc.gcf" . . . . . . "An ontology representing the gross anatomy of Drosophila melanogaster."^^ . "^\\d+$"^^ . . "https://www.worldwildlife.org/ecoregions/$1"^^ . . "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1"^^ . "^\\d+$"^^ . . "bugbase.expt" . . "ontology" . "false"^^ . "bioinformatics" . . "hovergen" . . "An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). "^^ . . . . . . . . . . "ExAC Transcript" . . . . "skos" . "civic.vgid" . . . . . . . . "pdb-ccd" . . . . "PharmGKB Drug" . "gdsc" . . . . "NIF Standard Ontology" . . . . "true"^^ . . . . "SNOMED" . . . "false"^^ . "^\\d{7}$"^^ . . . . "biology" . . . . . "16793"^^ . "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id="^^ . "S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix."^^ . "Name-to-Thing" . . "anatomy" . . . . . . "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^ . "Guangshun Wang" . . . . . . "gene" . . "0116"^^ . . . . . "SBGN Bricks data and ontology" . _:N639b47a900af489b96783cabd2d49df1 . . . . "RC00001"^^ . . "agriculture" . . "tchen@forsyth.org" . . "false"^^ . . "ontology" . _:N07c9995202684d52922d84b31e2f5ded "davem@umn.edu" . . "This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. "^^ . . . . . "Wikidata Property" . . "MESHCS" . . "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process."^^ . . . . . "obo" . "metabolomics" . . . "biological sample annotation" . "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . . . . . . . . "biomedical science" . . "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/"^^ . "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed."^^ . . . . "biocuration" . . . . . "splash" . . "http://purl.obolibrary.org/obo/MFOMD_"^^ . "^\\d{7}$"^^ . . . . . . . "Collection of European paediatric cardiac coding files"^^ . . . "https://icd.codes/icd10cm/$1"^^ . . . "false"^^ . . . "^\\d+\\.\\d+$"^^ . "http://www.jcvi.org/charprotdb/index.cgi/view/"^^ . . . . . . "Maciej Antczak" . . . . . . . . . . . "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities."^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"^^ . "plant development stage" . "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_"^^ . "PesticideInfo chemical ID" . . _:N0b947b7b473b4387b084765374d32e99 "Crop Ontology Helpdesk" . . . . . "Denny Vrandečić" . . . . "structure" . "prints" . . . . . . . "http://purl.org/sig/ont/fma/fma"^^ . "https://doi.org/"^^ . "Each OCI (Open Citation Identifier) has a simple structure: oci:-, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first is the identifier for the citing bibliographic resource, while the second is the identifier for the cited bibliographic resource."^^ . . . . . . "animal physiology" . "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation."^^ . "FuncBase Human" . "26957"^^ . "A01M1/026"^^ . "false"^^ . "anatomy" . . . "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . "Gene Ontology" . "4005"^^ . . . . . . . . "true"^^ . . . "http://mods.rna.albany.edu/mods/modifications/view/$1"^^ . . . . . . . . . . . . . "http://www.w3.org/1999/02/22-rdf-syntax-ns#"^^ . "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database."^^ . . . . . . "^\\d+$"^^ . "European Bank for induced pluripotent Stem Cells" . . "TransportDB" . . "version control" . "false"^^ . "false"^^ . "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks."^^ . . . . "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1"^^ . . "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1"^^ . "EGID" . . . . "Vertebrate Gene Nomenclature Committee" . "https://ssbd.riken.jp/database/dataset/$1"^^ . . "Heidi L. Rehm" . "http://www.whocc.no/atcvet/atcvet_index/?code=$1"^^ . . "bindingdb" . "food" . . . . . . "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns."^^ . "false"^^ . . . . "sael" . "systemic neuroscience" . . "ekaterina.chuprikova@eurac.edu" . "false"^^ . "van_slyke@zfin.org" . "0001998"^^ . "cellimage" . "Plant Environment Ontology" . . . . . "https://doulix.com/biomodules/"^^ . . . "Defunct vaccine information source from the He Lab"^^ . . "BioSample" . . . . "5621"^^ . . . . "spd" . . . . . . . "brenda" . "scopus.publication" . "transyt" . . "Lonza" . . . . . . . "HDAA2" . "Human Intermediate Filament Database" . . . . "structural bioinformatcs" . . . . . . . . . "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database."^^ . . "^ST[0-9]{6}$"^^ . . . . . . . "false"^^ . . . . "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary."^^ . . . . . . . . . . . . "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:"^^ . . . . "false"^^ . . . . "https://www.storedb.org/store_v3/download.jsp?fileId="^^ . . . "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract)."^^ . . "oryzabase.stage" . . "protocol" . "applied microbiology" . "data identity and mapping" . "genomics" . . "Metabolite and Tandem Mass Spectrometry Database" . . . . . . "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1"^^ . . . . . . . . "ontology" . "false"^^ . "2.16.840"^^ . "scpd" . . . "pba" . . "yeastintron" . . . "^\\d+$"^^ . . . . "ndf-rt" . "https://biopragmatics.github.io/providers/schem/$1"^^ . . . . . . "biology" . . "Korean Clinical Research Information Service" . "life science" . . "genetics" . "miriam.resource" . . . "^F\\d{4}$"^^ . . . . . . . "life science" . . . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1="^^ . . . . . . . . "https://www.cellbankaustralia.com/$1.html"^^ . . . . . . "http://purl.obolibrary.org/obo/FOBI_$1"^^ . "https://www.rebuildingakidney.org/id/$1"^^ . "kuiper@bio.ntnu.no" . "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books."^^ . . . "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^ . . . . . "GenAtlas is a database containing information on human genes, markers and phenotypes."^^ . . "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals."^^ . "edong@umich.edu" . "regulation" . "http://rebase.neb.com/rebase/enz/$1.html"^^ . "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:"^^ . . . "antibody" . "biology" . . . . . "http://purl.obolibrary.org/obo/TO_"^^ . . "Golm Metabolome Database Analyte" . "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations."^^ . "experimental measurement" . . "charprot" . . "https://data.terra.bio/ga4gh/drs/v1/objects/$1"^^ . . "mouse" . "CTD Disease" . . . . . . . "datacite" . . "go.resource" . . "UniProt" . "mutant" . "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$"^^ . . . . . . "RDFa Core is a specification for attributes to express structured data in any markup language. The embedded data already available in the markup language (e.g., HTML) can often be reused by the RDFa markup, so that publishers don't need to repeat significant data in the document content. (from https://www.w3.org/TR/rdfa-core/)"^^ . "disease" . . . "2.16.840.1.113883.6.88" . "http://tables.pseudogene.org/[?species_name]/$1"^^ . "131"^^ . "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo="^^ . . "ontology" . . . . . . "protein" . . . "Platynereis stage ontology" . . "disease" . "research" . . . . "protein" . "^SL-\\d+$"^^ . "false"^^ . . "Adverse Event Reporting Ontology" . "false"^^ . . . "Ruili Huang" . "genecards.geneannot" . "imsr.apb" . . "tokue" . . . "ontology" . . . "https://biopragmatics.github.io/providers/cemo/$1"^^ . "TA14985"^^ . "https://progenetix.org/services/ids/"^^ . . . "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . . . "Electron Microscopy Public Image Archive" . . . "https://www.scopus.com/affil/profile.uri?afid=$1"^^ . . . "http://purl.obolibrary.org/obo/CHEBI_"^^ . "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . "biomedical science" . . . "false"^^ . . . . . . . . "erik.vannimwegen@unibas.ch" . . . "exposure" . "Getty Thesaurus of Geographic Names" . . . "subject agnostic" . . . . "ontology and terminology" . . . . . . . "omop" . . . "Beilstein" . . "obo" . . . "ontology" . . . . . . "http://www.ebi.ac.uk/cmpo/CMPO_$1"^^ . . . . . "Ascomycete phenotype ontology" . "^DDB_G\\d+$"^^ . . . . . . "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology."^^ . "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms."^^ . . "anatomy" . . _:Nda1926f0128c406c8ef98fc6a27a0fc7 "David J. McLaughlin" . "ANOVA"^^ . . "cmf" . "^\\d{7}$"^^ . . "false"^^ . "^\\d{7}$"^^ . . "Elementary Multiperspective Material Ontology" . . . . "http://jcggdb.jp/idb/jcggdb/"^^ . "BioKC" . . "http://dictybase.org/gene/"^^ . "^\\d+$"^^ . "vaccine" . "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology."^^ . . . . . . "life science" . . . . . . . . "chemical" . . . . . "true"^^ . "http://www.w3.org/ns/shacl#"^^ . "Brazilian Registry of Clinical Trials" . "0000072"^^ . . . . "https://athena.ohdsi.org/search-terms/terms/"^^ . . "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes."^^ . . . . . "snp500cancer" . . "Plant Stress Ontology" . . "https://scicrunch.org/resolver/RRID:BCBC_$1"^^ . . "clustering" . . . . "https://metacyc.org/META/NEW-IMAGE?object=$1"^^ . . . . "plant breeding" . "Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)" . . . "pandey@jhmi.edu" . . "https://glytoucan.org/Structures/Glycans/"^^ . . "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"^^ . "false"^^ . "Consensus CDS" . . "https://s3.us-east-2.amazonaws.com/lg.cede/"^^ . . . "H00076"^^ . . . . "Complex Portal" . "^\\d+$"^^ . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/CTENO_"^^ . "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings."^^ . . . . . . . "^\\d+$"^^ . . . "https://proteinensemble.org/"^^ . "w3c rec" . "RISM Online" . "philosophy" . _:Nb6b37a7b77e34a5eb7eefc59be1db2d7 "Julie Thompson" . . . "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)"^^ . "SNOMEDCT_US_2021_07_31" . . . . . . . . . "https://doulix.com/constructs/$1"^^ . . . "An ontology covering the taxonomy of teleosts (bony fish)"^^ . "00000021"^^ . "ontology" . . "MediaDive Solution" . . "^spike\\d{5}$"^^ . . "Database of small human noncoding RNAs" . . . . . "Ontology for Immune Epitopes" . . . "genome" . "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant."^^ . . "false"^^ . . . "http://purl.obolibrary.org/obo/REX_$1"^^ . . "false"^^ . . . . "Sebastian Koehler" . "0000773"^^ . . "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^ . . "^[A-Za-z0-9-]+$"^^ . "mw.study" . . "^ECMDB\\d+$"^^ . . _:N15f1101e5afe405f9d53181d2c5a6e24 "Allotrope Foundation" . . "bioinformatics" . . "false"^^ . . . . . . "ontology" . "Jian Huang" . . "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors"^^ . "false"^^ . "comparative genomics" . . . . "https://scicrunch.org/resolver/RRID:"^^ . "ontology" . . . . . "ontology" . . . . . "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . . "artificial intelligence" . . . . . . . . . "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch="^^ . . . . "https://bioregistry.io/tokue:"^^ . . "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot="^^ . . "Model Card Report Ontology" . . . "https://www.ebi.ac.uk/interpro/set/pfam/"^^ . . "0000-0003-3738-3140" . "Microbial Protein Interaction Database" . . . . . "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1"^^ . . . . . . . "genotype" . "chemical biology" . . . . . . . . . . . . "Distributed Archives for Neurophysiology Data Integration" . "Carissa Park" . "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."^^ . . "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data."^^ . . "dbvar.variants" . "https://www.metanetx.org/chem_info/"^^ . . . "cgsc" . "Human Ancestry Ontology" . "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels."^^ . . "orthologous" . "A Systematic Annotation Package for Community Analysis of Genomes" . "flybase" . . . "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models."^^ . . "http://www.w3.org/ns/activitystreams#"^^ . . "0000630"^^ . . "FaBiO, the FRBR-aligned Bibliographic Ontology" . . "chemical biology" . "false"^^ . . . . . "life science" . . . . . . "http://foodb.ca/compounds/$1"^^ . "http://purl.uniprot.org/core/"^^ . . . . . . "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1"^^ . . "gfrishkoff@gsu.edu" . . . "obo" . . "https://cstr.cn/"^^ . . . . . "ontology" . . . . "https://fairsharing.org/$1"^^ . "modeldb" . . . . . . "MPATH" . "environmental science" . . "627"^^ . "GWAS Central Marker" . . . "life science" . . "http://www.cathdb.info/domain/$1"^^ . . "https://euclinicaltrials.eu/app/#/view/"^^ . . . . "maria.taboada@usc.es" . . "1000"^^ . . . . "https://flybase.org/reports/$1"^^ . "proteins" . "0001011"^^ . . . "MHC Restriction Ontology" . . . . . "https://github.com/$1"^^ . "systems biology" . "bioinformatics" . . . "inhand" . "^[A-Za-z-0-9_]+(\\@)?$"^^ . "http://purl.obolibrary.org/obo/MRO_$1"^^ . . . "life science" . "A controlled vocabulary to support the study of transcription in the primate brain"^^ . "false"^^ . . . . . "false"^^ . _:N121f99ad90c846da8913ff92b247ea48 "BioModels.net team" . . . "http://www.w3.org/ns/oa#$1"^^ . . . "psipar" . . "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"^^ . "4544"^^ . . "FlyBase_Cell_line" . "ukprn" . . "interaction" . . . . "life science" . . . "giacomo.lanza@ptb.de" . . "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF."^^ . . "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^ . "CORDIS Project" . . . "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList"^^ . "thermofisher" . . . . "aceview.worm" . "taxonomy" . . "false"^^ . . "mosquito" . . . . "http://purl.obolibrary.org/obo/OGG_"^^ . . . "ontology" . . . . . "1000001"^^ . "^JCRB\\d+$"^^ . . "13"^^ . . . . "small molecule" . . "Iranian Registry of Clinical Trials" . . "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . . . "^\\d+$"^^ . "KEGG.EDRUG" . "NONHSAG00001"^^ . . "^[A-Za-z_0-9]+$"^^ . "biomaterial" . . . "http://purl.obolibrary.org/obo/SPD_"^^ . "Xenobiotics Metabolism Database" . . . . . . . "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_"^^ . . "199/2168"^^ . . . . "https://w3id.org/semapv/vocab/$1"^^ . "GFAM" . . . "social and behavioural science" . . . . . . . . "protein" . . . . "dna" . . "ICD-O" . "KEGG Pathways Database" . _:Nee718a1169484f53b606356afc36575f "Pierre Sprumont" . . . . . . "mice" . . . . . "0015177"^^ . . . "false"^^ . "^\\d{7}$"^^ . . "efo" . "http://biohackathon.org/resource/faldo#$1"^^ . . "^\\d{7}$"^^ . "https://www.cytion.com/$1"^^ . . . _:Nd5000726c51a442e95b8c79d186a8132 "support@bioontology.org" . "false"^^ . . "The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2)."^^ . . "https://envipath.org/package/$1"^^ . "Clinical Trial Registries" . . . . . . . . "1000160"^^ . . . . "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$"^^ . . . . . . . . "https://www.vmh.life/#metabolite/"^^ . . . . . . . . . . . "nicole@tislab.org" . "false"^^ . "vido" . . "dashr@lisanwanglab.org" . . "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."^^ . "snctp" . . . . "GXA Expt" . . . . "REFSEQ_PROT" . "22RV1_12_2019"^^ . "void" . "false"^^ . . . . . "https://portal.gdc.cancer.gov/cases/$1"^^ . . "aop.stressor" . "false"^^ . . . . . . . . "0000487"^^ . . . "false"^^ . "http://purl.obolibrary.org/obo/BFO_$1"^^ . "DrugBank Drug Category" . "disease" . . . . "Collagen Mutation Database" . . . . . . "https://integbio.jp/dbcatalog/en/record/"^^ . . . . . . "http://bacmap.wishartlab.com/organisms/$1"^^ . . "P4355"^^ . . "bbtp" . . "phipo" . "protein" . "jonrkarr@gmail.com" . "morphology" . . . "metnetdb" . "https://datacommons.org/browser/$1"^^ . . . "catalog" . . "^[0-9][A-Za-z0-9]{3}$"^^ . . "http://purl.obolibrary.org/obo/MONDO_$1"^^ . "genomics" . "^\\d+$"^^ . . . "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1"^^ . . "false"^^ . "version Dec 2019"^^ . "Integrated Canine Data Commons" . . . "88"^^ . . "idot" . "life science" . "biology" . . . . . . "MultiCellDS collection" . "7499841"^^ . "image" . "false"^^ . . . "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank."^^ . . "11002"^^ . . . . . "data management" . . . "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information."^^ . . . . . "ontology" . "DSSTox_CID" . . . "^GPM\\d+$"^^ . "life science" . . . . . . "https://www.inaturalist.org/places/"^^ . "preclinical studies" . . . . "w3c rec" . "patrice.buche@inrae.fr" . . . . . "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . . "Dublin Core Types" . . "8cf84adb-b4db-4807-ac98-0004247c35df"^^ . "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"^^ . "1001"^^ . . . . . . . . . . "genome" . . . . . . . "developmental biology" . "mouse embryonic stem cell line" . "molecular interaction" . . . . "gudmap" . . . "WBPhenotype" . "Mouse Genome Informatics" . "TC" . "^[0-9]+$"^^ . . . . . . "ChEMBL_ID" . "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement."^^ . . . "SL-0002"^^ . . "https://glyconavi.org/hub/?id=$1"^^ . . . . . . "false"^^ . . "false"^^ . "https://id.loc.gov/authorities/"^^ . "https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1"^^ . . "Datanator Reaction" . . . . . "http://purl.obolibrary.org/obo/RO_"^^ . "00000099"^^ . . "^\\d{6,7}$"^^ . . . . . . . . "ICD" . . "PTM-0450"^^ . "electronic health record" . . . . "^DB\\d{5}$"^^ . "microbiome" . . "https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn"^^ . "22132778"^^ . "http://www.ontobee.org/" . . "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome."^^ . . "http://purl.obolibrary.org/obo/OCCO_"^^ . . "obo" . "ontology" . . "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^ . "Bill Duncan" . . . "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information."^^ . . . "Wasila Dahdul" . "http://elm.eu.org/elms/elmPages/$1.html"^^ . . . . . . . "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes."^^ . . . . . . "shibase" . . "false"^^ . . . . . . . . "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)."^^ . . . . . "false"^^ . . . . . . . "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation."^^ . "false"^^ . "thomas@luetteke-online.de" . "patient care" . "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . "life science" . . . "disease" . "https://browser.planteome.org/amigo/term/PECO:$1"^^ . "LNCRNADB" . "http://mycobrowser.epfl.ch/marinosearch.php?gene+name="^^ . . . "pazar" . . "disease" . . "isanchez@cnb.csic.es" . . "approved drug" . "mjyoder@illinois.edu" . "^[\\d.]+$"^^ . "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID="^^ . . . "WikiGenes" . "https://bioregistry.io/nbn:"^^ . "Charles Tapley Hoyt" . . . . . . . . "^MNEST\\d+$"^^ . . "pathway" . . "statistics" . "https://semanticscience.org/resource/CHEMINF_$1" . "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^ . . . "cell lines" . . . "Metabolome Express" . . "false"^^ . . "https://www.biorxiv.org/content/10.1101/$1"^^ . "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . . "co_327" . . "fungidb" . "Michael Szcześniak" . "inxight" . "^[a-z]{3}-[a-km-z0-9]{7}$"^^ . . . . . . . "life cycle" . "small molecule" . . . . . "20021"^^ . . . . "Developing Human Brain Atlas" . "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . . . "https://www.ncbi.nlm.nih.gov/pubmed/$1"^^ . . "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites."^^ . "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"^^ . . . . . . "systems biology" . "ontology" . _:Nc7df189bb5a84fff985817ad74147293 . . . . "http://purl.obolibrary.org/obo/GECKO_$1"^^ . "unit" . "^[0-9][A-Za-z0-9]{3}$"^^ . . . "https://easychair.org/cfp/$1"^^ . . . . "false"^^ . "false"^^ . "http://scop.berkeley.edu/sccs="^^ . "OpenAlex" . . "Progenetix" . "false"^^ . . "life science" . . "Maryann Elizabeth Martone" . . . . . "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates."^^ . . . "https://spdx.org/licenses/$1"^^ . "structural biochemistry" . . . "false"^^ . "PACTR202304525632216"^^ . "1"^^ . . "genome" . . . . . . . "ontology" . . . . "gene" . "false"^^ . "fbdv" . . . . "^\\d{7}$"^^ . "https://www.confident-conference.org/index.php/Event:$1"^^ . . "CPX-263"^^ . "^\\w+$"^^ . . . . . "0000639"^^ . "BloodPAC" . . . "co_358" . "macie" . . "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources" . . . "longevity" . "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^ . . "^\\d+$"^^ . . . . . . . . . "^\\w+$"^^ . "Python"^^ . . "environmental science" . . . "Information for ligands in the BRENDA database."^^ . . . "^\\d+$"^^ . "false"^^ . . "http://sugarbind.expasy.org/"^^ . "FAIRsharing.62qk8w" . "ModelDB" . . "https://mips.helmholtz-muenchen.de/corum/?id="^^ . . . . . "geonames" . . . . "https://archive.softwareheritage.org/browse/swh:$1"^^ . . . "pseudogene.org" . "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO)." . . "data model" . . . "cho"^^ . . "0001"^^ . . "^(C|D)\\d{6,9}$"^^ . . . . . . . "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol="^^ . "http://www.kegg.jp/entry/$1"^^ . . . "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."^^ . "Shuichi Kawashima" . . . "http://www.iresite.org/IRESite_web.php?page=view&entry_id="^^ . . "https://phytochem.nal.usda.gov/phytochem/chemicals/show/"^^ . "icd9cm" . . . . "false"^^ . "biomedical science" . "0100011"^^ . "10004892"^^ . . . . "antoine.danchin@normalesup.org" . . "4000027"^^ . "gabi" . . "http://purl.obolibrary.org/obo/CEPH_$1"^^ . "extraction_set"^^ . . "MIMPS" . "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"^^ . . . "data management" . "interaction" . . . . . "0000024"^^ . "life science" . . . "icdom:8500_3"^^ . . . . . . "protein" . "false"^^ . "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines."^^ . "^RBR-\\w+$"^^ . "1122888"^^ . "genome" . . . "http://purl.obolibrary.org/obo/ZFA_$1"^^ . "5.A.1.1.1"^^ . . . . "BDGP insertion DB" . "July 2018"^^ . "968"^^ . "pdb.ligand" . . . "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"^^ . . "Antibiotic resistance genes and mutations"^^ . "dna" . . "https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/"^^ . "false"^^ . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"^^ . . . . . . . . . "obo" . "enzyme" . . . . "dna" . . . "drug discovery" . . "^\\d{7}$"^^ . . "0000029"^^ . . "http://www.gramene.org/db/genes/search_gene?acc="^^ . . "http://www.proglycprot.org/detail.aspx?ProId="^^ . "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://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1"^^ . "^\\d{7}$"^^ . . . "https://loinc.org/$1"^^ . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . "GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group."^^ . "richard@cyganiak.de" . . . "ala"^^ . . "http://purl.obolibrary.org/obo/VTO_$1"^^ . "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^ . . . . "^\\d{7}$"^^ . "http://multicellds.org/MultiCellDB/$1"^^ . "false"^^ . . . . . . "http://purl.obolibrary.org/obo/$1_$2" . . . "false"^^ . . . . . . . . "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"^^ . . . . "4019477"^^ . . "https://bioregistry.io/gabi:"^^ . "obo" . . . "https://www.scopus.com/sourceid/$1"^^ . . . . "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . . . . . . . "ChemIDplus" . "http://pax-db.org/#!protein/"^^ . _:N8567bba41b474a04adf4491efb98c660 "jamsden@us.ibm.com" . . . . "reagent" . . . . "aero" . . . "UniProt provides proteome sets of proteins whose genomes have been completely sequenced."^^ . . . . . "MobiDB" . . "evolutionary biology" . . "^\\w{1,2}\\d+$"^^ . . . "literalForm"^^ . . "helpdesk@cropontology-curationtool.org" . . "dbg2introns" . "rdf" . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes."^^ . . "bootstrep" . . . . "NITE Biological Resource Center" . . "Linked Open Vocabularies" . "false"^^ . . "DiscoverX cell line products" . . . "http://purl.obolibrary.org/obo/MFO_$1"^^ . . . "genome" . . . . "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . . . . "^OSC\\d{4}$"^^ . "false"^^ . "openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item."^^ . . . . "http://purl.obolibrary.org/obo/DINTO_$1"^^ . . "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1"^^ . "bco" . "morpheus.lab/morpheus"^^ . . . . . "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln="^^ . . . . . . . . . "obo" . "comparative genomics" . "false"^^ . . . _:N13aaee59b0414bc887f8a768b19c3f7d . "Subcellular Anatomy Ontology" . . . . "http://purl.obolibrary.org/obo/DIDEO_"^^ . . "ontology" . . "Curated Drug-Drug Interactions Database - Interaction" . "^\\d+$"^^ . . . "bioinformatics" . "pid" . . "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"^^ . . "false"^^ . . . . . "cell" . . "publication" . . . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1"^^ . . "^\\d+$"^^ . "DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary."^^ . . "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data."^^ . "Cluster of orthologous genes" . . . . "http://www.fao.org/gsfaonline/additives/details.html?id=$1"^^ . "0000106"^^ . "ribocenter" . "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno="^^ . . "https://www.alzforum.org/mutations/$1"^^ . "^\\d{7}$"^^ . . . "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^ . . . . "life science" . . . . . . . "false"^^ . . . . . "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types."^^ . . "metabolites" . . . "^\\d+$"^^ . "UBERON" . "study design" . . . . "https://www.ebi.ac.uk/interpro/entry/pfam/"^^ . "protein" . "genetic" . . . . "ontology" . . "biomedical science" . "medicine" . . . . "0000038"^^ . . . "computer science" . "earth science" . . . "An identifier for a country in numeric format per ISO 3166-1"^^ . . "uniparc" . . "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."^^ . . . "genomics" . . . . . "TogoVar" . . "https://www.datascienceontology.org/concept/$1"^^ . "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression."^^ . . "false"^^ . . . . "^PED\\d{5}e\\d{3}$"^^ . "genome" . . . . . "false"^^ . . "6b1"^^ . . "health science" . "http://www.w3.org/XML/1998/namespace#"^^ . . . "1046"^^ . "https://reporter.nih.gov/project-details/$1"^^ . . . . "false"^^ . . "false"^^ . . "http://purl.obolibrary.org/obo/GAZ_"^^ . . . . . . "structure" . "false"^^ . "^\\d+$"^^ . . . "http://plugins.biogps.org/cgi-bin/wp.cgi?id="^^ . "live animal" . . . . "http://www.tcdb.org/search/result.php?tc="^^ . "genome" . "metagenomics" . "Richard H. Scheuermann" . "WikiPathways is a database of biological pathways maintained by and for the scientific community."^^ . "true"^^ . "https://www.emsl.pnnl.gov/project/$1"^^ . "Health Canada Clinical Trials Database" . . . . . "genetics" . . "ietf.language" . . . . . . "Ontology of Microbial Phenotypes" . . . . . . . . . "101"^^ . "emea" . . . "enzymology" . . "Tree of Life Web Project" . . "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"^^ . "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules."^^ . "^A[A-Z]+\\d+$"^^ . "cultured cell line" . . . "http://www.kegg.jp/entry/$1"^^ . . "0.7-123"^^ . "vo" . "^GN_[A-Za-z0-9_:]+$"^^ . . "NCI Metathesaurus" . . "https://web.expasy.org/cellosaurus/" . . "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"^^ . . . "cellular" . "Life cycle stages for Mus Musculus"^^ . . . "plana" . "16333295"^^ . . . . . "https://www.wikidata.org/wiki/Property:"^^ . . . "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid="^^ . . . "tkg" . . "food" . . "edam.operation" . . . "hms.lincs.dataset" . "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"^^ . . . . . "paolo.romano@hsanmartino.it" . . . . . . "false"^^ . "p3db.site" . . "false"^^ . . . . . "hsdb" . "model" . "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis."^^ . . . . . "^r3d\\d{9,9}$"^^ . . "http://zinc15.docking.org/substances/"^^ . . "^\\d+$"^^ . . . . . . . . . "https://www.cameo3d.org/sp/targets/target/$1"^^ . "1"^^ . . . . "cell biology" . "true"^^ . . "311935300"^^ . "proteomics" . . . . . "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1"^^ . . . "https://www.vmh.life/#reaction/"^^ . "combine.specifications" . . . . . . . . . "Nikolaos Moustakas" . "0003003"^^ . "https://publons.com/researcher/"^^ . . "life science" . . "ogms/OMRE" . "obo" . "transcriptomics" . "geology" . . "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"^^ . "http://opm.phar.umich.edu/protein.php?pdbid="^^ . "has canonical" . . . . . . . "Statistical Torsional Angles Potentials" . . "pdbe" . "omp" . . . "metabolomics" . . . . . "maizegdb.locus" . . "molecular medicine" . "ubprop" . . . . . . "vaccine" . . . . . . "gene" . . . "http://purl.org/vocab/frbr/core#"^^ . . . "http://purl.dataone.org/odo/ECSO_"^^ . . . . "SNOMEDCT_US_2021_09_01" . . "http://www.innatedb.ca/getGeneCard.do?id="^^ . "Ontology of Vaccine Adverse Events" . . . "https://gold.jgi.doe.gov/resolver?id=$1"^^ . . . "Gene Expression Ontology" . . "ontology" . . "false"^^ . . "ontology" . "http://www.yeastract.com/view.php?existing=locus&orfname=$1"^^ . . . . "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data"^^ . . . . "scopus.eid" . . . . . "annotation" . . . . "https://rrid.site" . . . . . "Drug_Central" . "ontology" . . "human" . "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive."^^ . "https://bioregistry.io/combine.specifications:"^^ . . . . . . "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^ . . . "life science" . . . . . . . "drug name" . . . . . "ontology" . "0000295"^^ . "ardb" . . . . . "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1"^^ . . . . . . . . . . . "1cukA01"^^ . . "https://glygen.org/glycan/$1"^^ . . . . . . . . "smid" . . . . . "^\\d+$"^^ . . . . . "grin.taxonomy" . "false"^^ . . . . "https://bioregistry.io/schema/#$1"^^ . . . "http://www.dpvweb.net/dpv/showdpv.php?dpvno="^^ . . _:Ne2eb2958e37a46608ca817d8e0d9ba50 . "^\\d+$"^^ . . . . . "http://cgsc.biology.yale.edu/Site.php?ID="^^ . . "^\\d{7}$"^^ . . "^\\d{7}$"^^ . "chembl.target" . "Franziska B. Grieder" . . . . . . "false"^^ . "go.ref" . . . . "785"^^ . "CTD Gene" . "The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]"^^ . "Software Package Data Exchange License" . . . "false"^^ . "report" . "Metadata Management and distribution system for Multiple GNSS Networks" . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available."^^ . . . . . . . . . "phylogeny" . "obo" . "^\\d+$"^^ . "Carlos Oscar S. Sorzano" . "data retrieval" . "https://www.ebi.ac.uk/gxa/genes/$1"^^ . . "https://biomodels.net/vocab/idot.rdf#$1"^^ . . . . "natural science" . . . "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera."^^ . "agricultural engineering" . . . . . . . . . . "https://www.ebi.ac.uk/ena/browser/view/"^^ . "interoperability" . "false"^^ . . "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception."^^ . "https://www.cropontology.org" . "BacMap Biography" . . . "true"^^ . "false"^^ . . . . "bioregistry"^^ . . . . "subject agnostic" . "ResearcherID" . . . . "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id="^^ . . "265"^^ . . "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output."^^ . . . "image" . . . "ontology" . "foaf" . "http://func.mshri.on.ca/fly/genes/list_functional_scores/"^^ . . . "https://purl.dataone.org/odo/MOSAIC_$1"^^ . . . . . . "Cell line databases/resources"^^ . . . "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code="^^ . . . . "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$"^^ . _:N2b9b6b3f37684d34bdfa4f00edbd153e . "http://purl.obolibrary.org/obo/IDO_$1"^^ . . . . "http://pathguide.org" . "development" . . . . "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC."^^ . . "false"^^ . . . "AY209920"^^ . . . "https://www.confident-conference.org/index.php/Event_Series:"^^ . . "tgma" . . . "GenPept" . . "subject agnostic" . . . . "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id="^^ . "https://bioregistry.io/fbol:"^^ . . "modeling and simulation" . . . "Paragraph"^^ . "life cycle stage" . "false"^^ . "Database of Arabidopsis Transcription Factors" . . "https://www.ncbi.nlm.nih.gov/probe/?term="^^ . "^[1-9]\\d*$"^^ . . . . . "Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource."^^ . . . _:N15429ae11b764183a9987e206494294c "Onard Mejino" . "assay" . . . . . "International Standard Name Identifier" . "Cell line collections (Providers)"^^ . . . . . "obo" . . . "phenotype" . "agro" . "false"^^ . . "ENSG00000139618"^^ . . . "health" . . "false"^^ . "^A\\d{6}$"^^ . "https://bioregistry.io/genecards.genenote:"^^ . . . . . . . "YRC PDR" . . . . . . . "0001056"^^ . . "biology" . . "Biomedical Informatics Research Network Lexicon" . . "mmp.fun" . . "idoo" . . "DAPK1"^^ . . "false"^^ . "protein" . . "Mark Gerstein" . "seed" . . . "ornaseq" . "^\\d+-\\d+$"^^ . . "10.1621/vwN2g2HaX3"^^ . . . . . _:Nfbe0e8521e37434badd542c98d5cadea "futo@stanford.edu" . . . "http://purl.org/spar/deo/$1"^^ . . "^KCT\\d+$"^^ . "LOTUS Initiative for Open Natural Products Research" . "false"^^ . . . . . "hom" . . . . "Plant Phenology Ontology" . . . . . . "life science" . . "Sheeba Samuel" . . . "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information."^^ . . . . . . . . "ontology" . . . "^\\d{7}$"^^ . . . . "gene prediction" . "http://bactibase.hammamilab.org/"^^ . "hcvdb" . . . "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"^^ . . . . . . "^\\d{7}$"^^ . . . . . "false"^^ . . . . . "https://pubchem.ncbi.nlm.nih.gov/compound/$1"^^ . . "SNOMEDCT_US_2023_02_28" . . "http://www.molmovdb.org/cgi-bin/morph.cgi?ID="^^ . . . . . . "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^ . . "040000"^^ . . . . . . . . "ppr" . "biomedical science" . "https://www.uniprot.org/diseases/$1"^^ . "0002959"^^ . . "The Prescription of Drugs Ontology" . "saddan"^^ . "^\\d{7}$"^^ . . . "biomedical science" . . . . . . "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date."^^ . . . _:N07c9995202684d52922d84b31e2f5ded "David J. McLaughlin" . "obo" . . . . . . "life cycle stage" . . "http://purl.obolibrary.org/obo/AERO_$1"^^ . . "Suzi Aleksander" . "interaction" . . . "HGNC gene family" . . . "so" . "life science" . . . . "phylogenetics" . . . "CellBank Australia" . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/TAXRANK_$1"^^ . . . "false"^^ . "NCBIGene" . "ontology" . . . . . "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^ . . "Scholarly Contributions and Roles Ontology" . "coconut" . . _:Nfa653585832f480d92bb1b122af31629 . . "biology" . . "A001094"^^ . . "cto" . . "^1\\d{4}-\\d{3}$"^^ . . . "g.gkoutos@gmail.com" . . "AB" . "Ax1"^^ . . . . "1426686"^^ . . . . . "https://ror.org/$1"^^ . . . . "rna" . . "SoyBase is a repository for curated genetics, genomics and related data resources for soybean."^^ . . "http://emmo.info/emmo/cif-core#"^^ . . . . "zfin" . . . . . . . . . . . . . . "jiezhen@med.umich.edu" . . "http://purl.obolibrary.org/obo/UO_$1"^^ . "plm" . . . . "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-"^^ . . . . . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information."^^ . . . "^.{2,}$"^^ . "https://envipath.org/package/"^^ . "AB016785"^^ . "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON."^^ . . . . "Spectral Database for Organic Compounds" . . _:Nd78e386571634ea5a7085ad29e0607bf "helpdesk@cropontology-curationtool.org" . "@biopragmatics/curies"^^ . . . . . . "25782"^^ . . . "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^ . . . . . . "KIAA0001"^^ . . . . . . . . . . . . . . . . . . "ppdb" . . . . . . . . "taxonomy" . "pigqtldb" . "systems biology" . . . . . "ontology and terminology" . . . "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc."^^ . . . . . . . . "A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods"^^ . . "false"^^ . . . "structure" . "false"^^ . . . . . "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments."^^ . . "KEGG Drug Group" . . "https://pharmacodb.ca/tissues/"^^ . "foodb.food" . . . "false"^^ . . . "wikidata" . . . . "Lindsey Anderson" . "life science" . . . . "life science" . . "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies."^^ . "http://purl.obolibrary.org/obo/PHIPO_"^^ . . . "https://covid19.sfb.uit.no/api/records/"^^ . "Francesco Vitali" . "gnd" . . . . . . . . . . . . "BibliographicRecord"^^ . "has provider formatter" . . "false"^^ . . "true"^^ . . . . . . . "phenotype" . "A0A009E7X8"^^ . . . . . . "1000000"^^ . "http://purl.obolibrary.org/obo/MMO_"^^ . . "livestock" . "erv" . . . . . . . . "genome" . "http://exac.broadinstitute.org/variant/"^^ . . . "^[m,M]{2}[0-9]{5}[0-9]*$"^^ . . "^A\\d+$"^^ . "Human Induced Pluripotent Stem Cells Initiative" . "surjeet.arya@uky.edu" . "NXPFA" . _:N080da5f29fdd435f9aaec76ffbd54dbb "Jonathan Bard" . "MIRIAM Registry collection" . "uniprot.journal" . . . . . . . . . . "translational medicine" . . . . "http://csbl.bmb.uga.edu/DOOR/operon.php?id="^^ . . "https://www.atcc.org/products/$1"^^ . . . . . "^\\d{4,6}$"^^ . . "https://flowrepository.org/id/"^^ . . "bio.tools" . . . . . "^\\w+$"^^ . . "https://bioregistry.io/cadsr:"^^ . "false"^^ . . "https://mobidb.org/$1"^^ . . . "Minoru Kanehisa" . . . "has responsible" . . . . . "itiswebmaster@itis.gov" . . "agriculture" . . . . . . . . "CHEBI" . . . . "life science" . . . "http://purl.obolibrary.org/obo/EHDAA_"^^ . "model organism database" . . . . . . . "true"^^ . "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"^^ . "002804"^^ . "depod" . . "metaregistry" . . . . . "vmhmetabolite" . . "false"^^ . . . "ClinVar Variation" . "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN."^^ . . "obo" . . . "clyh" . . "Lycalopex_vetulus"^^ . . "Identifier of an object from the ASTD database."^^ . . . "NOR00681"^^ . . "0000109"^^ . "sov:WRfXPg8dantKVubE3HX8pw"^^ . . . . . "oio" . . . "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . "mhucka@caltech.edu" . "e0333"^^ . . "http://purl.obolibrary.org/obo/PORO_"^^ . . "Rhea, the Annotated Reactions Database" . . . . . . . "http://www.depod.bioss.uni-freiburg.de/showp.php?gene="^^ . . . . "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi."^^ . . "^PS\\d{5}$"^^ . . "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line"^^ . . . . . . . . . . . "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^ . "The Arabidopsis Information Resource" . "igsr" . "^(G|P|U|C|S)\\d{5}$"^^ . . . "pmid" . . "MU9_3181"^^ . "48439"^^ . . . "pfbaldi@uci.edu" . "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . . "nuclear magnetic resonance (nmr) spectroscopy" . . . . . . "LINCS Cell" . . "000000024"^^ . . "true"^^ . . . . . . . . "Tohoku University cell line catalog" . "An ontology of core ecological entities" . "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID="^^ . . . . "false"^^ . . "http://purl.obolibrary.org/obo/MCO_"^^ . "false"^^ . . . "Cell line collections (Providers)"^^ . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$"^^ . . "Library of Congress Subject Headings" . . . . . . "obo" . . . "Animal Genome Sheep QTL" . . "^\\d+$"^^ . . _:Ndf8772f8d5b14f2a81291b8a225d1742 . . . . "selventa" . "http://purl.obolibrary.org/obo/MP_$1"^^ . "PA131"^^ . . . . "ncbi.resource" . . . . . . "GCF_000001405"^^ . . "protein" . "iuphar.receptor" . . . "Daniel.Kahn@toulouse.inra.fr" . . . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information."^^ . . . . "Vertebrate Genome Annotation Database" . "development" . "false"^^ . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene."^^ . . "Neil D Rawlings" . . . "metabolomics" . . "bcbc" . . . . "obo" . "interaction" . . . . . . . . "PMC" . . . . . "dbsnp" . . . "metabolites" . . . . "http://purl.obolibrary.org/obo/XPO_"^^ . . _:Nc7df189bb5a84fff985817ad74147293 "johardi@stanford.edu" . . . . "genetics" . . "population genetics" . . . . . "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^ . . "reaction" . . . "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."^^ . . . "false"^^ . "life science" . . . "nsc" . . "chebi" . . . "computational chemistry" . . . . . . "computational biological predictions" . "life science" . "genomics" . "UniGene" . "C0020004/4992"^^ . "Food Interactions with Drugs Evidence Ontology" . "false"^^ . "https://go.drugbank.com/indications/"^^ . "The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs."^^ . "https://vcell.org/biomodel-$1"^^ . . . "false"^^ . . . . . . . . "hamap" . . . . "faseb list" . . "^\\d+$"^^ . . . . "marilyn.safran@weizmann.ac.il" . . . . . . "TubercuList knowledge base" . "ontology" . "0000947"^^ . . . . . . "structural biology" . "whimar@ohsu.edu" . . "The Organisation for Economic Co-operation and Development (OECD) Harmonised Templates (OHTs) are standard data formats for reporting information used for the risk assessment of chemicals, mainly studies done on chemicals to determine their properties or effects on human health and the environment, but also for storing data on use and exposure."^^ . . . . "Liliana Andres Hernandez" . . . . . . . . . "false"^^ . . "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . "https://pir.georgetown.edu/cgi-bin/ipcSF?id="^^ . "publication" . . . . . . . . "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number."^^ . . "dna" . "owl" . . _:Nc4693202043b456eaa44488266112b67 "Crop Ontology Helpdesk" . "1466"^^ . . . "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . . "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId="^^ . "sequence" . "Lukas A. Mueller" . . "Judith A Blake" . . "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=$1"^^ . . . . . . "gene" . . "co_339" . . "P00266"^^ . "false"^^ . . "Virtual Fly Brain" . . "wos.researcher" . "gene" . . . . . "An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io)."^^ . "small molecule" . "false"^^ . "systems biology" . . "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . . "^\\d+$"^^ . "Rahuman Sheriff" . . . . . . "inbred" . "53d583d8-40c6-40e1-9296-23f821cd77a5"^^ . . . . "biomedical science" . "protein" . . . "false"^^ . "3403"^^ . . . "TIGR00010"^^ . "agriculture" . . . . "ExAC Variant" . "exac.variant" . "https://civicdb.org/links/drugs/$1"^^ . . . . . "data analysis" . . "The U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) is the main metadata archive for permanent storage of registered [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service) (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord) is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services)) and can be alternatively used as the main product identifier endpoint when [searching OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below). OSTI.GOV is the primary registry and search tool for all Department of Energy (DOE) funded science, technology, and engineering research and development (R&D) results and the organizational hub for information about the DOE Office of Scientific and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761 - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761 - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761 **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/ - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/"^^ . "false"^^ . "Helen Berman" . . . . . . "Continuous Automated Model Evaluation" . . . . . "semantic web" . . . "Yeast Intron Database v3" . "Epilepsy Ontology" . "Database of Genomic Structural Variation - Variant" . "true"^^ . "^\\d{7}$"^^ . . . . "Giacomo Lanza" . . "EasyChair Topic" . . . . . "false"^^ . . . "data sharing" . . "https://massbank.jp/RecordDisplay?id="^^ . "Multiple alignment" . . . "Scientific Event Ontology" . "Chickpea ontology" . . "NCI Drug Dictionary ID" . . . . "true"^^ . "https://scicrunch.org/resolver/RRID:$1"^^ . "true"^^ . . "marker" . "^WP\\d{1,5}(\\_r\\d+)?$"^^ . "https://comptox.epa.gov/dashboard/$1"^^ . . . . . . . "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID="^^ . "aspgd.protein" . . . . . "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations."^^ . . "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions."^^ . "gene" . . . "AGR" . . "false"^^ . . "Open Biological and Biomedical Ontologies" . . . "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid="^^ . . "e-yasugi@umin.ac.jp" . "Mammalian Feeding Muscle Ontology" . "false"^^ . . . "David Mendez Lopez" . "true"^^ . "true"^^ . . . . "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . . . . . "http://purl.obolibrary.org/obo/PLANP_"^^ . "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes."^^ . . "false"^^ . . . . . "http://stitch.embl.de/interactions/$1"^^ . . "sdbs" . . . "^\\d{8}$"^^ . . . . . . . . "dideo" . . . . "false"^^ . "hao" . . . . . . "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)."^^ . . . . . . "true"^^ . . . . "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. "^^ . "https://cropontology.org/rdf/CO_327:"^^ . "hancestro" . . . . "zebrafish" . . . "http://dictybase.org/gene/$1"^^ . "GitHub Pull Request" . "http://repository.topdownproteomics.org/proteoforms/"^^ . "^NRFC\\d+$"^^ . . . . . "false"^^ . . . . . "A repository of software packages written in Rust."^^ . . "A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates."^^ . . . . . . "^\\w+(\\.)?\\d+$"^^ . . . . . . . . "CATH Protein Structural Domain Superfamily" . . . . "ko00071"^^ . . . "grant application" . "life science" . "protcom" . . . "NCBI PubChem database of bioassay records" . . . . . . . . "https://bioregistry.io/odam:"^^ . . . . "odc.tbi" . . "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML)."^^ . . "SIDM01262"^^ . . . . "PRO" . . . . . "The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage)\n\nNote that the identifier in this semantic space is not the one used in the webpages"^^ . . "Os01g0883800"^^ . . . "evolutionary biology" . "https://www.internationalgenome.org/data-portal/sample/"^^ . . "decipher" . "false"^^ . "^\\d{7}$"^^ . "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#"^^ . "disorders" . "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines"^^ . "https://cropontology.org/rdf/CO_323:"^^ . . "aop.events" . "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . "0002-1975-61"^^ . . "Pocketome" . "Plant Anatomy Ontology" . "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR."^^ . . . . . . "https://www.gtexportal.org/home/gene/$1"^^ . "http://www.kegg.jp/entry/"^^ . . . . . . . . "false"^^ . . "http://purl.org/linked-data/cube#$1"^^ . . . "The pre-IND tracking number for submissions to the FDA"^^ . "A structured controlled vocabulary for the phenotypes of Ascomycete fungi."^^ . "^\\d{7}$"^^ . "Mutant Mouse Resource and Research Centers" . . "0000010"^^ . . "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature."^^ . . . "IHW09326"^^ . "International Genome Sample Resource" . . "https://pubchem.ncbi.nlm.nih.gov/substance/"^^ . . "false"^^ . "development" . . "max@soe.ucsc.edu" . "SP_KW" . "Cell line collections (Providers)"^^ . "wikigenes" . . . . "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins."^^ . . "https://fairsharing.org/" . "C. elegans development ontology" . "sgd.pathways" . . . . . . "functional genomics" . . . "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli."^^ . . . . "BioProject" . . . "false"^^ . . "molecule" . . . "https://assets.nemoarchive.org/$1"^^ . . . . . "https://cropontology.org/rdf/CO_341:$1"^^ . . . "dna" . . . . . . "false"^^ . . . . . . "false"^^ . . . . . . . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"^^ . "Cell line collections (Providers)"^^ . . "SPU_000001"^^ . "tcb" . "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code="^^ . . . . "metabolomics" . "ontology" . . . . "HL7 External Code Systems" . . "ontology" . . "biology" . . . . "4779"^^ . . "molecular structure" . "false"^^ . . . . . . . . "resource metadata" . . . "http://purl.obolibrary.org/obo/VO_"^^ . "false"^^ . . . . . "false"^^ . _:Nda1926f0128c406c8ef98fc6a27a0fc7 "davem@umn.edu" . "false"^^ . . "model" . "false"^^ . . . "^\\d+$"^^ . . . . . "^\\d+$"^^ . . "1981638"^^ . . "pdumdv" . "Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine."^^ . . . . "^[1-9]\\d*$"^^ . . "genomics" . "gene" . . "10007835"^^ . . "biocarta.pathway" . "^\\d+$"^^ . . . "tm.shah@cgiar.org" . . "HomoloGene" . "biozil" . "130502"^^ . _:N9e47917e61904b6ca52093f043990cdc "World Health Organization" . . "https://www.npmjs.com/package/$1"^^ . "http://purl.org/dc/terms/$1"^^ . "^MI\\d{7}$"^^ . . . . . . "genome" . "ontology" . "http://purl.obolibrary.org/obo/ZEA_$1"^^ . . "C00000001"^^ . . . . . . . "EC" . . . "false"^^ . . . "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . "https://lincs.hms.harvard.edu/db/proteins/$1"^^ . . "ontology" . . . "ICD10WHO" . "T3D0001"^^ . . . "ontology" . . "network model" . "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles."^^ . . . . "knowledge representation" . . "CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. "^^ . "MNEST029358"^^ . . "false"^^ . . "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1"^^ . . . "http://www.phosphosite.org/siteAction.do?id=$1"^^ . . "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^ . . . . . . . "bao" . "drug" . "https://bioregistry.io/gmd:"^^ . . . "0000319"^^ . "funding bodies" . "protein" . _:N39ab7487df2d480a9cb36e248b317eea "InterPro Help" . . "ontology" . . . . . . "https://biopragmatics.github.io/providers/dmba/"^^ . . . . "AntWeb" . "false"^^ . "aellenhicks@gmail.com" . . "johnbeverley2021@u.northwestern.edu" . . . "Gainesville Core Ontology" . "Cambridge Structural Database" . . . "Maciej.Antczak@cs.put.poznan.pl" . "rlwalls2008@gmail.com" . . "https://rarediseases.info.nih.gov/diseases/$1/index"^^ . . "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank."^^ . . "Nonribosomal Peptides Database" . . . . . . "^G[0-9]{5}[A-Z]{2}$"^^ . . . "ontology" . "^\\d+$"^^ . "obo" . . . "loinc" . . . . "abcam" . . "http://purl.obolibrary.org/obo/MmusDv_"^^ . "prgr_human"^^ . . . "https://aopwiki.org/events/"^^ . "^[0-9]+$"^^ . "http://purl.obolibrary.org/obo/CLAO_"^^ . . . "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form=$1"^^ . . . "algorithm" . "publication" . . "0000001"^^ . "CHEBIID" . . "wbbt" . "^[A-Za-z0-9-]+$"^^ . . . "obo" . . . "life science" . "http://purl.obolibrary.org/obo/GENO_"^^ . "diet" . . "ontology" . . . "pubchem_id" . . . . . . "ogata@kuicr.kyoto-u.ac.jp" . "Regulation of Gene Expression"^^ . "0000634"^^ . . "ensembl" . . . . . . . . "0000001"^^ . . "term"^^ . . "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name="^^ . . . . . . "knowledge and information systems" . "RCSB_PDB" . . . "485991"^^ . . . . "Prefix.cc" . . "idog" . . "PDB ligand" . . . . "ontology" . "uniprot.database" . "ontology" . . . "1"^^ . . . . "^\\w+$"^^ . . "https://cropontology.org/rdf/CO_357:"^^ . . "ontology" . . . . "Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)"^^ . . "0000205"^^ . . "chemical" . . . . "ExAC Gene" . . . . "false"^^ . . . . "k-12 teacher" . . . "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"^^ . . . "Ontology for Parasite LifeCycle" . . "co_338" . . . "false"^^ . . . "Genomics of Drug Sensitivity in Cancer" . . . . "^\\d{7}$"^^ . . . "life science" . "COVID-19 Surveillance Ontology" . . . "Adrian Gschwend" . "humanities" . "false"^^ . "true"^^ . . "^[0-9]+$"^^ . . . "false"^^ . . "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors."^^ . . . "^\\d+$"^^ . "Current Dental Terminology" . . . . . . "http://dicom.nema.org/resources/ontology/DCM/"^^ . "life science" . "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)"^^ . . "clustering" . . "^HIT\\d{9}(\\.\\d+)?$"^^ . "obo" . . . . "https://cropontology.org/rdf/CO_340:$1"^^ . "gene" . . . . . "false"^^ . "^SKIP\\d+$"^^ . . . . "https://togoid.dbcls.jp/#"^^ . . . . . . . "https://www.deciphergenomics.org/syndrome/$1"^^ . "false"^^ . "^\\d+$"^^ . . . "Japan Consortium for Glycobiology and Glycotechnology Database" . . . . "TF0001053"^^ . "true"^^ . "electronic health record" . . . . . "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . . . . . . . . . "astd" . "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)"^^ . . "ddinter.interaction" . . "http://purl.obolibrary.org/obo/VHOG_"^^ . . "protein" . "Ontology for Avida digital evolution platform" . . . "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. "^^ . . . "ClinVar Submitter" . . "https://www.ebi.ac.uk/arrayexpress/experiments/"^^ . "plant phenotypes and traits" . . . . "https://nanbyodata.jp/disease/NANDO:$1"^^ . . "structure" . . . "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^ . "4DNSR73BT2A2"^^ . "phosphosite.protein" . . . "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object="^^ . "RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments."^^ . . "ontology" . "Extensible Markup Language" . "biomedical science" . . "Hannele Laivuori" . "cell biology" . . . . . . . "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas."^^ . "http://ecoportal.lifewatch.eu/ontologies/$1" . . . "0000618"^^ . "geology" . "https://nmrshiftdb.nmr.uni-koeln.de/molecule/"^^ . . . . . "joanne.kamens@addgene.org" . . "false"^^ . . . . "http://purl.obolibrary.org/obo/FAO_$1"^^ . . . . "SNP500Cancer" . "false"^^ . . "CDC2"^^ . . "pandit" . "dan5@georgetown.edu" . . . "Mouse Developmental Anatomy Ontology" . . . "protein" . . . . . . . "hasDbXref"^^ . "Malachi Griffith" . . "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies."^^ . . "mfo" . . "maggot" . . . . "Xeni Kechagioglou" . . "Richard Cyganiak" . "bgee.organ" . "protein" . . . "small molecule" . "Ulrike Wittig" . "obo" . . . "biology" . "Val Wood" . . . . . . . . . . "gene expression" . . . "metanetx.reaction" . . . "plasmodb" . "http://purl.obolibrary.org/obo/NCRO_"^^ . . "dictyBase" . "http://purl.obolibrary.org/obo/FYPO_$1"^^ . . . . "fishbase.species" . . . "0000000"^^ . . "developmental biology" . "http://purl.obolibrary.org/obo/MOD_"^^ . . . "E-cyanobacterium rule" . "epidemiology" . . . . "spar" . . "false"^^ . . . _:N3e7c81cd11fa492a82b3573ccfdc6237 "CTCAE Help" . "crates" . "UBPROP" . . . . . . . . . "gmd.profile" . "https://bioregistry.io/go.rule:"^^ . "http://www.p3db.org/protein.php?id=$1&ref=0"^^ . "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources."^^ . "false"^^ . . . . . . . . . "identifier for a scientific journal, in the UniProt database"^^ . "http://purl.obolibrary.org/obo/EHDA_"^^ . . "proteomics" . . "Insect Cell Line Database" . "Cell line databases/resources"^^ . . . "signaling" . . . . . "bioinformatics" . "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^ . . . . "virus" . . . "prefLabel"^^ . . . "^(E|D|S)RR[0-9]{6,}$"^^ . "137"^^ . . . . "Platynereis Developmental Stages" . "0045310"^^ . "apetrov@ebi.ac.uk" . . . "obo" . . . . . . . . "Reactions in drugbank"^^ . "International Nonproprietary Names" . . . . . . "pathway" . "cell cycle" . . "Hugh P Shanahan" . . "1"^^ . "cell biology" . . "anzctr" . . . "splash10-0zq2000000-77302b0326a418630a84"^^ . . . . . "anatomy" . . . "^\\d+$"^^ . . . "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . . . . "^([hm]\\_)?\\w+Pathway$"^^ . . "immunology" . . . . . . . . . . . "omia" . . . "https://cropontology.org/rdf/CO_334:$1"^^ . . "model" . . "n.queralt_rosinach@lumc.nl" . . . . . . "false"^^ . . . . . "topics" . "genome" . "P23298"^^ . "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"^^ . . . "^\\d+$"^^ . . "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac="^^ . . . . . . . "phylogenetics" . "^C\\d{8}$"^^ . . "Food-Biomarker Ontology" . . . . . "https://www.checklistbank.org/dataset/"^^ . "Pfam" . . . . . . "https://www.ncbi.nlm.nih.gov/homologene/"^^ . . . . "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source."^^ . "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. "^^ . "TS-0285"^^ . . . . . "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"^^ . "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."^^ . . . . . "Classification of Transcription Factors in Mammalia" . . "false"^^ . . . "rapdb.locus" . . "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data."^^ . "dbpedia" . . . . . . "CLPUB00496"^^ . . . . "https://www.clinicaltrials.gov/study/$1"^^ . . . "false"^^ . . . . "richard.scheuermann@nih.gov" . . . . . "data management" . . . . "AC00963334"^^ . . . . . . "structural bioinformatcs" . "true"^^ . "biopragmatics/bioregistry/424"^^ . "Neuronal cell types"^^ . . . "mmusdv" . . . . . . "epidemiology" . "1.1.1.1"^^ . "reaction data" . . . . . . "false"^^ . . . "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^ . "GeneTree" . . "^5\\d{4}$"^^ . . . . . . . "^\\d+$"^^ . . . "mirtarbase" . "report" . . "umls" . . "sequence" . . . . "life science" . "oncotree" . . "false"^^ . . . "doap" . . "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . . . . "ensembl.bacteria" . "metadata" . . "National Microbiome Data Collaborative" . . "http://purl.org/phylo/treebase/phylows/study/$1?format=html"^^ . . "Fly taxonomy" . . . . "domain" . "https://www.rrrc.us/Strain/?x=$1"^^ . . . . "https://lotus.naturalproducts.net/compound/lotus_id/"^^ . . . . _:N684dfaa5304e4af58860ef3f4a47b23a . . . . . . . . . . . . "false"^^ . . . . "0003463"^^ . "repository" . . "ontology" . . . "nutritional science" . "ddpheno" . "false"^^ . . . . . . . . . . "ACYPI000159"^^ . "ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons."^^ . . . "LipidBank" . . . "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/"^^ . . . . "ontology" . . . . . . . "EMAPA_RETIRED" . "http://purl.obolibrary.org/obo/CEPH_"^^ . . "infection" . "peroxibase" . . . . . "https://cropontology.org/rdf/CO_333:$1"^^ . . "REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs)."^^ . . . "bacmap.map" . . . . "dc11" . "life science" . "Dictybase Gene" . . . . . "aop" . . . . "chebi" . . "ID in NIAID ChemDB"^^ . . . . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/SEPIO_$1"^^ . . . . . . "ecacc" . . "obo" . "2005080"^^ . "cdno" . . . . . . "protonet.proteincard" . . "ontology" . . . "CHEMBL465070"^^ . . "https://flybase.org/reports/"^^ . . "false"^^ . . "ndfrt" . . . "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy."^^ . "genome" . "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects."^^ . . "100101"^^ . . "biochemistry" . . . . "http://purl.obolibrary.org/obo/CHIRO_"^^ . . "eggNOG" . . . . . . "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns."^^ . . "true"^^ . . "bdgp.insertion" . "false"^^ . "^\\d+$"^^ . . "109082"^^ . . . . . "US4145692"^^ . . . . "activityBoundOf"^^ . . . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid="^^ . . . . "https://www.genenames.org/data/genegroup/#!/group/"^^ . . "classification" . . "http://www.w3.org/2004/02/skos/core#"^^ . "false"^^ . . . . . "true"^^ . . . "https://bioregistry.io/d1id:"^^ . "rna" . "Vivek Krishnakuma" . "sabiork.kineticrecord" . "https://www.addexbio.com/productdetail?pid=$1"^^ . . . "true"^^ . . . "http://purl.obolibrary.org/obo/SYMP_"^^ . . . . . . "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id="^^ . . . "doi" . . "^[a-zA-Z0-9_-]{3,}$"^^ . . "paleodb" . . . . . . "http://www.w3.org/2006/time#$1"^^ . . . . "https://www.uniprot.org/proteomes/"^^ . . . . . "gramene.gene" . "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity."^^ . "life science" . . "biology" . . . . . "false"^^ . "false"^^ . . . "Signaling Gateway" . . "https://icd.who.int/browse10/2019/en#/$1"^^ . "structure" . . . . "^\\d+$"^^ . "USA National Service Center Number" . . "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession."^^ . . "BSU29180"^^ . . "signaling-gateway" . . . . . "deficiency" . . "^\\d{4}-\\d+-\\d+-\\d+$"^^ . "nfdi4chem.ontocape" . . . "ChEMBL" . "eggnog" . . "mixs" . "dailymed" . . . . "obo" . "genbank" . "pathway" . . . "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1"^^ . "Reaxys" . . "disease" . "^\\w+$"^^ . "0005147"^^ . "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)."^^ . . "sonami@riken.jp" . . "KEGG Genome" . . . . . . . "C023"^^ . . . "false"^^ . . "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view."^^ . . . "citation" . . . . "An experimental run, served thrugh the ENA"^^ . "false"^^ . . "authoredBy"^^ . . "pgs" . . . "bitterdb.cpd" . "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name="^^ . "Chemical Information Ontology" . "structure" . . . "false"^^ . . . . . "BE0000048"^^ . "PubChem CID" . . . "BIOZIL" . . "false"^^ . "^\\d+$"^^ . "registry" . "ehdaa2" . . . "Kerafast cell lines" . . . . "An ontology to describe entities related to prescription of drugs"^^ . . . "false"^^ . . . "false"^^ . . . . "Saccharomyces genome database pathways" . . . . "http://purl.obolibrary.org/obo/RoleO_"^^ . . "^\\d+$"^^ . . . . . "true"^^ . . . "3546"^^ . "pharmacogenomics" . "drugs" . "false"^^ . . "^[A-Z-_0-9]+$"^^ . . . "orth" . "glycomics" . . . . "^\\d+$"^^ . "Indications and other conditions in drugbank"^^ . "ontology" . "https://ecocyc.org/gene?id=$1"^^ . "false"^^ . . "ontology" . . "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^ . "false"^^ . "anatomy" . "embryo" . "^\\d+$"^^ . . . "expression data" . . . "has prefix" . . . . . . . . . "eukaryotic" . . . . . . "plant" . . " The Creative Commons Rights Expression Language (ccREL) lets you describe copyright licenses in RDF. For more information on describing licenses in RDF and attaching those descriptions to digital works, see [ccREL](https://wiki.creativecommons.org/CC_REL) in the [Creative Commons wiki](https://wiki.creativecommons.org/)."^^ . . "http://agroportal.lirmm.fr" . "taxonomy" . . . . "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections)."^^ . . . . "Peroxibase" . . "Scopus Researcher" . "food" . . . . "G protein-coupled receptor database" . . . . . "false"^^ . . . "http://purl.bioontology.org/ontology/HOIP/HOIP_$1"^^ . . . "http://biohackathon.org/resource/hco#"^^ . . . . "false"^^ . "^\\d+$"^^ . . . "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons."^^ . . "The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website)"^^ . . . "dc.terms" . . "ontology" . "602"^^ . "http://purl.obolibrary.org/obo/UBERON_$1"^^ . "gene" . . "NIF Standard Ontology: Qualities" . "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . . "population genetics" . . . . "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO)."^^ . . . . . . "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis."^^ . "http://biobanknetwork.telethon.it/Sample/View?sampleId="^^ . . . "preprints" . . . _:Nd45bb82a739d443a9a81f0bffd8efefc "Crop Ontology Helpdesk" . . . . "life science" . . "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders."^^ . "muamith@utmb.edu" . . . . . . . . . . . . . "obo" . . "iceberg.element" . "Human Phenotype Ontology" . "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making."^^ . "^(\\d\\d\\d|V\\d\\d|E[8-9]\\d\\d)(\\.\\d{1,2})?$"^^ . . . . "UniProtKB-KW" . . . . . "mop" . . "classification" . . "ardan@ebi.ac.uk" . . . . . "protein" . "https://pathbank.org/view/$1"^^ . . . . . . . . . . . . "NLFFF Database" . "anatomy" . . . . . . "food" . . . . . "study design" . "ontology" . . "false"^^ . . "cohd" . . "InChI" . . . "false"^^ . "molecular interaction" . "^\\d+$"^^ . "gene" . "https://w3id.org/sssom/"^^ . "drugbank.category" . "obo" . "phosphopoint.protein" . . "life cycle" . "^\\d+$"^^ . "software" . . "^\\d{7}$"^^ . . . . "gene" . "DDB0191090"^^ . . . . "interaction" . . "hypercldb" . . . "shacl" . . . . . . . "genotype" . "phenotyping" . "chemical entity" . . . "http://purl.obolibrary.org/obo/TAO_$1"^^ . "UniPathway Compound" . . . . . "Cell line collections (Providers)"^^ . "false"^^ . "chebi" . "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders."^^ . "embryo" . . . . "OSR0818"^^ . "1018"^^ . . "joerg.overmann@dsmz.de" . "enzyme" . "target" . . . "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology."^^ . . . . "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce"^^ . "01.01.005"^^ . . "sustainability" . "interaction" . "^\\d{7}$"^^ . . "Silvio Peroni" . "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . "life science" . . . . . . . . "059486"^^ . . "http://purl.obolibrary.org/obo/MAXO_"^^ . . . . . "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data."^^ . "y3ax-8bq3-60"^^ . . . "Exposure ontology" . . "protein" . "OMOP" . "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$"^^ . "false"^^ . . . "mmartone@ucsd.edu" . . "Jason E. Stajich" . _:Nd1e9b7f7d97d4a2a83127f2390a8ce15 "Crop Ontology Helpdesk" . "Diagnostic and Statistical Manual of Mental Disorders (5th Edition)" . . "Ge Gao" . "https://odc-sci.org/data/$1"^^ . . "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s)."^^ . . . "18"^^ . . "chebi" . "life science" . . . . "^\\d+$"^^ . . "A nomenclatural ontology for biological names" . . "dna" . . . "Ion Channel Electrophysiology Ontology" . . . "false"^^ . "131392"^^ . "BindingDB is the first public database of protein-small molecule affinity data."^^ . . . . "metanetx.compartment" . . "data management" . "neurology" . "brycemecum@gmail.com" . "narcis.fernandez@gmail.com" . . "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other."^^ . "A vendor of antibodies and other biologics"^^ . "experimental measurement" . . "https://bioregistry.io/collection/"^^ . "UP" . . . . . . . . "HsapDv" . . . . . "https://www.cytion.com/"^^ . "International Fungal Working Group Fungal Barcoding." . . "Orphanet Rare Disease Ontology" . . "Swiss Personalized Health Network Schema" . "psychology" . . . . . . "https://www.phenxtoolkit.org/protocols/view/$1"^^ . "true"^^ . "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^ . . "Dongsheng Cao" . "assay" . . . . . . "Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a \"peer\"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs. "^^ . "Animal Genome QTL" . . "^AT[1-5]G\\d{5}(\\.\\d+)?$"^^ . . . . . . . . . . "subject agnostic" . . . . . "http://purl.obolibrary.org/obo/CARO_"^^ . "0000002"^^ . "Anatomical Therapeutic Chemical Classification System" . "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . . . "false"^^ . "Database of Aligned Ribosomal Complexes" . "https://www.kazusa.or.jp/huge/gfpage/"^^ . . "^\\d{7}$"^^ . "zhangzhang@big.ac.cn" . . "^\\d{7}$"^^ . . . "ASPL0000349247"^^ . . "CHEBI" . . . . "http://purl.obolibrary.org/obo/MA_"^^ . . "ontology" . "Liz Allen" . "Lars Bertram" . "false"^^ . . "http://purl.obolibrary.org/obo/RNAO_"^^ . "International Classification of Diseases, 10th Revision" . "false"^^ . "pathway" . . "false"^^ . . . . . . . . . . . . . . . . "biomedical science" . . . "Kidney and Urinary Pathway Ontology" . . . . . . "biomedical science" . . "anatomy" . . "^\\d{7}$"^^ . "Environment Ontology for Livestock" . . . . . . . . . . "GWAS Central Phenotype" . "dragondb.protein" . . . . "ino" . . . . . . . . . "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_"^^ . "false"^^ . . "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id="^^ . . . "http://www.cs.tau.ac.il/~spike/maps/$1.html"^^ . "CGNC" . "http://www.pharmgkb.org/drug/"^^ . . "^\\d+$"^^ . "^[a-zA-Z0-9][A-Za-z0-9_]+$"^^ . . . . . . . . "classification" . . "https://cropontology.org/rdf/CO_333:"^^ . . . . "molecular genetics" . . . "12929"^^ . . . . . . . . . . "ssbd.project" . . . . "false"^^ . . . . . "^4DN[A-Z]{2}[A-Z0-9]{7}$"^^ . "TTD Drug" . . "2gc4E"^^ . "Cell line databases/resources"^^ . . "chemistry" . . "sperm" . . "greengenes" . . "PAp00000009"^^ . . "wosuid" . "http://purl.obolibrary.org/obo/AEO_$1"^^ . . . "bto" . "^\\d+$"^^ . . . . "http://purl.obolibrary.org/obo/PCL_$1"^^ . "Bio-Pesticides DataBase" . . . . . "obo" . "ecao" . . . . . . . . . "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone="^^ . . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id="^^ . "Orthology Ontology" . . . "scop.sun" . . "biro" . . . . _:N1699cf1ea2754508a32e555023a392e4 "agrovoc@fao.org" . . . . . "beta-carotene"^^ . . . "LNCipedia" . . "genome" . . . "http://www.drugbank.ca/drugs/"^^ . . "disease" . . . "false"^^ . . . . "^PRI\\d*$"^^ . "^\\d{7}$"^^ . . "Rupert Kellner" . "Stacia R Engel" . . . "Hiroyuki Ogata" . . . "^\\d+$"^^ . . . "http://www.fao.org/gsfaonline/additives/details.html?id="^^ . "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . . . "http://champ-project.org/images/ontology/cao.owl#CAO_$1"^^ . . . . . . . "phylogenetics" . _:N4bb080adea3244668a33721fe25e6ef1 "gregg@greggkellogg.net" . "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"^^ . "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis."^^ . . . "false"^^ . . "gene" . "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way."^^ . "Dendritic cell" . . "http://modelseed.org/biochem/compounds/$1"^^ . "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules."^^ . . "100810"^^ . . "http://multicellds.org/MultiCellDB/"^^ . "BM0456"^^ . . "life science" . "false"^^ . . "^FB\\d{8}$"^^ . . . . . "^\\d+$"^^ . . "Unimod protein modification database for mass spectrometry" . . "small molecule" . . . . "glycomics" . . "data governance" . "protein" . . . . . "http://purl.obolibrary.org/obo/MP_"^^ . "Bill Hogan" . . "Drosophila Phenotype Ontology" . . . . "civic.gene" . . . . "false"^^ . . . "wuc@udel.edu" . "genomics" . . "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e="^^ . "BiGG Compartment" . "0000000"^^ . "plant" . "lincs.smallmolecule" . . . . "fovt" . _:N80cbcd52618948a5867f9c33561a4aeb "willisj@mail.nlm.nih.gov" . . "gwang@unmc.edu" . . . . . "IPD-IMGT/HLA" . . . . "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI."^^ . . . "One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]"^^ . "http://purl.obolibrary.org/obo/PR_$1"^^ . "https://w3id.org/biolink/vocab/"^^ . "28789"^^ . . "1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d"^^ . . "false"^^ . "NucleaRDB" . . . . . . . . "life science" . "thesaurus" . "Eukaryotic Genes" . "UniProt Keywords" . . "protein" . "An ontology for non-coding RNA, both of biological origin, and engineered."^^ . . . "cardiovascular disease" . . . . . "false"^^ . "^DP\\d{5}$"^^ . . . "An ontology of human and animal behaviours and behavioural phenotypes"^^ . "ontology" . . . . "virmirdb" . . . "George Gkoutos" . . "uspto" . . . . "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . . . . . . . . . "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^ . "regulation" . . "sperm" . . "IUPHAR family" . . . . "false"^^ . . . . . . "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits."^^ . . . "^[a-z]+(\\-[a-z]+)*$"^^ . . . . "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"^^ . "^[a-z_A-Z]+$"^^ . . . . "false"^^ . . "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^ . . . . . "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$"^^ . . . . "phebert@uoguelph.ca" . "vsao" . . "https://www.bgee.org/gene/$1"^^ . "Fission Yeast Phenotype Ontology" . . "false"^^ . "4214"^^ . . "life science" . . . "http://edamontology.org/operation_$1"^^ . . . "^T\\d{3}$"^^ . . "rbca.jackson@gmail.com" . "UBREL" . "0000093"^^ . . . "http://purl.obolibrary.org/obo/GSSO_"^^ . . . . . "dbd" . "false"^^ . . . "2.1.1"^^ . . . . . . "CHEBI"^^ . "2649230"^^ . . "sequence" . "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . . "1eec8393-e598-41ed-9d8b-6d5b0db94470"^^ . "amphx" . "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"^^ . . "^\\d{7}$"^^ . . . "^[a-z]+(\\..*?)?$"^^ . . "bioinformatics" . "https://trialsearch.who.int/Trial2.aspx?TrialID=$1"^^ . . "botany" . . . . _:N0a3b10f91bc9432d844ddbb98489eb84 "WHO Collaborating Centre for Drug Statistics Methodology" . . "annotation" . . . "small molecule" . . "natural producs" . . . "^NBK\\d+$"^^ . "BitterDB Receptor" . . . . . . "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^ . "false"^^ . . . . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"^^ . "obo" . . . . . . . "protein" . "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"^^ . "variant" . "https://foodb.ca/foods/"^^ . . . . . . . "dna" . . . . "The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO."^^ . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/VO_$1"^^ . "Semanticscience Integrated Ontology" . . . . . . . "jmwhorton@uams.edu" . "false"^^ . . . "Yongqunh He" . "Legacy site for IETF RFC proposals"^^ . "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all."^^ . "interaction" . . . "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . . . . . "Locus Reference Genomic" . . . . . "^\\D{4}\\d{6}(\\-\\D{2})?$"^^ . . . "gene" . "Cell line databases/resources"^^ . . . . "http://purl.obolibrary.org/obo/ADO_"^^ . "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1"^^ . . . . . . . . . . . "^\\d{7}$"^^ . "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found."^^ . "false"^^ . . . . . . . "UniRef90_P00750"^^ . . "Fernanda Dorea" . "ctis" . . . "0000208"^^ . . "CropMRepository" . . . . "^ACTRN\\d+$"^^ . . . "National Academic Research and Collaborations Information System" . "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$"^^ . "w3c rec" . "Tsute Chen" . . . "PubChem Cell Line" . "5688061"^^ . "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"^^ . . "Cell Line Ontology" . . . "wwf.ecoregion" . "PRO_0000016681"^^ . . . "true"^^ . "Stewart Thomas Cole" . . . _:Nd78e386571634ea5a7085ad29e0607bf "Crop Ontology Helpdesk" . . . . . . . . . . . . "ncim" . . . "raymond@caltech.edu" . . . . _:N8f287a15652444e6a1ab1f96fade6ae1 "willisj@mail.nlm.nih.gov" . "true"^^ . "Laia Subirats" . . "Reaxys" . "obo" . . _:N3f1124850c29450a9be0c635dfd41a59 "michael.lincoln@va.gov" . . . "Symptom Ontology" . . "^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$"^^ . . "Transcription Factor Database" . "genomics" . . "gene" . . . "false"^^ . . "^D\\d{4}$"^^ . "ratmap" . "astrophysics and astronomy" . . . . "pancreatic development" . . . "^\\d+$"^^ . . . "nlx.sub" . "WBls" . . . . "Experimental condition ontology" . "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . "2842"^^ . "dorothea.iglezakis@ub.uni-stuttgart.de" . . . . "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets."^^ . . . . . "bcgo" . . "true"^^ . . . "ontology" . . . . . . "vendor" . . "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance."^^ . "National Center for Advancing Translation Sciences BioPlanet" . _:Nc4693202043b456eaa44488266112b67 "helpdesk@cropontology-curationtool.org" . . . "false"^^ . "http://purl.obolibrary.org/obo/PPO_$1"^^ . "http://purl.org/net/orth#$1"^^ . "structural biology" . . . . "sequence annotation" . . . . . . "data identity and mapping" . . "https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?short_form=NMR:$1"^^ . . . . . . . "phenotype" . . . "preclinical studies" . . . "zebrafish line" . "life cycle stage" . "easychair.cfp" . . "https://www.enzolifesciences.com/$1"^^ . . . . . . . "https://w3id.org/seo#$1"^^ . . "disease phenotype" . "false"^^ . "rxno" . . "Identifier of a taxon or synonym in the Catalogue of Life"^^ . . . . . . . "Yasset Perez-Riverol" . . "phylogenetics" . . "https://www.imanislife.com/?s=$1"^^ . "linikujp@gmail.com" . . "9002859"^^ . . . . "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"^^ . . "^ENSGT\\d+$"^^ . . . . . "David Blackburn" . . . . "2679240"^^ . . . . "^(cd)?\\d{5}$"^^ . "https://www.nextprot.org/term/$1"^^ . "M94112"^^ . . "EU Clinical Trials" . . "metabolites" . . . . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid="^^ . . . . . "https://flybase.org/reports/FBtc$1"^^ . "genetics" . . . . . . "Rosa2"^^ . "http://purl.obolibrary.org/obo/XPO_$1"^^ . . "true"^^ . . . . "phenotype" . . . . . . . "1000"^^ . . "https://eds.gene.le.ac.uk/home.php?select_db="^^ . . . "life science" . . . . . "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . . "life science" . . . "^\\d{7}$"^^ . "^[a-zA-Z0-9 +#'*]+$"^^ . . . . "false"^^ . "tads" . "ChemIDplus" . . "medicine" . . "^\\d{4,}$"^^ . . . "Bioregistry" . . "monitoring" . "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records."^^ . "computational biology" . . . "owl" . . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information."^^ . "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information."^^ . . "Cell Cycle Ontology" . . . . "false"^^ . "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . "http://cutdb.burnham.org/relation/show/$1"^^ . . "genetics" . . . "obo" . "Annotated Regulatory Binding Sites" . . "metadata" . "false"^^ . . "molecular entity" . "https://lincs.hms.harvard.edu/db/datasets/$1"^^ . "47419"^^ . "2029"^^ . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . "regulation" . . . . . . . "ontology and terminology" . . . . . "variants" . . "Long Term Ecological Research Controlled Vocabulary" . . . . "false"^^ . . "false"^^ . "David Starns" . "Bambara groundnut ontology" . . . "5359"^^ . . . "fetal fibroblast" . . . . . . . . . . "molecules" . . . . "Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID]"^^ . . . . "molbase" . . . . . . . . "Jessica Kissinger" . "napp" . . . . "swisslipids" . "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.."^^ . . "Chicken Gene Nomenclature Consortium" . . "http://purl.obolibrary.org/obo/OGMS_"^^ . . "ontology" . . . "EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)"^^ . . . . . . . . "1784"^^ . "Cell Image Library" . . . "Narcis Fernandez-Fuentes" . "kegg.environ" . "Japan Collection of Microorganisms" . "rna" . "Shoshana J. Wodak" . . "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs."^^ . "organism supplier" . "Ramasubbu Sankararamakrishnan" . . "A person" . . "http://scop.berkeley.edu/sunid=$1"^^ . . . "vasilevs@ohsu.edu" . . . . . . . . "stweedie@ebi.ac.uk" . . . . . "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . . "false"^^ . . . "^BE\\d{7}$"^^ . . . . . . . . "M77F7JM"^^ . . . . . "development" . "false"^^ . . . "bioregistry" . "icf" . "Semantic Web Context" . . . . . . . "COG0001"^^ . . "uniprot.proteome" . . "GitHub is an online host of Git source code repositories."^^ . "obo" . "genetically modified pig" . . . . . . "obo" . . . . . "4QHKG"^^ . "CONSO00010"^^ . . "false"^^ . . "Common Access to Biological Resources and Information Project" . . "ontology" . "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."^^ . . . . . "^\\d+$"^^ . . "Registry of Research Data Repositories" . . "yeastract" . "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information."^^ . . "^\\d+$"^^ . "false"^^ . "CHEBI" . . "chemistry" . . "^osa-miR\\d{3,5}[a-z]{0,1}$"^^ . . . . . . . . "pdthomas@usc.edu" . . "scopus.affiliation" . "https://www.deciphergenomics.org/syndrome/"^^ . . "preprints" . "drug repositioning" . . . . . "careerPrizeMoney"^^ . "CTX" . . "53504"^^ . "subject agnostic" . . . . "Identifiers.org Ontology"^^ . . "http://purl.obolibrary.org/obo/FBbi_$1"^^ . . "biomedical science" . . "phenotype" . . . . . "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^ . . . . "http://www.pathwaycommons.org/pc/record2.do?id="^^ . . . . . . . . . . . . "false"^^ . . "http://purl.org/spar/doco/"^^ . . "obo" . . . . . . . . . "co_348" . . . . . "Physical Medicine and Rehabilitation" . "FAIR* Reviews Ontology" . "tmjlowe@ucsc.edu" . "mba" . "^\\d+$"^^ . "https://omia.org/OMIA"^^ . "^PM\\d{7}$"^^ . "false"^^ . "^\\d+$"^^ . . . "false"^^ . . . "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid="^^ . "ontology" . . "^\\d+$"^^ . . "https://biopragmatics.github.io/providers/cvx/"^^ . "ontoneo" . "faseb list" . . "http://www.cellsignal.com/products/$1.html"^^ . . . "^A\\d{4}$"^^ . . . . "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^ . . . "c"^^ . . . . . . "2.7.1.1"^^ . . "genomics" . . "hc.npn" . "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^ . . "The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)"^^ . "Mondo Disease Ontology" . "A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies)."^^ . . . . . "DataONE" . "dwelter.ontologist@gmail.com" . "fcb" . . . . "genetics" . . "BRENDA Enzyme" . . "brenda.ligand" . . . "thesaurus" . . . "sequence" . . . "PF00004"^^ . . "https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md"^^ . . . "wikipedia.en" . . "Database of validation results for ligands and non-standard residues in the Protein Data Bank."^^ . . . "false"^^ . . . . . "AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets." . . . "VegBank" . . . "^\\d+$"^^ . . . "EST database maintained at the NCBI." . "1000560"^^ . . . . . "1050"^^ . . "http://vocab.getty.edu/page/tgn/"^^ . "Simplified molecular-input line-entry system" . . . . . "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments."^^ . "System Science of Biological Dynamics project" . . . . . . "http://www.proteinatlas.org/"^^ . . . "data model" . . . "^[SCTAGMNU]\\d+$"^^ . . . . . . . "http://www.kegg.jp/entry/"^^ . . "Cephalopod Ontology" . _:N39ab7487df2d480a9cb36e248b317eea "interhelp@ebi.ac.uk" . "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . . . . . . . . . . . "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes."^^ . . . . . "Contributor Role Ontology" . "p3db.protein" . "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease."^^ . "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications."^^ . . "Sharkipedia Trend" . . . "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . . . . "https://www.ebi.ac.uk/chembl/entity/"^^ . . . "http://purl.obolibrary.org/obo/MFOEM_"^^ . "^CAL\\d{7}$"^^ . "HEX1"^^ . "stem cell" . "strain" . . . . "ncbi.genome" . . "environmental science" . . . . "https://www.cancerrxgene.org/translation/Drug/"^^ . . "false"^^ . . . "Tobias Schulze" . . "Sheng-Da Hsu" . "https://cropontology.org/rdf/CO_358:$1"^^ . . "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data."^^ . . "https://cordis.europa.eu/project/id/"^^ . "A collection of ontologies relevant for chemistry.\n\nThe NFDI program deploys a [custom instance](https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1) of the Ontology Lookup Service (OLS) that provides the ontologies in this list.\n\nA further analysis of the metadata landscape of the ontologies in this list can be found [here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat).\n\nOntoCompChem and OntoKin appear on the NFDI4Cat list but have not yet been registered in the Bioregistry because the resources are missing/incomplete such that they do not meet minimum Bioregistry metadata standards. These might be added in the future if additional metadata can be found." . "https://civicdb.org/links/molecular_profile/"^^ . . . . . "https://www.ncbi.nlm.nih.gov/protein/"^^ . . "drug" . "^\\d{7}$"^^ . . . . "https://www.ncbi.nlm.nih.gov/datasets/genome/"^^ . . . . . . . "jRCTs041220087"^^ . . . . "false"^^ . . "ontology" . "ali.syed@kaust.edu.sa" . . . "false"^^ . . . . "oa" . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"^^ . . . . . . . . "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages."^^ . . . "urmas.koljalg@ut.ee" . . . . "preclinical studies" . . . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances."^^ . "https://bioregistry.io/pscdb:"^^ . . . "^\\d{1,7}$"^^ . . . . . "03212fd7_abfd_4828_9c8e_62c293052d4b"^^ . . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"^^ . . . . . "alzforum.mutation" . . . "oxburl@mmc.org" . "http://www.unimod.org/modifications_view.php?editid1=$1"^^ . . . . . "ontology" . . . "http://purl.org/oban/$1"^^ . . . . . . . "Silvio C.E. Tosatto" . . . "cheminformatics" . "obo" . _:N7f6fc0e00f37489aa7d35d8d331533dc "fred@fgiasson.com" . . "life science" . . "ulrike.wittig@h-its.org" . . . "Fahim Imam" . . . . . . . "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_="^^ . "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . . . . . . . . . "17165"^^ . "9606117"^^ . "https://smid-db.org/smid/"^^ . "John Cottrell" . "0000003"^^ . . "gene" . "Chlamydia"^^ . . . . "SNR17A"^^ . . "false"^^ . "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#"^^ . "aallen@ascl.net" . . . . . "MESH_SUPPLEMENTAL_RECORD_UI" . "protein" . "false"^^ . . . . "Collection"^^ . "false"^^ . "rpcec" . . "life science" . "civic.therapy" . . . "false"^^ . "false"^^ . "http://purl.obolibrary.org/obo/BOOTSTREP_$1"^^ . . "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones."^^ . . "Allergy"^^ . "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id="^^ . . . . . "ontology" . "ECGOntology" . "life science" . "^MCDS_L_[a-zA-Z0-9]{1,10}$"^^ . . . "phismith@buffalo.edu" . . "0000048"^^ . "MIRT000002"^^ . . "microbiology" . "oharb@upenn.edu" . "xlmod" . . . "http://id.nlm.nih.gov/mesh/vocab#$1"^^ . "https://www.ebi.ac.uk/chembl/cell_line_report_card/"^^ . . "http://purl.obolibrary.org/obo/APOLLO_SV_"^^ . . . . "go.chemical" . . . "life science" . . "http://purl.obolibrary.org/obo/WBls_"^^ . . . "Ribocentre" . "Gene Ontology Annotation Database" . . . . . . "false"^^ . . . . "https://www.inaturalist.org/places/$1"^^ . . . "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions."^^ . "0000009"^^ . "embryonic stem cell" . "biodiversity" . . "Virtual International Authority File" . . . "^\\d{7}$"^^ . . . . . "http://purl.org/spar/scoro/"^^ . . "developmental biology" . . . "software and information systems" . . "taxonomy" . " Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . . . "togovar" . "ama-cpt" . "umls.aui" . "gene ontology enrichment" . "miw023@ucsd.edu" . "false"^^ . . . "civic.source" . . . . . . "disease" . "VirGen" . "The Bioregistry's meta-registry"^^ . "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue="^^ . . . . "behavior" . . . . "dna" . . "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources."^^ . . . . . "obo" . . . "https://www.ncbi.nlm.nih.gov/gene/$1"^^ . . . "http://purl.obolibrary.org/obo/TXPO_"^^ . . . "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images."^^ . . "civic.vid" . . . . "UniProt Post-Translational Modification" . . "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . . . . "^SMP\\d+$"^^ . "transcription factor binding site prediction" . "packagist" . "^(Q|P)\\d+$"^^ . . . "A frontend to Wikidata"^^ . . . "1038233"^^ . . . . . . . . "^\\d{8}$"^^ . . _:Nd34bbd7daf4e4f95b69eabbbfbb1663c "Jonathan Bard" . . "cogs@ncbi.nlm.nih.gov" . "life science" . . . "^Gm\\d+$"^^ . "Gramene Gene" . "https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code="^^ . "^\\d+$"^^ . "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1"^^ . . . . . "obo" . . . . "glida.gpcr" . . . . "International Classification of Diseases, 10th Revision, Procedure Coding System" . "life science" . . "mutation" . . "http://bigg.ucsd.edu/models/universal/reactions/$1"^^ . "http://jcggdb.jp/idb/jcggdb/$1"^^ . . "MultiCellDS Digital snapshot" . . "^\\w+$"^^ . "pseudogene" . . . . . . "protein" . . "UniProt Subcellular Locations" . . "false"^^ . . . . "false"^^ . . . . . "rex" . "subject agnostic" . "false"^^ . . . . . . . . . . "false"^^ . . _:Ndfc62fb6799e46b0be4ddad6be24c69c "albertgoldfain@gmail.com" . "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"^^ . "obo" . "catalog" . . "^\\d+$"^^ . . . . . "RNA ontology" . . _:Nc7df189bb5a84fff985817ad74147293 "Josef Hardi" . . . "90806"^^ . . "pmdb" . . . . . . . . "CAPS-DB" . . .