"archdb" . . "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." . . . "^\\d+$"^^ . . "^\\d+$"^^ . "interaction" . . . "GCF_000001405"^^ . . "http://www.innatedb.ca/getGeneCard.do?id=$1"^^ . . . . . . "gene" . . "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"^^ . . "edong@umich.edu" . "DALIA Open Educational Resource" . . _:N089183192451472da39f43d990695286 "Eionet Helpdesk" . . . . . . . "http://sabiork.h-its.org/newSearch?q=$1"^^ . . . "https://www.sharkipedia.org/trends/$1"^^ . . "biomedical science" . . "false"^^ . "handle" . . . "https://www.ncbi.nlm.nih.gov/datasets/genome/"^^ . . . "http://stitch.embl.de/interactions/$1"^^ . . . "http://tables.pseudogene.org/[?species_name]/"^^ . "ogi" . "0000011"^^ . . . . "bel" . . . "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information."^^ . . "Mike Cherry" . . "life science" . . . "jmwhorton@uams.edu" . "zhufeng@zju.edu.cn" . . . . . "false"^^ . . "https://goldbook.iupac.org/terms/view/"^^ . "false"^^ . . . . "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^ . "fairsharing.organization" . "covid19" . "false"^^ . "mondo.issue" . . . "false"^^ . . . "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."^^ . . . "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."^^ . "https://dialnet.unirioja.es/servlet/revista?codigo=$1"^^ . . "subject agnostic" . . . "COEXISTENCE" . "proteomics" . "protein" . . "http://purl.obolibrary.org/obo/AEON_"^^ . . "https://cellxgene.cziscience.com/collections/$1"^^ . . "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . . . . "icd9" . . . . "janna.hastings@gmail.com" . . . . "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns."^^ . . "ORCiD" . . . "10087"^^ . "^[0-9]+$"^^ . "human genetics" . . . . . "https://www.ncbi.nlm.nih.gov/nucest/"^^ . . . "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . . . . . . . . . . . . "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)"^^ . . "mite" . "false"^^ . . "^\\d+$"^^ . . . . . . . "false"^^ . "authoredBy"^^ . "Kim Dixon Pruitt" . "Ion Channel Electrophysiology Ontology" . "http://www-snorna.biotoul.fr/plus.php?id=$1"^^ . . . "mutation" . "^\\d+$"^^ . . . . . . . . "http://purl.obolibrary.org/obo/EHDAA2_"^^ . . . "trichdb" . . . . . . . . "tads" . "https://www.enzolifesciences.com/$1"^^ . . "obo" . "ega" . "mirbase.mature" . . "https://string-db.org/cgi/network?identifier=$1"^^ . "http://uri.neuinfo.org/nif/nifstd/birnlex_"^^ . "genomics" . "Data Use Ontology" . "https://biosimulators.org/simulators/$1"^^ . "BatchelorC@rsc.org" . . . "biology" . "http://www.receptors.org/nucleardb/proteins/"^^ . "life science" . . . . . . "ENST00000407236"^^ . . . . . "^\\d+$"^^ . "A small ontology expressing skills and competencies."^^ . . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . . . . "HPSI0114i-bezi_1"^^ . . . "rnaloops" . . . "expression data" . . "false"^^ . . . . . "Cotton ontology" . "aclame" . . "Polymorphism and mutation databases"^^ . . "botany" . "HMS-LINCS" . . . . . . . . . . . . "genome" . "^\\d+$"^^ . . "false"^^ . "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . . "classification-model"^^ . . . "0000000"^^ . . "life science" . . "Ribocentre is designed to contain comprehensive information of all natural ribozymes."^^ . . . "ppo" . . "https://www.ncbi.nlm.nih.gov/medgen/"^^ . "ontology" . . "Wikidata Property" . . . . . . "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^ . . . . "nmrxiv.project" . . "GND ID" . "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"^^ . . . "false"^^ . "SNOMEDCT_US" . . . . . . . . "http://purl.uniprot.org/core/"^^ . . . . "https://www.ebi.ac.uk/ols4/ontologies/fma/terms?obo_id=FMA:"^^ . "Clinical Trials Ontology" . . . "dna" . "srao" . . . "Satya S. Sahoo" . . "yeastract" . . . "Broad Fungal Genome Initiative" . . . "SNOMEDCT_US_2023_09_01" . . . . . . . "true"^^ . . . . "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."^^ . "pharmacy" . . . "genomics" . . "http://www.cathdb.info/cathnode/$1"^^ . . "false"^^ . . . . "https://loinc.org/"^^ . "false"^^ . . "http://ensembl.org/glossary/ENSGLOSSARY_$1"^^ . . . "biomedical science" . . . . "0100011"^^ . . . . . . "MESH_DESCRIPTOR_UI" . . "Christopher M. Overall" . . . "false"^^ . . . . "structure" . "false"^^ . "GLDS-141"^^ . . "http://www.unimod.org/modifications_view.php?editid1=$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 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."^^ . . . "https://www.scopus.com/authid/detail.uri?authorId=$1"^^ . . . . "http://uri.neuinfo.org/nif/nifstd/nifext_$1"^^ . . . . . "gene expression" . . . . . "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$"^^ . "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp="^^ . . "proteomics" . . . "repository" . "AddressBook"^^ . "^\\d+$"^^ . "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research."^^ . . . "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^ . "The ESCO occupations pillar is built on ISCO-08 which serves as its hierarchical structure. ISCO-08 provides the top four levels for the occupations pillar and ESCO occupations are located at level 5 and lower. In ESCO, each occupation is mapped to exactly one ISCO-08 code. [from homepage]"^^ . . . "^\\d+$"^^ . "false"^^ . . . "mice" . . . "false"^^ . . . . "Insect Resistance Ontology" . . . . . . . "^\\d+$"^^ . . . . . "alen.vodopijevec@cessda.eu" . "molecule" . . . "myco.marinum" . . . . . . "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"^^ . . . . "https://www.rebuildingakidney.org/id/"^^ . . . . . "NCBI_taxid" . "jeffvin.wong@utoronto.ca" . . . . "goa" . . . . "post-translational modification site prediction" . . "false"^^ . "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."^^ . . . . "lars.holm.nielsen@cern.ch" . "rdbsb" . . "ontology" . . "false"^^ . . . "http://www.pathoplant.de/detail.php?accNo=$1"^^ . . . . . . . . . "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/"^^ . . . "miRNA Target Prediction at EMBL" . "mentions" . "false"^^ . "false"^^ . . . "rdf" . . "false"^^ . . . . "Identifier for an animal, plant, or microorganism from the fossilworks website"^^ . . . . . . . . . "false"^^ . "true"^^ . . "0745-4570"^^ . . . "bko" . "dideo" . "^2\\d{4}$"^^ . "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082"^^ . . . "Provisional Cell Ontology" . "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"^^ . . "Nikolaos Moustakas" . . "kdbirp" . . "subtiwiki" . . "gitea/gitea"^^ . "lccn" . . "false"^^ . "sio" . . . . . "The aim of DALIA project is to build a platform for learning material for Research Data Management (RDM) and Data Science. The platform is based on a knowledge graph. We introduce MoDalia, the base ontology of DALIA knowledge graph. Modalia inherits some modules from EduCOR. It includes also modelling of micro -credentials and certificates"^^ . "sedml.language" . . "false"^^ . "ASRP1423"^^ . . . . "lncipedia" . . "https://bioregistry.io/resolve/github/pull/$1"^^ . . "geography" . . . . "project" . . . . . . . . "^\\w+$"^^ . "false"^^ . "agronomy" . "MGnify Study" . . . "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id="^^ . . . . "life science" . . . "ontology" . . "false"^^ . "false"^^ . "European Science Vocabulary" . . . . "ontology" . . "C023"^^ . "protein" . . "gavin.thomas@york.ac.uk" . "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"^^ . "8497"^^ . . . "ontology" . . "959"^^ . . . "iev" . "^[\\d.]+$"^^ . . "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"^^ . "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."^^ . "Human developmental anatomy, timed version" . . . . "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/"^^ . "http://purl.obolibrary.org/obo/SIBO_$1"^^ . . . . . . "computer science" . . "^[a-z]+/[0-9]+$"^^ . . . . . "https://portal.hubmapconsortium.org/browse/donor/"^^ . . . . "protein" . "https://www.eionet.europa.eu/gemet/en/group/$1"^^ . . . . "botany" . "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp="^^ . . "chembl.target" . . . "protein structure" . "410"^^ . "http://purl.obolibrary.org/obo/$1"^^ . . . "false"^^ . . . . . . "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id="^^ . . . "false"^^ . . "https://www.clinicaltrials.gov/study/"^^ . . "TTHERM_00648910"^^ . "The Mobilome Ontology describes bacterial mobile genetic elements, their mechanisms, and associated epidemiology."^^ . "ontology" . . . . "CTCAE" . . _:N1ddc4340664b4ee99de4ba14af5b0985 . . . . "Life cycle stages for Human"^^ . "agsd" . "lpt" . . . "false"^^ . . . "https://www.cytion.com/$1"^^ . . . . . "70"^^ . . . . "^\\d+$"^^ . . . "genome" . "Chris Sander" . "Drug_Central" . "mgi" . . "pathogen" . . . "http://cgsc.biology.yale.edu/Site.php?ID=$1"^^ . . . "00011461"^^ . "^\\d+$"^^ . "Linked Open Vocabularies" . . "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^ . . "person" . "AGRO" . . . . . . . . . "false"^^ . . . . "false"^^ . . "hsa00190"^^ . . . . . "structure" . "A controlled vocabulary of media resources, such as audio, cartographic, manuscript, multimedia, etc."^^ . "johannes.wittmann@dsmz.de" . . "false"^^ . . . "Merriam Webster Dictionary" . "^\\d{7}$"^^ . . "D00123"^^ . . "Comparative Data Analysis Ontology" . . . . . . . . . . "Marc Ciriello" . . "2A"^^ . . . "false"^^ . . "Jeremy D. Glasner" . "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . "disease" . . . . . "An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains"^^ . . "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$"^^ . . "false"^^ . . . . "kaken" . "SIDER Side Effect" . . . "Jie Zheng" . . "gene" . "dip" . "metabolite" . "true"^^ . . "HIX0004394"^^ . . . "http://w3id.org/nkos/"^^ . . . . . "^(\\w+(\\-\\w+)?(\\.\\w+)?\\/?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . "false"^^ . . "smiles" . . . "ChemBioSys Project" . "depmap" . . "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"^^ . . . "https://cstr.cn/$1"^^ . "https://dbpedia.org/ontology/"^^ . . . . "metadata standardization" . . "https://www.uniprot.org/tissues/"^^ . . . "http://purl.obolibrary.org/obo/MONDO_"^^ . . "phenotype" . . . . "gene expression" . . . . . "botany" . . "Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank."^^ . "experimental tools" . "protein family" . . . . . . . . . "Database of Genotypes and Phenotypes" . . . "Iconclass Classification" . . . . . . . . . "itmctr" . "Uber-anatomy ontology" . "false"^^ . "false"^^ . "Open Digital Rights Language Ontology" . . "https://gnomad.broadinstitute.org/variant/$1"^^ . . . . "https://fedirect.toolforge.org/?id="^^ . . "true"^^ . . . . "http://n2t.net/ark:"^^ . . . "brenda.ligandgroup" . "Sabine Oesterle" . . . . . "false"^^ . . . . "artificial intelligence" . . "https://www.fung-growth.org/page/Display%20page%20FG/$1"^^ . . . "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"^^ . "mingxun.wang@cs.ucr.edu" . "http://purl.obolibrary.org/obo/DERMO_"^^ . . . . "https://www.eionet.europa.eu/gemet/en/theme/"^^ . "false"^^ . . . "structural biology" . "dna" . . "Quality"^^ . . . "Karen R. Christie" . "pathways" . "false"^^ . . . . . . "duplication" . . . . . . . . . "EGID" . "huanglin36@mail.sysu.edu.cn" . . . "false"^^ . . "obo" . "NA06985"^^ . . . . "neuroname" . . "dna" . . . . . . . . . . . . _:N8feab9e44e98445393aad2ffd0819fe6 . . "esco.occupation" . . . . . . "biomedical science" . . . "602"^^ . . . . . "false"^^ . . . . "false"^^ . . "computer science" . "obo" . "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information."^^ . . . . . "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . "omics" . . "11"^^ . "Software Package Repositories" . . "The International Clinical Trials Registry Platform, originally called International Standard Randomised Controlled Trial Number (ISRCTN) registry, is a primary clinical study registry recognised by the World Health Organisation (WHO) and the International Committee of Medical Journal Editors (ICMJE) that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage)"^^ . "Kyoto Encyclopedia of Genes and Genomes" . . "^m\\w+$"^^ . "0000040"^^ . "^\\S+$"^^ . . . "https://www.ncbi.nlm.nih.gov/dbvar/studies/"^^ . "https://cells.ebisc.org/$1"^^ . . . "remote sensing" . . . "kegg_genomes" . "Research and learning in agriculture, the environment and the applied life sciences"^^ . . . "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants."^^ . . . . . . . "Anna L. Kaysheva" . "environmental science" . . . . . . . "interaction" . . . . "david.gloriam@sund.ku.dk" . . . "interaction" . . . . . . "1"^^ . . . "agricultural products" . "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid="^^ . . "http://purl.obolibrary.org/obo/MPIO_$1"^^ . . . . . "Terminologia Histologica" . "1009107926"^^ . . . . . . . "001000"^^ . . "^[A-Z-_0-9]+$"^^ . "Open Data Commons for Spinal Cord Injury" . "genome" . "pr" . "subject agnostic" . . . . . . . . . . . "small molecule" . "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1"^^ . "ontology" . . "ontology" . . "ontology" . . "false"^^ . . . "false"^^ . . "https://ceds.ed.gov/element/$1"^^ . "biomedical science" . . . "https://www.uniprot.org/diseases/$1"^^ . . "ontology" . . _:Nd96a2c997e5a4049a35901b620a94d63 . . "gene" . "opm" . "ovarian" . . "The ICD-11 Foundation is the comprehensive base layer of the International Classification of Diseases, encompassing all diagnostic concepts, definitions, and semantic relationships, designed for flexibility and adaptability across various use cases, including research, ontology development, and detailed health data analysis."^^ . . "true"^^ . "BioKC" . . . . . "false"^^ . . "biomedical science" . "asrp" . "biology" . . "transgenic" . . "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#"^^ . "function" . "dolce" . . . . . . . "false"^^ . "developmental biology" . . . "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."^^ . "disease" . "dhowe@zfin.org" . . . "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . . "INN_ID" . "^\\d+$"^^ . "Vendor for assays, cells, and antibodies"^^ . . . "biodiversity" . . "https://matrixdb.univ-lyon1.fr/association/"^^ . "CCLE_867"^^ . . . . . . "metadata" . . . . . "Ardan Patwardhan" . "articles" . "data management" . "00020134"^^ . . . . "^EMD-\\d{4,5}$"^^ . "^\\w+(\\.)?\\w+(\\.)?\\w+$"^^ . . "false"^^ . "Topology Data Bank of Transmembrane Proteins" . . . . . . . "1047874"^^ . . "Plant Anatomy Ontology" . . "false"^^ . . . . . . . . . . . . "false"^^ . . "oer" . . "https://www.uniprot.org/locations/"^^ . . "seinet" . . "https://grants.nih.gov/stem_cells/registry/current.htm?ID="^^ . . . "diabetes" . "http://hawaii.eagle-i.net/i/"^^ . "chemical" . . . "^\\d+$"^^ . . . . "http://purl.obolibrary.org/obo/ExO_$1"^^ . "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^ . "^\\d+$"^^ . . . . . "^\\d+$"^^ . . . "^\\d+$"^^ . . . "An issue on the UBERON GitHub Issue tracker"^^ . . "Toxic Process Ontology" . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_"^^ . . . "pathway" . . . . . . "Browser for the periodic table of the elements"^^ . . "NONCODE v4 Gene" . . "Doug Howe" . . . "https://packagist.org/packages/"^^ . . "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."^^ . . . "0000001"^^ . . . "education level" . . . . "biomedical science" . . "false"^^ . "data quality" . "Information for ligand groups (chemical classes)."^^ . "expression" . . . "https://mirgenedb.org/browse?qtype=mgid&org=ALL&query="^^ . "http://vocabularies.bridgedb.org/ops#"^^ . . . "food" . "20003"^^ . "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)"^^ . . . . "53504"^^ . "false"^^ . "http://purl.obolibrary.org/obo/CRO_$1"^^ . . . "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object="^^ . . . . . "NBK331"^^ . . "human disease model" . . . "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn="^^ . . . "life science" . . "organic chemistry" . "Spectral Database for Organic Compounds" . "life science" . . . . "maxo" . "https://ensaiosclinicos.gov.br/rg/$1"^^ . "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id="^^ . . . "Vertebrate Skeletal Anatomy Ontology" . . "clm" . . . . "cell" . "true"^^ . . . . "https://massbank.jp/MassBank/RecordDisplay?id=$1"^^ . . "ambystoma" . "https://data.chembiosys.de/organisms/$1"^^ . "0000038"^^ . . . "worldavatar.kin" . . "HMS Library of Integrated Network-based Cellular Signatures Datasets" . "https://www.genenames.org/data/genegroup/#!/group/"^^ . "false"^^ . . . "Johannes Wittmann" . . . . . . "17186"^^ . . "PhosphoSite Residue" . . . . . . . "nord" . . . "false"^^ . . . . . . . . . . . "Bgee stage" . . . . . . "SCC111"^^ . . "radlex" . . "https://omim.org/MIM:$1"^^ . . . . . "cran" . . . . "http://purls.helmholtz-metadaten.de/mwo/mwo_$1"^^ . "genome" . . . . . _:Ne3b81e66109543bd8b5f1e698db02f0c "Hajo Rijgersberg" . . . "biomedical science" . . "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . . . . . "0001"^^ . "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."^^ . "http://purl.org/gc/$1"^^ . . . "NASA Open Science Data Repository Hardware" . . . "19333"^^ . "KEGG_REACTION_CLASS" . "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . . . . . . . . . . . . . . . "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species."^^ . . . "^\\d+$"^^ . . "ontology" . "0000339"^^ . . "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"^^ . . . "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."^^ . "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."^^ . "C0017565"^^ . . "https://glytoucan.org/Structures/Glycans/"^^ . "Protein modification" . . "Spectra Hash Code" . "livestock" . . . . . . . . . "medical microbiology" . . _:Nfa934ac069554083883f6a0e265c393c "Eric Duchêne" . . "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^ . . . "^[A-Z0-9]+$"^^ . . "http://purl.obolibrary.org/obo/SLSO_"^^ . . "https://www.uniprot.org/unirule/"^^ . "https://www.gwascentral.org/marker/$1"^^ . "miseming@sfu.ca" . "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms."^^ . . . . . . . . . . . "Jianjiong Gao" . "oer" . "ontology" . "protein" . "ExAC Transcript" . . "false"^^ . . . "EPA Hazardous Wastes" . . . . "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."^^ . . . "https://cropontology.org/rdf/CO_333:$1"^^ . "http://purl.obolibrary.org/obo/PRIDE_"^^ . . "^\\d+$"^^ . . "omics" . . . . "physical geography" . . . . . . . "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^ . . . . . . . "true"^^ . "genatlas" . . . "strain" . . "pride.project" . "Mufaddal Naguthanawala" . . "https://aftol.umn.edu/glossary?category="^^ . "000260236"^^ . . "biomedical science" . "Yaroslava G Yingling" . . "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . . "Feng Zhu" . . "rs17852708"^^ . "genetics" . "Robert J. West" . . . . . "^(MNXM\\d+|BIOMASS|WATER)$"^^ . . . . . . . . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/TXPO_"^^ . "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."^^ . "kegg.ligand" . . . "ontology" . "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1"^^ . . "false"^^ . "diagnosis" . . . "Gene Normal Tissue Expression" . . . . "false"^^ . . . . . . . "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining."^^ . . . . . . . . "0000001"^^ . . . . . "TCTR20230429001"^^ . . "botany" . . "sbo" . . "Patent" . "An ontology for non-coding RNA, both of biological origin, and engineered."^^ . "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank."^^ . "http://purl.obolibrary.org/obo/IDO_"^^ . . . . . . . "A controlled vocabulary to support the study of transcription in the human brain"^^ . . . . "obo" . "depod" . . . . . "^\\w+$"^^ . . "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)."^^ . . . "obo" . . "life science" . . "817732"^^ . "false"^^ . . . "obo" . "false"^^ . . . "^OSR\\d{4}$"^^ . . "http://research.bmh.manchester.ac.uk/informall/allergenic-food/?FoodId="^^ . "https://cropontology.org/rdf/CO_357:$1"^^ . "false"^^ . . "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref="^^ . . "0000088"^^ . . . . "^\\d{7}$"^^ . "ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for chemoproteomic probes used to label human proteins in living cells."^^ . . "false"^^ . "https://www.ebi.ac.uk/interpro/entry/InterPro/$1"^^ . . _:Nbc5554f14fc14cbe9dd87f8245b8368b "davem@umn.edu" . . . . . "https://www.emouseatlas.org/emap/ema/DAOAnatomyJSP/anatomy.html?stage=TS$1"^^ . _:N922423823a164071873c18cd0da554a3 . . . "http://www.w3.org/ns/prov#"^^ . "PS00001"^^ . "genome-wide association study" . . "Genomes Online Database" . . "pirsf" . . . "rna" . . . "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"^^ . . "sequence annotation" . "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments."^^ . "^\\d{7}$"^^ . "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis="^^ . . "https://mmp.sfb.uit.no/databases/marref/#/records/"^^ . "OMIMPS" . . . "https://www.npatlas.org/explore/compounds/"^^ . . . "flopo" . . "pathogen" . "https://data.chembiosys.de/strains/"^^ . "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"^^ . "RHEA" . . . . "https://civicdb.org/links/sources/$1"^^ . "study design independent variable" . . _:N605a47747bae443ca9926391a8181797 . "food" . "ncit" . "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."^^ . . . "http://www.semanticdesktop.org/ontologies/2007/03/22/nco#$1"^^ . . "reto" . . . . . . "26957"^^ . "jakkbl@gmail.com" . "false"^^ . "Kenan Azam" . "phosphosite.sitegroup" . . "CHEBIID" . . "decimal"^^ . . . "nif.grossanatomy" . . _:N5fb757cbe6c640f5932a18d812860cd9 . . "https://w3id.org/kim/isced-2013/"^^ . . . . . . . "genomics" . . . . "^\\d+$"^^ . . "https://prefix.zazuko.com/prefix/$1:"^^ . "PPJ_100024"^^ . . "dna" . . . "Maximilian Haeussler" . . . . "health science" . . . . . . "An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects."^^ . "biochemistry" . "true"^^ . "E00002"^^ . . "model organism" . . "Radiomics Ontology" . . . "11061"^^ . . . . "metacyc.compound" . . . "Disease Class" . . "http://www.ubio.org/browser/details.php?namebankID=$1"^^ . "taxonomic classification" . . . . . . . "compound" . "antibody" . . "vegbank" . "COMBINE specifications" . . . . . . . "Human Unidentified Gene-Encoded" . . _:N89147f83abed402a8bbc6aa743fcf60b "gary@sourceauditor.com" . . . "100"^^ . "false"^^ . . . . . . . . "transcription factor" . "Identifier of an entry from the AAindex database."^^ . . "hipsci" . . "ontology" . . . . . . _:N6321c68bb95043c780afe7f03dba1a5c "mejino@u.washington.edu" . "sugarbind" . . . . . . "Veterans Health Administration (VHA) unique identifier" . . "NBC00001"^^ . . . "phenotype" . . "ontology" . . . "NLXBR" . . . "http://www.fairsharing.org/ontology/domain/DRAO_$1"^^ . . . . . "NeuroVault Image" . "exac.gene" . . "beetlebase" . . . . . "https://www.uniprot.org/unirule/$1"^^ . . "geography" . . . "http://purl.obolibrary.org/obo/PD_ST_$1"^^ . . "http://publications.europa.eu/resource/dataset/$1"^^ . . . . . "http://www.ymdb.ca/compounds/"^^ . . . . . . . . "neuroscience" . . . "Ontology for Parasite LifeCycle" . "sed-ml.level-1.version-1"^^ . . "dc11" . . "European Genome-phenome Archive" . "apid.interactions" . . "^\\d{7}$"^^ . "false"^^ . "hj@uestc.edu.cn" . . . . . "medicine" . . . . "ontology" . . "78073"^^ . "http://www.whocc.no/atc_ddd_index/?code=$1"^^ . . "upper-level ontology" . "life science" . . "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases."^^ . . "false"^^ . . . . "ISCED is designed to serve as a framework to classify educational activities as defined in programmes and the resulting qualifications into internationally agreed categories. The basic concepts and definitions of ISCED are therefore intended to be internationally valid and comprehensive of the full range of education systems."^^ . . . "ISO 639 3-Letter Language Code" . "KEGG_RCLASS" . . . . "type"^^ . . . . . . "^\\d{6}$"^^ . "^\\d+$"^^ . . "false"^^ . . . . "single-cell multimodal omics" . "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"^^ . . "^\\d+$"^^ . . . . . "PRI10"^^ . . . . "Data Catalog" . . . . . . . "molecule" . "^\\d{7}$"^^ . "4447"^^ . . "Thai Clinical Trials Registry" . . . . . "bioschema" . . . . . "cell biology" . . "https://biofactoid.org/document/"^^ . . . . . . . . . "https://grch38.togovar.org/variant/$1"^^ . . . . . "Software Licenses Ontology" . . . "kclb" . . "http://purl.org/dc/dcam/$1"^^ . "NIF Standard Ontology: Brain Regions" . . "http://www.ecogene.org/gene/"^^ . "Rutger Vos" . . . "https://cropontology.org/rdf/CO_359:"^^ . . . . . . . . . . . . . . "^\\d+$"^^ . . "protein" . . "stweedie@ebi.ac.uk" . . "cohesin" . . . . . . . . "https://terminology.hl7.org/CodeSystem-v3-"^^ . . . . . "npm" . . "oxburl@mmc.org" . . "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession="^^ . . "classification" . "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."^^ . . . . "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"^^ . "structure" . "GeneAnnot: Microarray Gene Annotation" . . "drug" . . "false"^^ . "Dialnet book ID" . "go.gpi" . "environmental science" . "life science" . . . "Aceview Worm" . . . "variant" . "http://purl.obolibrary.org/obo/MI_"^^ . . . . "https://w3id.org/biolink/vocab/$1"^^ . . . "http://www.orpha.net/ORDO/Orphanet_"^^ . . "paxdb.organism" . . . . . "icechem" . "atfdb.family" . . . . . . "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."^^ . . . . . "http://ictv.global/id/MSL40/$1"^^ . . . "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1"^^ . . . . . "http://arabidopsis.org/servlets/TairObject?accession=Gene:"^^ . . "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. "^^ . "http://purl.obolibrary.org/obo/PORO_"^^ . "rgd.qtl" . . . . "http://purl.obolibrary.org/obo/DOID_$1"^^ . "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"^^ . "feolo@ncbi.nlm.nih.gov" . "NameRXN" . "http://purl.obolibrary.org/obo/CMF_"^^ . . "ganesh.swaminathan@sanger.ac.uk" . "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . . . . . "molecular biology" . . "obo" . . . "life science" . . . "proteomics" . . . "health" . . . "RGD Disease Ontology" . "^[a-zA-Z0-9_\\-]+(/.*?)?$"^^ . "obo" . . "ChEBI Data Sources" . . . "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . . . . . . . "icd11" . . "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"^^ . . . "false"^^ . . . . . . "0000400"^^ . . "disease" . "molecules" . . "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."^^ . "biomedical science" . . . . "https://bioregistry.io/mesh.2012:"^^ . "pathway" . "Bill Duncan" . . "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."^^ . "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^ . . "https://portal.hubmapconsortium.org/browse/collection/$1"^^ . "https://civicdb.org/links/molecular_profile/$1"^^ . . . . . "apollosv" . . . . . "Glyma0021s00410"^^ . . "Tanay Shah" . . "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus."^^ . "ICDCM_2005" . . . . "animal genetics" . . . . "https://gold.jgi.doe.gov/resolver?id="^^ . . . "0000016"^^ . . "46977"^^ . . . . "doqcs.model" . . . "tissue" . . . "false"^^ . "false"^^ . . . "Shuichi Kawashima" . "^\\d{7}$"^^ . "false"^^ . "https://health-products.canada.ca/dpd-bdpp/info?lang=eng&code="^^ . "atcc" . . "https://www.nwo.nl/en/projects/"^^ . . "^\\w+$"^^ . . . . . . . "taxonomy" . "http://purl.obolibrary.org/obo/RoleO_"^^ . "ontology" . "false"^^ . "expression data" . "https://trialsearch.who.int/Trial2.aspx?TrialID=$1"^^ . . "sequence" . . "false"^^ . "^\\d+$"^^ . "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1"^^ . "https://www.cancerrxgene.org/translation/Drug/$1"^^ . . "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. \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."^^ . . . . "false"^^ . . . . "experimental measurement" . . . "usda.cvb.pcn" . "dna" . . . . "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."^^ . . "IP" . "ogata@kuicr.kyoto-u.ac.jp" . . . . . . "gene" . . . "microbial ecology" . "sep" . . "Ontology of RNA Sequencing" . . . . . "interaction" . . "Rebecca Jackson" . . "A collection of ontologies relevant within the [NFDI4Chem project](https://www.nfdi4chem.de/) that is mostly based on the overview paper [Ontologies4Chem: the landscape of ontologies in chemistry](https://doi.org/10.1515/pac-2021-2007).\n\nNFDI4Chem deploys a [custom instance](https://terminology.nfdi4chem.de/ts/) of the Ontology Lookup Service (OLS), called NFDI4Chem Terminology Services (TS), that provides the ontologies in this list. This list contains ontologies that cover various domains of chemistry (e.g. ChEBI, CHMO, and RXNO), those that are dependencies of these chemistry specific ontologies (e.g. BFO, RO, IAO, and OBI) as well as those ontologies, which where indexed in the NFDI4Chem TS for interoperability research purposes (e.g. PROV-O, SOSA, and OBOE)." . "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."^^ . "false"^^ . "Food Interactions with Drugs Evidence Ontology" . . "dna" . . . "Database of Quantitative Cellular Signaling: Model" . "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."^^ . . "^[0-9]+$"^^ . . . . . "1000160"^^ . . . . . . . . . . . . . "chemical" . "http://tolweb.org/"^^ . . "Metabolome Express" . . "ontology" . . . "subject agnostic" . . "protein" . . "http://purl.obolibrary.org/obo/CHIRO_"^^ . "patient care" . "taxonomy" . . "http://uri.neuinfo.org/nif/nifstd/"^^ . . "lonza" . . . . "false"^^ . "msio" . "carole.goble@manchester.ac.uk" . . . . . . "ontology" . . "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^ . . . . "vaccine" . "hagr.gendr" . . "Subcellular Anatomy Ontology" . . "xpo" . . . . . . . "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."^^ . "https://pubseed.theseed.org/SubsysEditor.cgi?page=FunctionalRolePage&fr=$1"^^ . "ontology" . "small molecule" . . . . "Jörg Wicker" . . "https://osdr.nasa.gov/bio/repo/data/studies/$1"^^ . "ISBN-10" . . . . "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO="^^ . . . "https://pubseed.theseed.org/SubsysEditor.cgi?page=ShowSubsystem&subsystem="^^ . . . . . . . . . . . . . . "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN="^^ . . . . . "http://reg.clinicalgenome.org/allele?hgvs="^^ . "co_348" . . . . . . . "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."^^ . . "chempro.probe" . "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . . . . . . . "diseaseclass" . . "jkissing@uga.edu" . . . . . . . . "pathbank" . "pco" . . . "ontology" . . "https://www.ebi.ac.uk/chembl/cell_line_report_card/"^^ . . "small molecule" . . . _:Nd9e2a85080184e66ae3d6137d39a4341 . . . . . . . "https://www.clinicaltrialsregister.eu/ctr-search/search?query="^^ . "https://metabolicatlas.org/identifier/MetabolicAtlas/$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."^^ . "bao" . . "Genome Taxonomy Database" . . "food" . . "The Behaviour Change Intervention Ontology" . . "kisao" . "small molecule" . . . . . "enzyme" . . "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."^^ . . "false"^^ . . . . . . . "life science" . . . "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"^^ . "virology" . "Identifier for a species on the noaa fisheries website"^^ . "^[0-9a-zA-Z]+$"^^ . "Linear double stranded DNA sequences" . . "co_367" . . . "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid="^^ . "https://www.synapse.org/Synapse:syn$1"^^ . "protein analysis" . . . "aio" . "ontology" . . . . . "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . "https://units-of-measurement.org/"^^ . "clb" . "Conferences in EasyChair"^^ . . "obo" . . . "methods" . . "global health" . . . "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . . . . . . "https://www.gbif.org/species/$1"^^ . . . . "marine environment" . "wgs84" . "LINCS Cell" . . "http://purl.obolibrary.org/obo/VBO_"^^ . . . "gramene.ref" . "1"^^ . . . "false"^^ . . . . . "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . "biomedical science" . . . "false"^^ . . "molecular infection biology" . "goldbook" . "https://purl.dataone.org/odo/SASAP_"^^ . "false"^^ . "Antibiotic Resistance Ontology" . "http://purl.obolibrary.org/obo/CEPH_"^^ . . . "^[WAICV]\\d{2,}$"^^ . "http://purl.obolibrary.org/obo/OMIABIS_$1"^^ . "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features."^^ . . . . . . . . "https://humap3.proteincomplexes.org/displayComplexes?complex_key=$1"^^ . "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . . . . "interaction" . . "5.1"^^ . . "bdgp.est" . "life science" . . "Identifiers correspond to curated associations between diseases and tRNA-derived small RNAs (tsRNAs) in the tsRNADisease database."^^ . . . . . . "Amphibian gross anatomy" . . . "ABE-0009634"^^ . . . . "genome" . . . "kenan@ucsd.edu" . . . "https://www.ncbi.nlm.nih.gov/clinvar/submitters/"^^ . . . . . . "^[0-9][A-Za-z0-9]{3}$"^^ . "annotation" . . . . "ontology" . . . _:N2fc03ae361414470a8c0bda5edf04557 . . "^(conceptualization|data-curation|formal-analysis|funding-acquisition|investigation|methodology|project-administration|resources|software|supervision|validation|visualization|writing-original-draft|writing-review-editing)$"^^ . "0000029"^^ . "^\\d+$"^^ . . . . . . "^\\d{7}$"^^ . "ontology" . "interaction" . . . "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium."^^ . . "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . . . . . . "structure" . "ontology" . "BAMSC981"^^ . "C138986"^^ . "drug" . . "major histocompatibility complex" . "life science" . . . . . . "CP0041613"^^ . . "FAIR* Reviews Ontology" . "2029"^^ . . "https://bioregistry.io/metaregistry/biocontext/$1" . _:N5a4bd7511e0e47b3a297104dc280dedc "helpdesk@cropontology-curationtool.org" . "^PPR\\d+$"^^ . . . "Antony Williams" . "erik.vannimwegen@unibas.ch" . "PF" . . _:Na6e5ebb17d90415f947106893f425627 . . . "Wasila Dahdul" . . "biology" . . "europe.pic" . . . . . "Natural Product Activity and Species Source Database" . . . . . "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1"^^ . . . "^\\d+$"^^ . . . "http://purl.obolibrary.org/obo/FAO_"^^ . "4900"^^ . "Collections of images, based on topics, such as the human skull collection"^^ . . . . . "plant phenotypes and traits" . "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."^^ . . . . "biomedical science" . _:N1cd40c152ac54ccf9674b630f1e1c5ff "SEP developers via the PSI and MSI mailing lists" . "nikolaos.moustakas@catalysis.de" . . . "100010"^^ . . . "ENSG00000136147"^^ . "BCRTi001-A"^^ . . . . . "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"^^ . . . "Dynamic Ecological Information Management System - Site and Dataset Registry - Locations" . "http://purl.obolibrary.org/obo/AAO_$1"^^ . . "https://www.internationalgenome.org/data-portal/sample/"^^ . . . "Animal Genome Chicken QTL" . . "http://nbn-resolving.org/$1"^^ . . . . . . "https://rapdb.dna.affrc.go.jp/locus/?name=$1"^^ . "^PED\\d{5}e\\d{3}$"^^ . "https://w3id.org/BCI-ontology#"^^ . . . . _:N6835ccee24b84375ab1206252243e893 "michael.lincoln@med.va.gov" . "obo" . . "phylogeny" . "bioinformatics" . "ontology" . "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."^^ . . "ghr" . "drugbank.reaction" . . . . . "http://purl.obolibrary.org/obo/MOP_"^^ . "0000013"^^ . . "^\\d{4}$"^^ . . "hgmd" . . "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . . . . . . "small molecule" . "false"^^ . "comparative genomics" . . "^\\d+$"^^ . . "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."^^ . . "false"^^ . . . "Cell line databases/resources"^^ . "bmbf.glossary" . . "Job.Dekker@umassmed.edu" . . . . . . . . "^\\d+$"^^ . . "false"^^ . . . "http://www.proteinatlas.org/$1"^^ . . "false"^^ . "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France)."^^ . "faircookbook" . . "antibiotic resistance" . "https://pk-db.com/data/"^^ . . . . . . "mod" . . "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^ . . "false"^^ . "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way."^^ . . . "^D\\d{4}$"^^ . "nasaosdr.biospecimen" . . "sioc.core" . "http://uri.neuinfo.org/nif/nifstd/nlx_mol_"^^ . . . . "icdom:8500_3"^^ . . "ontology" . . . . "obo" . "Apple Ontology" . "worm" . . "436605"^^ . "^[0-9][A-Za-z0-9]{3}$"^^ . "Life cycle stages for Mus Musculus"^^ . "aao" . . . . . "^\\d+$"^^ . "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . . . "nasaosdr.experiment" . "https://www.ebi.ac.uk/chembl/compound/inspect/"^^ . . . . "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_"^^ . "packagist" . "small molecules" . . . . . "biology" . . "vac" . "genome" . . "Renato Iannella" . . . "Antibiotic resistance genes and mutations"^^ . _:N545a1e7afef5492895e4bbec0b47af47 "Alain J. Cozzone" . "https://www.ncbi.nlm.nih.gov/research/cog/cog/"^^ . . . "drug target" . . . . . . . "https://bioregistry.io/hovergen:"^^ . . . . "diagnosis" . "PGOHUM00000289843"^^ . . . "false"^^ . "Identifiers.org Terms" . . . . . "obo" . . . . "NIA Mouse cDNA Project" . "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . "https://assets.nemoarchive.org/"^^ . . "unicarbdb" . "^\\d+$"^^ . . . . . . "^PM\\d{7}$"^^ . "sage.socialsciencethesaurus" . "^WBRNAi\\d{8}$"^^ . "http://vocabularies.unesco.org/thesaurus/concept"^^ . . . . . "nlx.sub" . "cath.superfamily" . "agriculture" . "cc" . . . . . "atol" . "false"^^ . . . . "study design" . . . . . "0000586"^^ . "A representation of variables appearing in models in the environmental research space."^^ . "biomedical science" . "Maxwell L. Neal" . . . . . "Cell line collections (Providers)"^^ . . "niclas.karlsson@medkem.gu.se" . "Aclame" . . "pathway" . "movie" . "bgee.family" . "genome" . . . . . . "http://purl.obolibrary.org/obo/FLOPO_$1"^^ . "epidemiology" . . "^\\d+$"^^ . "DBPedia Ontology" . . . "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)."^^ . . "genetic engineering" . . . "anatomy" . . "https://terminology.hl7.org/CodeSystem-v3-$1"^^ . . "^[a-zA-Z0-9_\\.]+$"^^ . "false"^^ . . . "This vocabulary was created in the FOAF project, based on experience with FOAF, Dublin Core and other early RDF vocabularies. Deployment experience shows that changing namespace URIs is expensive and unrewarding, so this vocabulary provides terms to support in-place evolution of structured data vocabularies. By indicating status at the level of terms rather than vocabularies, dictionary-style, fine grained improvements become easier. Different organizations and parties can agree or disagree on the status of a vocabulary term; however the status published alongside the term may deserve special attention. Future work could include patterns for citing announcements and decisions, or using SKOS to decentralise the extension of the basic status levels. (from artifact)"^^ . . . . "https://mobidb.org/"^^ . . "dna" . . "nlfff" . . . "statistics" . "https://www.devtox.org/nomenclature/ml_manus.php?mno="^^ . . . . . "https://www.biozol.de/en/product/$1"^^ . "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . . . _:N15ef3856e9974f1ba44c136fd9b90bcd . "false"^^ . . . "open educational resources" . "ontology" . "centrally registered identifier" . . . . "1"^^ . "https://deims.org/activity/$1"^^ . . . . "informatics" . "^[A-Za-z0-9]+$"^^ . . . "rfc" . . "^SCV\\d+(\\.\\d+)?$"^^ . "proteomics" . . . . . . . "https://www.ncbi.nlm.nih.gov/nucleotide/$1"^^ . "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . . "crossref.funder" . . . "structural bioinformatics" . . . "cpd15380"^^ . . . . "http://fossilworks.org/?a=taxonInfo&taxon_no="^^ . . . . . "expression data" . "http://www.proglycprot.org/detail.aspx?ProId="^^ . "true"^^ . . . . "^\\d{7}$"^^ . . "977869"^^ . . . . . . "^\\d{7}$"^^ . "UniProt Cross-ref database" . . . . "37"^^ . . . . "life cycle stage" . . "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . . . . "nicole@tislab.org" . "https://mite.bioinformatics.nl/repository/"^^ . . . . . . "knockout" . "false"^^ . "National Uniform Claim Committee Taxonomy" . "antibody" . . . . "comparative genomics" . . "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia.variant' prefix is used for genetic variants associated with phenes listed in OMIA"^^ . . . "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."^^ . . "https://osdr.nasa.gov/bio/repo/data/subjects/$1"^^ . . . . . "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records."^^ . "NLXORG covers organisms."^^ . . "^\\d+$"^^ . . . "protein" . . "https://www.ebi.ac.uk/metagenomics/projects/$1"^^ . . . . . "^SAMEA\\d{8}$"^^ . "ontology" . "morpheus" . . . . . . . . "false"^^ . . . . "^[SCTAGMNU]\\d+$"^^ . . . . . . "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."^^ . "pathogen" . . . "603903"^^ . . "Banana ontology" . "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^ . "true"^^ . "https://www.genenames.org/data/gene-symbol-report/#!/symbol/"^^ . "http://elm.eu.org/elms/elmPages/$1.html"^^ . . . . "74.186"^^ . . . "VIAF cluster ID" . . "false"^^ . "false"^^ . . . "false"^^ . "DrugBank Target v4" . "0000001"^^ . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^ . . . . . . . . . . . . . "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite."^^ . . . "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies."^^ . "false"^^ . "GLIDA Ligand" . . . . . "PED00017e001"^^ . "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced."^^ . . . . "false"^^ . . . "^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$"^^ . . . "https://ibdc.dbtindia.gov.in/icpd/study-view-home/$1"^^ . "Tomohiro Oga" . "icd11.foundation" . "kim.license" . . . . "life science" . . . . "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"^^ . . "0000066"^^ . "UPPRO" . "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId="^^ . . "earl" . . "endlessforms.unit" . . . . "obo" . . . "BioSchemas" . "^KIAA\\d{4}$"^^ . "MGI" . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1"^^ . "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 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."^^ . . "false"^^ . "false"^^ . . . "comparative genomics" . "https://www.datascienceontology.org/concept/$1"^^ . . "false"^^ . . . . . . "false"^^ . . "https://www.inaturalist.org/taxa/"^^ . "^\\d+$"^^ . "cstr" . "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data."^^ . . "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"^^ . "dictyBase Expressed Sequence Tag" . "swan" . . . "0000005"^^ . . . . "true"^^ . "ferroliganddb" . "false"^^ . "false"^^ . "MetaCyc" . _:N788b89c2ed584aac8b10a82c0e990232 . "chembiosys.organism" . "medicinal chemistry" . _:N7821e843498b4fc482592503dae946a4 . . . "false"^^ . "https://europepmc.org/article/CTX/$1"^^ . . . "https://nmrxiv.org/sample/"^^ . "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."^^ . "A list of values for class levels. Created in the context of the OpenEduHub"^^ . _:Nb05f67102810430c80a5c82956a65323 "more.info@allotrope.org" . . . . . "vertebrate" . . . . "Ambystoma Genetic Stock Center" . . . "UK Provider Reference Number" . . . . "Identifiers represent antibody-antigen complexes in the Antigen-Antibody Complex Database (AACDB), which provides comprehensive structural and functional annotations including paratope and epitope information, antibody developability data, and antigen-drug target relationships to support immunoinformatics research and therapeutic antibody development."^^ . "http://purl.obolibrary.org/obo/REO_$11"^^ . . . . "deims.network" . "rna" . "Evan E Bolton" . . "The Arabidopsis Information Resource" . . . . . . "obo" . "http://purl.obolibrary.org/obo/PO_$1"^^ . . . . . . . "https://w3id.org/oc/meta/$1"^^ . . . . . . "ontology" . . . . . "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege."^^ . . "hypercldb" . "Fossilworks Taxon" . . . . "^\\d{7}$"^^ . "000140" . "obo" . . . "protein" . . "false"^^ . "environmental science" . . . . . "gene group" . . "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." . . . . "Sonia Balyan" . . . "ontology" . . . . . . "Metadata Management and distribution system for Multiple GNSS Networks" . "obo" . "https://uniresolver.io/#did:$1"^^ . "structure" . "LinJ.20.0070"^^ . . "https://cropontology.org/rdf/CO_356:"^^ . . . "food" . . . "Research Organization Registry" . "genetic disorder" . . . "610"^^ . . . "false"^^ . . . . "^TC\\d+$"^^ . "rxn00001"^^ . "^\\d+$"^^ . "^\\d+$"^^ . "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]"^^ . . . "http://sabiork.h-its.org/reacdetails.jsp?reactid="^^ . . . . . . . "Asteraceae Genome Database - Plant" . "true"^^ . "Creative Commons Schema" . . "tred" . "UniProt Post-Translational Modification" . . . . . . . . . "obo" . "pathways" . "28463"^^ . "mfoem" . . "domain" . . "http://www.jcvi.org/charprotdb/index.cgi/view/$1"^^ . . . . "https://bioregistry.io/bacmap.map:"^^ . "Comprehensive Resource of Mammalian protein complexes" . . . . . . "A formal represention for drug-drug interactions knowledge."^^ . . . "agriculture" . . . "^[A-Z0-9][A-Z0-9-]*$"^^ . . . . . "false"^^ . . . . . "2u4tf"^^ . . . . . "An ontology describing the anatomical structures and characteristics of Porifera (sponges)"^^ . "cghdb" . "SWRL enables Horn-like rules to be combined with an OWL knowledge base."^^ . . . . "https://inspire.ec.europa.eu/theme/$1"^^ . "karel.berka@upol.cz" . . . . "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"^^ . . . . . . . . "false"^^ . . . . . . . . . "chenyuzong@sz.tsinghua.edu.cn" . . . . "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid="^^ . "CiteXplore" . . . "Maria Gould" . . "obo" . . . "a.kranz@fz-juelich.de" . . "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^ . . . "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=$1"^^ . . " Hendrik Borgelt" . . . . "Wikidata Entity" . . . . . . . "Werner Müller" . . "CLO" . "dbprobe" . "false"^^ . "95-0166C6"^^ . . . "David Clunie" . . "false"^^ . . "^\\d+$"^^ . "prgr_human"^^ . . . . . . . . "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . . . . "P00266"^^ . . "vasilevs@ohsu.edu" . . "http://thebiogrid.org/"^^ . . . "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)"^^ . . . "biology" . "http://hdl.handle.net/11459/$1"^^ . . . . "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1"^^ . "Johannes B. Goll" . . "3567"^^ . "cell biology" . "128796-39-4"^^ . . . . "rdf" . . . . . "reagents" . "icd10" . . . . . "k-12 teacher" . "Ilene Karsch-Mizrachi" . . "^\\d+$"^^ . . "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities."^^ . "^\\d+$"^^ . "pfam.clan" . . . "ontology" . . . . . . . . . . "molecular entity" . "http://purl.obolibrary.org/obo/MFMO_$1"^^ . "^\\d+(\\w+)?$"^^ . "true"^^ . . . . "General Multilingual Environmental Thesaurus Relation" . "ecmdb" . . . "plasmid" . . . "false"^^ . . . "empty" . "small molecule" . . . . "3000001"^^ . "a3bc9e6193c47998758ac9d9bf9ddbb6"^^ . . "kyinno" . . "https://www.kegg.jp/brite/"^^ . "pibase" . "chemical" . "false"^^ . "translational medicine" . "^[A-Za-z-0-9_]+(\\@)?$"^^ . . . . "Molecular Interactions Controlled Vocabulary" . "obo" . . "ODAM Data explorer" . . . . . "computer science" . . "omics" . "https://www.loc.gov/preservation/digital/formats/fdd/"^^ . . "^\\d{7}$"^^ . . . . . . "identifier of an author or reviewer, in Semion"^^ . . . "An international LGBTQ+ linked data vocabulary"^^ . . "ExO" . "000001"^^ . . . . . . . . "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."^^ . "DIP-743N"^^ . "region" . . . . "metabolites" . . "false"^^ . . . "PubMed Central" . . "Rat Genome Database strain" . "false"^^ . "The COVID-19 epidemiology and monitoring ontology" . "https://glytoucan.org/Structures/Glycans/$1"^^ . . "classification" . . "The S/MAR transaction DataBase" . . . . . . "https://www.metanetx.org/comp_info/"^^ . . . "European Food Information Resource Network" . "PA166156302"^^ . . . . "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world."^^ . . . "true"^^ . . . . "ogsf" . "meetings" . _:Na6e5ebb17d90415f947106893f425627 "eVOC mailing list" . . "^\\d{7}$"^^ . "decipher" . "ontology" . . . . . . "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"^^ . . "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . . . . . . "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 )."^^ . "oga.t@northeastern.edu" . "Protein covalent bond" . . "http://www.gramene.org/db/protein/protein_search?protein_id="^^ . "phenotype" . . . . . . . . . "ontology" . "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."^^ . . . "https://mycobrowser.epfl.ch/genes/$1"^^ . . . . _:N173b76cb92df4b748c1e838498a75183 "Steven John Zimmerly" . "pid" . . "Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models."^^ . . . . "metabolites" . . . . . . . . . "https://ice.ntp.niehs.nih.gov/api/v1/search?chemid=$1"^^ . . "https://unicarb-db.expasy.org/msData/$1"^^ . . . . "ontology" . "false"^^ . "anatomy" . . "Olivier Bodenreider" . "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)."^^ . "ontology" . . "false"^^ . . "http://modelseed.org/biochem/compounds/"^^ . . . "eukaryotic" . . . . . . . . "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1"^^ . "NCI Metathesaurus" . . "https://www.cabi.org/cabebooks/ebook/"^^ . . "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments."^^ . . . . . . . . "http://cor.esipfed.org/ont/earthcube/srt_"^^ . . . . . . . . . . "false"^^ . "ontology" . "The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes."^^ . "AffyProbeset" . "PesticideInfo chemical ID" . . . . . "quality" . . "igrhcellid" . "kinetics" . "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)." . . . "gene expression" . "http://purl.bioontology.org/ontology/CSP/"^^ . . . . . . . "adverse reaction" . "Wheat ontology" . . . . . . "life science" . . . . . . "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept"^^ . . "CATH superfamily" . "false"^^ . . . . "^[0-9]{15}[0-9X]{1}$"^^ . . . . . . . "T06648"^^ . . . "CQG5"^^ . . "kegg.genome" . "false"^^ . "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^ . "An ontology to support comparative effectiveness researchers studying claims data."^^ . "https://www.ebi.ac.uk/metagenomics/genomes/$1"^^ . "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."^^ . . . . . "An ontology designed to support the semantic annotation of epidemiology resources"^^ . . "semapv" . "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein="^^ . "yrcpdr" . . "Ontology about the development and life stages of the C. elegans"^^ . "MassBank" . "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id="^^ . "Dynamic Ecological Information Management System - Site and Dataset Registry - Activity" . . "https://www.drugbank.ca/categories/$1"^^ . . "https://bioregistry.io/iceberg.cime:"^^ . . "disease" . . "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . . . "ontology" . "2673500"^^ . . . "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\"."^^ . . . . . . . "GrainGenes symbol" . . . "Scholarly Contributions and Roles Ontology" . "matus.kalas@uib.no" . "https://bioregistry.io/ccdc:"^^ . . "^(\\w+)?\\d+$"^^ . . . . . . . "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . . . . . "^\\d{7}$"^^ . "https://omabrowser.org/oma/hog/HOG:$1"^^ . . "https://medlineplus.gov/genetics/condition/"^^ . . _:Nd96a2c997e5a4049a35901b620a94d63 "NIH Reporter Helpdesk" . "2.16.840.1.113883.6.88" . . . . . . "rnajunction" . . . . . . . . "http://purl.obolibrary.org/obo/UPHENO_$1"^^ . "gudmap" . "http://purl.org/ontology/rec/core#$1"^^ . . . . . . "hgnc.genefamily" . "ICD10" . . . . "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc."^^ . "http://purl.uniprot.org/annotation/"^^ . "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."^^ . . . . "false"^^ . . "27267"^^ . "25512"^^ . "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"^^ . . . . "affy.probeset" . . . . . . . "cheminformatics" . . . . "Atsushi Yoshiki" . . "obo" . . . . . . . "false"^^ . "informatics" . . . "Gene Ontology Database references" . . "plant" . . . "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."^^ . . . "https://europepmc.org/article/ppr/$1"^^ . . . . . . "fernanda.farinelli@gmail.com" . "sitex" . "anatomy" . . . "domain" . "Identifiers for references, typically linking to sources of evidence such as publications that support data within IEDB."^^ . . "Human Developmental Stages" . "^spike\\d{5}$"^^ . "linkedin" . . . "National Drug Code" . "Hugh P Shanahan" . . "clinical studies" . "false"^^ . "false"^^ . "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"^^ . "epidemiology" . . . . . "cameo" . . . "GDS1234"^^ . . . . "funcbase.mouse" . . "EDAM Topic" . . "DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry) is an information management system powered by eLTER. It allows you to discover long-term ecosystem research sites around the globe, along with the data gathered at those sites and the people and networks associated with them. DEIMS-SDR describes a wide range of sites, providing a wealth of information, including each site’s location, ecosystems, facilities, parameters measured and research themes. It is also possible to access a growing number of datasets and data products associated with the sites."^^ . . . "https://bioregistry.io/vipr:"^^ . . . "https://www.cellrepo.com/repositories/$1"^^ . . "Ontology of Genetic Susceptibility Factor" . . . . . "false"^^ . . "Paul David Neil Hebert" . "VFDB Genus" . . . . . "Ontology for Biomedical Investigations" . . "0000404"^^ . "AgentIdentifierScheme"^^ . . "Prefixes relevant for the [Data Literacy Alliance (DALIA)](https://dalia.education/en) project" . . "researcher" . . "regulation of gene expression" . . . "IUPHAR_LIGAND_ID" . . . . . . . . . "catalogs" . "VEuPathDB ontology" . "Genome Properties" . . . "bioinformatics" . "long-finned-pilot-whale"^^ . . . . . . . . "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . . . . . . "^\\d+$"^^ . . . . . . "false"^^ . "genomics" . . "article" . "ligandbook" . . . . "genecards.genenote" . . "https://www.kaggle.com/$1"^^ . "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . . . "dorothea.iglezakis@ub.uni-stuttgart.de" . . "http://pax-db.org/#!species/"^^ . . . "ontology" . . "false"^^ . "EARL is a vocabulary, the terms of which are defined across a set of specifications and technical notes, and that is used to describe test results. The primary motivation for developing this vocabulary is to facilitate the exchange of test results between Web accessibility evaluation tools in a vendor-neutral and platform-independent format. It also provides reusable terms for generic quality assurance and validation purposes. [from homepage]"^^ . . . "single cell rna-seq" . . "ChemBioSys Strain" . . . . . "https://fanta.bio/cre/"^^ . "SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases."^^ . . "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . "^\\d+$"^^ . "dna" . . . . "false"^^ . . "false"^^ . . . . "annotation" . . . "jmcl@ebi.ac.uk" . . . . . . . . . . . . "michelle.scott@usherbrooke.ca" . . . "agriculture" . "An identifier for an organization"^^ . . "https://cropontology.org/rdf/CO_348:$1"^^ . . . . . . "biology" . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"^^ . . "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . "biomedical science" . . "cp390@cam.ac.uk" . "^F\\d{4}$"^^ . "https://cropontology.org/rdf/CO_345:"^^ . . . . "embryo" . "Structural Classification of Proteins - Unique Identifier" . . "Human Dermatological Disease Ontology" . . . . . "March 2017 version "^^ . "simulation"^^ . . "pesticides" . . . "http://scop.berkeley.edu/sunid="^^ . . "Uberon" . . . . . "^U\\d+$"^^ . . "dbg2introns" . . "metagenomics" . "subject agnostic" . . "^\\d+$"^^ . . . "Fly taxonomy" . "false"^^ . . "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^ . . . . . "greatchen@cdutcm.edu.cn" . . "19210-3"^^ . . "false"^^ . "false"^^ . . "false"^^ . . . . "epidemiology" . "MagnitudeValueType"^^ . "http://purl.obolibrary.org/obo/NCIT_"^^ . "BioDeep Database" . "ElementNumber"^^ . . . . "https://bioregistry.io/metaregistry/ncbi/$1"^^ . . "opl" . "uniprot.keyword" . "rgd.strain" . . . . "A disease/condition-specific instantiation of a canonical biomarker"^^ . . . . . . "bioinformatics" . . "https://mycobrowser.epfl.ch/genes/"^^ . "mim.ps" . . . . . . . . "S0960-9822(11)01319-4"^^ . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1="^^ . _:N83343f3eac114bfabaf9d0c12d45d92f "pierre.sprumont@unifr.ch" . . "evidence" . "^[1-9]\\d{0,5}$"^^ . "http://modelseed.org/biochem/reactions/$1"^^ . . "190000021540"^^ . . . . . "PjrpzUIAAAAJ"^^ . . . . . "https://portal.hubmapconsortium.org/browse/sample/"^^ . . "A semantic space of small molecules"^^ . "^\\d{7}$"^^ . "ontology" . "http://purl.obolibrary.org/obo/OGI_$1"^^ . . "^\\d+$"^^ . . "Ensembl Gene" . . . . . . . "1"^^ . . . "geography" . "genetic resource" . . . . "MESHCS" . . "http://purl.enanomapper.org/onto/ENM_$1"^^ . "3000887619"^^ . "Genderal Ontology for Linguistic Description" . "A database of GlycoMaps containing 2585 conformational maps."^^ . "https://chemprosquare.idrblab.net/data/competitor/details/$1"^^ . . . . . . . "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data"^^ . . . "phylogenetics" . "^\\S+$"^^ . "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^ . "CLAVAS: ISO 639-3 Language Codes" . . . "funcbase.human" . "obo" . "Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant."^^ . . "false"^^ . "ontology" . . . "2.1.1"^^ . "morphology" . "fd8d0743-344a-4758-bb97-f8ad84a37357"^^ . "false"^^ . "data integration" . "life science" . "A data model describing machine learning experiments"^^ . . . . "https://ocid.ontochem.com/prefname?ocid="^^ . "classification" . . _:Nc47ec4ead5d14c2ca67e8fa44e0b94d8 "laura@codata.org" . . "ama-cpt" . . "inchikey" . . . . . "genomics" . "https://osdr.nasa.gov/bio/repo/data/hardware/$1"^^ . . "Identifiers for Major Histocompatibility Complex (MHC) restrictions of immune cells, detailing genetic factors that influence immune recognition."^^ . "structure" . . . "worfdb" . "npatlas" . "The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collections refers to the broader phenotypic and genetic resources of Asteraceae plants."^^ . . . . "MolBiC provides information about cell-based molecular bioactivities along with associated compounds, proteins and cell lines. This prefix maintains identifiers for cell lines used in assays measuring molecular bioactivity, linking them to associated compounds and proteins."^^ . . . "anatomy" . . . "jiezheng@pennmedicine.upenn.edu" . "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#"^^ . . "0000072"^^ . "S000002493"^^ . "assays" . . "hgnc.family" . "https://www.tib.eu/digitrubber#DIGITRUBBER_"^^ . . . "FlyMine Chromosome Band" . "REBASE Enzyme Number" . . . "false"^^ . . . "ontology" . . . "DG00301"^^ . . . . "https://bioregistry.io/zazuko:"^^ . "false"^^ . "https://cordis.europa.eu/project/id/$1"^^ . "https://ligandbook.org/package/$1"^^ . . . "^\\d{7}$"^^ . . "cell line" . . . "Leif Oxburgh" . . . "https://biopragmatics.github.io/providers/icepo/"^^ . . . "false"^^ . . . . . "https://www.sharkipedia.org/species/"^^ . . . . . . . "http://www.pantree.org/node/annotationNode.jsp?id=$1"^^ . "provenance"^^ . "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond."^^ . "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . . "^\\d+$"^^ . . "https://drks.de/search/en/trial/"^^ . "https://go.drugbank.com/bio_entities/$1"^^ . "nemo.competence" . "false"^^ . . "Biomedical Informatics Research Network Lexicon" . "Daniel Marschall" . . . . . . . . . "gitlab" . "SNOMEDCT_US_2023_10_01" . "Tim Robertson" . "An ontology for dengue fever."^^ . . . "Costal and Marine Ecological Classification Standard" . . . . . "glycosylation" . . . "chemrof" . "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . "zazuko" . . . "0000013"^^ . "Asset"^^ . "false"^^ . . . . "false"^^ . . "Identifiers.org" . . _:N5b03584c81674192b841994dd3875efa . "http://purl.obolibrary.org/obo/HSO_$1"^^ . . "https://modeldb.science/$1"^^ . . . . . "nmrxiv.sample" . . . "has identifier space owner" . "^\\d{7}$"^^ . . . "Don Gilbert" . "cmf" . . "Pierre Cosson" . . . . "https://cropontology.org/rdf/CO_325:"^^ . "dna" . "false"^^ . . . . "Willy Wong" . "hovergen" . . . . . . . . . "http://purl.org/pav/$1"^^ . "supply" . . . . . . . . "patient care" . "identifier for species classified under the New Zealand Threat Classification System"^^ . "http://www.signaling-gateway.org/molecule/query?afcsid=$1"^^ . . . . . . . . . . . "https://cropontology.org/rdf/CO_326:"^^ . . . "gene expression" . "http://purl.obolibrary.org/obo/DDPHENO_$1"^^ . . "Núria Queralt Rosinach" . . . . . . . . "false"^^ . . . . . . "biology" . "trait" . . . "https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_"^^ . "Japan Registry of Clinical Trials" . "molecular microbiology" . . . "false"^^ . . . . "ontology" . "https://www.ncbi.nlm.nih.gov/gtr/tests/"^^ . "http://purl.obolibrary.org/obo/SWO_"^^ . "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$"^^ . . . . . . "false"^^ . . . . . . . "https://nfdi4culture.de/id/"^^ . . "obo" . "0000194"^^ . . . . . "nsf.award" . . . . . . . . "GO Evidence Code" . . "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . "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."^^ . . "mutant mouse strain" . "MoDALIA Ontology" . . . . "https://purl.brain-bican.org/ontology/dhbao/DHBA_$1"^^ . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"^^ . "zebrafish" . . "http://purl.obolibrary.org/obo/MCO_"^^ . . . "tanja.bekhuis@tcbinfosci.com" . "https://fairsharing.org/users/$1"^^ . "protein" . "C. elegans development ontology" . "CIAT Common bean trait dictionary - version August 2014"^^ . . . . "false"^^ . "https://catalog.hathitrust.org/Record/$1"^^ . . . . . "4007166"^^ . "false"^^ . "^\\w+$"^^ . . "lam87@cornell.edu" . "false"^^ . . "http://purl.org/dcx/lrmi-terms/$1"^^ . "cheminformatics" . "ontology" . . . "ontology" . "https://www.ncbi.nlm.nih.gov/books/"^^ . . . "false"^^ . "ps048"^^ . "ontology" . "Plant Phenology Ontology" . "life science" . "SRS086444"^^ . . . . . "vaccine" . . "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]"^^ . . . "Edison Ong" . . . . "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"^^ . . . . . "^\\d{7}$"^^ . . . . "229"^^ . "false"^^ . . "life science" . . . "MEDLINE" . . "false"^^ . "Animal natural history and life history" . . . "bioinformatics" . . "subject" . "kegg.orthology" . . "Philippe Le Mercier" . "pathogen" . "0000001"^^ . . . "kegg.enzyme" . . "ENSG00000169174"^^ . "protein" . "0010034"^^ . "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . "http://purl.obolibrary.org/obo/PR_$1"^^ . "^\\d+$"^^ . . . . . . "Montana Smith" . . "https://graphics.endlessforms.info/library?id="^^ . . . . . . "- 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."^^ . . "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . . "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."^^ . . "false"^^ . "Guide to Pharmacology Target" . . . "nsv3875336"^^ . "drug discovery" . . . . "false"^^ . . "w3c rec" . . . . . . . "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . "vbo" . . "^[A-Za-z0-9]+$"^^ . "ZFIN" . . "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."^^ . "ricecyc" . . . . . . . "obo" . . . "false"^^ . . . . . "000912"^^ . "https://www.ebi.ac.uk/metagenomics/proteins/"^^ . . . "^\\d+$"^^ . . . . "Rudolf T. Pillich" . "smp-m3w9hbe"^^ . . . "diabetesomic" . "https://www.pombase.org/gene/"^^ . "^\\d{7}$"^^ . "obo" . . . . . "google.scholar" . . . . "obo" . . . "genome" . "arxiv" . "anatomy" . . . "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . . "protein" . "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."^^ . . "https://disprot.org/$1"^^ . "High-quality Automated and Manual Annotation of microbial Proteomes" . _:Nef8ae6522f4047df9b7c2ae9afbe76eb . "nucleotide" . . "Colleen Xu" . . "a.39.1.1"^^ . . . "csp" . "pgxbs-kftva5zv"^^ . . . "disease" . "https://www.wwpdb.org/pdb?id="^^ . "false"^^ . . "^\\d+$"^^ . . . "protein interactions" . . . . . "^\\d+$"^^ . . . . . "http://sideeffects.embl.de/se/"^^ . "srodriguez142857@gmail.com" . . . . "life science" . . . "life science" . . . "obo" . . . . . . . "Osamu Ohara" . . . "medlineplus" . . . "Homology Ontology" . . "darc" . . . "https://w3id.org/kim/schularten/"^^ . "Integrated Microbial Genomes Taxon" . "genome" . "electroencephalography" . . "depends on" . "^[0-9]+(LR)?$"^^ . . "15"^^ . . . . . "AHR"^^ . "0000890"^^ . "ChEBI Integrated Role Ontology" . "Fab.Schreiber@gmail.com" . . "false"^^ . "Q13485"^^ . "st00576"^^ . . "false"^^ . . . . "CCR_C-3784_55fa12c9-35ad-7b55-b7a5-f9926c801952"^^ . "The International Harmonization of Nomenclature and Diagnostic criteria" . . . . . "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."^^ . . . . . . . . . "true"^^ . . "DDB0016567"^^ . . "090201"^^ . . "taxonomic classification" . . . "USA National Service Center Number" . "^\\d{7}$"^^ . . "obo" . "NCITt" . . . . "http://data.europa.eu/89h/"^^ . "Food-Biomarker Ontology" . "false"^^ . . . . "The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data."^^ . . "https://deims.org/sensors/"^^ . . . . . . . "^\\d+$"^^ . . . . . . . "protein" . . . . "Biocuration Conference 2025 Collection" . "Thomas Lütteke" . . "^\\d{7}$"^^ . "major histocompatibility complex" . . . . "biomedicine" . . . . . . . . "ZINC is not Commercial" . "statistics" . . "gene" . . . . . "http://purl.obolibrary.org/obo/COLAO_"^^ . . "false"^^ . . "co_346" . . "biochemistry" . . . "false"^^ . . . . _:Nb039f65249c74fabb39262758d9cba60 . . . "https://cropontology.org/rdf/CO_339:$1"^^ . . "false"^^ . . "clinical LABoratory Ontology" . "^\\w+$"^^ . "earth science" . . . . . . "false"^^ . . . . . . "Creative Biolabs Antigen provides identifiers for antibody-based entities such as recombinant, functional, engineered, and format-specific antibodies as well as antibody processing tools, which are essential for applications in diagnostics, therapeutics, and immunology."^^ . . . "Chemistry resources"^^ . "Megan S. Kane" . "http://www.oid-info.com/get/2.16.840.1.113883.6" . . . . . "odor" . . "faldo" . . "biogrid.interaction" . . . . "false"^^ . "https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema=$1"^^ . . "hgnc.symbol" . . . "^(T0\\d+|\\w{3,5})$"^^ . . "sharkipedia.species" . . . . . "PseudoGene" . . "ADA"^^ . . . "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$"^^ . . "^[A-Za-z_][A-Za-z0-9\\.\\-_]*$"^^ . "environmental science" . . "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.."^^ . . "ontology" . "go.issue" . . . "umbbd.pathway" . . . "Gainesville Core Ontology" . . . . . . . . . "cellrepo" . "anatomy" . . . . "1023371"^^ . "events" . . . . "medical informatics" . . . . "^PDC\\d+$"^^ . . "http://purl.obolibrary.org/obo/OAE_"^^ . . "Raja Mazumder" . . . . . . . . . . . . "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."^^ . . "disease" . "Stephen Fisher" . "paolo.romano@hsanmartino.it" . . "false"^^ . . . "ChemBioSys Dataset" . . . . "biomedical science" . "0032571"^^ . . "http://purl.obolibrary.org/obo/AERO_"^^ . "animal husbandry" . "evolutionary biology" . "protein" . . . . "phenomics" . . . . . "true"^^ . . . . . . "clarin.clavas" . . . . . . "familyName"^^ . . . . "obo" . "http://www.obofoundry.org/" . "P12345"^^ . "false"^^ . . "The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/)."^^ . . . "UPVAR" . . "rna" . . "Rice ontology" . "Basic Formal Ontology" . "gtdb" . . . . "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."^^ . . "animal physiology" . "UM-BBD compound" . . . . . . . . . "https://catalog.integbio.jp/dbcatalog/en/record/$1"^^ . . . . "false"^^ . . . "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."^^ . . "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"^^ . . "microRNA Gene Database" . "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli."^^ . "^nbdc\\d+$"^^ . "domain" . . . "false"^^ . . . . . . "MIRBASE_FAMILY" . "Yossih@tauex.tau.ac.il" . "https://w3id.org/biolink/vocab/"^^ . . . "http://purl.obolibrary.org/obo/ARO_$1"^^ . . . . "https://fda.report/applications/"^^ . . . . . . . "false"^^ . "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."^^ . "http://purl.obolibrary.org/obo/OBI_$1"^^ . . . "health monitoring" . "https://cropontology.org/rdf/CO_345:$1"^^ . . . . . "satyasahoo@ieee.org" . . . "^[0-9A-Z]+(\\.[0-9A-Z]+)?$"^^ . "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . . . . . "Data Privacy Vocabulary" . . . "http://jcggdb.jp/idb/jcggdb/$1"^^ . . . . . . . "NASA Open Science Data Repository Subject" . . "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^ . "license" . . . . . . "ontology" . "A assay in the ChemBioSys data platform"^^ . . . . . . "hubmap.collection" . . "BindingDB is the first public database of protein-small molecule affinity data."^^ . . . "plant phenotypes and traits" . "gene group" . "http://purl.obolibrary.org/obo/TO_$1"^^ . . "ontology" . . . . . . "translational medicine" . . "marine biology" . . . . . "000000001"^^ . . . . "^\\d+$"^^ . . "eNanoMapper ontology" . "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."^^ . . "^\\d+$"^^ . "pd_st" . . . . "^[a-f0-9]+$"^^ . . . . "^[1-9][0-9]*$"^^ . . "chmo" . . "false"^^ . . . "Categories in the AFTOL database"^^ . . "Heather Piwowar" . "http://www.ecogene.org/gene/$1"^^ . "structural biology" . "developmental biology" . . . "^\\d+$"^^ . . . . . . . . . "knowledge graph" . . "nmpdr" . . "^OS-\\d+$"^^ . "dbgap" . "false"^^ . "structural biology" . . . . . . "^\\d+$"^^ . . "selventa" . "false"^^ . . . . . . . "bioinformatics" . . . "July 2018"^^ . . . . . . "gene expression" . "small molecule" . . "^HGVPM\\d+$"^^ . . "grid.225360.0"^^ . . "obo" . . "rna" . "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."^^ . . . . . . "HomologyRelation"^^ . . . . "ribonucleic acid" . "PNS12@cam.ac.uk" . "T30002"^^ . . . . . "a.kikhney@embl-hamburg.de" . . "gaz" . . "uminctr" . "http://www.w3.org/2004/02/skos/core#$1"^^ . "mircoRNA Gene Database is a collection of animal microRNA genes. This database allows researchers to analyze mircoRNA properties like secondary structure and features in a phylogenetic context."^^ . "deepak.unni3@lbl.gov" . . . . "credit" . . . . . "dna" . "ontology" . "nasaosdr.payload" . "gene expression" . . "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^ . "http://purl.obolibrary.org/obo/GENO_$1"^^ . . . "^\\d{7}$"^^ . . "Deepak Unni" . . . . . . . "mass spectrometry assay" . "NeuroNames" . "false"^^ . . "cell biology" . "http://purl.obolibrary.org/obo/OARCS_"^^ . . . . . "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"^^ . "^\\d{7}$"^^ . . "Ontology for General Medical Science" . . . "Collection of European paediatric cardiac coding files"^^ . . . . . . . "Software Functions Ontology" . "PD10000"^^ . "co_336" . . . . . "http://www.vbase2.org/vgene.php?id="^^ . . . . . "crates" . "false"^^ . "merops.inhibitor" . "^[a-z]+(\\-[a-z]+)*$"^^ . . "http://www.peptideatlas.org/PASS/"^^ . "school type" . . . "Vitro is a full stack framework for building semantic web applications. It is not domain specific."^^ . "dcid" . . . . "^UPC\\d{5}$"^^ . . . . . . . . . . "Common Entity Data Standards - Domain Entity Schema" . . "^GenProp\\d+$"^^ . . . "Carl F. Schaefer" . . "https://v31.homd.org/genome/genome_description?gid="^^ . . "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^ . "false"^^ . "dermo" . . . "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."^^ . . . . . "http://phylomedb.org/?seqid="^^ . . . . "model organisms" . . . _:N08f9068afd1c46f6b9dc8651c6a1086e . . . . "eropmoscow" . "protein" . . . . . . "PharmacoDB Cells" . . . . . "classification" . . "^\\d{7}$"^^ . . "GenProp0699"^^ . . "false"^^ . "ontology" . "https://deims.org/taxonomy/term/$1"^^ . . . . . "^\\d+$"^^ . "has URI prefix" . . . . "ontology" . . . "^\\d{7}$"^^ . "http://purl.obolibrary.org/obo/CTENO_$1"^^ . . . . "anatomy" . . "Drosophila Genomics Resource Center" . "https://bioregistry.io/ncbiortholog:"^^ . "http://purl.org/phylo/treebase/phylows/study/$1?format=html"^^ . "Database of Quantitative Cellular Signaling: Pathway" . . "http://purl.obolibrary.org/obo/HsapDv_"^^ . . . "Statistical Torsional Angles Potentials" . . . . . . . . . . "transposon" . "https://www.wormbase.org/get?name="^^ . . "^RF\\d{5}$"^^ . . . "Research Resource Identification" . . . "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."^^ . . "computer science" . "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1"^^ . . . "ontology" . "https://w3id.org/evorao/$1"^^ . "CHEBI" . . . . . "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^ . . . "false"^^ . . "false"^^ . "https://prefix.zazuko.com/prefix/$1:" . . . . . "life science" . "ac" . . . "http://dbpedia.org/resource/"^^ . . "6819"^^ . . "Leszek Vincent" . . "^\\w+$"^^ . "wikipedia.en" . . . . "phenotype" . "PS" . . . . . "false"^^ . . . "E12768"^^ . . "http://cor.esipfed.org/ont/earthcube/AUT_"^^ . . . "interaction" . "http://edamontology.org/format_$1"^^ . . . "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . "obo" . "smtifahim@gmail.com" . . "NASA Open Science Data Repository Experiment" . "obo" . . . "C. elegans phenotype" . "https://elsst.cessda.eu/id/3/$1"^^ . . . . . . . . "ontology" . "https://pypi.org/project/"^^ . "regulation" . . . . . . "Rice Genome Annotation Project" . "https://www.dublincore.org/specifications/skos-thes/ns/#$1"^^ . "knowledge and information systems" . . "Bob Thacker" . . "agriculture" . . . "Ge Gao" . "http://sabiork.h-its.org/newSearch?q="^^ . "dg.4dfc" . . . . "subject agnostic" . . "violinID" . "0000027"^^ . . . . . . . "AT1402"^^ . . "genome" . . . . . "hammer"^^ . "3905431"^^ . . . "false"^^ . . . "http://vocab.nerc.ac.uk/collection/P06/current/$1"^^ . . . . "MIRIAM Registry collection" . "proteomics" . "MGYP000261684433"^^ . . . . . . "https://w3id.org/aio/$1"^^ . . . . "false"^^ . "false"^^ . . . "Person" . . . . . . "false"^^ . . . "did" . . . . . "false"^^ . "0000029"^^ . "Google Scholar Researcher" . . . . . "VB.Ob.3736.GRSM125"^^ . . "virus" . "ontology" . . . "genetic polymorphism" . . . "^\\d{7}$"^^ . "image" . . "^\\d+$"^^ . . . . . . . "3966782"^^ . . "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."^^ . "https://www.inaturalist.org/users/$1"^^ . "^C\\d{4}$"^^ . . "https://www.biocatalogue.org/services/"^^ . . . "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^ . "preclinical studies" . . "paul.fabry@usherbrooke.ca" . . "https://www.uniprot.org/arba/"^^ . "https://w3id.org/babelon/"^^ . "gene" . . . . "Dendritic cell" . "00026f50-858a-446b-8ed9-b0e3ecd7b20e"^^ . . "https://www.biolegend.com/Default.aspx?ID=6664&productid="^^ . "0000254"^^ . . . "botany" . . . . "life science" . "http://purl.obolibrary.org/obo/PROCO_$1"^^ . "BRENDA Tissue Ontology" . "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^ . . . . "Thermo Fisher Scientific" . . "http://www.bioassayontology.org/bao#BAO_$1"^^ . . "50943"^^ . . "miaa" . "https://biocomputeobject.org/BCO_$1"^^ . . . . . . . "^([0-9A-F]{4}-){2}[0-9A-F]{4}$"^^ . "SMP" . "0000006"^^ . . "Library of Congress Subject Headings" . . "https://europepmc.org/article/AGR/"^^ . . . "variants" . . . "ontology" . "http://purl.obolibrary.org/obo/CLAO_"^^ . . "https://plantreactome.gramene.org/content/detail/"^^ . . . . "idr" . . . . "https://deims.org/$1"^^ . . . . . . "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:"^^ . . "https://www.ncbi.nlm.nih.gov/nucest/"^^ . . . . . . "^\\d{8}$"^^ . . . "MycoBrowser leprae" . "TogoVar" . . "103"^^ . . . "GeneID" . . "GALEN" . "2526"^^ . . . . . "^[1-9]\\d*$"^^ . . . . "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains."^^ . . "ontology" . . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . "^AC[0-9]{8}$"^^ . . . "ontology" . . "false"^^ . "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/)"^^ . "jz@mamot.fr"^^ . "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."^^ . "phenotype" . . . "taxonomy" . . . . "Human Dephosphorylation Database" . . . . "Yeast Phenotype Ontology" . . "This ontology is designed to support data search, retrieval and information identification in the EJP-RD catalogs which covers the registries and biobanks for rare diseases. (from repository)"^^ . . "Daniel N. Wilson" . "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."^^ . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"^^ . "TA_H3"^^ . . . . . "prodom" . . "http://purl.obolibrary.org/obo/VHOG_$1"^^ . . . . . . . "https://www.ncbi.nlm.nih.gov/nlmcatalog/"^^ . . "^\\w{1,3}$"^^ . "The set of prefixes used in the Cellosaurus resource" . . . "Plant Genome Network" . "https://arxiv.org/abs/$1"^^ . . . . . "biochemistry" . . . "Electrocardiogram Ontology" . . . "ADH1"^^ . . . "false"^^ . "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^ . "faseb list" . "^[0-9]+$"^^ . . "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"^^ . . "International Generic Sample Number" . . "false"^^ . . . "S7000002168151102"^^ . "false"^^ . "UM-BBD_pathwayID" . "false"^^ . . . . . "resource metadata" . . . "Tsute Chen" . "gene" . "biology" . . "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^ . . "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1"^^ . . . "Paul Fabry" . . . . . "zoology" . "98034"^^ . "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."^^ . "https://dgrc.bio.indiana.edu/product/View?product="^^ . "joerg.overmann@dsmz.de" . "https://rarediseases.org/?p="^^ . "https://metacyc.org/META/NEW-IMAGE?object="^^ . . . . . _:Nb5631ff21e9f4f0d986745314038884d "custserv@nlm.nih.gov" . . "oboinowl" . "https://molmedb.upol.cz/mol/$1"^^ . "life science" . "https://github.com/geneontology/go-ontology/issues/$1"^^ . . "phenotype" . . "R00100"^^ . . "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI."^^ . . "https://proteinensemble.org/"^^ . . "^\\d{7}$"^^ . . "mass spectrometry assay" . . "CAPS-DB" . _:N497e98e36c7a48cda5c1bf9c66da51ee "po-discuss@plantontology.org" . . . "Cotton ontology from CottonGen database - June 2019"^^ . "https://w3id.org/bervo/BERVO_"^^ . "http://lexvo.org/ontology#"^^ . . . . . . "drao" . . . . . "https://plantreactome.gramene.org/content/detail/$1"^^ . . "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . "IRCT20080904001199N7"^^ . "Global LEI Index" . "biochemistry" . . . . . . . . . "false"^^ . . "ontology" . "http://erop.inbi.ras.ru/result2.php?PepName="^^ . "A project in the ChemBioSys data platform"^^ . . "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes"^^ . "phenotype" . . . "false"^^ . . "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^ . "Randi Vita" . "obo" . . . . "https://cohesindb.iqb.u-tokyo.ac.jp/browsepeak/eachpeak/$1"^^ . . . . . "bsg-000052"^^ . "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."^^ . "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^ . "As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including:\n- Research team and institution\n- The EMSL project DOI\n- Link to project data available in EMSLs Data Portal\n- Project type"^^ . . "http://purl.jp/bio/4/id/"^^ . . "false"^^ . "life science" . . "http://scicrunch.org/resolver/SCR_"^^ . "^[0-9]*$"^^ . . "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1"^^ . . . . . "genotype" . "life science" . "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"^^ . "Cellosaurus" . . . . . . "kronkcj@mail.uc.edu" . "Lonza" . . "PubChem compound" . "^[A-Za-z 0-9]+$"^^ . "^(([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]+)?)?)?)$"^^ . "drug repositioning" . "00000268"^^ . . . . . "microbiology" . "biomedical science" . . . "false"^^ . . . . "S-EPMC6266652"^^ . "controlled term" . . . "immunology" . . . "An ontology of information entities about an individual"^^ . . . . . . "0000574"^^ . . "false"^^ . . . "^\\d{7}$"^^ . "https://lincs.hms.harvard.edu/db/cells/$1"^^ . . "Medaka fish anatomy and development" . . . "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^ . . . "Transcriptional Regulatory Element Database" . . . . . "http://purl.obolibrary.org/obo/ATO_"^^ . "false"^^ . "^[A-Z0-9]{6,7}$"^^ . "biomedical science" . . . "^rs[0-9]+$"^^ . . "Crates.io" . . . "French National Center for Scientific Research - Research Group Identifier" . . . . . . . "chembiosys.assay" . . "http://www.iclc.it/details/det_list.php?line_id=$1"^^ . . . "sepio" . . . . "IntellectualContribution"^^ . . "0000088"^^ . "false"^^ . . . "This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from )"^^ . . . . . . . . . . "http://www.wikidata.org/entity/$1" . . . . . . . "bgee@sib.swiss" . "anatomy" . "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^ . . . "oboformat" . "uniprot.core" . . . . . . . . "bcp47" . . "X58356"^^ . . . . "mop" . "^TA\\d+$"^^ . . . . "ontology" . . "wikidata.entity" . "ehdaa" . . . . . . . . "obo" . . . "false"^^ . . . . . . "Yohann Paris" . . "^\\d+$"^^ . . . . . "https://mycobrowser.epfl.ch/genes/"^^ . "https://sciflection.com/"^^ . "https://rpcec.sld.cu/en/trials/$1"^^ . . . "obo" . "sequence" . "false"^^ . . "http://purl.obolibrary.org/obo/MRO_$1"^^ . "^\\d+$"^^ . "c0000005"^^ . . . "fbtc" . . "Manufacturers of Vaccines" . "19-T4"^^ . . . . "^[a-zA-Z0-9\\-:#\\.]+$"^^ . . "transgenic" . "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode="^^ . "MOSAiC Ontology" . "experimentally determined" . "false"^^ . . "measurement" . . . . . . "false"^^ . "aellenhicks@gmail.com" . "life science" . "arraymap" . . . . . . "true"^^ . . "^NONHSAT\\d{6}$"^^ . . . . "http://purl.obolibrary.org/obo/OPL_"^^ . . "pathway" . . . "life science" . . "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^ . . . . "false"^^ . . "false"^^ . "omop" . . "Cathy Wu" . "Ontology for Chemical Kinetic Reaction Mechanisms" . "https://bioregistry.io/registry/$1" . . . . . . . "This is a vocabulary collection utilized by XHTML Family modules and document types using XHTML Modularization, including XHTML Role and XHTML + RDFa as defined in rdfa-syntax. The XHTML specifications are developed by the W3C XHTML 2 Working Group as part of the W3C HTML Activity. [from homepage]"^^ . . "Clement Jonquet" . . . "BiGG Reaction" . "http://purl.obolibrary.org/obo/TAXRANK_"^^ . "functional genomics" . "https://www.authenticus.pt/"^^ . . . "ontology" . . "disease" . . . "false"^^ . . . . . . . "The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]"^^ . . "^\\w+(\\.)?\\d+$"^^ . "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]"^^ . . . . . "pharmvar" . "glida.ligand" . "structural biology" . . . "biochemistry" . . . . "^\\d+$"^^ . . . . . . . "Molecular database for the identification of fungi" . . . "false"^^ . . . . "Eschmeyer's Catalog of Fishes" . . "PF3D7_1328700"^^ . "frbr" . . . "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^ . "antimicrobial peptides" . "Amos Bairoch" . . "obo" . "wiktionary" . "http://purl.obolibrary.org/obo/ECO_$1"^^ . "ontology" . "false"^^ . "false"^^ . . "ontology" . "0007807"^^ . "^FB\\d{8}$"^^ . "^\\d{7}$"^^ . . . . . "Lindsay.Cowell@utsouthwestern.edu" . "http://purl.obolibrary.org/obo/RoleO_$1"^^ . . . . "Gemina Symptom Ontology" . . . . "health science" . "ontology" . . . . . . . . "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^ . . . . . "https://www.mlcommons.org/mlc-id/"^^ . . . . . . . . . . "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."^^ . . "https://www.checklistbank.org/dataset/3LR/taxon/$1"^^ . . . . . . . . . . . . . . . . . . "abm" . . "reaction" . . . "structrual bioinformatics" . . . . . . . . . "Inge.Jonassen@uib.no" . "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances"^^ . . . "^\\d{7}$"^^ . "Space Life Sciences Ontology" . . . "051"^^ . "International Fungal Working Group Fungal Barcoding." . . . . "molecular entity" . . . . . "systems biology" . "ontology" . . . "sioc.access" . "computational biology" . "reagent" . . . "http://champ-project.org/images/ontology/cao.owl#CAO_$1"^^ . . . . "open educational resources" . . "Odor Molecules DataBase" . . "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" . "alayne.cuzick@rothamsted.ac.uk" . . . . . "https://jjj.bio.vu.nl/models/"^^ . . . . . "The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains."^^ . . "structure" . . . . . "Yongqun Oliver He" . "nucleic acid" . "VMH metabolite" . "_fe65f286"^^ . "false"^^ . . . "Ontological Interpretations for Web Property Graphs" . . "LINCS Protein" . . "developmental biology" . "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community."^^ . "https://osdr.nasa.gov/bio/repo/data/experiments/"^^ . "https://www.ribocentre.org/docs/"^^ . "http://geneontology.org/docs/gene-product-information-gpi-format/#"^^ . . . "LINCS Small Molecule" . . "aero" . "^\\d{7}$"^^ . . "fobi" . "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^ . . . . . . "ChemBioSys Organism" . . "61467"^^ . . "4544"^^ . . "true"^^ . . . . . . . . . . . . "idoden" . . "National Library of Medicine Catalog" . "Identifiers represent experimental growth profiles documenting fungal species' ability to utilize specific carbon sources (plant biomass components, polysaccharides, and monosaccharides) in the FUNG-GROWTH database, which provides phenotypic data to support functional genome annotation and comparative analysis of carbohydrate metabolism across fungal species."^^ . . . "hinv.locus" . "health science" . . . . . . . "false"^^ . "Degradome Database" . . . . "https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/"^^ . . "epo" . "^\\d{7}$"^^ . . "^SAM[NED](\\w)?\\d+$"^^ . . "https://bioregistry.io/iceberg.ime:"^^ . . . "ChemFOnt Chemical" . . . "false"^^ . . . . "xlmod" . . . "2116"^^ . "https://biopragmatics.github.io/providers/hog/$1"^^ . . "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . "false"^^ . . . . . . "https://semanticscience.org/resource/SIO_$1"^^ . "selventa" . "http://www.orpha.net/ORDO/Orphanet_$1"^^ . . . . "upper-level ontology" . "geneotype" . . . . . . "http://118.178.132.53/tsRNADisease/detail.php?entry_ID="^^ . . . "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."^^ . "The anatomy of the Tick, Families: Ixodidae, Argassidae"^^ . "https://w3id.org/class/sectors/$1"^^ . . "tissue" . . . "industry" . "https://www.ebi.ac.uk/arrayexpress/experiments/$1"^^ . . . "false"^^ . . . . . . . "r.shrestha2@cgiar.org" . . . "http://rna.rega.kuleuven.be/rnamods/rnashow.pl?"^^ . . "organic molecular chemistry" . . "https://neurovault.org/collections/"^^ . . . . . "^\\w+:[\\w\\d\\.-]*$"^^ . . . . . . . "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line="^^ . . "BE0000048"^^ . "Registry of Research Data Repositories" . "The upper level ontology upon which OBO Foundry ontologies are built."^^ . "sequence" . "true"^^ . . "5UTR_107_ENST00000517291.2"^^ . "The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved." . . . . "http://purl.obolibrary.org/obo/GENO_"^^ . . . "http://id.loc.gov/vocabulary/resourceTypes/$1"^^ . "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment."^^ . . . . "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid="^^ . "Gene Location" . . . "http://jcggdb.jp/idb/jcggdb/"^^ . . " 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."^^ . "disease" . "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . . "ontology" . . . . . . . "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"^^ . . "evr" . . "subject agnostic" . . . "dsmz" . . "bpdb" . . . "true"^^ . . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . "http://purl.obolibrary.org/obo/FLU_$1"^^ . _:N9756a95d55d04316b98ac063b1e03879 . "Clare Pilgrim" . . . . . "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^ . "LDCM0160"^^ . . . "hcao" . . . . . . "obo" . "MAR11851"^^ . "^\\d+$"^^ . . . "geno" . "chemistry" . . "ontology" . . "false"^^ . . "gene expression" . . "hasDbXref"^^ . "attachedTo"^^ . . "false"^^ . . . "This prefix is for FDA application identifiers. There are multiple types of FDA applications (https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications), including New Drug Application (NDA). FDA.report provides access to all FDA databases, including applications, in a single portal, and can resolve FDA application identifiers."^^ . . . "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."^^ . "protein" . . "UniProt Protein" . . . . . . . . "Sensors in DEIMS SDR"^^ . "Decentralized Biomedical Ontology" . . "https://humap3.proteincomplexes.org/displayComplexes?complex_key="^^ . "^\\d{7}$"^^ . . . "TripleExpression"^^ . . . . . "https://cbcb.cdutcm.edu.cn/AGD/genome/details/?id=$1"^^ . "false"^^ . "P-008-GD6"^^ . "http://www.semanticdesktop.org/ontologies/2007/08/15/nao#"^^ . . . . . "Encyclopedia of Life Schema" . . . "chebi" . . . "Educational Sectors Vocabulary" . . "mavedb" . "https://www.brenda-enzymes.org/php/result_flat.php4?ecno="^^ . . . . . . "conso" . "omics" . . "gene" . "http://purl.obolibrary.org/obo/HSO_"^^ . "human" . "false"^^ . . "obo" . . . . . . . "Adrian Gschwend" . . "906801"^^ . . . . . "uberon.issue" . . . . . "https://deims.org/sensors/$1"^^ . "plant phenotypes and traits" . "00023232"^^ . . . . . "ISCW007415"^^ . . . . "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^ . "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1"^^ . . . "^([3-5][A-Z])\\w+[^A-Z][0-9]$"^^ . "Identifier for a species in iNaturalist"^^ . . "^[1-9]\\d*$"^^ . . . . . "http://purl.obolibrary.org/obo/MOBIO_"^^ . "http://www.kegg.jp/entry/$1"^^ . . . . . . . . . "https://www.mycobank.org/page/Name%20details%20page/"^^ . . . . . "obo" . "^[AEP]-\\w{4}-\\d+$"^^ . . "Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions"^^ . "https://fungi.ensembl.org/id/$1"^^ . "dcelem" . . "https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/"^^ . . "seconary school type" . "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers."^^ . . . . . "elvira@imbb.forth.gr" . "cell" . . . . . . "70"^^ . "Roman Baum" . . . "http://purl.obolibrary.org/obo/EMAPA_"^^ . . "^\\d+$"^^ . . . "PubChem Classification" . . "KEGG.EDRUG" . . . "vsdb" . "http://metlin.scripps.edu/metabo_info.php?molid="^^ . "^\\d{8}$"^^ . . . . "DDB_G0267522"^^ . . . . . . . . "ENSG00000139618"^^ . "protein" . . "http://purl.obolibrary.org/obo/LABO_"^^ . "pandey@jhmi.edu" . "F0001"^^ . "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."^^ . "PASS01237"^^ . "http://cor.esipfed.org/ont/earthcube/SFO_"^^ . . "https://w3id.org/kim/hochschulfaechersystematik/"^^ . . . . . "http://purl.org/ontology/bibo/"^^ . "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"^^ . . . . . . . "protein" . "PANTHER Family" . . . . . . . "true"^^ . . "^[a-f0-9]{32}$"^^ . "Sofia Robb" . "false"^^ . . . . "Work"^^ . . "anatomy" . . "ontology" . "small molecule" . . . . . "urmas.koljalg@ut.ee" . "false"^^ . . . . "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR."^^ . "Primate Brain Atlas" . "Semantically-Interlinked Online Communities Argumentation Ontology" . . . . . . "^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})$"^^ . . . "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . "ipi" . . "Allyson Lister" . . . . "sosa" . . "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."^^ . "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."^^ . "Ismail Fliss" . "http://purl.obolibrary.org/obo/ICEO_$1"^^ . . "animal" . . . . . . . "natural product" . "ontology" . . "https://molbic.idrblab.net/data/cellline/details/"^^ . . . . "http://www.pocketome.org/files/$1.html"^^ . . . "ATCC(in host)" . . . "vita" . "hubmap.donor" . "http://purl.obolibrary.org/obo/OBA_"^^ . "CAL0003079"^^ . "co_333" . "^\\d{7}$"^^ . . . . . "MESH_SUPPLEMENTAL_RECORD_UI" . . "omim" . "pseudogene" . . . . "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^ . "T0599"^^ . "organic chemistry" . . . . . . . . . . "ecg" . . . "life science" . "https://pharmacodb.ca/datasets/"^^ . "ComplexPortal" . . . . "small molecule" . . . "http://purl.obolibrary.org/obo/ICO_$1"^^ . . . . . . "^\\d+$"^^ . . "Social Insect Behavior Ontology" . . . . "dsm5" . . "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."^^ . . . "SBGN Bricks data and ontology" . "genome" . "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 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."^^ . "1"^^ . . . . . . "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."^^ . . . . . "metabolite" . "https://www.arabidopsis.org/locus?accession="^^ . . "Pankaj Jaiswal" . . "false"^^ . . . . . . . . . "https://animaldiversity.org/accounts/$1"^^ . . "engelsta@ohsu.edu" . . . "Assigns persistent identifiers to multidisciplinary research outputs with focus on research originating in Africa, such as in cultural heritage and indigenous knowledge."^^ . . . . . . "SNOWMEDCT_US_2018_03_01" . "0000044"^^ . "Cell line collections (Providers)"^^ . . . . "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data."^^ . . . "Barry Smith" . . . "^\\w+\\_\\d+(\\.\\d+)?$"^^ . . . . "disease course" . "ohmi" . . "icf" . . . . "n.queralt_rosinach@lumc.nl" . . . . "http://purl.obolibrary.org/obo/OPL_$1"^^ . . "protcom" . "^\\d+$"^^ . "https://pdc.cancer.gov/pdc/study/$1"^^ . . . "vto" . . . "life cycle" . . . . . "protein" . . . "0002233"^^ . . . . "Global Proteome Machine Database" . . . . . . . . . . "bt0001"^^ . "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families."^^ . _:N497e98e36c7a48cda5c1bf9c66da51ee . . . "Carlos Oscar S. Sorzano" . "contributor"^^ . "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^ . . . "cropping systems" . . . "bioregistry"^^ . "kim.educationlevel" . . . . "life cycle stage" . . . . "data visualization" . "^[a-z0-9]+$"^^ . . "https://mmp.sfb.uit.no/databases/marcat/#/records/"^^ . . . "Gemma L. Holliday" . . "^2-s2\\.0-\\d+$"^^ . . . . "false"^^ . . "false"^^ . "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/)" . . "Health Canada Natural Product Number" . . . . . . . "20000614040"^^ . . "false"^^ . . "https://bioregistry.io/abcam:"^^ . "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)"^^ . "5"^^ . "Multiple alignment" . "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."^^ . . . "http://purl.obolibrary.org/obo/PAO_"^^ . "BG11523"^^ . "larvae" . "1200"^^ . "http://vivoweb.org/ontology/core#"^^ . "NMR-instrument specific component of metabolomics investigations" . . "ontology" . "ubprop" . . "Identifiers for missions associated with experiments that investigate biological and health responses of terrestrial life to spaceflight"^^ . "false"^^ . "false"^^ . "https://registry.dome-ml.org/review/$1"^^ . "assay" . . "0000022"^^ . "resource metadata" . . . "venom" . "food" . "Manually curated collections of resources stored in the bioregistry"^^ . . "0000009"^^ . "false"^^ . . "^(HOM)?\\d{7}$"^^ . "https://www.fishbase.ca/summary/$1"^^ . "dron" . . "Properties and classes used for protein annotation"^^ . . . . "false"^^ . . . "false"^^ . . . . "Swiss Personalized Health Network Schema" . "ascl" . "rna" . "^[1-9][0-9]*$"^^ . "obo" . "sumirp77@gmail.com" . "GeneCards Gene" . . . . . . "bioinformatics" . . "nist" . "cells" . "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."^^ . "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . . "http://purl.org/spar/pwo/"^^ . . "human genetics" . . "Sol Genomics Network" . . "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^ . "^\\d{7}$"^^ . . . "life science" . . . "ontology and terminology" . . . "FuTRES Ontology of Vertebrate Traits" . . . . "https://bioregistry.io/combine.specifications:"^^ . "https://www.gwascentral.org/study/$1"^^ . "ontology" . . "http://data.europa.eu/esco/occupation/"^^ . . . . . "ontology" . . "http://www.pharmgkb.org/pathway/$1"^^ . . "ricenetdb.compound" . "https://hdl.handle.net/hdl:20.500.12633/$1"^^ . "false"^^ . . . . . "false"^^ . . . . "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"^^ . . . . . "ontology" . . "Human BioMolecular Atlas Program Donor" . "SABIO-RK Reaction" . . "0000111"^^ . . . "https://molbic.idrblab.net/data/protein/details/"^^ . . "http://synbip.idrblab.net/data/bts/details/"^^ . . . . "Darwin Core is a vocabulary standard for transmitting information about biodiversity. This document lists all terms in namespaces currently used in the vocabulary."^^ . . "SNOMEDCT_US_2020_09_01" . . . . . . "^\\d+$"^^ . . . . "true"^^ . . _:N737c82f1d18947caa3d2c88fd2aea61d "Intellectual.PropertyServices@ama-assn.org" . . . . "0000004"^^ . . "BUNA790102"^^ . . . . . . . "e-yasugi@umin.ac.jp" . . "Lin Huang" . "LiceBase" . . . "http://purl.obolibrary.org/obo/PdumDv_$1"^^ . . . . . . "https://github.com/obophenotype/uberon/issues/$1"^^ . . "Entity in Wikidata"^^ . . "^\\d{7}$"^^ . . . . "anatomy" . . . "https://cropontology.org/rdf/CO_322:"^^ . . . "sequencing assay" . . . "Wes Schafer" . "http://data.europa.eu/esco/skill/"^^ . . . . . . "AllSomeInterpretation"^^ . "bto" . . . . . "roman@ebi.ac.uk" . "zengxian@fudan.edu.cn" . . . "^\\d{7}$"^^ . . . "life cycle stage" . . "TDR" . "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)."^^ . . . "National Center for Advancing Translation Sciences BioPlanet" . "http://www.ebi.ac.uk/cmpo/CMPO_$1"^^ . . "A tag in the ChemBioSys data platform"^^ . . . "rsk00410"^^ . "49"^^ . "http://www.kegg.jp/entry/$1"^^ . . . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes."^^ . . . . "Human Protein Complex Map" . . . "r3d100010772"^^ . "^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$"^^ . . . . . . . . . "obo" . . "G00123"^^ . . . . "https://www.merckmillipore.com/catalogue/item/$1"^^ . "UniProt Variants" . "3771992"^^ . "Genomic Epidemiology Ontology" . "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . "https://sumlineknowledgebase.com/?page_id=$1"^^ . "plant_reactome" . . "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."^^ . . "expression" . . . . "http://purl.obolibrary.org/obo/EXMO_$1"^^ . . . . "^\\d+$"^^ . . . . . . . "false"^^ . "https://biosimulations.org/projects/"^^ . "BOLD Systems taxon" . . . . . "gene expression" . . "^\\d+$"^^ . "Protege Ontology" . . . . "NCBI Data Repository Service" . "O80725"^^ . . . "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^ . . . "false"^^ . . . "^SKIP\\d+$"^^ . . . . . . . "https://tetrahymena.vet.cornell.edu/display.php?stockid="^^ . . . "http://dicom.nema.org/resources/ontology/DCM/$1"^^ . . . . "false"^^ . "^\\d+$"^^ . . . "http://www.kegg.jp/entry/"^^ . . . "^[1-9]\\d{0,6}$"^^ . "agriculture" . . "https://rnaloops.cs.put.poznan.pl/search/details/$1"^^ . . "togovar" . . "knockout" . . . "smid" . "IHW09326"^^ . "https://www.ebi.ac.uk/pdbsum/$1"^^ . . "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. "^^ . . . . "proteomics" . . . . . . "http://usefulinc.com/ns/doap#"^^ . "OSR00185W"^^ . . "gene name" . "phenotype" . "molecular interaction" . . . "chemistry" . . "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . . . "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/"^^ . "ECU03_0820i"^^ . . "false"^^ . "false"^^ . . . . . . . . "false"^^ . . "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes."^^ . . "gro" . . . "molecule" . . "small molecule" . "vo" . . . . . . "chembl.mechanism" . . "biospecimen" . . "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."^^ . . "Multiplexed Assays of Variant Effect Database" . . . . "http://www.bootstrep.eu/ontology/GRO#$1"^^ . "anatomy" . "false"^^ . "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."^^ . "PharmacoDB Datasets" . . "http://purl.obolibrary.org/obo/TAO_"^^ . . "Integbio" . "true"^^ . . "https://abrc.osu.edu/stocks/number/SALK_$1"^^ . . "henrich@embl.de" . "true"^^ . . . "https://biopragmatics.github.io/providers/cvx/$1"^^ . "01001"^^ . "Perry Miller" . . "software engineering" . . . . . "ProteomicsDB Protein" . "false"^^ . "ALX-210-175"^^ . "^R\\d+$"^^ . . "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1"^^ . "0019171"^^ . . . "Prefix.cc" . . "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"^^ . "Guoqing Zhang" . "000000024"^^ . "Orphanet" . "false"^^ . . "https://data.chembiosys.de/data_files/$1"^^ . . . . . "0000008"^^ . . . "http://exac.broadinstitute.org/gene/$1"^^ . "ontology" . . "Chemical Book" . . . . "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"^^ . "National Drug Data File" . . "isced2013" . . . . . . . . . . . . . "obo" . . _:N3b2e5a75e65c4b6ebb253a66b8a9073c . . "antimicrobial agent" . . . . "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1"^^ . . "hpath" . "ontology" . . . "forest management" . "plant breeding" . "isanchez@cnb.csic.es" . "false"^^ . . . "sheriff@ebi.ac.uk" . . "agriculture" . . . "endlessforms.element" . . . . "^\\d{1,9}$"^^ . . . . . . . "European Registry of Materials" . "false"^^ . . . "http://unite.ut.ee/bl_forw.php?nimi=$1"^^ . "^\\d+$"^^ . . . . . _:N25c1a4a229e849899b9c7c47fd32918b "takeya.kasukawa@riken.jp" . . "https://medlineplus.gov/genetics/condition/$1"^^ . "biogrid" . "biomedical science" . . . . "A type for entries in the Bioregistry's collections" . . "jhc@lbl.gov" . "0005250"^^ . . . "^\\w+$"^^ . . "https://panoramaweb.org/$1.url"^^ . . "false"^^ . . "0003463"^^ . "TubercuList knowledge base" . . "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access."^^ . . . "Daniel Himmelstein" . . . . . . . . . . "1731"^^ . "^\\d{7}$"^^ . "dbsnp" . . . . "Cellosaurus Registry" . . . . . . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/EHDAA_$1"^^ . . . . . "comparative genomics" . . "International Classification of Diseases, 10th Revision" . . "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1" . "Bibliographic Reference Ontology" . . "text mining" . "disease phenotype" . "ontology" . "http://purl.org/spar/scoro/"^^ . . "sustainability" . . "false"^^ . . . "Teresa K. Attwood" . . "infectious disease medicine" . . "epcc" . . "http://oncotree.mskcc.org/api/tumorTypes/search/code/"^^ . . "FEMA provides identifiers for flavor ingredients deemed safe for food use. These entities include chemical compounds and natural substances used as flavoring agents, each reviewed by the FEMA Expert Panel for GRAS (Generally Recognized As Safe) status. The identifiers link to safety data and regulatory assessments, including evaluations by the U.S. FDA and, where applicable, the Joint FAO/WHO Expert Committee on Food Additives (JECFA)."^^ . . "https://www.langual.org/langual_thesaurus.asp?termid="^^ . "http://purl.dataone.org/odo/SENSO_$1"^^ . "false"^^ . . . . _:N605a47747bae443ca9926391a8181797 "Vivian Lee" . "cell lines" . . . . "b97957"^^ . . "zinc" . . . . "https://go.drugbank.com/reactions/"^^ . "toby.gibson@embl.de" . "protein" . . _:N9756a95d55d04316b98ac063b1e03879 "NLM Customer Service" . "ontology" . . . . . . . . . . _:N680b661fb12648a886d0881f4fabc9fc . . "dna" . . . "nuclear" . "lcnaf" . "environmental science" . "ietf.language" . . "7943"^^ . "ID of a researcher in Authenticus website"^^ . "https://psskb.org/motif/card/"^^ . . . . . "longevity" . . . . "^[\\w0-9\\-&_'’\\.]+$"^^ . . . "http://opm.phar.umich.edu/protein.php?pdbid=$1"^^ . . . . "NFDI-MatWerk aims to establish a digital infrastructure for Materials Science and Engineering (MSE), fostering improved data sharing and collaboration. This repository provides comprehensive documentation for NFDI MatWerk Ontology (MWO) v3.0.0, a foundational framework designed to structure research data and enhance interoperability within the MSE community. To ensure compliance with top-level ontology standards, MWO v3.0.0 is aligned with the Basic Formal Ontology (BFO) and incorporates the modular approach of the NFDIcore mid-level ontology, enriching metadata through standardized classes and properties. The mwo addresses key aspects of MSE research data, including the NFDI-MatWerk community structure, covering task areas, infrastructure use cases, projects, researchers, and organizations. It also describes essential NFDI resources, such as software, workflows, ontologies, publications, datasets, metadata schemas, instruments, facilities, and educational materials. Additionally, mwo represents NFDI-MatWerk services, academic events, courses, and international collaborations. As the foundation for the MSE Knowledge Graph, mwo facilitates efficient data integration and retrieval, promoting collaboration and knowledge representation across MSE domains. This digital transformation enhances data discoverability, reusability, and accelerates scientific exchange, innovation, and discoveries by optimizing research data management and accessibility. (from repository)"^^ . . . "Long Term Ecological Research Controlled Vocabulary" . . . . . "carnegie.stage" . . . "false"^^ . "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . . "megan.kane@nih.gov" . . . "false"^^ . "^\\d+$"^^ . . . . "false"^^ . . . . . . . "http://purl.uniprot.org/annotation/$1"^^ . "LIPID MAPS" . "RNA Modification Database" . . . . "^\\d+$"^^ . "co_325" . . "false"^^ . . "ceph" . . "^(application|audio|font|haptics|image|message|model|multipart|text|video)(/.*)?$"^^ . . . "Workspace (Git repository) for modeling projects managed by the Physiome Model Repository"^^ . . . "false"^^ . . "life science" . "pseudomonas" . . . . "https://n2t.net" . . . . . . . . . . . "chemical entity" . . . "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]="^^ . "https://search.dalia.education/communities/$1"^^ . . . "^\\d{7}$"^^ . "false"^^ . "https://www.confident-conference.org/index.php/Event_Series:$1"^^ . . . "TreeFam" . . "genomics" . . . . . . . "cancer" . . . . "^[1-9]\\d{2,6}$"^^ . . . . . "s1000"^^ . . "protein" . . . . . . "life science" . . "agriculture" . "false"^^ . . . . . . "https://nanbyodata.jp/disease/NANDO:"^^ . "^\\d+$"^^ . . "^NBR\\d+$"^^ . "Pathguide" . . . "false"^^ . "^E(S|D)i\\d+-\\w$"^^ . . . _:N4a37364fe53a4e4d92048112b84cc3d0 "radlex-feedback@lists.rsna.org" . . . . "biomedical science" . "false"^^ . . . "true"^^ . . . . . . . "Human Genome Variation Society Nomenclature" . . . . "Homeostasis imbalance process ontology" . "dandi" . "The pattern for expanded URIs in the given resource" . "1455"^^ . "chris@gigasciencejournal.com" . "0000447"^^ . "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."^^ . "Cross-linker reagents ontology" . . . "https://odc-tbi.org/data/"^^ . . . "institution" . . . "false"^^ . "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1"^^ . . "chemistry" . . . . "belongsToCluster"^^ . . . . "http://purl.obolibrary.org/obo/OMIT_"^^ . "medgen.cid" . . . . "life science" . "0000046"^^ . "epigenetics" . "Akt_PKB"^^ . "https://cropontology.org/rdf/CO_367:$1"^^ . "genomics" . . . . . . . "Silvio C.E. Tosatto" . "drsanv0" . "Ensembl Plants" . "SP_KW" . . . "biomodels.kisao" . . . . "https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1"^^ . "Cell line collections (Providers)"^^ . . "International Classification of Diseases, 11th Revision (Foundation Component)" . "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . . "A manually curated resource for the representation and annotation of metabolic pathways"^^ . "baeverma@jcvi.org" . . "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . "http://phenol-explorer.eu/foods/$1"^^ . . "https://bioregistry.io/cst.antibody:"^^ . "false"^^ . "2.16.840"^^ . . "OMA HOGs" . . . . "data analysis" . . . . . . . . "microbiome" . "^\\d{6}$"^^ . . . . "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."^^ . "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^ . . "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)."^^ . "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."^^ . . "https://cropontology.org/rdf/CO_326:$1"^^ . . . "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."^^ . "75"^^ . "https://ferr.gulab.org.cn/browse/$1"^^ . "false"^^ . . . "mwitt@purdue.edu" . . "inn" . . . . "false"^^ . . "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."^^ . . "imotdb" . . "http://www.w3.org/2004/02/skos/core#"^^ . . . . "yetfasco" . . . . . . . "https://registry.identifiers.org/registry/"^^ . "nmdc" . . "drug name" . "http://plugins.biogps.org/cgi-bin/wp.cgi?id="^^ . . "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"^^ . . . . "https://vcell.org/biomodel-$1"^^ . . "false"^^ . . . . . . . . . . . . . . _:N2fc03ae361414470a8c0bda5edf04557 "Sean Roberts" . . "agronomy" . "4019477"^^ . . "wiley"^^ . . . "U49845"^^ . "ecology" . "https://pubchem.ncbi.nlm.nih.gov/substance/"^^ . "false"^^ . . . . . . . "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_"^^ . "CIViC Assertion" . . "http://www.proteinmodelportal.org/query/uniprot/"^^ . . "589462"^^ . . . . . . "eol.schema" . "MentionType"^^ . "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."^^ . . . "false"^^ . "https://genelab-data.ndc.nasa.gov/genelab/accession/"^^ . . "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^ . . "ssrn.article" . . "http://purl.obolibrary.org/obo/INO_$1"^^ . "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database."^^ . . . . . . . . . . . . "taxonomy" . . . . "false"^^ . "ssn" . . . . . . . . . "pathway" . "biomedical science" . "^\\d+$"^^ . . "OpenEduHub Education Level" . "wormmart" . . . . . . "Metabolite and Tandem Mass Spectrometry Database" . . "false"^^ . "https://www.disprot.org/idpo/IDPO:$1"^^ . . . . "https://github.com/tibonto/educor#$1"^^ . . "Bong Hyun Sung" . . "false"^^ . . . . . . . "https://www.ebi.ac.uk/interpro/set/pfam/$1"^^ . "^\\w{5}\\.\\d{2}\\..*$"^^ . "John Wieczorek" . . . "true"^^ . . . "aacdb" . . "https://umgear.org/p?id="^^ . . . "131"^^ . "^IPR\\d{6}$"^^ . "agricultural engineering" . . . "RCV000033555.3"^^ . "ulrike.wittig@h-its.org" . "CFo000000197"^^ . "tree" . "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . "A controlled vocabulary to support the study of transcription in the mouse brain"^^ . . . "https://www.ncbi.nlm.nih.gov/gene/"^^ . . "metascience" . "xsd" . . "hao" . . . . . "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team."^^ . "^\\d{7}$"^^ . . . . . . "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name="^^ . "false"^^ . . "P06"^^ . . . . "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."^^ . . . "http://purl.obolibrary.org/obo/YPO_"^^ . "Giacomo Lanza" . . . "emolecules" . "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."^^ . . . . "ncro" . . "http://www.scopus.com/record/display.url?origin=inward&eid=$1"^^ . . "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"^^ . . "http://www.kegg.jp/entry/$1"^^ . . . . "Leigh.Carmody@jax.org" . "ontology" . . . "Biomarker Knowledgebase - Biomarker" . "strain" . . . . . . "data retrieval" . "obo" . . . "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management."^^ . . "javier.millanacosta@maastrichtuniversity.nl" . "64ba"^^ . "^\\d{7}$"^^ . "imaging" . . . "embryo" . "NP_012345"^^ . _:Ne8f59032a90d4fe18933465e973bd258 "brennan.thomas@epa.gov" . . "microbe-host interaction phenotype" . . . "Orientation of Proteins in Realistic Lipid Membranes" . "obo" . "ontology" . . . . . . . . "https://gpcrdb.org/protein/$1"^^ . . . . "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1"^^ . "false"^^ . . . . . . "false"^^ . "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . "https://data.4dnucleome.org/biosources/$1"^^ . . "ontology" . . . . . . . . "genomics" . "botany" . "https://www.inaturalist.org/places/"^^ . . . . "https://graphics.endlessforms.info/element?id=$1"^^ . . . . "100101"^^ . . . "omics" . "Henriette Harmse" . . . . . "false"^^ . . "genome" . . . . "biology" . "gramene.protein" . "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id="^^ . . . "SPCC13B11.01"^^ . "pathway" . . "edda" . "https://osf.io/$1"^^ . "cell" . . "rna" . . "ontology" . . . "http://www.co-ode.org/ontologies/galen#$1"^^ . "veterinary medicine" . "pathway" . "Zazuko Prefix Server" . "ontology" . . . . "https://www.gwascentral.org/marker/"^^ . "HUMAN16963"^^ . "Ontology for Modeling and Representation of Social Entities" . . "^PA\\d+$"^^ . "https://www.nextprot.org/term/"^^ . . . . . . . . . . . . . "life science" . . . . . . "transcript" . "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. "^^ . "Database of Interacting Proteins" . . "oboe.standard" . . . . . . "http://purl.obolibrary.org/obo/ECTO_"^^ . . . "http://purl.obolibrary.org/obo/MOD_$1"^^ . . . . . . . . "false"^^ . . . "^[0-9]+$"^^ . . . . . . "0000ffeb-36e0-4a29-b21d-84423bda979d"^^ . "^\\d+$"^^ . . . . "ontology" . "MJoachimiak@lbl.gov" . . . "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id="^^ . . . . . "false"^^ . "ontology" . . . "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_"^^ . "Social Science Research Network Author" . "https://world-2dpage.expasy.org/repository/$1"^^ . . . . . . "false"^^ . "https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?curie=NMR:$1"^^ . . "clao" . . "^[a-z_A-Z0-9]+(\\[[c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y]\\])?$"^^ . "raid" . "anatomy" . . "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."^^ . "subject agnostic" . . "version Dec 2019"^^ . . . _:N5a29923746d74e12b425843c144a6e90 . "life science" . . . "BT20_BREAST"^^ . "epigenetics" . . . . "false"^^ . . . "molbase.sheffield" . . . . "Cancer Cell Line Encyclopedia Cells" . "ontology" . . . . . "bmont" . . . . . . "UMLS_ICD9CM_2005_AUI" . . . "mgnify.samp" . "biomedical science" . . . . . . . "glycosciencesdb" . "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . "Richard Cyganiak" . "^\\d{1,7}\\-\\d{2}\\-\\d$"^^ . "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology."^^ . . . . "eukaryotic" . . . "epidemiology" . . . . . "DBPedia Property" . . "Maaya Manoj" . . . . "The Food Ontology" . . "EAWAG Biocatalysis/Biodegradation Database reaction" . "cba" . . . "^\\d+$"^^ . . . . . "true"^^ . . "090701"^^ . . . . . "jp@senescence.info" . . "https://dblp.org/pid/$1"^^ . "RISM Online" . "American Type Culture Collection" . "http://rebase.neb.com/rebase/enz/$1.html"^^ . "UBERON Issue Tracker" . . "ND50028"^^ . . . . "A catalogue of mouse strains supplied by The Jackson Laboratory. Each identifier corresponds to a mouse strain."^^ . . "false"^^ . . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME"^^ . . "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^ . "^\\d+$"^^ . . "false"^^ . "HDAA2" . . . . . "http://purl.org/spar/deo/"^^ . "The COVID-19 Infectious Disease Ontology" . . "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1"^^ . "rwinslow@jhu.edu" . . . . . . . "hpscreg" . . "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."^^ . . . . . . . "dc" . "go.rule" . . . . . . _:N13428b66cf7a4f6f956195d5354d505e "Stephen Larson" . . "Joint Genome Institute Proposals" . "protein" . "604090889"^^ . . . "obo" . . "sibo" . "http://purl.obolibrary.org/obo/AfPO_"^^ . "EasyChair Topic" . . "Ontology for simulation, modelling, and optimization" . . "false"^^ . "electronic health record" . . . "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."^^ . . "UBREL" . "@biopragmatics/curies"^^ . "CDBP00415501"^^ . . . "isacorreia@tecnico.ulisboa.pt" . . . "authenticus" . . . "ontology" . "Gene"^^ . . . _:N5a29923746d74e12b425843c144a6e90 "Patricia Brooks" . . . . "obo" . . . . "chemistry" . "http://purl.obolibrary.org/obo/WBls_$1"^^ . . "0000071"^^ . "https://github.com/tibonto/educor#"^^ . "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . . . . . . "chebi" . . . "Pearl millet ontology" . . "PRIDE Project" . "co_370" . "^\\d+$"^^ . "Loop ID" . . "^\\d+$"^^ . "edeutsch@systemsbiology.org" . "comparative neurobiology" . . "ScerTF" . . . . . . . . "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"^^ . "life science" . "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"^^ . . . "protein" . . "structure"^^ . . . "civic.assertion" . . . . "false"^^ . "false"^^ . . . "biokc" . . . . . "enzyme" . . "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^ . . "Michael Y Galperin" . . "Flora Phenotype Ontology" . . . "andreas.ledl1@fhnw.ch" . . "small molecule" . "http://purl.org/spar/datacite/"^^ . . . "^C\\d+$"^^ . . . . "13"^^ . . "http://purl.org/ontology/bibo/$1"^^ . "false"^^ . . "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"^^ . . "deoxyribonucleic acid" . . . . . . . . . . "Genatlas" . "http://hdl.handle.net/"^^ . . "International Medical Device Regulators Forum" . "0C1F-DA6C-4B02"^^ . . . . . . "anatomy" . "Packagist" . . "Linguist" . "2200934"^^ . "Susan Tweedie" . . . . "https://www.ncbi.nlm.nih.gov/cdd?term="^^ . . "false"^^ . . . "mibig" . "KEGG BRITE" . "genome" . . . . "https://bioregistry.io/metaregistry/cellosaurus/"^^ . . "https://datanator.info/reaction/"^^ . . "systems biology" . . . . "http://purls.helmholtz-metadaten.de/mwo/mwo_"^^ . "false"^^ . . "false"^^ . "^\\d{7}$"^^ . "false"^^ . . . . "^[0-9]+$"^^ . . "life science" . . . "obo" . _:N6835ccee24b84375ab1206252243e893 . . . . "https://bioregistry.io/cellbank.australia:"^^ . . "false"^^ . . . . . . "http://biomodels.net/rdf/vocabulary.rdf#$1"^^ . "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract)."^^ . "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1"^^ . . . "NASA Open Science Data Repository Biospecimen" . "protein" . "https://spdx.org/licenses/$1"^^ . . . . . "tropicalis" . . "https://mmp.sfb.uit.no/databases/marref/#/records/$1"^^ . . "http://purl.obolibrary.org/obo/AERO_$1"^^ . . "GitHub is an online host of Git source code repositories."^^ . . "false"^^ . "rna" . "https://unicarb-db.expasy.org/msData/"^^ . . "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"^^ . "false"^^ . "http://www.w3.org/2003/11/swrl#$1"^^ . . "false"^^ . . . . . . . . . . "enzo" . "0000002"^^ . "A metadata model for Dublin Core metadata"^^ . . . . "omics" . "^[8-9]\\d{3}(/[0-3])?$"^^ . . "N21"^^ . "^[A-Za-z0-9\\/]+$"^^ . . . . "false"^^ . . . . "nlx.qual" . "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . . "https://dialnet.unirioja.es/servlet/revista?codigo="^^ . "^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . . "false"^^ . . . . . "https://www.ebi.ac.uk/pdbe/entry/emdb/"^^ . . . "false"^^ . . "MFCD00011659"^^ . "http://ascl.net/$1"^^ . . "false"^^ . "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS."^^ . "^\\d+$"^^ . . . . . "ontology" . "000059"^^ . . . . "gsfa" . . . . . . "http://planttfdb.cbi.pku.edu.cn/tf.php?uid="^^ . . . . . . . "phenotype" . . "^\\S+$"^^ . . "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"^^ . . . "kim.schularten" . . . . "phosphopoint.protein" . "Homeodomain Research" . . "vcell"^^ . . "chemistry" . . . "^\\d{7}$"^^ . . . "AnVIL DRS" . . . . . . . . "decides"^^ . . . . . "genome" . . "pepbank" . . . . . "functional genomics" . . . . "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/"^^ . . . "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$"^^ . "biology" . "Novus Biologicals" . . "language" . . "DBCOND0066902"^^ . "Lars Eisen" . . "http://purl.obolibrary.org/obo/ONTONEO_"^^ . "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString="^^ . . . . "false"^^ . . "^\\d+$"^^ . . . "Tom Gilbert" . . . . "http://publications.europa.eu/resource/dataset/"^^ . . "AntiBody Sequence Database" . . "false"^^ . . . "false"^^ . . . . "ontology" . "^\\d{7}$"^^ . . "1001"^^ . "life cycle" . "Horizon Discovery cell line collection" . "https://odc-tbi.org/data/$1"^^ . . . . "semantic web" . . . . "http://purl.obolibrary.org/obo/ZFA_"^^ . . "CHEBI" . . . . . "ohara@kazusa.or.jp" . . . . "inaturalist.user" . "TDWG Taxon Rank LSID Ontology" . "miRBase pre-miRNA" . . . . . . . . "true"^^ . "A collection of ontologies relevant for chemistry.\n\nThe NFDI program deploys a [custom instance](https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1) of the Ontology Lookup Service (OLS) that provides the ontologies in this list.\n\nA further analysis of the metadata landscape of the ontologies in this list can be found [here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat).\n\nOntoCompChem and OntoKin appear on the NFDI4Cat list but have not yet been registered in the Bioregistry because the resources are missing/incomplete such that they do not meet minimum Bioregistry metadata standards. These might be added in the future if additional metadata can be found." . . . . . "https://massbank.jp/MassBank/RecordDisplay?id="^^ . "sonia.balyan@ibdc.rcb.res.in" . . . "multicellds.snapshot" . . . "false"^^ . . "life science" . . . . "false"^^ . . "http://purl.obolibrary.org/obo/IAO_$1"^^ . "cbioportal" . "ncats.drug" . "http://purl.obolibrary.org/obo/PATO_"^^ . . . . . . "NFDI4Culture Metadata API" . "supfam" . . "EDAM Format" . . "false"^^ . . "Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle"^^ . . . . "Zenodo" . . "lipidomics" . . . "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."^^ . "https://pubchem.ncbi.nlm.nih.gov/classification/#hid="^^ . . "false"^^ . . . . "http://www.daml.org/2003/01/periodictable/PeriodicTable#$1"^^ . . "^[a-zA-Z0-9_-]{3,}$"^^ . "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."^^ . "false"^^ . "Identifiers for chemicals used as solvents in SupraBank"^^ . . "false"^^ . "agriculture" . "eroshkin@burnham.org" . . . . "interfil" . . . "false"^^ . "https://bioregistry.io/spike.map:"^^ . "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_"^^ . . "organic chemistry" . . "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."^^ . . . . "pandura@mrc-lmb.cam.ac.uk" . "cohesindb.gene" . . . . "https://ensaiosclinicos.gov.br/rg/"^^ . "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"^^ . "https://www.ebi.ac.uk/interpro/entry/antifam/$1"^^ . . . "https://data.gesis.org/gesiskg/schema/$1"^^ . . "blast" . "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales. This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 894215."^^ . . . . "http://www.radiomics.org/RO/"^^ . . . . . "disease phenotype" . . . "https://precision.fda.gov/uniisearch/srs/unii/"^^ . . . _:Nb2862f37c4784127bdc22eaf7bb6b0a6 . "Five Stars of Online Research Articles Ontology" . . . . "A UUID for an open educational resource indexed in the Data Liteacy Alliance (DALIA) web application"^^ . "opb" . . . "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI)."^^ . . . . . . . . "genetics" . . "tahe" . "resource metadata" . . . "ontology" . . "genetic disorder" . . . "2h6o"^^ . "protein" . "EndlessForms Studio Graphic" . "Gene Ontology Rules" . "rnao" . . "true"^^ . . . "ajacobs@cas.org" . "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^ . . "biopixie" . . . . . "allele" . . . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . "0005147"^^ . . . "Geonamaes" . . . . . . . "false"^^ . . . . . "neuroscience" . . . . "Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID]"^^ . "ec-code" . . . "peteremidford@yahoo.com" . "^PTM-\\d{4}$"^^ . "phenotype" . . "WGS84 Geo Positioning" . _:N1d785bfb0097444c98bd8c0a54ebdb63 . . "60025709"^^ . "http://www.ncbi.nlm.nih.gov/clinvar?term="^^ . . "rx00408"^^ . . . . "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid="^^ . . "animal husbandry" . . . "interaction" . . . "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No="^^ . "loc.relator" . "Competence Ontology" . . "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."^^ . "FamPlex" . . "https://clinicalgenome.org/affiliation/$1/"^^ . . "https://www.rrrc.us/Strain/?x="^^ . . "chemistry" . . . "dpvocab" . "M58335"^^ . "true"^^ . . . "SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.)."^^ . "life science" . "^\\d+$"^^ . "false"^^ . "dwelter.ontologist@gmail.com" . . . . . . . . . . . . . "C00000001"^^ . "https://data.chembiosys.de/institutions/"^^ . "https://www.probes-drugs.org/compound/$1"^^ . . . . . "sequence" . . . "mmmp.biomaps" . "organ" . "obo" . "^\\w{14}$"^^ . . . "Virtual Fly Brain" . . "insertion" . . . . . . "Sorghum ontology" . . "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."^^ . . . . "Sabrina@tislab.org" . . . . "mutant" . "false"^^ . . "functional genomics" . . "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database."^^ . "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"^^ . "proteins" . _:N8feab9e44e98445393aad2ffd0819fe6 "Hossein Beygi Nasrabadi" . . . "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . . . "10153"^^ . . . . . . . . . . "Mobilome Ontology" . . "omon" . . . "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms."^^ . "homologous" . "Cardiovascular Disease Ontology" . "Coconut ontology" . "Be"^^ . "^\\d{6}$"^^ . . . "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . . . . . "ardan@ebi.ac.uk" . . "Virus Pathogen Resource" . . . . . "obo" . . . "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . . . . . . . "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^ . . "https://www.kazusa.or.jp/huge/gfpage/"^^ . . "kegg.disease" . . "00000001"^^ . . . "Vertebrate Gene Nomenclature Committee" . "ontology" . "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . . "lgai.cede" . "0000061"^^ . . . . . . "spike00001"^^ . "https://www.ebi.ac.uk/chembl/id_lookup/$1"^^ . . . . . "transcriptomics" . . "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors."^^ . . . . "false"^^ . "https://w3id.org/gaidet/$1"^^ . . . "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs."^^ . "0000001"^^ . . "^IS\\w+(\\-\\d)?$"^^ . "154022"^^ . "rna" . . "chris.overall@ubc.ca" . "https://herv.img.cas.cz/s/"^^ . "http://www.kegg.jp/entry/"^^ . . . . . . . "true"^^ . "^\\d+$"^^ . . . . "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^ . "1466"^^ . "topics" . "atmospheric science" . . "^\\d+$"^^ . "Identifiers for proposals/projects at the Joint Genome Institute"^^ . "teddy" . "Richard John Roberts" . . . . "oryzabase.strain" . . "33"^^ . . . "genepio" . . "Livestock Breed Ontology" . . "computational biology" . "molecules" . . . . . . . "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."^^ . "https://dbpedia.org/ontology/$1"^^ . "competence" . . . "https://db.idrblab.net/ttd/data/drug/details/"^^ . . . "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."^^ . "http://purl.obolibrary.org/obo/VSAO_$1"^^ . "Systems Biology Ontology" . . . . . "protein" . "bioinformatics" . . . . "ASPL0000349247"^^ . . . . "Ontology of Core Data Mining Entities" . . . . "CIP - potato ontology - december 2018"^^ . . "ecology" . . . . . . . . . "true"^^ . "http://purl.obolibrary.org/obo/COVIDO_$1"^^ . "Pfam protein family" . . . . "^ZDB\\-\\w+\\-\\d+\\-\\d+$"^^ . "3851"^^ . . . . . . . "Yvonne Bradford" . "https://www.cytion.com/"^^ . . . "j.harry.caufield@gmail.com" . "pathology" . "false"^^ . . . "false"^^ . . . . . . "false"^^ . . "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^ . . "William R. Sellers" . . . . . "false"^^ . . "ontology" . . . . . . . . "http://www.receptors.org/nucleardb/proteins/$1"^^ . "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID="^^ . . "Sebastian Lobentanzer" . . . . "false"^^ . "metanetx.chemical" . . "life science" . "ncrna" . "^(ENSFM|ENSGTV:)\\d+$"^^ . "dlxc" . . . "co_347" . . . . "http://purl.obolibrary.org/obo/TTO_$1"^^ . . . "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."^^ . . . "organism supplier" . . . . "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."^^ . "AD834"^^ . "Human Proteome Map Peptide" . . . "http://purl.obolibrary.org/obo/CHEMINF_"^^ . . . "chromium"^^ . . . . "https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/"^^ . . "co_345" . . . . . "Cell line collections (Providers)"^^ . . "false"^^ . . "The Echinoderm Anatomy and Development Ontology" . "BlastRule" . "glycomedb" . "OntoDM-core defines the most essential data mining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. (from abstract)"^^ . . . . . "false"^^ . . . . "http://purl.obolibrary.org/obo/GALLONT_$1"^^ . . "http://purl.obolibrary.org/obo/MFOMD_"^^ . . . . . . . "false"^^ . . . "sickle cell disease" . . . . . "4623"^^ . . "325.4"^^ . "francesco.vitali@ibba.cnr.it" . . "http://data.europa.eu/esco/isco/$1"^^ . . . . . "Lehrplan Ontology" . . "https://schema.org/"^^ . . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/SPD_$1"^^ . "andreas.ruepp@helmholtz-muenchen.de" . "1"^^ . . . . . . . . "ggplot2"^^ . _:N72e9805822a84a57af392e18424ae7e5 "João Paulo A. Almeida" . . . "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . . "spradling@ciwemb.edu" . "http://www.phosphosite.org/proteinAction.do?id="^^ . . . "mutant mouse strain" . "medgen.gtr" . . "300108/p3934_A-172"^^ . . . . . "genomics" . . . . "plant anatomy" . . . . . . . "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."^^ . . . . . . "Human BioMolecular Atlas Program Sample" . . . . . "structure" . "false"^^ . . . "0010039"^^ . "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)." . . . "daniel.gautheret@u-psud.fr" . . "MolBiC Compound" . . . . . . . "MESHC" . . . . . . "HSALNG0006197"^^ . "proteomicsdb.protein" . . "https://www.ebi.ac.uk/biomodels/$1"^^ . "https://www.flymine.org/come/entry?gn=$1"^^ . "PSI Extended File Format" . . "aftol.taxonomy" . . . . . . . "Ontology for PREMIS 3, the international standard for metadata to support the preservation of digital objects and ensure their long-term usability."^^ . "Dynamic Ecological Information Management System - Site and Dataset Registry - Sensor" . . . "ontology" . "000204"^^ . "^CDBG000\\d{5}$"^^ . "chemical" . . . "oharb@pcbi.upenn.edu" . . . "00000105"^^ . "false"^^ . "helpdesk@cropontology-curationtool.org" . "xmetdb" . "ontology" . . . "http://purl.obolibrary.org/obo/FOVT_$1"^^ . "biomedical science" . . "hbvar" . "cio" . "dialnet.journal" . "https://www.ebi.ac.uk/pride/archive/projects/"^^ . . "dna" . "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . . "authorList"^^ . "TRQ"^^ . "coconut" . "Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog."^^ . . "false"^^ . "^\\d{7}$"^^ . . . . "data science" . . "^(ev\\:)?E\\d+$"^^ . . . "^(?:[a-zA-Z]+\\/)?[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . "ehda" . "PIR Superfamily Classification System" . "0000006"^^ . . . . . "http://purl.obolibrary.org/obo/COVOC_"^^ . . . "Database of structurally defined protein interfaces" . . . . . . . "^FR\\-FCM\\-\\w{4}$"^^ . . . "http://kgi.services.base4nfdi.de/entity/$1"^^ . . "ontology" . . . . . "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"^^ . "http://bigg.ucsd.edu/models/universal/metabolites/"^^ . . "https://cropontology.org/rdf/CO_336:$1"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_dys_"^^ . . "phylomedb" . "^[a-z0-9\\_]+$"^^ . "https://bartoc.org/en/node/"^^ . . . . . . "http://emmo.info/emmo#EMMO_"^^ . . . "0000079"^^ . "http://biohackathon.org/resource/faldo#$1"^^ . . . "^ENSG\\d{11}$"^^ . . "MetaNetX chemical" . "gene" . "IEEE Xplore document ID" . . "A database containing predicted viral miRNA candidate hairpins."^^ . . . . . . "insdc.cds" . "http://purl.obolibrary.org/obo/ORNASEQ_"^^ . . . . "PolBase" . . . . . . "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . . "molecular biology" . "semapv_voc" . . . . "An _gentle_ implementation of the Unified Foundational Ontology (UFO), which is an upper level ontology like BFO that is concerned with e.g. expressing temporal relationships between events."^^ . . "GrainGenes reference" . . "Ath_AT1G01030.1"^^ . "umls.aui" . . . . . . . "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . "asin" . "^\\d+$"^^ . . . . . "hospital" . . "EAWAG Biocatalysis/Biodegradation Database enzyme" . . "CAMEO Chemicals ID" . "github.issue" . "false"^^ . . . "Immune Epitope Database Receptors" . . . . . . . . "genetic code" . . . . "false"^^ . "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease."^^ . "^DG\\d+$"^^ . "false"^^ . . . . "false"^^ . "Alvis Brazma" . . . . "protein" . "2"^^ . "life science" . "false"^^ . "NHMRC Australian PhenomeBank" . . . "preclinical studies" . . . "false"^^ . "Christophe Dunand" . . . . . . . . . . "protein" . "obi" . "http://purl.obolibrary.org/obo/EHDAA_"^^ . "Vertebrate skeletal anatomy ontology."^^ . . "http://purl.obolibrary.org/obo/MA_$1"^^ . "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . . "Evan Patterson" . . "person" . "^[A-Za-z0-9]+$"^^ . . . . . "pubchem.substance" . . "dg.4503" . "biology" . . "nif.dysfunction" . "togoid" . . "domain" . "hölzel" . . . . . . . . . . . . . . . . . "general & upper" . . . "false"^^ . . . . . . "IUPAC Gold Book Compendium of Chemical Terminology" . . "annotation" . "pscdb" . "^XB\\-\\w+\\-\\d+$"^^ . . . . . "https://w3id.org/kim/isced-2011/level$1"^^ . . "gaidet" . . . . "Lozana Rossenova" . "faseb list" . "The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada."^^ . "Namespace"^^ . . "taxonomy" . . "protein" . . . . . "Plant Gall Ontology" . "false"^^ . "Stefanie Seltmann" . . "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."^^ . . . . . "dan5@georgetown.edu" . . . "https://www.biorxiv.org/content/10.1101/$1"^^ . . "classification" . . . . "vt" . "0000001"^^ . . . . _:Nebc150d4fddc45f6ac674abbf114e164 "Natalie L Catlett" . "https://smc.jgi.doe.gov/sources/$1"^^ . "agriculture" . "^\\d{7}$"^^ . "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/"^^ . "https://biokb.lcsb.uni.lu/fact/$1"^^ . . . . "CSP2005" . . . . . "LDPC0032"^^ . "WikiPathways" . . "InChIKey" . "disease" . . . . . "ontology" . . . . "false"^^ . "0000015"^^ . . . . . "CAA71118.1"^^ . "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology."^^ . "0000685"^^ . "Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science."^^ . . "biology" . . . . . . "FishBase" . . "pathway" . "ontology" . . "false"^^ . . . . . . . "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot="^^ . . "false"^^ . . . . . "biology" . "^KW-\\d{4}$"^^ . "^\\d{7}$"^^ . . . . "rrid" . . "The State of Alaska's Salmon and People Ontology" . "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."^^ . "WikiPathways Ontology" . . "false"^^ . . "false"^^ . . "Nucleotide" . . "ICD11" . "The ALlele FREquency Database" . . . "http://www.alanwood.net/pesticides/$1.html"^^ . . . . . "National Microbial Pathogen Data Resource" . . . . . "^\\d+$"^^ . . . . . "genome" . . . . "https://cropontology.org/rdf/CO_358:"^^ . . . . . . "false"^^ . . . "structure" . "http://neuromorpho.org/neuron_info.jsp?neuron_name="^^ . _:Nee497bc5e1e74254bf03610e9dc5dc0f . . "http://edamontology.org/topic_$1"^^ . "Medical Dictionary for Regulatory Activities Terminology" . "Hs635"^^ . . . . "NP_003997.1:p.Trp24Cys"^^ . "^P\\d+$"^^ . "^\\d+$"^^ . . . . "false"^^ . "phenotype" . . "Langua aLimentaria Thesaurus" . "wuc@udel.edu" . "Dictyostelium discoideum phenotype ontology" . . . "http://purl.org/nemo/gufo#$1"^^ . "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . . . "Network Data Exchange" . . . . . "https://bioregistry.io/lrg:"^^ . . . . "A_24_P98555"^^ . "data analysis" . . _:N05c9d168646a4a7a8670b28e92dd190e "af8d@nih.gov" . . . . "^B\\d+$"^^ . . "pathway" . . "9606"^^ . "T039"^^ . . "false"^^ . . "https://ice.ntp.niehs.nih.gov/api/v1/search?chemid="^^ . "neuroscience" . "Gramene QTL" . . . . . . "918902"^^ . "https://drugs.ncats.io/drug/$1"^^ . . . . . . "molbic.compound" . . . "has alternative prefix" . . . "martin.pospisek@natur.cuni.cz" . . "^\\d+$"^^ . "^ECMDB\\d+$"^^ . . . . . "^\\d+$"^^ . "Hugh.Shanahan@rhul.ac.uk" . "http://purl.obolibrary.org/obo/ORNASEQ_$1"^^ . . "NCIt" . "https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?curie=NMR:"^^ . . . "life-cycle" . "^NPA\\d{6}$"^^ . "pubchem.assay" . "pathway" . "scopus.author" . "molecular" . "Ontology of Microbial Phenotypes" . . "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . . . . . "biomedical science" . "ensembl.metazoa" . . . . . . . "drugbank.target" . "https://www.kegg.jp/entry/"^^ . . . . . "isced1997" . . "nmrshiftdb2" . . . . . "https://cropontology.org/rdf/CO_330:$1"^^ . "ctcae" . . "raymond@caltech.edu" . "ttd.drug" . "adriano.rutz@ik.me" . . . . "https://assets.nemoarchive.org/$1"^^ . . . "pba" . . . "biomedical" . . "^\\d{8}$"^^ . . . . . . . "https://www.loc.gov/preservation/digital/formats/fdd/$1"^^ . "journal" . . . . . "true"^^ . "false"^^ . . . "https://deims.org/"^^ . . . "false"^^ . . . "http://stitch.embl.de/interactions/"^^ . . . . "^T3D\\d+$"^^ . "^\\d{7}$"^^ . . . . . "http://purl.org/spar/bido/"^^ . "true"^^ . "ontology" . . "EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)"^^ . "^UPI[A-F0-9]{10}$"^^ . . . . "false"^^ . . . "false"^^ . . . "glyconavi" . "protein" . "Erik van Nimwegen" . . . . . "http://purl.obolibrary.org/obo/ATO_$1"^^ . . . "ontology" . "^[0-9]+:[0-9]+$"^^ . . . "sleep" . "AY321118"^^ . . "ClassyFire" . . "9-1-1 Complex"^^ . "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."^^ . "iot" . "COG_Cluster" . "Gene Ontology Causal Activity Model" . . . "false"^^ . . "peptideatlas.peptide" . . "zhu@iastate.edu" . . . . . "lipidmaps" . . . . . "false"^^ . "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1"^^ . . . "Gene Product Information Schema" . "http://www.imgt.org/ligmdb/view?id="^^ . . . . "false"^^ . . "false"^^ . "proteomics" . . "Publishing Roles Ontology" . . "ontology" . . "business administration" . . . . "xyz19940216@163.com" . . . . . . . . . . . . . "diagnosis" . . . . . "^A(N|O)\\d+$"^^ . . . "phylogenomics" . "sstoss" . . "Southwestern Environmental Information Network" . . . . . . "SIDM01262"^^ . "false"^^ . . "^\\d{1,5}$"^^ . . . "biology" . . . . "^[0-9a-z]{24,24}$"^^ . . . . . . "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."^^ . . . "false"^^ . "false"^^ . "c"^^ . . "Bgee gene" . "dsmz_mutz-id:ACC 291"^^ . . . "people/11035"^^ . . "CADAFLAT00006211"^^ . "The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure."^^ . . . . "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information."^^ . . . . . . "false"^^ . . . . "life science" . . . . . "^GLDS-\\d+$"^^ . "^\\d+$"^^ . . . . "80001"^^ . . . . "http://ecoliwiki.net/colipedia/index.php/$1:Gene"^^ . "https://github.com/information-artifact-ontology/IAO/issues/$1"^^ . . . "matthias.samwald@meduniwien.ac.at" . . . . "false"^^ . "genomics" . . . . . . "false"^^ . "https://civicdb.org/links/variant_group/"^^ . . . "inchi" . "d.a59037e8"^^ . . "^\\d+$"^^ . . . . . . "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."^^ . "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."^^ . "http://rdf-vocabulary.ddialliance.org/lifecycle#"^^ . . . . . "Milton H. Saier, Jr." . "oma.grp" . . . . . "snoRNABase" . . . . . . . . "Scopus affiliation ID" . . "skos.thes" . . "^\\d{7}$"^^ . "M1"^^ . . . . "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid="^^ . . . "botany" . . . . "NIF Standard Ontology: External" . . "metadata" . "34665743"^^ . . . "^P\\d{5}$"^^ . . "exac.variant" . "Liz Allen" . "swrl" . . "18125"^^ . "doqcs.pathway" . . . "^[1-9]\\d*$"^^ . . . . . . "cnt" . . . "^\\d+$"^^ . "false"^^ . "https://pharmacodb.ca/datasets/$1"^^ . . . . . "life science" . "1"^^ . "https://bioschemas.org/profiles/$1"^^ . . . . . . . . . "data analysis" . "false"^^ . "MTBLS1"^^ . . "^\\d{7}$"^^ . "Identifiers.org Ontology" . . . . "obo" . . "false"^^ . . "^\\d+$"^^ . "Identifers for natural products isolated or mutasynthesized by bacteria of the genus Streptomyces."^^ . . . . . . . . . . . "http://kgi.services.base4nfdi.de/entity/"^^ . "true"^^ . "false"^^ . . . . . "^(\\wT?)?\\d{5}$"^^ . "structural bioinformatcs" . . . . . "OrthoDB" . "skos-xl" . "microbiology" . . . "false"^^ . "neurobiology" . . "biospecimen" . "anatomy" . . "Pre-K"^^ . . " http://edamontology.org" . . . . . "lbctr" . . "true"^^ . . . . "gaoj@mskcc.org" . . "https://cran.r-project.org/web/packages/$1"^^ . "http://www.pantherdb.org/panther/family.do?clsAccession=$1"^^ . . "http://rdfs.org/sioc/actions#"^^ . "data analysis" . . . . . . . . "life science" . "bel" . "Adrien Coulet" . . "ontology" . . . . "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^ . "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^ . "^[1-9]\\d*$"^^ . "sustainability" . . . . . "^\\d{7}$"^^ . "Ontology of Organizational Structures of Trauma centers and Trauma systems" . "ontology" . "true"^^ . "uniprot" . . . "srvoss@uky.edu" . "https://eol.org/pages/$1"^^ . . . . "http://usefulinc.com/ns/doap#$1"^^ . . "perkinelmer" . . . . . . . "http://purl.obolibrary.org/obo/OMRSE_$1"^^ . _:N410f639c709b4c8d9eb5be58cfdf385c . . "Tissue List" . . . "orthology" . "http://purl.obolibrary.org/obo/ZFA_$1"^^ . "research" . . . "https://lobid.org/gnd/$1"^^ . . . . "euvoc"^^ . "https://permalink.obvsg.at/"^^ . "4145692"^^ . . . . . . "https://www.abmgood.com/search?query="^^ . . . . "wwpdb" . . "linked open data" . . . "gene" . "SNR17A"^^ . "life science" . "https://web.expasy.org/abcd/ABCD_$1"^^ . . . "chemistry" . . "ontology and terminology" . . "https://www.e-cyanobacterium.org/bcs/entity/"^^ . . . . "Damian Smedley" . . . "^RID\\d+$"^^ . . . "true"^^ . . "https://cbcb.cdutcm.edu.cn/AGD/plant/details/?id="^^ . "reo" . "reaction data" . . "biomedical science" . "attribution" . . "http://purl.obolibrary.org/obo/OHPI_"^^ . "functional genomics" . . . . "The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number. [wikipedia]"^^ . "https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip"^^ . _:Nfe756a5fb0a64141bd9927ac3b82174b . . . . . . . "Molecular Design Limited Hash" . "small molecule" . . "ontology" . "false"^^ . . "faseb list" . . . . "true"^^ . . "Toshiaki Katayama" . . . "Peroxibase" . . . . . . . . "http://purl.org/vocab/frbr/core#$1"^^ . . . "0000062"^^ . "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders"^^ . . . . "ontology" . . "^.*/.*$"^^ . . . . . . . . . "ontology" . . "https://www.iana.org/assignments/media-types/"^^ . "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."^^ . . "^UCR\\d{5}$"^^ . "false"^^ . . . . "false"^^ . . "The Genetic Testing Registry 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."^^ . "The Euvoc ontology, published by the Publications Office of the European Union, supports the development of authority tables (Name Authority Lists or NALs), Eurovoc and EU corporate datasets. It contains a set of classes and properties enabling all the information to be expressed in multilingual format. It helps define relationships between terms and concepts across multiple domains, supporting interoperability and standardization across European Union documentation and databases. It also defines a set a commonly use properties (i.e: start date, end dates, status), and supports the reusability on common data (currencies, languages, countries).\n\nThe Euvoc ontology is maintained by the Publications Office of the European Union and disseminated on the EU Vocabularies website."^^ . . "proteomics" . . "false"^^ . . . . . . . "person" . "cell cycle" . . "disease" . "Ivan Herman" . . . "A database-specific registry supporting curation in the Gene Ontology" . . "Nematode & Neglected Genomics" . "https://tools.ietf.org/rfc/rfc$1"^^ . . . . "vivo" . . "Beilstein" . "true"^^ . "true"^^ . "obo" . . . "John L. Markley" . . "go-term enrichment data" . . . . "false"^^ . . . . . "^\\d+$"^^ . "ssbd.project" . "pathology" . . . . . . . . "DBCAT000600"^^ . "classification" . . "transcript" . "^\\d{8}$"^^ . "go.chebi" . "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1"^^ . . . . . . . . . "tto" . . . . "^\\w+(\\.\\d+)?(\\.\\d+)?$"^^ . "co_337" . "false"^^ . "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."^^ . . . . . . "life science" . . _:Nbbeee860628a45b49201041d290f1664 "Evangelos Katis" . . . . . . . _:N4654dbf5c0074a959f1cf5467bab33e1 "Jonathan Bard" . . "https://ontology.iedb.org/ontology/ONTIE_"^^ . "http://www.w3.org/2007/05/powder#$1"^^ . "ised" . . "dsm4" . "earth science" . . . . . "structure" . "biomedical science" . "^\\d{7}$"^^ . . "ontology" . . . . "00000085"^^ . _:N1f4a0c25aeec4f6ebb4e66593f74a4e2 "Caty Chung" . . "biodiversity" . . . . . "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."^^ . . . . . "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^ . . "ontology" . . . "dna" . "A vocabulary about species to support the environmental research community in Arizona and New Mexico"^^ . . "Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database"^^ . "biomedical science" . "^\\d{7}$"^^ . . . . "Bioregistry" . "12"^^ . . "Peter Midford" . . "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data."^^ . "metascience" . . . "00000098"^^ . . "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^ . . . . "medicine" . "Plant Environment Ontology" . "^\\d+$"^^ . "osf" . . . . . . . . "Intelligence Task Ontology" . . "M0001"^^ . "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."^^ . . "https://www.kyinno.com/?s=$1"^^ . . . . . . . . "false"^^ . "International Traditional Medicine Clinical Trial Registry" . . "pathway" . "taxon" . . . . . . . . . . . . . . "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^ . "abandrowski@ncmir.ucsd.edu" . . . . . "C_AA001108.1"^^ . "has reviewer" . . . . "^\\d+$"^^ . . . . . "http://www.ontodm.com/OntoDM-core/OntoDM_$1"^^ . . "^\\d+$"^^ . . . . . "unirule" . "44259"^^ . "true"^^ . "UniProt Chain" . . . "http://www.bioinfo.org/NONCODEv4/show_rna.php?id="^^ . . . "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . "blast" . . . . . . . . . "https://coicatalogue.uc.pt/index.php?t=specimen&COINumber="^^ . "https://www.scopus.com/authid/detail.uri?authorId="^^ . "repository" . . "false"^^ . . . . . . "Small Molecule Pathway Database" . "genome" . . . "metadata" . "^\\d{7}$"^^ . "AlignmentObject"^^ . . "false"^^ . "Shuichi Onami" . . "L000001"^^ . . . . . . . "nepomuk.nco" . "false"^^ . "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."^^ . "Alan Rubin" . . . . "immunology" . "https://www.storedb.org/store_v3/download.jsp?fileId="^^ . "Sri Lanka Clinical Trials Registry" . "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."^^ . "https://cropontology.org/term/$1:$2" . . "^\\d+$"^^ . . . "Maciej Antczak" . . "^\\d+$"^^ . . . . . "cordis.project" . . . . . . "Domain Resource Application Ontology" . "h.doerpholz@fz-juelich.de" . . "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." . . "omics" . . "epio" . "medicinal chemistry" . . . . "AA0001"^^ . "https://www.uniprot.org/locations/$1"^^ . "labo" . . "0000066"^^ . . . . "http://uri.neuinfo.org/nif/nifstd/nifext_"^^ . _:Nb05f67102810430c80a5c82956a65323 "Allotrope Foundation" . "antibodies" . . "ontology" . "TF0001053"^^ . "false"^^ . "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^ . . . . . . . . . "https://civicdb.org/links/diseases/"^^ . "classification" . . . . . "false"^^ . . "https://scicrunch.org/resolver/RRID:NXR_$1"^^ . "laia.subirats@gmail.com" . . "A0014"^^ . . "patricia.siguier@univ-tlse3.fr" . "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]" . "Mutant Mouse Resource and Research Centers" . . . "miro" . . . . "ontology" . . . . . . . "y3ax-8bq3-60"^^ . "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."^^ . . "ontology" . . . . . . . . . . . "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded."^^ . . "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . . . . . . . . "^\\w+$"^^ . . . "ontology" . . . . . "g.gkoutos@bham.ac.uk" . . . . "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^ . . "chemspider" . . "Philippine Health Research Registry" . "0000000"^^ . . "sasap" . . . "gtr.test" . "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . "ICTV19990991"^^ . "false"^^ . "biosamples" . "false"^^ . . "^\\d{7}$"^^ . . . . "structure" . . "^S\\d+$"^^ . . . . . "https://www.cameo3d.org/sp/targets/target/"^^ . . . . . "CategorialBibliometricData"^^ . . . . "Identifiers for the binding targets of synthetic binding proteins (SBP), describing the specific molecules or complexes that SBPs interact with for their intended applications"^^ . "Computational Chemistry Ontology" . "cdt" . "bykdb" . . . "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)"^^ . . . . . . "The BioDeep database is a comprehensive database of metabolite information in living organisms: by aggregating metabolite information from multiple public databases and large-scale natural language text mining work, we have built a large scale knowledge network for biological knowledge interpretation. By using the BioDeep database, it is possible to query such large scale metabolic knowledge network."^^ . . . . . . . . "https://www.nextprot.org/term/$1"^^ . . . . . "12039302"^^ . . . . . "protein families" . . "spp" . "Gene Ontology" . . . . "http://purl.obolibrary.org/obo/CDNO_$1"^^ . . "protein" . "genomics" . . "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."^^ . "false"^^ . . . "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^ . "Protein Model Database" . "careerPrizeMoney"^^ . "mbrochhausen@uams.edu" . . . . "life science" . . . "0000858"^^ . . "http://n2t.net/ark:$1"^^ . "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"^^ . "3532759"^^ . . "000254"^^ . . "ricenetdb.mirna" . . "ChemBioSys Institution" . "false"^^ . "biochemistry" . "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."^^ . . . "Carsten Linder" . . "Kangho Ji" . . . "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^ . "Database of small human noncoding RNAs" . "http://purl.obolibrary.org/obo/AEO_$1"^^ . . . . "medicinal chemistry" . . . "life science" . "obo" . . "development" . . . . . "wd" . "subject agnostic" . . "semion" . . . "fdb8a927-45c3-48b7-9743-cbb5e16837fa"^^ . "obo" . . . . _:N94c2ea8167254c9a89ccab8a27c6161e "NLM Customer Service" . . "Pointer"^^ . . . "http://dicom.nema.org/resources/ontology/DCM/"^^ . "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . "protein" . . . . . "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."^^ . . "cordis.article" . . . . . . "biology" . "ko00002"^^ . . "false"^^ . "lipidbank" . "true"^^ . "false"^^ . "https://www.wwpdb.org/pdb?id=$1"^^ . "hydrogeology" . "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1"^^ . "Mingxun Wang" . . "http://en.wikipedia.org/wiki/"^^ . . "An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date."^^ . . "Agent"^^ . . . "General Multilingual Environmental Thesaurus Theme" . . . . . "MolMeDB" . "biology" . "https://portal.hubmapconsortium.org/browse/collection/"^^ . "gene" . . "false"^^ . "^\\d{7}$"^^ . . . . . "obo" . "false"^^ . . "https://uts.nlm.nih.gov/uts/umls/concept/"^^ . "https://purl.dataone.org/odo/MOSAIC_"^^ . . . "vaccine" . . "rna" . "foaf" . "^[-\\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)$"^^ . . . . . . . "small molecule" . . . . . . . . "ricegap" . . "developmental biology" . "resource metadata" . "Olfactory Receptor Database" . "life science" . . . . . . . "http://www.w3.org/2003/g/data-view#$1"^^ . . "false"^^ . _:N2d5072dd9d104290839761e23aeca8f0 . . . "computational chemistry" . "preclinical studies" . . _:N11dd3fa437e74139a6d614b106621ce9 . "goccid" . . . . "unii" . . . "emapa" . . "false"^^ . "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation."^^ . . . . . "false"^^ . . "0000093"^^ . "^([hm]\\_)?\\w+Pathway$"^^ . "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."^^ . . . "https://bioregistry.io/genpept:"^^ . . "KEGG pathway" . . . . "http://tolweb.org/$1"^^ . . "GOLD genome" . "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications."^^ . "A vocabulary for embedding provenance metadata into webpages via RDFa"^^ . "phenomics" . "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . . . . . . . "wikidata.property" . . . . "ecso" . . "^\\d+$"^^ . "false"^^ . "^\\d{7}$"^^ . "ontology" . "Selventa Families" . . . . "neurobiology" . . . . . . . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . "https://bartoc.org/" . . . "http://phenol-explorer.eu/foods/"^^ . . . . "allergome" . "http://purl.org/dc/terms/$1"^^ . "^\\d{5}$"^^ . . . "Unified Foundational Ontology" . . "Sandra Orchard" . "World Wildlife Fund Ecoregion" . . "data schema" . "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."^^ . "Pazar Transcription Factor" . . . "http://bigg.ucsd.edu/models/"^^ . "pictar-vert" . . _:Nb05f67102810430c80a5c82956a65323 . "98346"^^ . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/"^^ . . _:Nea3693d03c2b40ebbbc21a04344079c1 . . _:Nb7e85f58056b4253a68baea08ef24c12 . . "ontology" . "chembiosys.study" . . . "reaction" . "nihreporter.project" . . . "^\\d{7}$"^^ . "biomedical science" . "^PRJ[DEN][A-Z]\\d+$"^^ . . "PrefixOrTermMapping"^^ . . "Homologous Organ Groups" . . . . "http://purl.org/dcx/lrmi-terms/"^^ . "ecyano.model" . . . . "environmental science" . "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."^^ . "Datasets in DEIMS SDR"^^ . . "epigenomics" . "igsr" . . . . "https://bioregistry.io/prints:"^^ . . . . . . "imke.tammen@sydney.edu.au" . "0000080"^^ . "^T\\d{8}$"^^ . "false"^^ . "^\\d+$"^^ . . . "HMDB" . . "OTTHUMG00000169812"^^ . "conferences" . "^MI\\d{7}$"^^ . "contributor roles" . . "ecocyc" . . "life science" . . . . "Bactibase" . . . . "harkemaj@msu.edu" . "Paragraph"^^ . "cells" . "PaxDb Organism" . "http://www.fairsharing.org/ontology/subject/SRAO_"^^ . "https://www.nextprot.org/db/entry/$1"^^ . "^\\d+$"^^ . . . . . "FBdv" . . "Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining basic information on community-related web services."^^ . "^CA\\d+$"^^ . "nmrcv" . "life science" . "nlx.chem" . "http://purl.obolibrary.org/obo/TAXRANK_$1"^^ . . "MaizeGDB" . "^\\d+$"^^ . "Regulatory Elements Database for Drosophila" . . . "neurobiology" . "j.a.moore@dundee.ac.uk" . . "Human Phenotype Ontology" . . . . "http://purl.obolibrary.org/obo/OBI_"^^ . . "interaction" . "false"^^ . "spdx" . . . "CRW_00469"^^ . . . "Gene Ontology Issue Tracker" . "false"^^ . . "AB_262044"^^ . "false"^^ . . "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . "vfdb.genus" . "^\\w+$"^^ . "dbSNP Reference SNP number" . "data management" . . . "subject agnostic" . . . . . "Online Computer Library Center WorldCat" . . "obo" . . . "gnpis" . . . . . . . . . . "https://id.loc.gov/vocabulary/languages/$1"^^ . "obo" . "https://www.abcam.com/$1.html"^^ . . . . . . "MedlinePlus Health Topics" . "PSI-MI" . . . "Maize gross anatomy"^^ . . "gene" . . . . . . . . "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:"^^ . . . . . . . . . "pombase" . "strain" . . . . . . . "https://w3id.org/dpv#$1"^^ . . . "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^ . . . "https://hl7.org/fhir/us/$1"^^ . "prefLabel"^^ . . . "^\\d+$"^^ . "immunogenetics" . "chemistry" . . . . "false"^^ . _:Nba63b9197e1b4f7d9250736af3631bbb . "Digical Object Container Identifier" . "environmental science" . "mouse" . . "HBG004341"^^ . "ontology and terminology" . "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^ . "20021"^^ . . . . . . "true"^^ . "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"^^ . "life science" . . . "false"^^ . . . . "false"^^ . . "mass spectrometry" . . . "false"^^ . . . "^Gm\\d+$"^^ . "sequence" . "3G6A5W338E"^^ . "Anatomical Therapeutic Chemical Classification System" . "Neural ElectroMagnetic Ontology" . "toxicity" . "digital humanities" . "hubmap.dataset" . . . . . . "limore" . "http://purl.org/spar/deo/$1"^^ . . "skosxl" . . . . . . . "chemistry" . . . . . "chemistry" . "Zachary King" . . "Contains identifiers for genes that are part of cohesin regulated CRMs (cis-regulatory modules) from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each identifier represents a single cohesin-related CRM. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information."^^ . . . "bco" . . "Minimal Anatomical Terminology" . . . . . "^DTXSID\\d+$"^^ . . . . "data set" . "Cell Line Ontology [derivative]" . . . "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."^^ . . . . "http://drugcentral.org/drugcard/$1"^^ . . "https://www.eionet.europa.eu/gemet/en/group/"^^ . . "Media Types" . . . . "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."^^ . "Neuronal cell types"^^ . . "http://uri.neuinfo.org/nif/nifstd/sao"^^ . "https://www.disprot.org/"^^ . . . . . . . . "obo" . . . . . . . . "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1"^^ . "http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1"^^ . "medicine" . "obo" . . "https://www.flymine.org/flymine/report/ChromosomeBand/$1"^^ . "42840"^^ . "life science" . "Jawahar Swaminathan" . . . . . . . . . . "metagenomics" . . . . . "molecular interaction" . "bibliometrics" . "^[0-9]+$"^^ . . . . . . . "life science" . "http://purl.obolibrary.org/obo/LPT_$1"^^ . . "false"^^ . . . "http://purl.obolibrary.org/obo/OMIT_$1"^^ . "molecular biology" . . . "sioc.swan" . . . . . . "eukaryotic" . "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . . . "http://purl.obolibrary.org/obo/MIAPA_$1"^^ . "https://www.novusbio.com/products/"^^ . . . . "ontology" . "false"^^ . . "semantic web" . "assay" . . "phenomics" . "http://purl.obolibrary.org/obo/SEPIO_$1"^^ . . . . . "MITE0000001"^^ . . "0000057"^^ . . . . "biomedical science" . . . "false"^^ . "An issue in any public repository on GitHub."^^ . . "molecule" . "deims.taxonomy" . "nkos" . . . "environmental material" . . . . . . . . . "host" . "people" . "regulation" . "https://mged.sourceforge.net/ontologies/MGEDontology.php#"^^ . . . . . . "https://cropontology.org/rdf/CO_337:"^^ . "HMDB00001"^^ . . . . "https://mirgenedb.org/browse?qtype=mgid&org=ALL&query=$1"^^ . . . . . . . "leen.vandepitte@vliz.be" . . "life science" . "nif_subcellular" . "false"^^ . "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . . "earth science" . "obo" . "African Population Ontology" . "ontology" . . "recombinase" . . . . . . . . "VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host."^^ . . . "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^ . . . "proccaserra@gmail.com" . . "phenotypes" . "^\\d+$"^^ . "^S\\d+$"^^ . "This ontology is a formal representation that captures the fundamental concepts and their relationships to one another in the field of curriculum design and implementation of the German school system."^^ . . . "mco" . . . "molbic.protein" . "https://biopragmatics.github.io/providers/peff/"^^ . "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."^^ . "ontology" . . "DateTimeDescription"^^ . . . "https://idr.openmicroscopy.org/search/?query=Name:idr"^^ . . . . . "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code="^^ . "https://bioregistry.io/pscdb:"^^ . "classification" . . "namerxn" . . . . "http://purl.obolibrary.org/obo/PLANA_$1"^^ . . "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . . "kdurante@stanford.edu" . . . . . "bel" . "ontology" . . "small molecule" . . . . "^[A-Za-z0-9]+$"^^ . . . "PharmGKB Disease" . "http://purl.obolibrary.org/obo/HANCESTRO_$1"^^ . . . "https://go.drugbank.com/indications/$1"^^ . . . . . . . "false"^^ . "semantic web" . . "AT1G73965"^^ . "^DIP(\\:)?\\-\\d{1,}[ENXS]$"^^ . . . . "structure" . . . . . . . . "microbiome" . . "MGYG000004903"^^ . . . . . . "SNOMEDCT_US_2019_03_01" . "Human BioMolecular Atlas Program Collection" . "https://bioregistry.io/proteomicsdb.protein:"^^ . "protein" . "^ML\\w+$"^^ . "gene" . "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . "genome" . "Matthias König" . . . "^DB-\\d{4}$"^^ . . "https://www.jax.org/strain/$1"^^ . . "DSMZCellDive" . . . . "Annika Jahnke-Bornemann" . . "gene" . "life cycle" . "^\\d+$"^^ . . . . . . . . . "European Collection of Authenticated Cell Culture" . . "241"^^ . . . "DDB0191090"^^ . "bolton@ncbi.nlm.nih.gov" . "Database of biopesticides maintained by the University of Hertfordshire"^^ . . . "https://data.chembiosys.de/data_files/"^^ . "MultiCellDS Digital snapshot" . . "disease course" . "00005643"^^ . "https://iconclass.org/"^^ . . . "431472"^^ . "http://www.proteinatlas.org/"^^ . _:N1d785bfb0097444c98bd8c0a54ebdb63 "alexey.melnikov@isode.com" . "classification" . . "^(E|D|S)RR[0-9]{6,}$"^^ . . . . "https://graphics.endlessforms.info/unit?id="^^ . . . "glycomics" . . . "false"^^ . . . . "These resources represent software repositories" . . "Sugar Kelp trait ontology"^^ . . "protein" . . . . . "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions."^^ . . "obo" . . . . "annotation" . . _:Ne8f59032a90d4fe18933465e973bd258 . . . . . . "FlyBase Qualifiers" . . "Dimension"^^ . . . . "protein" . . . . . . "Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a"^^ . "https://cropontology.org/rdf/CO_367:"^^ . . . "ontology" . . . . "gnps.task" . . . . . "subject agnostic" . . . "tcb" . "cath.domain" . "obo" . . . "false"^^ . . . "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^ . "ontology" . . . "noncodev3" . . . . "David Osumi-Sutherland" . . . . "Tetrahymena Stock Center" . . "^[a-z_A-Z0-9]+$"^^ . "BP100000"^^ . . "false"^^ . . . . . . "^\\d+$"^^ . "The Statistical Methods Ontology" . . . . . . . "http://purl.obolibrary.org/obo/PGDSO_"^^ . . "go.chemicals" . . "Variation Modelling Collaboration" . "safisher@upenn.edu" . . "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId="^^ . "https://molbic.idrblab.net/data/protein/details/$1"^^ . . . . . . . . "dunand@lrsv.ups-tlse.fr" . . . "hsa-mir-200a"^^ . . . "pathogen" . "Deutsche Sammlung von Mikroorganismen und Zellkulturen" . "emmo" . . . "chemidplus" . . "biomedical science" . . "ontology" . . "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities."^^ . . . "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]"^^ . "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."^^ . "diagnosis" . . "protein" . . . "social and behavioural science" . . . . . . . . "The reviewer of a prefix" . . "rpillich@ucsd.edu" . . . . . "fbrf" . . "GT10"^^ . . "Global Research Identifier Database" . "biomedical science" . . . . . . "ontology" . . . . . "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC="^^ . . . . "false"^^ . . "http://purl.obolibrary.org/obo/TRANS_"^^ . "eagle-i" . . . . "SD00043"^^ . "achcar11"^^ . "22-46615880-T-C"^^ . "mirnao" . . "https://urgi.versailles.inra.fr/gnpis/#result/term="^^ . . "An identifier for a country in numeric format per ISO 3166-1"^^ . "http://purl.obolibrary.org/obo/IDOMAL_"^^ . . "mesh.2013" . . . "^M\\d+$"^^ . . . . "pathwaycommons" . . . "Ontology for Nutritional Epidemiology" . . . "data retrieval" . . "https://www.enzolifesciences.com/"^^ . . . . "addexbio" . . . "Ronald C. Beavis (Ron Beavis)" . . "Gender, Sex, and Sexual Orientation Ontology" . . . "https://scholar.google.com/citations?user=$1"^^ . . "cognition" . . "host" . . "Reagent Ontology" . "http://search.sisuproject.fi/#/variant/"^^ . . . "false"^^ . "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . "http://www.cathdb.info/domain/$1"^^ . "BioTop" . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"^^ . . . . "A study in the ChemBioSys data platform"^^ . . . . . "rdf" . "Locations in DEIMS SDR"^^ . "http://virtualflybrain.org/reports/"^^ . . "true"^^ . . . . . . . "Synapse Data Repository" . . . . "Agronomy Ontology" . "http://purl.obolibrary.org/obo/FOBI_"^^ . . "biomaterial supply resource" . "bkc640"^^ . . . "pride" . . . "disease" . . . . . "subject agnostic" . . . "anatomy" . "false"^^ . "chemical" . . "ChEMBL mechanism" . . "Serhii Nazarovets" . "false"^^ . "RNACentral" . "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^ . "cheminf" . "^\\d+$"^^ . "21723"^^ . . "life science" . "JECFA provides identifiers for flavors, food additives, contaminants, toxicants, and veterinary drugs. Each entry includes chemical details, acceptable or tolerable intake limits, and links to related reports and monographs."^^ . "false"^^ . . . "^\\d{7}$"^^ . . . "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . . . . "biomarker" . "false"^^ . . "MSBNK-IPB_Halle-PB000166"^^ . "https://chem.nlm.nih.gov/chemidplus/rn/$1"^^ . . . . . . . . . "ontology" . "https://biopragmatics.github.io/providers/sdis/$1"^^ . . . . . . . . . . . "genomics" . "David Brodbelt" . . "Christine Orengo" . "Sebastian Koehler" . "life science" . . . "NIF Gross Anatomy" . . . "CODATA Research Data Management Terminology" . . . . "dmendez@ebi.ac.uk" . "ontology" . . . "https://cells.ebisc.org/"^^ . . . "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information."^^ . "genomics" . . "Colin Groom" . . . . . . "bdgp.insertion" . . . "gene" . "^[A-Za-z_]+$"^^ . "BibliographicRecord"^^ . "https://www.genenames.org/data/genegroup/#!/group/$1"^^ . "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . . . . . . . "00005254"^^ . "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId="^^ . . . . . "fdd000613"^^ . . . . "ontology" . "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . . . . . "Jakob Voß" . . "http://thesauri.dainst.org/en/concepts/"^^ . "animal organ development" . "life science" . "obo" . "subject agnostic" . "false"^^ . . . . "genomics" . "gc" . "hc.npn" . "FDA Submission Tracking Number" . "http://bitterdb.agri.huji.ac.il/Receptor.php?id="^^ . . . "false"^^ . "gas chromatography" . . "phenotype" . . . . . _:N6c77afbbeff44c7997cc11c8306e2d79 "evorao@evora-project.eu" . "angiology" . "repeatsdb.protein" . . . . . "hesa" . . "Decentralized Identifier" . "environmental material" . . "19803"^^ . . . . "biomedical science" . . . . "Paleobiology Database" . . . . . "subject agnostic" . . . . . . . . "protein" . "life science" . . . "quality" . . . "77"^^ . "BioStudies database" . "^\\d+$"^^ . . "^(\\d|\\w)+-\\d$"^^ . . . . . . "co_338" . . . . "Sequence-Structural Templates of Single-member Superfamilies" . . . . . "https://www.ndexbio.org/viewer/networks/$1"^^ . "^\\w+$"^^ . . "Database of the dielectric properties of biological tissues."^^ . "Glenn King" . "René Ranzinger" . "A0001"^^ . . "ensemblglossary" . "efo" . "botany" . "^[A-Z0-9]{6,7}$"^^ . . . "structure" . "small molecule" . "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . . . "0000010"^^ . "rdb20@pitt.edu" . . . . . "david.wishart@ualberta.ca" . "https://www.linkedin.com/in/$1"^^ . . . . "relations" . . . "false"^^ . . . . . . . . "false"^^ . "The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible ontology describing the functions and actions of biologically important chemicals including primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals. The identifiers in this semantic space correspond to individual chemicals."^^ . . "1664"^^ . . "http://purl.obolibrary.org/obo/GNO_$1"^^ . "http://purl.org/obo/owlEOL_$1"^^ . . . "^MF_\\d+$"^^ . . . . . . "ontology" . . "^\\d{7}$"^^ . "ABC"^^ . "^\\d{7}$"^^ . "^([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+)?(-\\d+)?(#PRO_\\d+)?$"^^ . "false"^^ . "German Federal Ministry of Education and Research Glossary" . . . . "SEED Compound" . . . "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/"^^ . "ontology" . . . . "Data Science Ontology" . "https://herv.img.cas.cz/s/$1"^^ . "false"^^ . . "life science" . . . . . "genome" . . . . "http://purl.obolibrary.org/obo/PROPREO_$1"^^ . . . "https://fanta.bio/cre/$1"^^ . "vrandecic@gmail.com" . "https://civicdb.org/links/gene/$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."^^ . . "http://purl.obolibrary.org/obo/EMAP_$1"^^ . . . "http://www.gramene.org/db/ontology/search?id=GRO:$1"^^ . "drug" . "Bacillus subtilis genome sequencing project" . . . . . . . "4"^^ . "^.*?--%3E.*?$"^^ . "https://www.phosphosite.org/curatedInfoAction.action?record=$1"^^ . . . "Vibrational Spectroscopy Ontology" . . . "https://pathbank.org/view/"^^ . "col" . . . . . . "dso" . "^\\d{3}$"^^ . "metatlas.reaction" . . . "life science" . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID="^^ . "Wiktionary" . . . "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . . "https://cropontology.org/rdf/CO_334:$1"^^ . "protein" . . "false"^^ . . . . . . "Experimental Measurements Purposes and Treatments ontologY" . . . "https://bmrb.io/data_library/summary/index.php?bmrbId=$1"^^ . "meddra" . "life science" . "Cellosaurus Publication" . "cell" . "http://qudt.org/schema/qudt#$1"^^ . . "chemical entity" . "ino" . "http://multicellds.org/MultiCellDB/$1"^^ . "biomedical science" . "http://bioportal.bioontology.org/ontologies/$1"^^ . . . "Digital Object Identifier" . "expression" . . "^c\\d+$"^^ . "ontology" . "Nikkaji number" . . . . . . "ontology" . "drug name" . . . . . . . "0278"^^ . . "ReviewVersion"^^ . . "Identifier for a user in iNaturalist"^^ . . . . . . . . "2004-2820"^^ . . . "http://purl.obolibrary.org/obo/PLANP_$1"^^ . "protein" . . "Alliance of Genome Resources Knowledge Base" . . . "0000141"^^ . "Salk Institute for Biological Studies" . . . "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F"^^ . . "P10636"^^ . . . . . . . "https://bioregistry.io/pubmed:"^^ . . . . . . "http://data.europa.eu/8mn/euroscivoc/$1"^^ . "Colorectal Cancer Atlas" . "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. "^^ . _:Nd7f53041e68a4488a557dc99f51861e8 "Michael J. Lincoln MD" . . . . . "28789"^^ . "https://mycobrowser.epfl.ch/genes/"^^ . . . "The EMI ontology is used to structure spectrum annotation provenance by reusing the PROV-O ontology (a W3C recommendation) and sample and observation data by applying the SOSA ontology. EMI reuses the SOSA ontology as a data schema for struturing the Sample and Observation data. SOSA (Sensor, Observation, Sample, and Actuator) is a subset of SSN (Semantic Sensor Network Ontology) that is a W3C recommendation. [from homepage]"^^ . "dna" . . "63"^^ . . . . . "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId="^^ . "mutant" . . . . "^\\d+$"^^ . "true"^^ . . . "Assembly" . . . "Alen Vodopijevec" . "http://worfdb.dfci.harvard.edu/html/index.php?search_type=name&page=showresultrc&race_query=$1"^^ . . . "disprot.region" . . . . "strain" . "false"^^ . . "A0118748"^^ . . . "oclc" . "https://labsyspharm.github.io/lspci/$1"^^ . . . . "true"^^ . . . . "Shorthand representations of languages and their subtypes"^^ . "The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations."^^ . "ClinGen Clinical Genome Expert Panel" . "mihail.anton@chalmers.se" . . "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE."^^ . . "^virsi\\d+$"^^ . . "ontology" . . . . . . . . . . . . . . . "false"^^ . "true"^^ . . "Molecular Interaction Database" . . . "false"^^ . "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."^^ . . "goche" . . . . . . "gene expression" . . . . . . . . . . "medicine" . "^EDI_\\d+$"^^ . "dbpedia" . . . . . . . . . . . . . . . . "false"^^ . . . "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1"^^ . . . "certain"^^ . . "Castor bean ontology" . "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^ . "obo" . "molecule" . _:N63b95b51add14c3ca7df76ffc79d54dc "sschurer@med.miami.edu" . . . . . "false"^^ . . . . "proco" . . . "http://purl.unep.org/sdg/SDGIO_"^^ . "jens.klump@csiro.au" . . . "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . . . "Ceri Van Slyke" . . . "evolutionary biology" . "shex" . "false"^^ . . . "obo" . . . "hubmap.sample" . . . . . . "life science" . . . "api" . "ontology" . . . . . "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians."^^ . . . . _:Nc47ec4ead5d14c2ca67e8fa44e0b94d8 . . . . "bioinformatics" . "^\\d+$"^^ . "w.simpson@orcid.org" . "obo" . . . . . . . "false"^^ . . . . . . . . . . . "Leafsnap" . "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^ . . . . . . "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . "Registry and database of bioparts for synthetic biology" . . "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^ . . "^[0-9]{12}$"^^ . "145"^^ . . . "botany" . . . . . "academy" . . . "UBERON" . "^[SCTAGMNUIX]{1,2}\\d{2}\\.([AB]\\d{2}|\\d{3})$"^^ . "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies."^^ . "http://pax-db.org/#!protein/$1"^^ . "SNOMEDCT_2005_07_31" . . "life science" . . . "genome" . . . . . "true"^^ . "1000003"^^ . "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^ . . . "^[0-9]+$"^^ . . "SMID-DB" . "qafeQTWIWmcC"^^ . "^[A-Za-z0-9_-]+$"^^ . . . . "http://www.genomesize.com/result_species.php?id=$1"^^ . . . . "Identifier for a journal article in the fossilworks website"^^ . . "Dynamic Ecological Information Management System - Site and Dataset Registry - Dataset" . . . . . "uniprot.var" . . . . . . . . "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId="^^ . . . . "^[a-z0-9]{10}$"^^ . . "European Language Social Science Thesaurus" . . . . "0001707"^^ . _:Nedbc275e04954fc697a3f356038185e2 "PLOS Taxonomy Team" . . . . "SDY2614"^^ . . "MO000027"^^ . "ontology" . "ontology" . . "^\\w+$"^^ . "http://arabidopsis.info/StockInfo?NASC_id=$1"^^ . "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."^^ . "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . "false"^^ . "BGC0000001"^^ . . "scop.sid" . . . . . . "false"^^ . . "https://pharmacodb.ca/cell_lines/"^^ . "neXtProt family" . . . "https://cropontology.org/rdf/CO_359:$1"^^ . "ontology" . . . "Kyoto Stock Center" . . . . "Funding, Research Administration and Projects Ontology" . . . . . . . . . "ontology" . . . . "geochemistry" . . "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease."^^ . . "Human Gene Mutation Database" . "SAMEA10104908"^^ . . . "false"^^ . . . . . . . . . . . "^\\d+$"^^ . . . "^\\w+$"^^ . "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."^^ . . . . . . . "obo" . . . . . . "mpid" . "KIM German School Types" . . . . "earlyChildhood"^^ . . . "http://purl.obolibrary.org/obo/BSPO_$1"^^ . . . . "pdumdv" . "true"^^ . "obo" . . . . "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."^^ . . . . . . "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."^^ . . "true"^^ . "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^ . . . "basic research" . "ftt" . "This collection contains various brain atlases from the Allen Institute." . . "https://e-cyanobacterium.org/bcs/rule/"^^ . "genpept" . . . . "bigg.compartment" . . "false"^^ . . "FlyBase internal citation identifiers"^^ . "false"^^ . . . . . "Unified Medical Language System Concept Unique Identifier" . "earth science" . . . "false"^^ . . . . "mgnify.analysis" . "co_331" . "centrally registered identifier" . . "obo" . "http://www.semanticdesktop.org/ontologies/2007/03/22/nco#"^^ . . . "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . "http://purl.bioontology.org/ontology/IDODEN_"^^ . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models."^^ . "life cycle" . . "131392"^^ . . . . "DSSTox_CID" . . "false"^^ . . "pathway" . . . . . _:Nab3f592f14fe401faf7eb3b4f40c6466 "cs@firstdatabank.com" . . "Os01g0883800"^^ . . . . "4005"^^ . "dramp" . . . . "otol" . . "obo" . . "msig" . . . . . "preclinical studies" . . "a formalization of concepts and relations relevant to evolutionary comparative analysis"^^ . . . . "ECOCYC" . . "false"^^ . . . "E-cyanobacterium Experimental Data" . "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view."^^ . . "taxonomy" . . "^ENSGT\\d+$"^^ . . . "KEGG Drug Group" . . . . "http://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . . . . "life science" . . . "cvx" . "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."^^ . . . . . . . . "http://purl.obolibrary.org/obo/MmusDv_$1"^^ . . . . . "https://archive.gramene.org/db/ontology/search?id=GR_tax:"^^ . . "dwc" . . . "false"^^ . . . "Ian Foster" . . . "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . "^\\d+$"^^ . . . "biomedical science" . . . . . . . "https://biopragmatics.github.io/providers/peff/$1"^^ . "alignedWith"^^ . . . . . . . "e.arnaud@cgiar.org" . . . "Regulation of Transcription Ontology" . "NASA Open Science Data Repository Mission" . . . . . . . "ILMN_129894"^^ . . . . . "antibody" . "gaog@mail.cbi.pku.edu.cn" . . . . . "voss@gbv.de" . . . "dcam" . . . "false"^^ . "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information."^^ . . "biomedical science" . . "life science" . . . . . "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$"^^ . . "embryonic stem cell" . . . . . . . . . "Online Mendelian Inheritance in Animals" . . . . _:Nd96a2c997e5a4049a35901b620a94d63 "report@mail.nih.gov" . . . . . . . "life science" . . . "merriam_webster" . "enzymatic reaction" . "phenomics" . . "plant phenotypes and traits" . . . "false"^^ . . "anatomy" . "life science" . "genprop" . . . . . . "bioinformatics" . . . . . . "Raimond Winslow" . . . . . "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."^^ . "data management" . . "ontology" . . . "rare disorder" . "organelle" . "obo" . . . . . "ontology" . . . "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^ . "0000252"^^ . . "^\\d+$"^^ . "https://cropontology.org/rdf/CO_340:$1"^^ . . "aggregated-data"^^ . "phenotype" . . . "dermatology" . . "glycomics" . . . . "subject" . "meghan.balk@gmail.com" . . . "false"^^ . . . "The Ontology of Genes and Genomes" . . . . "protein" . "co_330" . . "mfmo" . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . . . . . . "obo" . . . "Identifiers for microbially derived natural products that contains compound structures, producing organism taxonomy, biosynthetic and chemical properties."^^ . "life cycle" . "catalog" . "odc.tbi" . "^\\d{7}$"^^ . "1443"^^ . . . . "ontology" . . . "G1"^^ . . "MolBase" . . "protein-protein interactions" . . "The Bibliographic Ontology" . . . "annotation" . "http://www.hprd.org/protein/"^^ . "http://purl.obolibrary.org/obo/FLU_"^^ . . "^\\d+$"^^ . . . . . "AURKA"^^ . . "https://dcmi.github.io/openwemi/ns#$1"^^ . . . "BSU29180"^^ . "false"^^ . . . . . . . . . . "The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)"^^ . . "false"^^ . "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^ . . . . "^[A-Z]{2}\\d+$"^^ . . . . "metabolic model" . "http://xmlns.com/foaf/0.1/$1"^^ . . . . . . "false"^^ . "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . . . . . . . . . . . . . . "assay" . . "^\\d+$"^^ . . "SRX000007"^^ . "Tuan Amith" . "life science" . . . . . "Edgar Wingender" . "3546"^^ . . "OMIM Phenotypic Series" . . "imsr.apb" . . . . . . . "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1"^^ . . . . . . . "http://genomics.senescence.info/genes/details.php?id="^^ . "Disease Drivers Ontology" . "349124"^^ . . . "cryoem" . . "false"^^ . . . . . "http://dbpedia.org/property/"^^ . "life science" . "false"^^ . . "cell" . "life science" . . . . "immunology" . . . . . . . "157"^^ . . . . "ontology" . . . "https://www.geonames.org/$1"^^ . "open educational resources" . "https://sciprofiles.com/profile/$1"^^ . . "https://www.pgscatalog.org/pgs/"^^ . "suprabank.interaction" . . "life science" . . . . . . . . . "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases."^^ . . . "false"^^ . "Amos.Bairoch@sib.swiss" . "false"^^ . . . . "Banco de Celulas do Rio de Janeiro" . . . . . . . "zachll@umich.edu" . "spectra (samples) in the nmrXiv database"^^ . "mouse strain" . . "SIGNOR" . . "ab275461"^^ . . . . . "^\\d+$"^^ . "http://purl.org/spar/cito/$1"^^ . . . "Ontology of rat strains"^^ . . . "^\\d{7}$"^^ . "false"^^ . . . . . . . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . . . . "http://purl.obolibrary.org/obo/FIDEO_$1"^^ . . . "0020"^^ . "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information."^^ . . . . . . "^A[A-Z]+\\d+$"^^ . . "structural bioinformatcs" . . . . . . . . "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data."^^ . . . "sbp000002"^^ . . "cell lines" . . . . . . . . "https://dcmi.github.io/openwemi/ns#"^^ . . "units" . "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. "^^ . . "https://search.dalia.education/items/$1"^^ . . . "http://purl.uniprot.org/uniprot/$1"^^ . . . . . . . "wot" . "Data Documentation Initiative Vocabulary" . "tcdb" . . . "https://w3id.org/citedcat-ap/$1"^^ . "Genomic Distribution of structural Superfamilies" . . "Asteraceae Genome Database - Genome" . "http://sideeffects.embl.de/drugs/"^^ . . . . . "Bambara groundnut ontology" . . "psdo" . . . "phipo" . . "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id="^^ . "protein" . . . "structural biology" . . "true"^^ . . . "https://www.biocatalogue.org/services/$1"^^ . "^\\d{7}$"^^ . . "2329"^^ . . "metabolomics" . "SUM Breast Cancer Cell Line Knowledge Base" . "chemistry" . "true"^^ . . . "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object="^^ . "ptr" . "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$"^^ . . . "false"^^ . "Neuro Behavior Ontology" . . . "https://data.chembiosys.de/organisms/"^^ . . "https://elsst.cessda.eu/id/3/"^^ . . . . "C34"^^ . "mipmod" . "antifam" . . "Jose P. Faria" . "CHEBI" . "gene" . . "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id="^^ . . "false"^^ . "life science" . . . . . . . . . . . . . . "vendor" . "data classification" . "ontology" . . "bcbc" . "biomarkerkb.biomarker" . . "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^ . "fortuna@ebd.csic.es" . "http://purl.obolibrary.org/obo/TAO_$1"^^ . . . . "structure" . . . . "NASA Open Science Data Repository Payload" . . . . . . . . . "cabri" . . . "protonet.proteincard" . . . "false"^^ . . "2VM6_A55_A135"^^ . "Layla Michán Aguirre" . . "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. "^^ . . "organ" . . . . . . . "false"^^ . . . . . . "Bilateria anatomy" . . . . . "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene="^^ . . "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^ . "co_358" . "cteno" . "https://meshb.nlm.nih.gov/record/ui?ui="^^ . . . "DB-0174"^^ . "false"^^ . "true"^^ . "https://github.com/$1"^^ . . "00000000"^^ . . . "false"^^ . . "https://omabrowser.org/oma/hog/HOG:"^^ . . . . . . . . . . . . . . . . . . "false"^^ . . "false"^^ . . "https://www.ebi.ac.uk/ega/studies/"^^ . . . . . . "astrophysics and astronomy" . "^\\d+$"^^ . "NCIT_Thesaurus" . . . "false"^^ . "vs" . "molecular dynamics" . "Catalog of purchasable reagents and building blocks"^^ . "biocuration" . . . "^ERM[0-9]{8}$"^^ . "human" . . . . "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^ . . . "false"^^ . . . . "Stefan Kuhn" . . "http://purl.obolibrary.org/obo/NBO_"^^ . . . . "http://uri.neuinfo.org/nif/nifstd/oen_"^^ . . "https://data.chembiosys.de/models/"^^ . _:Nc565f4c724574369978f4501b9fa42de . . . "life science" . "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . . "^\\d+$"^^ . . "rna-seq" . "https://hamap.expasy.org/unirule/"^^ . . . "genomics" . . "LifeWatch Metadata Catalogue" . . . . . . . . "genetic interaction (sensu unexpected)" . . . . . "^\\d{8}$"^^ . . "568815597"^^ . . . . . "cell reprogramming" . . "true"^^ . "true"^^ . "https://www.eionet.europa.eu/gemet/en/relations/"^^ . "treefam" . . . "https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/$1"^^ . "Pfam protein clan" . . . . "^\\d{8}$"^^ . . . "life science" . . . . . . . . "^jRCT\\w?\\d+$"^^ . "Rat Resource and Research Center" . "environment" . "true"^^ . "false"^^ . . . "phylogenetics" . "https://chemprosquare.idrblab.net/data/target/details/"^^ . "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"^^ . "^PASS\\d{5}$"^^ . "http://purl.obolibrary.org/obo/HP_"^^ . "false"^^ . . . . . "https://cropontology.org/rdf/CO_343:"^^ . . . . " 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://deims.org/activity/"^^ . "immunology" . . . "life science" . "curated information" . "http://bigg.ucsd.edu/compartments/"^^ . . "knapsack" . . . . . . . "https://mobidb.org/$1"^^ . . . "^[a-z]+(\\..*?)?$"^^ . . "PLOSTHES" . . . . "Pierre.Cosson@unige.ch" . "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."^^ . . . . "life science" . "LL379-9"^^ . . . . . . . . . . "false"^^ . "https://models.physiomeproject.org/exposure/$1"^^ . . "oral surgery" . . . . . . . "life science" . . . "^\\d+$"^^ . . . "^\\d{7}$"^^ . . "life science" . "BioSystems" . . "fypo" . "false"^^ . "authorea.author" . "CIViC Source" . "false"^^ . "Gmelin's Handbook of Inorganic Chemistry" . "obo" . . "enm" . . "Mike Tyers" . . . . "http://bigg.ucsd.edu/models/universal/metabolites/$1"^^ . . "Javier Millán Acosta" . "false"^^ . . "InterLex" . . . "linguistics" . . . . . "http://purl.obolibrary.org/obo/FBcv_$1"^^ . . . "Activity"^^ . . . . . . . . . "fao" . . "http://eol.org/schema/terms/$1"^^ . . "oban" . "data analysis service" . . . "plant phenotypes and traits" . . . "MassIVE" . "biomedical science" . "computer science" . "false"^^ . . . . . "genome" . "0000001"^^ . . . . . "gene" . "https://omia.org/variant/omia.variant:$1"^^ . "metabolomics" . . "^L\\d+$"^^ . . "53d583d8-40c6-40e1-9296-23f821cd77a5"^^ . . . . "publications" . "computer science" . . . "metadata model" . . . . "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . . "statistics" . . . . . "https://cn.dataone.org/cn/v2/resolve/%7B$1%7D"^^ . . "unit" . . . . "HsapDO:0000004"^^ . . . "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."^^ . "false"^^ . "https://w3id.org/BCI-ontology#$1"^^ . . . . . "life sciences" . "food" . "false"^^ . . . "^(G|P|U|C|S)\\d{5}$"^^ . "https://www.kegg.jp/entry/$1"^^ . . . . . "false"^^ . . . . "SASDAX8"^^ . "smc.source" . "has resource example" . "genome" . . . . . . "false"^^ . "https://covid19.sfb.uit.no/api/records/$1"^^ . . "false"^^ . . . . "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"^^ . . . _:Nb657f519dd284b5090487aa5136011e0 . . . "https://i.uestc.edu.cn/AACDB/details.php?id="^^ . . . "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover."^^ . "0002066"^^ . . "FB00000917"^^ . . . "Simple Knowledge Organization System eXtension for Labels" . . "These are the terms that are improted for FOVT to describe vertebrate traits."^^ . . . . . . . . "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download."^^ . "epidemiology" . . "resid" . . . . "0000547"^^ . . . "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions."^^ . . "Dialnet article ID" . . . . "SciCrunch Registry" . "Genetic Testing Registry" . . "reactome.pathway" . . . . . . . . . . "true"^^ . "false"^^ . . "^SL-\\d+$"^^ . . . . "C2584994"^^ . . "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:"^^ . "dna" . "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"^^ . "https://glyconavi.org/hub/?id=$1"^^ . . . . . . "^[A-Za-z0-9]+$"^^ . "huge" . "bacmap.map" . . "false"^^ . . . . "false"^^ . "IID00001"^^ . . "78"^^ . . "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^ . "^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$"^^ . . "http://purl.obolibrary.org/obo/BCO_"^^ . . . . . "phenxtoolkit" . . . . . . "https://ximbio.com/reagent/"^^ . . "A terminology for the skills necessary to make data FAIR and to keep it FAIR."^^ . "insdc.run" . . . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes."^^ . "bioinformatics" . "false"^^ . "CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains. Note that while still available and included in Unified Medical Language System (UMLS), it has not been updated since 2006."^^ . "faseb list" . . "false"^^ . "201022999"^^ . . . . "aquaculture" . "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels."^^ . . . "life science" . "plwhetzel@gmail.com" . "false"^^ . . "^(SMP|PW)\\d+$"^^ . . "miriam" . . . "gene" . . . . . . "life science" . "DICOM Controlled Terminology" . "http://purl.obolibrary.org/obo/OlatDv_"^^ . "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." . . . "transcriptomics" . . . "https://vcell.org/biomodel-"^^ . . . . . . . "https://www.ebi.ac.uk/pride/archive/projects/$1"^^ . . . "http://purl.obolibrary.org/obo/RNAO_$1"^^ . "commoncoreontology" . . . . . . . "^[a-zA-Z_][a-zA-Z0-9\\-_]+$"^^ . . . . . . . "qb" . . "structural biology" . . "data management" . . "environmental science" . . . . . "uniprot.database" . "^\\d+$"^^ . "qualo" . . "Logical Observation Identifiers Names and Codes" . "^ACTRN\\d+$"^^ . "rna" . "false"^^ . . . . "UniProt provides proteome sets of proteins whose genomes have been completely sequenced."^^ . . . . "NanoParticle Ontology" . . "http://purl.obolibrary.org/obo/GECKO_"^^ . . "^\\d+$"^^ . "Method"^^ . . . . "viroligo" . . . "obo" . . . "false"^^ . . . "Os01t0883800-02"^^ . "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes."^^ . "https://www.arraymap.org/pgx:$1"^^ . . "imex" . "genome" . . . . . . . . . . . . . . . . . . . . . "NFDI Knowledge Graph Registry" . . . "_3dmet" . . . . . "ClinVar Record" . . "7dfd3f10-d410-45a4-983d-8fbd6dfbc374"^^ . . "BRAF"^^ . "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^ . _:Nb7e85f58056b4253a68baea08ef24c12 "William Bug" . . "4685"^^ . . "ieee.author" . "false"^^ . "false"^^ . . . . "lifengcheng@zju.edu.cn" . "LOC_Os01g49190"^^ . . "false"^^ . . . . "https://ogp.me/ns#$1"^^ . "plant breeding" . "true"^^ . . "Datasets inside StoreDB at University of Cambridge"^^ . . . . . . "GLAndersen@lbl.gov" . . . . . "andrew.mcshan@chemistry.gatech.edu" . . . "true"^^ . "https://models.physiomeproject.org/exposure/"^^ . . . . . . "Toni Gabaldón" . "ontology" . . "anatomy" . . . . . . . "http://purl.obolibrary.org/obo/GECKO_$1"^^ . . "tao" . "dbpedia.property" . . . . . "false"^^ . "protein" . "Reactome" . "ontology" . . "Database of experimentally verified IRES structures" . . "false"^^ . "false"^^ . "nasaosdr.mission" . "00573"^^ . . . "botany" . . "antoine.danchin@normalesup.org" . . . "ligandbox" . "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . . "gary.bader@utoronto.ca" . "openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item."^^ . "life science" . "controlled vocabularies" . . . . . . . . "URS0000759CF4"^^ . "Coriell Institute for Medical Research" . "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]"^^ . "Transcription Factor Database" . "DP00003"^^ . . . . . . "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.)."^^ . . . . "http://www-snorna.biotoul.fr/plus.php?id="^^ . "A user in DockerHub"^^ . "^[dp]\\.[a-z0-9]{8}$"^^ . . . "bacdive" . . . . . . "loqate" . "genome" . . "fyler" . . "phenotype" . "database" . . "Literature references in the Hymenoptera Anatomy Ontology Portal"^^ . . . . "214100"^^ . "http://www.onto-med.de/ontologies/gfo.owl#$1"^^ . . "nucleotide" . . . "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . . . "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."^^ . . . "gregory.landrum@phys.chem.ethz.ch" . . . _:N7b0d2fd1573e45fcbf2aa497c5505152 "pierre.sprumont@unifr.ch" . . . . "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."^^ . "medical informatics" . . "bgee.organ" . _:N5f25bcb1b0db421f830a0cc3fcc06c6d "marc@geonames.org" . . . . "functional genomics" . "https://www.diseasesdatabase.com/ddb$1.htm"^^ . "agriculture" . . "false"^^ . . . . "^G(PL|SM|SE|DS)\\d+$"^^ . . . "Citation Counting and Context Characterisation Ontology" . . . "tgilbert@sund.ku.dk" . "gc_id" . . . . . "^\\d+$"^^ . . . "^\\d+$"^^ . "Lycalopex_vetulus"^^ . "FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors."^^ . . . . . . . . _:Nb5631ff21e9f4f0d986745314038884d . . . . "^YMDB\\d+$"^^ . "0.7-123"^^ . . "false"^^ . . . . . "true"^^ . . "ypo" . . "https://www.kazusa.or.jp/rouge/gfpage/$1"^^ . . "protein" . . . . . . "http://flowrepository.org/id/"^^ . "Clytia hemisphaerica Development and Anatomy Ontology" . . . . . . . . "OriDB Saccharomyces" . "GenInfo Identifier" . "identifier for chemicals linked to information on occurrence in plants"^^ . "metadata" . . . . "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^ . . . "Marie-Paule Lefranc" . . . "protein" . . "false"^^ . . "molecule" . . . . "false"^^ . . "16333295"^^ . "90062901"^^ . "alan.rubin@wehi.edu.au" . "https://www.metanetx.org/chem_info/$1"^^ . "Pesticide Properties DataBase" . . "integbio" . . "jstuelk@gwdg.de" . . "protein" . "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . "embryology" . . _:N47b8474538d9407cb8dfc4a0f5ea868c "elzanowski@biol.uni.wroc.pl" . . . "41455251.1"^^ . "proteomics" . . "imsr_em" . . . . "obo" . . . "combine.specifications" . "ZDB-GENE-041118-11"^^ . . "https://cgap.nci.nih.gov/Pathways/BioCarta/"^^ . "https://iso639-3.sil.org/code/"^^ . . . "donny@polyneme.xyz" . . . "fish" . . . "https://data.gesis.org/gesiskg/schema/"^^ . "Sabine.Oesterle@sib.swiss" . . . . "EndlessForms Studio Element" . "^\\d+$"^^ . . . . . . . "https://nztcs.org.nz/nztcs-species/"^^ . . . . . . "^\\d+$"^^ . . . "HL7 External Code Systems are stored within the greater OID system" . "MIRIAM Legacy Registry Identifier" . "https://bioregistry.io/chemspider:"^^ . "https://radlex.org/RID/"^^ . "life science" . . . . . . "false"^^ . . . . . "http://purl.obolibrary.org/obo/PW_"^^ . "chemical entity" . "nrfc" . "^UDB\\d{6}$"^^ . . "199/2168"^^ . . . . "https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/"^^ . . . "earthcube.sfo" . "stacia@stanford.edu" . . "biology" . "translational medicine" . . . "^\\d{7}$"^^ . . "false"^^ . "CHEBI" . . . . "life science" . . "The Bibframe vocabulary consists of RDF classes and properties used for the description of items cataloged principally by libraries, but may also be used to describe items cataloged by museums and archives. Classes include the three core classes - Work, Instance, and Item - in addition to many more classes to support description. Properties describe characteristics of the resource being described as well as relationships among resources. For example: one Work might be a \"translation of\" another Work; an Instance may be an \"instance of\" a particular Bibframe Work. Other properties describe attributes of Works and Instances. For example: the Bibframe property \"subject\" expresses an important attribute of a Work (what the Work is about), and the property \"extent\" (e.g. number of pages) expresses an attribute of an Instance."^^ . . . . . "false"^^ . . "https://hamap.expasy.org/unirule/$1"^^ . "life cycle stage" . . . "Andrew C. McShan" . . . "chemistry" . "life science" . . "Database of Aligned Ribosomal Complexes" . . . . . "health science" . "http://purl.obolibrary.org/obo/TAHH_$1"^^ . "ontology" . . . . . "karr@mssm.edu" . "Science Data Discovery Ontology" . . "Theiler stages (TS) define mouse development by a set of morphological criteria ([Theiler, 1989](https://doi.org/10.1007/978-3-642-88418-4)). This staging scheme is used because embryos at the same gestational age can have developed at different rates and therefore exhibit different morphological characteristics. Theiler stages may in some cases correspond to a single gestation age, but more often cover a range of ages. (from [https://www.informatics.jax.org/glossary/theiler](https://www.informatics.jax.org/glossary/theiler))"^^ . "UDB000691"^^ . . . . . . . . . "Biolink Model Registry" . . . "agriculture" . . . "cabi" . . . . . . . . . . "diseasesdb" . "miRBase Families" . . . "false"^^ . . "Human Medical Genetics" . . . . . . "https://nfdi.fiz-karlsruhe.de/ontology/NFDI_$1"^^ . "https://cropontology.org/rdf/CO_370:"^^ . . . . . . . . "The Comprehensive R Archive Network" . . . "http://purl.obolibrary.org/obo/MSIO_"^^ . . . . . "3771877"^^ . . . . . "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1"^^ . . . "rism" . . . . . "experimental condition" . . . "GPIb_IX_V"^^ . "knowledge and information systems" . "genome" . "biomedical science" . "https://www.ebi.ac.uk/interpro/entry/pfam/$1"^^ . . . . . . . . . "deoxyribonucleic acid" . . . "http://edamontology.org/data_$1" . . . . . "addiehl@buffalo.edu" . "^\\d+$"^^ . . . "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."^^ . . . . "protein" . "Semantic Web Context" . . . . . "PT00819"^^ . "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"^^ . "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . . . "lotus" . "^\\d{5}$"^^ . . . . . . . . . "jrc-eurl-ecvam-chemagora"^^ . . . . . . . . "Sam Griffiths-Jones" . . "protein" . . . . . . . . . . . . . . . . _:N25c1a4a229e849899b9c7c47fd32918b . . . "jorvis@gmail.com" . . "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."^^ . . "false"^^ . . . . "neurovault.collection" . "dal.alghamdi92@gmail.com" . "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."^^ . . . "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)"^^ . . . . . . "hsdb" . "A website containing information about rare diseases, powered by Wordpress."^^ . "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."^^ . . . . "ontology" . "false"^^ . "bioinformatics" . . . . . "false"^^ . "skos" . "NCBITaxonomyID" . "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"^^ . "An expanded example URL for a resource or metaresource." . . . . "false"^^ . . . . "European Genome-phenome Archive Dataset" . . . "biomedical science" . . . "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"^^ . . . "true"^^ . "LinkML" . . . . "Datanator Reaction" . "false"^^ . "dailymed" . "Zhang Zhang" . "http://purl.obolibrary.org/obo/OGI_"^^ . . . . . "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."^^ . . . "MIPF0000002"^^ . . "Todd W Harris" . . . _:N7d8ef3b598314e69805b74e833189665 "Jonathan Bard" . . "Australian New Zealand Clinical Trials Registry" . . "nckyrpides@lbl.gov" . "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23"^^ . . . . "confident.event" . . . . . "MEROPS Family" . "homd.taxon" . . . . "https://go.drugbank.com/metabolites/$1"^^ . "Protein Ensemble Database" . . . "rtecs" . . . "http://psb.kobic.re.kr/STAP/refinement1/result.php?search="^^ . "https://odc-sci.org/data/"^^ . . . . "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^ . . "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . "GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio."^^ . "civic.variantgroup" . "storedb.study" . "geography" . . . "0000012b-5661-2f63-2f73-b43980000000"^^ . "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$"^^ . "^\\d{7}$"^^ . . . . "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality."^^ . . . . "MediaDive Medium" . . . . "0000144"^^ . "false"^^ . . . . "identifier for a person, on the LinkedIn website"^^ . . . _:Nb2862f37c4784127bdc22eaf7bb6b0a6 "gary@sourceauditor.com" . . . . "ProteomeXchange" . . . . . . . "KEGG Glycan" . "0009089"^^ . . "IPI00000001"^^ . "Guangshun Wang" . "gene expression" . "551115"^^ . . "ChemDB" . . . "functional genomics" . . "https://phagedive.dsmz.de/strain/"^^ . "GO Chemicals" . _:Ncf5bc35010ea4cbc9dc2b7102df539d2 . . "^\\d{7}$"^^ . . . "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."^^ . . . . . . . "1257009"^^ . . "data_1664"^^ . "^\\d{7}$"^^ . . "false"^^ . . . . . . . . . . "agsc" . . "ccso" . . "Identifiers.org Ontology"^^ . . . . . "feature"^^ . "anatomy" . . "life science" . . . "KEGG-path" . "0001021"^^ . . "false"^^ . "false"^^ . . "false"^^ . . . . . "developmental biology" . . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid="^^ . . "PACTR202304525632216"^^ . . . . . . "31623"^^ . . "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]."^^ . "false"^^ . "rna" . "ontology" . . "data sharing" . "genome" . "classification" . "http://viroligo.okstate.edu/main.php?vid=$1"^^ . "The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science."^^ . "chemical structure image" . . . . . _:N47b8474538d9407cb8dfc4a0f5ea868c "Andrzej Elzanowski" . "alleles" . . "0000001"^^ . . "biomedical science" . . "https://civicdb.org/links/sources/"^^ . "1"^^ . . . . . "An open, community-driven registry of conference and event venues.\n\nEVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research organizations.\n\nThis benefits researchers assembling information about in-person conferences and events by enabling them to refer in an unambiguous way to the venue where it takes place.\n\nThis repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w), meaning that the data and code are all in one repository that anyone can contribute to."^^ . . . . . "Clinical Trial Registries" . "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . "NeuroVault Collection" . . . . . . "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . "false"^^ . . . "bioinformatics" . . . . "SKOS Thesaurus Extension" . . "Oral Health and Disease Ontology" . "Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate."^^ . . "life science" . "database" . "^PIRSF\\d{6}$"^^ . "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."^^ . . "https://www.genenames.org/cgi-bin/genefamilies/set/"^^ . . . "http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#$1"^^ . "molecular genetics" . . "E4330"^^ . . . "^\\d+$"^^ . . . "0001003"^^ . "Physical Medicine and Rehabilitation" . . . . . . . . . . . . . . "https://biopragmatics.github.io/providers/schem/$1"^^ . "http://cegg.unige.ch/orthodb/results?searchtext=$1"^^ . "biomedical science" . "Common Terminology Criteria for Adverse Events" . . "A registry of life science prefxes"^^ . . . "cell biology" . . . . "Arabidopsis Small RNA Project" . . . . . . . . "protein" . . "FAIRsharing User" . . "slime-mould" . . "gtex" . "biomedical science" . . . . . "ChEBI" . . . . "Open Data for Access and Mining" . . . . . . . . . "http://www.w3.org/1999/xhtml/vocab#$1"^^ . . "ontology" . "prefixcommons" . "https://bioregistry.io/metaregistry/scholia/$1"^^ . "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)."^^ . . . "false"^^ . . "nihgeneid" . "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide."^^ . . "Earth Metabolome Ontology" . . "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)."^^ . "FAIRsharing" . "Virus-HostDB" . . "dcterms" . "false"^^ . . . . . "^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$"^^ . . . . . . "CCDC Number" . . "ncbi.assembly" . "agriculture" . . . "Variants in dbVar."^^ . . . "bibliometrics" . . . . . . "bspo" . . . . . . . "idpo" . . . . . . "Metabolic Encyclopedia for Pathway/Genome Databases" . "Grant"^^ . "MAMpol005339"^^ . . "protein" . . "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . . . "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://smpdb.ca/view/"^^ . . . . "ligea" . . "MMP3312982.2"^^ . . "taxonomy" . _:Nedbc275e04954fc697a3f356038185e2 "subjectareas@plos.org" . "life science" . . "true"^^ . . "https://aopwiki.org/aops/"^^ . "0000005"^^ . . "Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining subclasses and subproperties of SIOC terms."^^ . . "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"^^ . "http://www.kegg.jp/entry/"^^ . . . . . "https://www.uniprot.org/uniparc/$1"^^ . . "https://fungidb.org/fungidb/app/record/gene/$1"^^ . "Genotype-Tissue Expression" . . "PubMed" . "ICDO" . "http://purl.obolibrary.org/obo/T4FS_$1"^^ . "^\\d{2,7}-\\d{2}-\\d|DTXSID\\d{7,9}|[A-Z]{14}-[A-Z]{8}[SN][A-Z]-[A-Z]$"^^ . . . . "2gc4"^^ . _:N7821e843498b4fc482592503dae946a4 "Michelle Futornick" . "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"^^ . . . . "langual" . . . "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . . "Alzforum Mutations" . "false"^^ . . . . . . . "^\\d{7}$"^^ . "6237"^^ . . . "559"^^ . _:N4aae48270bd349dc849eaacb9ce5cb04 "whocc@fhi.no" . . . "Genomics of Drug Sensitivity in Cancer" . _:Nc10b32e9694e4396ad2b5acd0f88abfa . . "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . . "zea" . . "annotation" . "lipid" . "markerdb" . . . "http://purl.obolibrary.org/obo/SBO_$1"^^ . "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN="^^ . "https://identifiers.org" . . . . "life science" . . . "false"^^ . . _:N2a175dfd0cf54fcfa643f5a7965e801e . . . . . . "https://www.holofooddata.org/sample/"^^ . "https://bioregistry.io/p3db.protein:"^^ . . "https://w3id.org/lehrplan/ontology/LP_"^^ . "chemistry" . . . "sequence" . "ontology" . . . "owl" . . . . "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."^^ . . . . . . "http://flowrepository.org/id/$1"^^ . . . "false"^^ . . . . "laevis" . "orthodb" . "GlyTouCan" . "138488"^^ . . "false"^^ . "^\\d+$"^^ . . . . "plant phenotypes and traits" . . "schober@imbi.uni-freiburg.de" . . "^\\d+$"^^ . . . . . . . "https://doulix.com/biomodules/"^^ . _:N13428b66cf7a4f6f956195d5354d505e . . . "LCCN Permalinks are persistent URLs for bibliographic records in the LC Catalog and authority records in LC Authorities. These links are constructed using the record's LCCN (or Library of Congress Control Number), an identifier assigned by the Library of Congress to bibliographic and authority records. LCCN Permalinks are also available for citation records in the Handbook for Latin American Studies (HLAS). [from homepage]"^^ . . "PGS000018"^^ . . "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^ . "https://www.fishbase.ca/summary/"^^ . "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^ . . _:N2bb389bb394b47d885e945a4eb073ee5 . . "VirGen" . "PED00037"^^ . . . . . "ontology" . . "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . . . . "false"^^ . "MMP743597.11"^^ . "http://ciliate.org/index.php/feature/details/$1"^^ . "statistics" . "http://purl.obolibrary.org/obo/FBbi_$1"^^ . . . . . . . . "false"^^ . . "loop" . . . . . . "false"^^ . . . "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_"^^ . . "Mark Engelstad" . . . "ror" . . "0000000"^^ . . "exac.transcript" . . "50885"^^ . . "microbiology" . . . . . . . . "ontology" . "ontology" . . . "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^ . . "^\\d+$"^^ . "A dataset in the ChemBioSys data platform"^^ . . . . "InfragenericTaxon"^^ . "https://protists.ensembl.org/id/$1"^^ . "https://ximbio.com/reagent/$1"^^ . . "umbbd.rule" . . "subject agnostic" . . . . . "mutant strain" . "knowledge and information systems" . . "civic.did" . . . "TS-0001"^^ . . "AMDEFA"^^ . . "This database provides identifiers for catalytic bioparts which are fundamental to the design, construction, and optimization of biological systems for specific metabolic pathways. It provides basic information, function information (including catalytic functions, qualitative and quantitative parameters, and biopart expression), and sequence information (nucleotide sequence and amino acid sequence)"^^ . . . . "structure" . "http://ecoinformatics.org/oboe/oboe.1.2/oboe-standards.owl$1"^^ . "cellbank.australia" . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/FOVT_"^^ . . . . . "researcher" . "Steven E. Wilson" . "van_slyke@zfin.org" . "https://ceds.ed.gov/element/"^^ . "https://molbic.idrblab.net/data/compound/details/$1"^^ . "LCSCCPN"^^ . . . . . "fly" . "Justin Whorton" . "lter" . . . . . "false"^^ . . . "https://chem.nlm.nih.gov/chemidplus/rn/"^^ . "false"^^ . . . . . . . "dna" . "skosthes" . . . . . "false"^^ . "https://bioregistry.io/dbd:"^^ . . "oai:cwi.nl:4725"^^ . . . "https://mips.helmholtz-muenchen.de/corum/?complex_id="^^ . . . . . . . "CE28239"^^ . "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."^^ . . "clustering" . "http://ratmap.org/Showgene.php?gene_stable_id=$1"^^ . . . "false"^^ . "-LHR8P7WS-K"^^ . "Xenopus Anatomy Ontology" . "Yeast Deletion and the Mitochondrial Proteomics Project" . . . . "^\\d{7}$"^^ . . "Ctibor Škuta" . "^\\d{7}$"^^ . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"^^ . . "23"^^ . . "0002989"^^ . "false"^^ . "https://graphics.endlessforms.info/library?id=$1"^^ . . . "structure" . "synthetic biology" . . "Merck Index Reaction" . "http://www.cathdb.info/cathnode/"^^ . "Jessica Kissinger" . . "imsr_tac" . . . "Database containing promotor sequences found in Saccharomyces cerevisiae."^^ . "http://cor.esipfed.org/ont/SWL_"^^ . "endocrinology" . "KEGG.COMPOUND" . "kaysheva1@gmail.com" . "https://lov.linkeddata.es" . . "hrehm@mgh.harvard.edu" . . . "false"^^ . . "canal"^^ . "gene" . . . "genomics" . . . . . . "^[a-z][a-z0-9_]+[a-z0-9]$"^^ . . . . "uniprot.taxonomy" . "obo" . . "false"^^ . . . "sweetrealm" . . . . . . . . . . . . . "Danielle Welter" . . . . "classification" . . . . . "false"^^ . "DB14938"^^ . "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."^^ . . . "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . "false"^^ . "chemistry" . "morpheus.lab/morpheus"^^ . "http://www.rcsb.org/ligand/"^^ . . . "DrugBank Condition" . "https://bioregistry.io/metaregistry/$1"^^ . "structure" . "RF00230"^^ . . . "uniparc" . . "BQJCRHHNABKAKU"^^ . "life science" . "https://biopragmatics.github.io/debio/$1"^^ . . "MarDB" . "snp2tfbs" . . "macie" . . . . . . . . . "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#$1"^^ . . . "http://purl.org/dc/dcam/"^^ . "false"^^ . . . "David Linke" . "^[0-9]+$"^^ . "suprabank.additive" . "A subspace of Metabolic Atlas for compartment-specific records for metabolites."^^ . . "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."^^ . . . "PhosphoSite Curation" . . . . "true"^^ . "^\\d{7}$"^^ . "^\\d{7}$"^^ . "^HIX\\d{7}(\\.\\d+)?$"^^ . . . . "false"^^ . . . "^\\w.+$"^^ . . . "mirbase.family" . . "^\\d+$"^^ . . "false"^^ . . "omim.ps" . "http://purl.obolibrary.org/obo/OGG_$1"^^ . . . . . . "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment."^^ . "protein" . _:Nd64ff50fbeeb4373853e6b7314155a9c "NCI Thesaurus Mailbox" . "PEPhub" . . . "PhosphoPoint Kinase" . "E5.11.2.0.0.0.4"^^ . . . "pathway" . . . "David Sehnal" . "FBtr0084214"^^ . . "genomics" . "^(CN)?\\d{2,7}$"^^ . . . . . "167047"^^ . "^RC\\d+$"^^ . . . . "virology" . "resource metadata" . "has resolver formatter" . . . . . . . "true"^^ . . "false"^^ . "The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are:\n\n- [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.)\n- [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC)\n- [GENCODE](https://www.gencodegenes.org/) (uses GenBank)\n- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc)\n- [STRING](https://string-db.org/) (uses UniProt)" . . . . "^MAM\\d{5}\\w$"^^ . . . "Selventa legacy complex namespace used with the Biological Expression Language"^^ . . . . "false"^^ . . . "^\\d{4}$"^^ . . "molecular biology" . "SM00015"^^ . . . . "rna" . . . "https://www.sharkipedia.org/species/$1"^^ . . . . "anatomy" . . . "351"^^ . . . . . "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting" . "obo" . "http://purl.obolibrary.org/obo/FBdv_"^^ . . . . "biology" . . . . . . . . . . . "CAS_RN" . "cdao" . "cohesin" . . . . . . "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^ . . . "false"^^ . "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."^^ . . . "https://bioregistry.io/skm:"^^ . "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"^^ . "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . "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."^^ . . . . . . . "phosphorylation" . "50-00-0"^^ . "false"^^ . . . "genome" . . "Brazilian Registry of Clinical Trials" . . "85dc6019-9654-4ba0-8338-08c4ffe8fe47"^^ . . . "false"^^ . . . . . "^\\d+$"^^ . "nextprot.family" . . . "0000001"^^ . "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical" . . . "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections."^^ . "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^ . . . "lectins/172"^^ . . "proteomics" . . . . . . . "radiology" . "^\\d{7}$"^^ . . "Anne Thessen" . "The Addiction Ontology (AddictO) is an ontology being developed all aspects of addiction research."^^ . . . . . . . . . "adverse reaction" . . . "A comprehensive compendium of human long non-coding RNAs"^^ . . "0000021"^^ . "person" . . . . "rcameron@sfu.com" . . "CO_325" . . . . . . "Documentation of the Phenoscape Curation Workflow"^^ . . . . . "http://purl.obolibrary.org/obo/FBSP_"^^ . . "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^ . . "http://www.unimod.org/modifications_view.php?editid1="^^ . . . . . "Human Metabolome Database" . . "14"^^ . . "false"^^ . . "Rebuilding a Kidney" . . . . . . . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . . . "dorloff@ncmir.ucsd.edu" . . "Philip Strömert" . "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . . "http://purl.obolibrary.org/obo/VO_"^^ . "true"^^ . . "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . . . . . "http://purl.obolibrary.org/obo/DC_CL_"^^ . . "https://omim.org/MIM:PS"^^ . . . . "yongqunh@med.umich.edu" . . . . . . "Mosquito insecticide resistance" . "^CCDS\\d+(\\.\\d+)?$"^^ . . "ngl" . "invertebrate" . . . "ontology" . . "^\\d+$"^^ . . "Stephen R. Heller" . . . . . . "Jian Huang" . "biology" . . . "Environmental conditions, treatments and exposures ontology" . . . . . "^\\d+$"^^ . "splash10-0zq2000000-77302b0326a418630a84"^^ . "^([a-zA-Z]+-)?\\d+(\\.\\d)?$"^^ . . "http://edamontology.org/operation_"^^ . "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"^^ . . "^\\d+$"^^ . "unit" . . . "https://w3id.org/qualo/id/$1"^^ . . . "obo" . "Orientations of Proteins in Membranes Database" . . . . . . . "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . "2"^^ . . . . . "true"^^ . "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"^^ . "false"^^ . "ontology" . "polypeptide region" . . . "https://terms.codata.org/rdmt/"^^ . . . . . "false"^^ . . "obo" . "ChemBioSys Tag" . . . "true"^^ . . . . "cho"^^ . . "model" . . . "false"^^ . . "^\\d+$"^^ . . . "false"^^ . . "http://purl.obolibrary.org/obo/KISAO_$1"^^ . . . "FlyBrain Neuron Database" . "ChEMBL-Cells" . . . . . . "false"^^ . . . . "false"^^ . "ontology" . . "molecular entity" . "https://string-db.org/cgi/network?identifier="^^ . . . . . . . . . . . . . "IMGT/HLA human major histocompatibility complex sequence database" . . . "http://snomed.info/id/$1"^^ . "protein" . "235" . "https://bioregistry.io/schema/#$1"^^ . . "rutgeraldo@gmail.com" . "false"^^ . "knowledge and information systems" . . . . "false"^^ . _:N851ebc0692b14a7b8f922a0351f3d2c5 . "https://v31.homd.org/genome/genome_description?gid=$1"^^ . . "deims.sensor" . "https://bdsc.indiana.edu/stocks/$1"^^ . . . . . . . "760050"^^ . . . . . . . . "false"^^ . . . . . "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements."^^ . . . . . . "license" . . . . "biology" . "PaxDb Protein" . . "ExAC Gene" . "^FDB\\d+$"^^ . . . . . "CHEMBL4303805"^^ . "Medical Subject Headings Vocabulary" . "British Oceanographic Data Centre data storage units" . . . . "structure" . "obo" . . . "http://www.yeastract.com/view.php?existing=locus&orfname=$1"^^ . "https://id.loc.gov/authorities/"^^ . . "Lars Bertram" . "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . . . . . "https://www.ncbi.nlm.nih.gov/probe/?term="^^ . "Gm00047"^^ . . . . . . . "AOPWiki (Stressor)" . "^PRO_[0-9]{10}$"^^ . . . . . . "polysaccharide" . . . . "false"^^ . "DataONE" . . . . "https://www.ncbi.nlm.nih.gov/protein/"^^ . "genetics" . . . . "isbn" . "napp" . . . "http://www.gramene.org/db/literature/pub_search?ref_id="^^ . "CHEBI" . "http://www.w3.org/ns/earl#"^^ . "Description of Plant Viruses" . . . . . "mamo" . . "informatics" . . . "059486"^^ . . "genome" . "Abcam" . "structure" . . "false"^^ . "H-InvDb Locus" . _:N2d5072dd9d104290839761e23aeca8f0 "marc@geonames.org" . "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]"^^ . . . . _:Nee497bc5e1e74254bf03610e9dc5dc0f "Harry Caufield" . "sbml.level-3.version-2"^^ . . . . . . "genes" . . "Imanis Life Sciences cell line products" . "Peruvian Clinical Trial Registry" . "false"^^ . "ESCO Skill" . . . . "https://n2t.net/$1:" . "Terms from the source appear in the target resource" . "http://purl.obolibrary.org/obo/AISM_"^^ . . . . . . . . "false"^^ . . . . "SWAN ontology consists in a collection of ontologies used to create, manage and share scientific knowledge bases."^^ . . "swiss-model" . . . . "The samples subsection of HuBMAP provides metadata about individual tissue samples collected from donors, and are the downstream experimental datasets for scRNA sequencing. Each sample has a unique identifier that links it to donor information, anatomical source, and related datasets."^^ . . "BioContext contains modular JSON-LD contexts for bioinformatics data." . . . . . . . . . "A001094"^^ . "wikipathways" . . "environmental science" . "^[a-z_A-Z0-9]+$"^^ . . . . "An ontology to support disciplinary annotation of Arctic Data Center datasets."^^ . . "http://www.pantree.org/node/annotationNode.jsp?id="^^ . . "Groundnut ontology" . . "^\\d+[a-d]?$"^^ . . . "zenodo" . "https://www.vmh.life/#metabolite/$1"^^ . . "animal breeding" . "https://bioregistry.io/panorama:"^^ . . "http://pathguide.org" . . . . . . . . "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"^^ . "medicine" . . "1174"^^ . "true"^^ . "gene" . . "celia.michotey@inrae.fr" . . . "false"^^ . . . "biomedical science" . . . . "Biological Collections Ontology" . "Electron Microscopy Public Image Archive" . . . . . "ontology" . "ontology" . . . . . . . . "Pigeonpea ontology" . "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."^^ . . "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo="^^ . . _:N72e9805822a84a57af392e18424ae7e5 . "https://cryptodb.org/cryptodb/app/record/gene/$1"^^ . . . "contributor roles" . . . "http://zinc15.docking.org/substances/$1"^^ . . "imaging" . . "false"^^ . "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols."^^ . "^\\d{7}$"^^ . . "RiceNetDB miRNA" . "MDB00000001"^^ . "datanator.reaction" . "ML0224"^^ . "peptideatlas.dataset" . . "arrayexpress.platform" . . . "life science" . "false"^^ . "false"^^ . "Enzo Life Sciences is an antibody vendor."^^ . "false"^^ . "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."^^ . "ppr" . . . . . . "http://purl.obolibrary.org/obo/CTO_$1"^^ . . . . "^\\d+$"^^ . "^\\d+$"^^ . . . "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"^^ . . "Plant Growth and Development Stage" . "http://vbrc.org/gene_detail.asp?gene_id=$1"^^ . "skos.xl" . . . "nvs.P06" . . "Oryza Tag Line" . . "population genetics" . "051"^^ . . "http://purl.obolibrary.org/obo/BCO_$1"^^ . "knowledge and information systems" . . "^\\d+$"^^ . "classification" . . . . "https://fairsharing.org/"^^ . "http://nava.liacs.nl/cgi-bin/nava.py?id="^^ . . "https://web.expasy.org/cellosaurus/cellopub/$1"^^ . . . . . . . . . . "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . . . "ontology" . . . . . "false"^^ . . . . . . . . . "Birgit Meldal" . "biology" . "gene" . "obo" . "T01B6.1"^^ . . . . . . "A01M1/026"^^ . . . . . . "biological_process" . . . . . . "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^ . . "true"^^ . . "1374"^^ . "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . . "KEGG Reaction" . . . . "http://purl.obolibrary.org/obo/BCGO_"^^ . . "Exposure ontology" . . "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications."^^ . "https://loinc.org/$1"^^ . "Eukaryotic Genes" . . "1776"^^ . "social and behavioural science" . . . . . . . . "^\\d+$"^^ . . . . . . "FHIR External Terminologies" . "life science" . "UniCarb-DB" . . "Regulation of Gene Expression Ontology" . "https://zenodo.org/record/$1"^^ . "dictyBase" . . "^C\\d{8}$"^^ . . . "mediadive.solution" . "SAMEA112904733"^^ . "^\\d{7}$"^^ . . . "sequence feature" . . . . . "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes."^^ . . "^\\w+$"^^ . "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."^^ . . . "life science" . . "functional genomics" . . . "phenx" . . "PA447218"^^ . . . "http://multicellds.org/MultiCellDB/$1"^^ . "ProGlycProt" . . "false"^^ . . . . . . "Synthetic Binding Protein Epitope" . . "false"^^ . . "IMGT/PRIMER-DB" . "mental health" . . . . "http://ecmdb.ca/compounds/$1"^^ . . . . . "PathBank" . "proteomics" . "exposure" . . . . "3517823"^^ . "chemical biology" . . "ontology" . "biology" . . . "life science" . "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id="^^ . "victorinolavida@ciencias.unam.mx" . . . . "https://www.ebi.ac.uk/complexportal/complex/$1"^^ . "http://vocab.getty.edu/page/tgn/"^^ . "bioinformatics" . . . . . . . . . . . "Bacterial Tyrosine Kinase Database" . . . . "https://civicdb.org/links/drugs/"^^ . . "https://cropontology.org/rdf/CO_338:"^^ . . "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)"^^ . "pii" . . . . . . . . . "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated."^^ . . "Paul D Thomas" . . . . . "false"^^ . . "pieter.mestdagh@ugent.be" . . "chemical biology" . . . "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."^^ . . "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#"^^ . . . . . . "genome" . "https://www.fung-growth.org/page/Display%20page%20FG/"^^ . "rna" . . . . . "http://pombe.oridb.org/details.php?id=$1"^^ . . . . . . . . "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."^^ . "MIMIC III Database" . . . . "Malachi Griffith" . "Charles Ettensohn" . "NCBI Taxonomy" . . "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^ . . . . "pathway" . . "life science" . . . . "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . "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."^^ . . . "false"^^ . . . . . "chemistry" . "nmr" . . "protein" . . "Symptom Ontology" . . . . _:Nd7f53041e68a4488a557dc99f51861e8 "michael.lincoln@va.gov" . "1351341"^^ . . . . . "sequence" . "false"^^ . . "Identifier for a place in iNaturalist"^^ . "https://viperdb.org/Info_Page.php?VDB="^^ . . "mirgenedb" . . . "spdx.licenses" . . "http://search.sisuproject.fi/#/variant/$1"^^ . . . "chromatin loop" . . "Hypertension Ontology" . . "^CAL\\d{7}$"^^ . . "audience type" . . "Secondary Metabolism Collaboratory - biosynthetic gene cluster" . . "^\\d+$"^^ . "C. elegans Gross Anatomy Ontology" . . . "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis."^^ . . . "false"^^ . "false"^^ . . . . . . . . . "genomics" . "gpcrdb" . . . . . . "http://lincsportal.ccs.miami.edu/datasets/#/view/"^^ . . "^\\d{3}-\\d{3}-\\d$"^^ . "https://www.osti.gov/biblio/$1"^^ . "^\\w+$"^^ . . . . . "Sequencing Initiative Suomi" . . "https://ssrn.com/abstract=$1"^^ . . "proteomics" . "^\\d{7}$"^^ . "CB82546919"^^ . "true"^^ . . . . . . . "3"^^ . . . . . "ontology" . "Joshua Orvis" . . "kegg_genome" . . "lreha@ualberta.ca" . "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."^^ . "gene expression" . . . "German Clinical Trials Register" . . . . "Gene Expression Ontology" . "taxonomy" . . . "PepBank Peptide Database" . "A collection of graphics that relate to a theme"^^ . . . "11478"^^ . . "Cellosaurus identifeirs for publications, like Pubmed"^^ . . "Fungal Growth Database" . . "skos-thes" . . "http://www.kegg.jp/entry/$1"^^ . "OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX."^^ . . . . . . "false"^^ . "The international standard for identifying health measurements, observations, and documents."^^ . . . . "body_symmetry"^^ . . "false"^^ . . . "^[FKPU]\\d{3}$"^^ . . "ontology" . . . "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."^^ . "https://cropontology.org/rdf/CO_320:"^^ . "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms."^^ . . . . . . . "https://dialnet.unirioja.es/servlet/libro?codigo="^^ . "people" . . . . "^PST_\\d+$"^^ . "http://yeastrc.org/pdr/viewProtein.do?id=$1"^^ . . . "0002927"^^ . . "health science" . . . . "Data Commons" . "ontology" . "life science" . "agriculture" . . . . . . . . . . "false"^^ . . . "http://uri.neuinfo.org/nif/nifstd/nlx_"^^ . . "transposon insertion" . . . . . . . "false"^^ . "284196006"^^ . . . . . "PTPN1"^^ . . . "mgriffit@wustl.edu" . . "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^ . . "https://purl.brain-bican.org/ontology/hbao/HBA_$1"^^ . . "enzyme commission number" . "Sharkipedia Trend" . "https://hpscreg.eu/cell-line/$1"^^ . "^Q[A-Z0-9]+$"^^ . . "sequence annotation" . "civic.tid" . "Bjoern Peters" . . . "identifier for an author in IEEE Xplore"^^ . "ribocentre" . "false"^^ . . "corrdb" . . . . . "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^ . "phenotype" . "MSH" . . . . "muamith@utmb.edu" . . . . . "ontology" . . . . "Wikipedia" . . . . "soybase" . . "Tree of Life Web Project" . . "botany" . "Platynereis stage ontology" . "https://bioregistry.io/collection/"^^ . "0000000"^^ . . "AB0"^^ . . "disease" . "false"^^ . "https://www.ncbi.nlm.nih.gov/gtr/conditions/"^^ . "0000210"^^ . . . . . . . "BDGP insertion DB" . . . . . . . . "biology" . "sparcdrs" . . . "https://comptox.epa.gov/dashboard/$1"^^ . "nucleic acid sequence" . . . . . . . . . . "VEGA" . "true"^^ . . . "genome" . "alzheimer's disease" . . . "false"^^ . "chemistry" . . . . . . "https://www.cellosaurus.org/CVCL_$1"^^ . "bootstrep" . . . . . . "A vocabuarly for describing the background and methodology for the design of the DataCite profile of DCAT-AP (CiteDCAT-AP), as well as the defined mappings."^^ . "false"^^ . . "false"^^ . . "iceberg.family" . "zty2009@hit.edu.cn" . . . . . "wdduncan@gmail.com" . . "false"^^ . . . . "false"^^ . . "obo" . "gabi" . "TB2:S1000"^^ . "human" . . . "mint" . . "Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network"^^ . . . . . . . . "https://uts.nlm.nih.gov/uts/umls/semantic-network/"^^ . "Vilma Hualla Mamani" . "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . "PPR103739"^^ . "physiology" . "SNOMED_CT_US_2018_03_01" . . . "developmental biology" . "mazumder@gwu.edu" . . . "The China National Center for Bioinformation's (CNCB) Genome Warehouse (GWH) is a public repository holding genetic information for a wide range of species including humans, plants, animals, and microorganisms. Identifiers in this resource correspond to genomes of various species. The goal of the resource is to make genomic data accessible to researchers in areas like precision medicine and biotechnology."^^ . "glycomics" . "biodiversity" . . . . "0002959"^^ . "George Gkoutos" . "https://catalog.hathitrust.org/Record/"^^ . . "hinv.transcript" . "^\\d{8}$"^^ . . "giant.plankton@gmail.com" . . "BugBase Expt" . "Generative Artificial Intelligence Delegation Taxonomy" . . . . . . . . . . . . . . . . . . . "https://mediadive.dsmz.de/medium/$1"^^ . "http://purl.obolibrary.org/obo/MFMO_"^^ . "obo" . "http://purl.obolibrary.org/obo/GEO_$1"^^ . "molecular biology" . . . "genecards.geneloc" . "0001998"^^ . "Protein Structure and Stability Knowledge Base" . . "protclustdb" . . "biodiversity" . "Ontology about C. elegans and other nematode phenotypes"^^ . "An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io)."^^ . . "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NDFRT&code=$1"^^ . . "http://purl.obolibrary.org/obo/PdumDv_"^^ . "umbbd.enzyme" . . . "false"^^ . "has local unique identifier example" . "bork@embl.de" . "0015177"^^ . . "protein" . . "Lars Holm Nielsen" . . . "^\\d+$"^^ . "false"^^ . . . . . . . . . "fig|306254.1.peg.183"^^ . "small molecule" . . "^LDCM\\d+$"^^ . . "^\\d{7}$"^^ . . "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^ . . "Oryzabase Reference" . . "knowledge and information systems" . . . "Sickle Cell Disease Ontology" . . "false"^^ . "obo" . . "http://edamontology.org/data_"^^ . "HGNC Gene Group" . "^SEQF\\d+(?:\\.\\d+)?$"^^ . . "10.1038/s41597-022-01807-3"^^ . . . . "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages."^^ . "caps" . "Snapshot" . . "Ali Syed" . "earth science" . . . . . . "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)"^^ . "UK Universities and Colleges Admissions Service" . "life science" . "true"^^ . "Tzong-Yi Lee" . . . . "adeans@psu.edu" . "pathway" . "Bgee organ" . "^[A-Za-z_0-9]+$"^^ . "structure" . "Adriano Mari" . . . . . "identifier for a physical constant"^^ . . "Shapes Constraint Language" . . . . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"^^ . . . "true"^^ . . . . . . . . . . . "pancreatic islet" . . "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term="^^ . "organism supplier" . . "Mental Disease Ontology" . . "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors."^^ . "false"^^ . . . . "0000015"^^ . . . . . . . . . . "alternate"^^ . . "B2067"^^ . . . "^[a-z][a-z]/[0-9]+$"^^ . . . . . . "TAX" . . . . "atcvet" . "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."^^ . "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id="^^ . . "snoDB0001"^^ . "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_"^^ . . . . . . . "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID="^^ . . . . . . . . "true"^^ . "chemistry" . "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations."^^ . . "false"^^ . "Resources mentioned in \"Sharing biological data: why, when, and how\"" . . "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."^^ . . . "spar" . . . . "data analysis" . . "http://www.gramene.org/db/ontology/search?id=GRO:"^^ . "bitterdb.cpd" . . . . . "Ruben Abagyan" . . "https://scicrunch.org/resolver/RRID:AGSC_$1"^^ . . "8cf84adb-b4db-4807-ac98-0004247c35df"^^ . . "amoebadb" . . . . . "compound" . "https://cropontology.org/rdf/CO_356:$1"^^ . . . "ACTRN" . . . . "0471491039"^^ . "vso" . . . . "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^ . "http://purl.obolibrary.org/obo/TTO_"^^ . . "Progenetix" . . "3304"^^ . . "data retrieval" . . . . "31"^^ . . "ecology" . . . . "http://biomeddb.org/Disease/Details?DISEASEID="^^ . . "^[A-Z0-9]{1,10}_[A-Z0-9]{1,5}$"^^ . "false"^^ . . . . "Python"^^ . . . . . . _:Nd64ff50fbeeb4373853e6b7314155a9c . "Creative Biolabs protein" . . "^\\d{7}$"^^ . "sequence" . . "Bitbucket" . . . . . . "ontology" . "^DRAMP\\d{5}$"^^ . . "1859"^^ . . . . "https://www.ebi.ac.uk/biomodels/"^^ . "easychair.cfp" . "arba" . . . _:N9d97cb603fef4486af9c2f180e0a3a6c . "^PR\\d{5}$"^^ . . . . . . . . "Open Graph protocol" . . "drug" . "Philipp.Bucher@sib.swiss" . . "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . . . "true"^^ . . . . . . . . . "obo" . "ontology and terminology" . . "obo" . . . . "protonet.cluster" . "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read."^^ . . . . "^\\d+$"^^ . "false"^^ . "environmental science" . . "1kfv"^^ . "ontology" . "epidemiology" . "DAML Periodic Table of the Elements" . . . . "phylogenetics" . . . . . "https://prefix.zazuko.com/$1:$2" . . . "false"^^ . . "Cell line databases/resources"^^ . . "48439"^^ . . . . . . "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"^^ . . . . "ordo" . . . . "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . . "0000106"^^ . . "ontology" . "0016"^^ . . "afo" . . . "drug repositioning" . . "phylogenetics" . . "life science" . "^((S\\d{4}-\\d{4}\\(\\d{2}\\)\\d{5})|(B\\d-\\d{3}-\\d{5}-\\d/\\d{5}))-[\\d|X]$"^^ . "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."^^ . . . "Reaxys eMolecules" . "1"^^ . "obo" . "berman@rcsb.rutgers.edu" . . . . "https://portal.hubmapconsortium.org/browse/sample/$1"^^ . "false"^^ . "0000095"^^ . . . . . . . . . "r.huntley@ucl.ac.uk" . "disease" . "umls.cui" . . . . . . "The LifeWatch Metadata Catalogues plays a crucial role in managing metadata for digital objects, including Datasets, Services, Workflows and Virtual Research Environments. This catalogue serves as the central repository, ensuring that resources are accessible and reusable by stakeholders."^^ . "OMIA" . . . . "homosaurus" . "http://purl.obolibrary.org/obo/CL_$1"^^ . . . . . "software engineering" . "^[-_0-9A-Za-z]{12}$"^^ . . . "3"^^ . "https://www.ncbi.nlm.nih.gov/biosystems/$1"^^ . "John Cottrell" . . "genome" . . "Lipid"^^ . . . . . "genbank" . "Electron Microscopy Data Bank" . . . "0000008"^^ . . . "genetic variation" . "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"^^ . . . . "aquaculture" . . . "false"^^ . . "fanta" . . "biochemistry" . . . . . . "http://purl.obolibrary.org/obo/DUO_$1"^^ . . "B-5720-2018"^^ . . "BioDolphin" . . "agriculture" . . . "^[A-Z0-9]+$"^^ . . "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."^^ . . . . "life science" . "single nucleotide polymorphism" . "Thomas Keane" . . "https://lccn.loc.gov/$1"^^ . "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene."^^ . . "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."^^ . . . . . . . "genome" . . . "https://bitbucket.org/$1"^^ . "Anita Bandrowski" . . "https://scicrunch.org/resolver/RRID:AGSC_"^^ . "^oai\\:cwi\\.nl\\:\\d+$"^^ . . "false"^^ . . . . . . "Kai Blin" . "biology" . "^\\d{7}$"^^ . "interaction" . "false"^^ . . . "022586"^^ . "regulation" . . . . . . . . "SNOMED" . "ontology" . "CHEBI" . "OBO Metadata Ontology" . . . . . . . . . "Distributed Archives for Neurophysiology Data Integration" . "false"^^ . . . . . . . "BioKC (Biological Knowledge Curation), is a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML)."^^ . . . . . . "clinical studies" . "pathway" . . . . "small molecule" . . "population dynamics" . . . "PDC000351"^^ . "sider.effect" . "000040"^^ . "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass="^^ . "https://www.dublincore.org/specifications/skos-thes/ns/#"^^ . . . "icdc" . "^FC(HS|MM)_\\d+$"^^ . . "https://www.dbgi.org/earth_metabolome_ontology/#$1"^^ . . . "plant breeding" . "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"^^ . "MNEST029358"^^ . "chembiosys.data" . . "Cooperative Patent Classification" . . "dna" . "^D\\d+$"^^ . . . . "phenomics" . . . . . . . . "16941567"^^ . "http://purl.obolibrary.org/obo/ONE_$1"^^ . . . "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1="^^ . . . . . . . . "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . . "graph" . . "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)."^^ . "ontology" . . . . . "https://omia.org/phene/omia:$1"^^ . . "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."^^ . "https://morpheus.gitlab.io/models/$1"^^ . . "https://biopragmatics.github.io/providers/scomp/"^^ . . . . . . . . "EcoliWiki from EcoliHub" . _:Ndb1e5a981dc841498d6b55b7a3393cac "World Health Organization" . . . . "ymdb" . "human geography" . "Matt Yoder" . . "http://purl.obolibrary.org/obo/SYMP_$1"^^ . . . . . "Handle" . . . . "genetree" . . . . . . . . . . . . . . "http://www.chemspider.com/Chemical-Structure.$1.html"^^ . . "Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)"^^ . "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."^^ . . . . "https://www.scopus.com/affil/profile.uri?afid=$1"^^ . . "false"^^ . . . "https://web.expasy.org/cellosaurus/cellopub/"^^ . . "This ontology integrates cell type markers for cells in the Cell Ontology from various sources along with details of marker context (anatomical context, assay), confidence (where available) and provenance. [from repository]"^^ . . . . "chemistry" . . . "plant phenotypes and traits" . . . "staylor@vertosolutions.net" . . . "sample annotation" . "GrassBase" . "_4dn.biosource" . _:N28f417fe9b3c44bc93409fd79fad1d81 "Heinrich Herre" . . . "rdf" . . "Structural Classification of Protein - Stable Domain Identifier" . . . "life science" . . "molecular interaction" . . . . . "cell lines" . . "cell" . . . "030719"^^ . "3403"^^ . . . . . . "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition."^^ . . . . . . . "false"^^ . . . "swisslipids" . . "false"^^ . . . . . . "A controlled vocabulary for education levels, such as primary eduation, secondary education, and post-secondary education"^^ . . "https://www.ebi.ac.uk/interpro/set/pfam/"^^ . "https://e-cyanobacterium.org/models/model/$1"^^ . . . . . . "obo" . . "TTD Drug" . . "1eec8393-e598-41ed-9d8b-6d5b0db94470"^^ . "malaria" . "117145750"^^ . "lexvo.ontology" . "Note"^^ . . . "^M\\d{5}$"^^ . "vocabularies" . . . . . . . "biopragmatics/bioregistry/424"^^ . "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."^^ . "false"^^ . "resource metadata" . "grin.publication" . . "2200950"^^ . . "Traits and phenotypes of flowering plants occurring in digitized Floras"^^ . "https://cropontology.org/ontology/$1" . . . . . . . . . . . "mmusdv" . "obo" . . "ontology" . . . "MCDS_S_0000000001"^^ . . . . "drug discovery" . "AT1G01030.1"^^ . . "subject agnostic" . "https://caps.ncbs.res.in/pass2.8/?q=superfamily/"^^ . . "http://purl.org/oban/"^^ . . "VFDB Gene" . . . "58788"^^ . . . "cell_model_passport" . . . . "structure" . "https://www.inaturalist.org/taxa/$1"^^ . "The Generative Artificial Intelligence Delegation Taxonomy (GAIDeT) assigns identifiers to contributor roles as an extension to the Contributor Roles Taxonomy (CRediT) to support promoting transparency and accountability in academic publishing when AI contribtors are involved in research. It is operationalized in the [GAIDeT Declaration Generator](https://panbibliotekar.github.io/gaidet-declaration/), an interactive tool for researchers to disclose the delegation of tasks to generative AI (GAI) tools in accordance with the GAIDeT taxonomy."^^ . . . . "ncbi.gi" . . "genome" . . "life science" . . "Ugis Sarkans" . . . . "http://api.hymao.org/api/ref/$1"^^ . . . "sdgio" . "ID in NIAID ChemDB"^^ . "^\\w+$"^^ . "^\\d{8}$"^^ . "ugis@ebi.ac.uk" . "Tick Cell Biobank" . . . "chemical entity" . "false"^^ . . . . . "mtbd" . "^\\d+$"^^ . . . . . "life science" . "false"^^ . "BioGRID" . "https://www.ebi.ac.uk/QuickGO/GProtein?ac="^^ . . . . . "Dan Berrios" . "An additional Japanese clinical trial registry"^^ . . "ncbitaxon" . "NMRShiftDB" . "http://www.geneontology.org/formats/oboInOwl#$1"^^ . . . . . . . "21393"^^ . "^\\d+$"^^ . "immunology" . . . "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)"^^ . . . "iedb.reference" . "disease" . "José Victorino Ruiz Lavida" . "false"^^ . . . "false"^^ . . "http://purl.obolibrary.org/obo/LPT_"^^ . . . . "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^ . "ontology" . . . "package/8ca67504-3167-4cc8-ba74-98137bb7cd0a"^^ . _:N593c178482fa4d9297fdf9d7014db005 . "false"^^ . . . "Tohoku University cell line catalog" . "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . . . . . "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."^^ . "obo" . . . . "http://www.hmdb.ca/metabolites/$1"^^ . . "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters."^^ . . "http://www.peptideatlas.org/PASS/$1"^^ . "http://stormo.wustl.edu/ScerTF/details/$1"^^ . "digitrubber" . "http://www.wikipathways.org/instance/$1"^^ . . . . "International Standard Name Identifier" . "false"^^ . "subject agnostic" . . "^[0-9a-z_-]+$"^^ . . "false"^^ . "P4355"^^ . . "https://w3id.org/kim/schularten/$1"^^ . . . "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."^^ . . . . "ISO 15926-14" . "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1"^^ . . . . "false"^^ . "https://flybase.org/reports/"^^ . . . . . . . . . . . "intact.molecule" . "expression" . "https://phytochem.nal.usda.gov/phytochem/chemicals/show/"^^ . . "ontology" . . . . . . "life science" . . . "WormBase" . . . . . "gerhard.mayer@rub.de" . . . "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt="^^ . "odamexplorer" . "ontology" . "^B\\d{5}$"^^ . . . . . "https://sumlineknowledgebase.com/?page_id="^^ . "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."^^ . . . . "http://dictybase.org/gene/"^^ . . . "E-cyanobacterium model" . . . "^\\d+$"^^ . . . . . "kegg.compound" . . . . . "preclinical studies" . . . . "false"^^ . . . . . "PMC3084216"^^ . . . . "life science" . . "^\\w+$"^^ . . . "genome" . . . . . . . . . . . . . . . . . "F-SNP" . . . . . . . . "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."^^ . "Biomarker Knowledgebase - Canonical Biomarker" . . "genomics" . . "^FB\\w{2}\\d{7}$"^^ . . . "uniprot.chain" . . . "https://giardiadb.org/giardiadb/app/record/gene/$1"^^ . "rna" . . "gene" . "gbif" . . "J. Michael Cherry" . "Curated Drug-Drug Interactions Database - Interaction" . "life science" . "https://bioregistry.io/go.rule:"^^ . "171"^^ . . . "false"^^ . . . . . . . . "classification" . "biospecimen" . . . . "Veterinary Nomenclature" . . "^sbp\\d+$"^^ . "Diagnostic and Statistical Manual of Mental Disorders (5th Edition)" . . . . "false"^^ . . "biomedical science" . "James C. Hu" . . . "https://foodb.ca/foods/"^^ . "^T[A-Z]\\d{7}$"^^ . . . "biomedical science" . . . . . . . "https://bioregistry.io/phosphopoint.protein:"^^ . . "protein" . "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$"^^ . . "ontology" . . "https://amphibiaweb.org/species/"^^ . . "protein" . "http://purl.obolibrary.org/obo/ADO_"^^ . "https://www.ebi.ac.uk/complexportal/complex/"^^ . "pigqtldb" . . . "pharmacodb.cell" . . "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . . . "frim1"^^ . . . . "organization" . "87"^^ . "false"^^ . "UTRdb" . . "gobp" . "isrctn" . . . . . . . . . . "^CHEMBL\\d+$"^^ . "false"^^ . . . . "BirdBase" . . . "^[a-f0-9]{32}$"^^ . "^.{2,}$"^^ . "clinical studies" . . . . "SNOMEDCTCT_2018_03_01" . . . . . . . "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"^^ . "cell" . "Identifiers for the protein scaffolds of synthetic binding proteins (SBP), detailing their structural frameworks and roles in facilitating SBP function."^^ . . . "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."^^ . . "https://www.rebuildingakidney.org/id/$1"^^ . "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^ . "CNBG_0001"^^ . "false"^^ . "microbial" . "false"^^ . . . "TF101014"^^ . "Tudor Oprea" . "quality" . "Minimal Viable Identifier" . . "Pennsieve" . . . . . "true"^^ . . . "Croissant Format Specification" . . . . "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions."^^ . "Damion Dooley" . "3"^^ . "^IID\\d+$"^^ . . . "biology" . . . "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."^^ . . "genetic disorder" . "protein interactions" . "life science" . . . . . . "MetaCyc Reaction" . "subject" . "https://reporter.nih.gov/project-details/$1"^^ . . "SpliceNest" . "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . . "false"^^ . . . . "^\\d+$"^^ . . . . "chembl.tissue" . . . . . . "^\\d+$"^^ . . . . . "A modeling paradigm-specific registry of prefixes and their URL expansions" . "tumor" . . . . . . . . "Edward A Dennis" . "ecology" . "Gene Expression Ontology"^^ . . "^\\d{7}$"^^ . . "4685"^^ . "Helen Berman" . . "PF11_0344"^^ . . . . . . "ecology" . . . . . . . . "andreadega/systems-biology-compiler"^^ . "GitHub username" . . "false"^^ . . "^[a-f0-9]{32}$"^^ . . "false"^^ . "Organization" . "https://www.kegg.jp/brite/$1"^^ . "ontology" . . "false"^^ . "small molecule" . . "1058367"^^ . "marc.hanauer@inserm.fr" . "skills" . . . . . "Christian-Alexander Dudek" . "false"^^ . . . . "AKR-270"^^ . . "classification" . . "alistair.miles@linacre.ox.ac.uk" . . . "http://purl.obolibrary.org/obo/RXNO_$1"^^ . . "dmba" . . . . . . . . "Lipid Ontology" . . "Taconic Biosciences" . "false"^^ . . . . . . "Cell line collections (Providers)"^^ . "wasila.dahdul@usd.edu" . . . . . "OBO Foundry" . . "^P\\w+$"^^ . "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."^^ . . . "https://bioregistry.io/metaregistry/scholia/"^^ . . "^\\d+$"^^ . "phenotyping" . . "CGNC" . "COlleCtion of Open Natural ProdUcTs" . . . . . _:N05c9d168646a4a7a8670b28e92dd190e "Anita Ghebeles" . . "derivatives%2Fthiocyclam%20hydrochloride"^^ . "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^ . "assay" . . "FuncBase Mouse" . . . . . . "obo" . . . . "genomics" . "Sigma Aldrich is a life sciences supply vendor."^^ . . . "NLXCHEM" . "obo_rel" . "true"^^ . . "false"^^ . . . "fhir.implementation" . . . . . "https://mmp.sfb.uit.no/databases/marfun/#/records/"^^ . . "https://neurovault.org/images/$1"^^ . . "metacyc.reaction" . "7123"^^ . . . "Fetal Calf Serum-Free Database" . . "http://purl.obolibrary.org/obo/WBbt_$1"^^ . . . "https://scicrunch.org/resolver/RRID:BCBC_$1"^^ . "Application ontology for entities related to insecticide resistance in mosquitos"^^ . "drugbank" . "zdoucmm@gmail.com" . "Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations"^^ . . . . . . . . . "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1"^^ . . . "Samuel Friedman" . "^\\d{7}$"^^ . . "regulation" . . . . . . "http://118.178.132.53/tsRNADisease/detail.php?entry_ID=$1"^^ . . . . . "Sucharitha Balu" . "^[A-Z-_0-9]+$"^^ . . "software engineering" . . . . . "Units in OBOE"^^ . . "infectious disease medicine" . . . "19"^^ . "https://europepmc.org/article/CBA/$1"^^ . "false"^^ . "https://www.addexbio.com/productdetail?pid="^^ . . . . "pharmacogenomics" . "ChemBioSys Study" . . "http://purl.org/oban/$1"^^ . . . . . "classification" . "https://metacyc.org/compound?orgid=META&id="^^ . . . . "NIF Standard Ontology" . "false"^^ . . . . . "biodiversity" . . . . . . . . . . . "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^ . . "Ensembl Glossary" . "https://www.fao.org/fishery/en/species/$1"^^ . . . "sylvain.v.costes@nasa.gov" . . "AntWeb" . "https://progenetix.org/services/ids/$1"^^ . . . . . . "false"^^ . "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information."^^ . . . "^[A-Z_]{3}[0-9]{4,}$"^^ . . "http://lincsportal.ccs.miami.edu/cells/#/view/"^^ . . "A vocabulary for the catalysis disciplines" . . . . "http://purl.obolibrary.org/obo/SCDO_$1"^^ . . . . "149"^^ . "Cell Line Ontology" . . . . . . . "mathematics" . "0000550"^^ . . "2"^^ . "ontology" . . "false"^^ . . . . . . . . "false"^^ . . "https://www.ebi.ac.uk/metabolights/$1"^^ . "nucleotide" . . . . . "https://w3id.org/oc/corpus/$1"^^ . . _:N680b661fb12648a886d0881f4fabc9fc "Gregg Kellogg" . . "rna-seq assay" . "https://pubchem.ncbi.nlm.nih.gov/compound/"^^ . . . "http://mirbase.org/cgi-bin/mature.pl?mature_acc="^^ . "false"^^ . "https://rism.online/$1"^^ . . . "With the DataPLANT biology ontology (DPBO), DataPLANT provides an intermediate ontology that acts as a broker and bridge between the individual researcher/domain experts and main ontology providers. DPBO enables easy and agile collection of missing vocabulary as well as relationships between terms for (meta)data annotation using DataPLANT’s Swate tool."^^ . "http://purl.obolibrary.org/obo/CARO_$1"^^ . "ontology and terminology" . "false"^^ . . . . "sopharm" . "pfam" . "biomedical science" . . "life science" . . . . . . . "foaf" . . . . . . "http://web.resource.org/cc/$1"^^ . . . . . . . "natural science" . "0005"^^ . "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements."^^ . . . "life science" . "false"^^ . . . "^\\d+$"^^ . . . . "glasner@svm.vetmed.wisc.edu" . . "life science" . "^\\d{7}$"^^ . . "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."^^ . "https://pmb-bordeaux.fr/maggot/metadata/$1"^^ . "^\\d+$"^^ . . "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."^^ . . "false"^^ . "With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [Fellowship for Interpretation of Genomes (FIG)](http://thefig.info/) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.\nThis prefix provides identifiers for molecular roles that describe the function of one or more proteins in microbes and plants."^^ . "Woody Plant Ontology ontology" . . "unipathway.pathway" . . "false"^^ . . . "obo" . "false"^^ . . "The SPARC Data Repository Service (DRS) is an implementation of the Global Alliance for Genomics and Health (GA4GH) DRS specification that provides a standardized API that enables researchers and other data consumers to access and retrieve data objects from various data repositories in a consistent and cloud-agnostic way. This implementation provides information for data objects in the SPARC repository (sparc.science)."^^ . "false"^^ . . . "Soybean ontology" . "https://cropontology.org/rdf/CO_347:"^^ . . "hsa-let-7a-2-3p"^^ . . "Arctic Data Center Academic Disciplines Ontology" . . . . "P3DB Site" . . . . . . . . "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^ . "citedcat" . "fovt" . . . "false"^^ . . . . . . . . "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."^^ . "gene expression" . . "false"^^ . . "nasaosdr.study" . . . "Pierre Grenon" . . "false"^^ . . . . "http://purl.obolibrary.org/obo/BFO_"^^ . "^GE\\d+$"^^ . . "http://purl.obolibrary.org/obo/IAO_"^^ . . . . . . . "true"^^ . . . "EU Clinical Trials" . . . . . "tccd" . "Fernanda Dorea" . "begdb" . . "^[-A-Za-z0-9\\_]*$"^^ . "https://scicrunch.org/resolver/RRID:NXR_"^^ . . "life science" . . . . "obo" . . "https://tetrahymena.vet.cornell.edu/display.php?stockid=$1"^^ . "http://www.narcis.nl/publication/RecordID/$1"^^ . "dna" . . "http://purl.obolibrary.org/obo/MSIO_$1"^^ . . "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."^^ . . "genome" . "https://dialnet.unirioja.es/servlet/autor?codigo="^^ . . . . "http://www.bindingdb.org/rwd/entry/$1"^^ . "metadata standardization" . . "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."^^ . "https://nf.synapse.org/Explore/Tools/DetailsPage?resourceId=$1"^^ . . . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"^^ . . "0000031"^^ . "AY209920"^^ . "Higher Education Resource Types" . . "mirbase" . . . . "^\\d+$"^^ . . "An ontology with predicates to formalization of the concept of mentions. The mentions may be either explicit (e.g. as when well stated into an article \"Dr. Johnson's groundbreaking research on climate change\") or implicit (e.g. such as discussing \"seminal studies in the field\"). MiTO contains the object property mito:mentions and its inverse mito:isMentionedBy."^^ . . . . "53367"^^ . . "kcoyle@kcoyle.net" . "https://dataguids.org/ga4gh/dos/v1/dataobjects/"^^ . . "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."^^ . . "^\\d+$"^^ . . . . . "Meng LIU" . . . . . . "NeuroMorpho" . "BioTools" . . "https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md"^^ . "^\\d+$"^^ . . "https://cropontology.org/rdf/CO_325:$1"^^ . "^\\d+$"^^ . "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id="^^ . "tredup@pharmchem.uni-frankfurt.de" . "This vocabulary is intended to provide a flexible framework within different usage scenarios to semantically represent any type of content, be it on the Web or in local storage media. For example, it can be used by web quality assurance tools such as web accessibility evaluation tools to record a representation of the assessed web content, including text, images, or other types of formats. In many cases, it can be used together with HTTP Vocabulary in RDF 1.0, which allows quality assurance tools to record the HTTP headers that have been exchanged between a client and a server. This is particularly useful for quality assurance testing, conformance claims, and reporting languages like the W3C Evaluation And Report Language (EARL). [from homepage]"^^ . "A repository of software packages written in Rust."^^ . . "http://ctdbase.org/detail.go?type=gene&acc="^^ . "helpdesk@cropontology-curationtool.org" . . "Transporter Classification Database" . . "frim1"^^ . "molecular biology" . "http://api.hymao.org/api/ref/"^^ . "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species="^^ . . . "Health Data Research Innovation Gateway" . . "^\\d+$"^^ . . . . . "0100002"^^ . . "molecular biology" . "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1"^^ . . . . "ido" . _:N3c26ef7ec133462e85e04ed7ddf135d2 "ClinicalTrials.gov Helpdesk" . . . . . "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."^^ . . . . "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1"^^ . . . . . "https://www.wikidata.org" . . . . "database" . . . "PF11779"^^ . . . . . . "tm.shah@cgiar.org" . "4195"^^ . . . . . . . "SysBioCancer2022"^^ . "baseDimensionEnumeration"^^ . . . . "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^ . "j.huerta@csic.es" . . . . "Epidemiology Ontology" . . . . . . . "infection process" . . . . . "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch="^^ . "obo" . "http://purl.obolibrary.org/obo/ONTOAVIDA_$1"^^ . . . "https://nfdi.fiz-karlsruhe.de/nfdi4dso/$1"^^ . "seo" . . . . "gxa.gene" . . . . "RNA ontology" . "Potato ontology" . . . "chembank" . . . "^\\d{7}$"^^ . . . . . "false"^^ . . . . "https://www.proteomicsdb.org/#human/proteinDetails/"^^ . "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])?$"^^ . . "CUT"^^ . . . . "variation" . "sheeba.samuel@uni-jena.de" . . "anatomy" . "12300"^^ . . "pmap.substratedb" . . "Chris Grove" . "https://cropontology.org/rdf/CO_366:"^^ . . . . "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1"^^ . _:Nef8ae6522f4047df9b7c2ae9afbe76eb "COI Catalogue" . . "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac="^^ . _:N7b0d2fd1573e45fcbf2aa497c5505152 "Pierre Sprumont" . "gramene.reference" . . "^[1-9]\\d{0,11}$"^^ . "oryzabase.gene" . . "^\\d{7,8}$"^^ . . "http://purl.obolibrary.org/obo/AfPO_$1"^^ . . "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . . "http://www.wikidata.org/entity/$1"^^ . "European Searchable Tumour Line Database" . "37271072100"^^ . . . . "ontology" . . . . "dbpedia.resource" . "PST_100013"^^ . "human" . . . . . "drugbank.condition" . . "true"^^ . . . "https://biopragmatics.github.io/providers/goche/$1"^^ . . _:N6c77afbbeff44c7997cc11c8306e2d79 "d3fk" . "1537"^^ . "VMH reaction" . "Genetic Testing Registry Tests" . . . "Pseudomonas Genome Database" . . . . "cell line" . . "false"^^ . "ecn" . "false"^^ . "kegg.dgroup" . . "ontology" . . "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^ . "http://vegbank.org/cite/"^^ . . "institution" . . "consulting" . . . "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."^^ . "A vocabulary of knowledge, skills and competences relevant to the European labour market. In ESCO v1.2.0, the skills pillar is structured in a hierarchy which contains the following four sub-classifications: 1) Knowledge, 2) Language skills and knowledge, 3) Skills, and 4) Transversal skills. [adapted from homepage]"^^ . . "0000106"^^ . . . . "http://www.w3.org/ns/shex#$1"^^ . . "https://biopragmatics.github.io/providers/pba/$1"^^ . . . "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . "Registry" . "electronic health record" . . "Cell line collections (Providers)"^^ . . "obo" . . "ontology" . . . . "BIOMD" . . . . "Cell Ontology" . . . "Nematode Expression Pattern DataBase" . . "obo" . . . "nbdc01071" . "http://ddinter.scbdd.com/ddinter/drug-detail/"^^ . . "http://dbpedia.org/resource/$1"^^ . . "development" . "taxonomy" . . "Proteomic Data Commons" . "EGAD00001008392"^^ . "http://purl.obolibrary.org/obo/EUPATH_"^^ . . . "MNXC15"^^ . . . . . "^MIRT\\d{6}$"^^ . "false"^^ . . . . . . . . "http://www.knapsackfamily.com/knapsack_core/information.php?word="^^ . . . . . . . . "ontology" . . "^[cdfgops]__\\w+\\S+$"^^ . "PhylomeDB" . . "https://coicatalogue.uc.pt/index.php?t=specimen&COINumber=$1"^^ . . . "project management" . . "Plasmodium Life Cycle" . "https://e-cyanobacterium.org/models/model/"^^ . "sample_002"^^ . "bandrow@gmail.com" . . . . "lattes" . . . "kegg.metagenome" . "http://aber-owl.net/ontology/$1" . . . . "Shoshana J. Wodak" . . . . _:Nb039f65249c74fabb39262758d9cba60 "Lars Juhl Jensen" . "The Common Entity Data Standards (CEDS) Domain Entity Schema (DES) provides a hierarchy of domains, entities, categories, and elements. It is intended for use primarily by people as an index to search, map, and organize elements in a logical way. [from homepage]"^^ . . "food" . _:N660a55a7ed6a461481924dd0b463a5f0 "noreply@bioontology.org" . . . . "human" . . "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"^^ . . . . . . . "Donovan Parks" . . . . . . "http://purl.obolibrary.org/obo/GOREL_$1"^^ . . . . _:N15ef3856e9974f1ba44c136fd9b90bcd "MedDRA MSSO" . . . . . "gene" . "false"^^ . _:Nd8d641a7ff3047728eaeb8c847a7e158 "jamsden@us.ibm.com" . . "medical informatics" . . . . . . . . . . "David Blackburn" . "false"^^ . . . . . . . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id="^^ . . "ontorxn" . "subject agnostic" . . . "bioinformatics" . "Sabrina Toro" . "http://ratmap.org/Showgene.php?gene_stable_id="^^ . . "obo" . "GeoNames Feature Code" . "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^ . . . . "fplx" . . "true"^^ . . "MSH2010_2010_02_22" . "CHEMBL465070"^^ . . . "anatomy" . . . . "small molecule" . "has responsible" . . . "sgn" . . "^BSU\\d{5}$"^^ . "^[a-z0-9\\-_]+$"^^ . "immune system" . . . . . "^\\d{7}$"^^ . . "richard.scheuermann@nih.gov" . . . . "ontology" . . "Development Data Object Service" . "life science" . "https://biopragmatics.github.io/providers/goche/"^^ . "The prefixes appearing in this collection correspond resources whose entities could appear as values for target groups, media types, educational levels, and other fields in OER data models.\n\nIt was originally curated as part of the publication [_Teaching RDM in a smart advanced inorganic lab course and its provision in the DALIA platform_ (arxiv:2509.18902)](https://arxiv.org/pdf/2509.18902)." . . . . . . . . . . "http://rs.tdwg.org/dwc/terms/"^^ . . . . . . _:Nee88b7db3bb94ad38302a3495582d71e "Patricia Brooks" . . . . "Research Resource Identifiers" . . . . . "Common Bean ontology" . . . "https://www.webofscience.com/wos/author/record/"^^ . . . . . . "https://n2t.net/$1:$2" . . . . . . . . . "National Organization for Rare Disorders" . . . . . . "^GCA_[0-9]{9}(\\.[0-9]+)?$"^^ . . "clo" . "gene expression" . "https://www.kegg.jp/entry/$1"^^ . "^\\d{5}$"^^ . "stock" . . "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."^^ . . . . . . "1"^^ . "https://uts.nlm.nih.gov/uts/umls/concept/$1"^^ . "http://www.onto-med.de/ontologies/gfo.owl#"^^ . "false"^^ . "botany" . . . "false"^^ . "false"^^ . . "bind" . "000001"^^ . "https://www.enzyme-database.org/query.php?ec="^^ . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . . . "http://purl.obolibrary.org/obo/TADS_"^^ . "sedml.format" . . "true"^^ . . . "https://www.confident-conference.org/index.php/Event_Series:"^^ . . . . "G protein-coupled receptor database" . . "gorel" . "^\\d+$"^^ . "cognition" . . "nist.codata" . "http://www.w3.org/2006/time#"^^ . . . . . . "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)."^^ . . . "structure" . . . . "false"^^ . . "https://polbase.neb.com/polymerases/$1#sequences"^^ . "https://biosimulators.org/simulators/"^^ . . . "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm"^^ . . . . . "false"^^ . "Q9UKQ2"^^ . . . "Schema.org" . . . "GE86325"^^ . "mampol" . "13"^^ . . . . "systems biology" . "^\\d+/.+$"^^ . "ontology" . "SCancerRNA provides identifiers for non-coding RNA biomarkers, including long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA, with data on their differential expression at the cellular level in cancer."^^ . . . . . . "ontology" . . "kegg.module" . . "mcarthua@mcmaster.ca" . "false"^^ . _:Nbc5554f14fc14cbe9dd87f8245b8368b "David J. McLaughlin" . "^\\d{7}$"^^ . . "florianv/swap"^^ . "model organism database" . . "protein" . . . "ChEMBL target" . . . "gwang@unmc.edu" . . . . . "preclinical studies" . . "true"^^ . "gene" . "https://eol.org/pages/"^^ . "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1"^^ . "person" . . . "http://purl.obolibrary.org/obo/INO_"^^ . . _:Nf1e1ab922e6f4149b4c3fddb86110c0d . . . . "epidemiology" . "RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments."^^ . . . "KCT0008394"^^ . "http://purl.obolibrary.org/obo/CMO_"^^ . . "^(5?)\\d{7}$"^^ . . . "false"^^ . . "xao" . . "MTHICD9_2006" . . . . "regulation" . . "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)."^^ . . "chemistry" . . "false"^^ . "r@iannel.la" . "Vir-Mir db" . . . . . . . "false"^^ . . "^[A-Z_a-z]+$"^^ . "ChemSpiderID" . "mjj@ebi.ac.uk" . "CropMRespository is a database of soil and crop biophysical process models."^^ . . . . . "https://w3id.org/class/sectors/"^^ . "mmp.fun" . . . . "kim.esv" . . "http://www.w3.org/1999/xhtml/vocab#"^^ . "^\\d+$"^^ . . . "KEGG Compound" . . . . "UniProt" . "minid.test" . . . "Library of Congress Format Description Document" . "TA14985"^^ . "Daniel Kahn" . . . "molecules" . "^\\d{7}$"^^ . "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"^^ . . . . . . "^SM\\d{5}$"^^ . . . . . "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1"^^ . . . . . . "the European Hepatitis C Virus Database (euHCVdb, euhcvdb.lyon.inserm.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses."^^ . . . . . . "Selventa Chemicals" . . "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"^^ . . . . . "GXA Expt" . . . . . . . . . "Paula.Duek@sib.swiss" . . "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"^^ . . . "Veterans Administration National Drug File" . "false"^^ . "https://dialnet.unirioja.es/servlet/autor?codigo=$1"^^ . "Citation Typing Ontology" . "BioGRID Interactions" . "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"^^ . . . . . . . "Identifiers represent RNA-protein interaction entries with quantitative kinetic data in the Kinetic Data of Biomolecular Interactions for RNA-Protein database (KDBI-RP), which is an open-access database cataloging association rates, dissociation rates, and equilibrium dissociation constants for RNA-protein interactions."^^ . "health_care_quality_assessment"^^ . . "immunology" . . "vendor" . . . "ontology" . "descriptionAnnot"^^ . "RNAloops" . "Kristian Axelsen" . . . . . "edam.format" . . . . . "false"^^ . "ontology" . "^CDBP00\\d{6}$"^^ . "^\\d+$"^^ . . . . . . . . "obo" . . "http://www.w3.org/2011/content#"^^ . . "https://suprabank.org/molecules/$1"^^ . . "systems biology" . . "ideal" . . . "Hymenoptera Anatomy Reference" . . . . . . "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^ . "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^ . "false"^^ . . . . . . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/LABO_$1"^^ . "^5\\d{4}$"^^ . "false"^^ . . . "7207"^^ . "ontology" . . . . "http://www.co-ode.org/ontologies/galen#"^^ . "false"^^ . "HGVM15354"^^ . "Integbio" . . . . . . "opmi" . . . _:Nf7c00a8535ea4cf3857a950c86008370 "IIS Helpdesk" . . . "Information Resource Registry" . . "natural science" . . . . . . . . . . . . . "FlyBase Gene" . . . . "rdf" . "6472"^^ . "https://www.wikidata.org" . "gene" . . "false"^^ . "Andrea Gaedigk" . "vocabularies" . "genome" . "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^ . "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan="^^ . "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."^^ . "Darren Natale" . . "101"^^ . "pathway" . "mmartone@ucsd.edu" . . "Capability"^^ . . . "Genotype Ontology" . . . . . . "genome" . . . "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."^^ . "https://credit.niso.org/contributor-roles/$1"^^ . . . . "Influenza Sequence and Epitope Database" . . . . . "http://degradome.uniovi.es/cgi-bin/protease/"^^ . "https://archive.softwareheritage.org/browse/swh:$1"^^ . . "false"^^ . . . . . . . . "sample annotation" . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid="^^ . . . . . "^A\\d+$"^^ . . . . . "medicine" . . . . . . "true"^^ . . "Ruili Huang" . "^\\d{6}$"^^ . . . . . "SpBase" . . "0000003"^^ . . "false"^^ . . . "glycoepitope" . . . . "^\\d{7}$"^^ . "developmental biology" . "reactions" . . . . "https://suprabank.org/additives/$1"^^ . . . "obci" . . . "^[0-9]+$"^^ . "dictybase" . "GSTA1"^^ . _:N5f25bcb1b0db421f830a0cc3fcc06c6d . "computational biology" . . . "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"^^ . . . "adult" . . . . . "Amelanchier laevis"^^ . "cncb.gwh" . . "ontology" . . "The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts."^^ . "iot" . "https://www.npatlas.org/explore/compounds/$1"^^ . . "d.craik@imb.uq.edu.au" . "https://bioregistry.io/nsrrc:"^^ . . . "hasProperty"^^ . . . "false"^^ . . . . "mcmelek@msn.com" . . "^M\\d+$"^^ . . . . . . . "false"^^ . "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . "covid-19" . . . . . . "false"^^ . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME"^^ . . "^\\d{7}$"^^ . "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets"^^ . . "http://www.pseudomonas.com/feature/show/?locus_tag=$1"^^ . . . "mo" . . "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."^^ . "false"^^ . . . . "https://www.biosino.org/rdbsb/bioparts_detail/"^^ . . "ChemIDplus" . "biomedical science" . . . . "ddanat" . . . "http://purl.org/pav/"^^ . "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."^^ . . "chebi"^^ . . "geo" . . "ontology" . . . "NCBI Registry" . . "http://data.europa.eu/89h/$1"^^ . "02069237"^^ . . . "false"^^ . "ontology" . . "6e3b1371-59d7-481a-9db4-cd0d0de98436"^^ . . . . "vendor" . "loc.resourcetype" . . . "Semanticscience Integrated Ontology" . . "Health Surveillance Ontology" . . . . . "false"^^ . . "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."^^ . "ontology" . . "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^ . "wikigenes" . . . . . . . . . . "false"^^ . . "12"^^ . . "Catalogue of Life" . "true"^^ . . . "spectra" . . "false"^^ . . "nmr" . "10194"^^ . . . . . . . "Environment Ontology" . . . . . . "false"^^ . . . . . . . "ceaf4ca0-9b09-4313-85a5-2edf1762e443"^^ . . . . "nicolas.matentzoglu@gmail.com" . . . . "Quantities, Units, Dimensions, and Types Ontology" . . "Integrated Resource for Domestic Dog" . . . "live mouse" . "zhaoxuetong@big.ac.cn" . "clarin.concept" . . "The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible ontology describing the functions and actions of biologically important chemicals including primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals. The identifiers in this semantic space correspond to entries in the ChemFOnt ontology that are used to organize individual chemicals. Terms can be looked up using the following URL (https://www.chemfont.ca/ontology_browse/term_info/18), but not directly by ID"^^ . "chemical" . "ohd" . . "MGnify Genome" . . . . . . . "false"^^ . . . . "glycopost" . "https://cropontology.org/rdf/CO_330:"^^ . . "Vitro Application Ontology" . "EGAS00000000001"^^ . "medical imaging" . "Heng Zheng" . . . "Cell Cycle Ontology" . . . . "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^ . "Sheeba Samuel" . . "http://autism.mindspec.org/GeneDetail/$1"^^ . . "bmrb" . "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone="^^ . . . . "ontology" . . . "false"^^ . . . . "computational biology" . . . . . . . . "protein" . "false"^^ . "ontology" . . . . "pharmacology" . . . . . "obo" . . "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1"^^ . "classification" . . "centrally registered identifier" . . "structure" . . "vaccine" . "Cell line collections (Providers)"^^ . "Dorothea Iglezakis" . "^MCDS_L_[a-zA-Z0-9]{1,10}$"^^ . "http://purl.obolibrary.org/obo/IDO_$1"^^ . "nlx.anat" . . . . . . . . . "Sivaram Arabandi" . . . "^\\d{7}$"^^ . . "12e8LH"^^ . "PWY3O-214"^^ . "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo"^^ . "enzyme" . . . "^MNEST\\d+$"^^ . . . . "genomic sequence" . "CC2(C)C\\1CCC(C)/C=C/12"^^ . "obo" . . . . . . _:Nd9e2a85080184e66ae3d6137d39a4341 "Jonathan Bard" . "knowledge and information systems" . . "false"^^ . . . "A user of FAIRsharing"^^ . . . . "gtr.lab" . . "Shur-Jen Wang" . . "SWISS-MODEL Repository" . . . . "^AT\\d+$"^^ . "Cell line collections (Providers)"^^ . . . "obo" . "beta cell" . "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."^^ . . . "behavior" . "https://mednet-communities.net/inn/db/ViewINN.aspx?i="^^ . "false"^^ . "http://purl.obolibrary.org/obo/MFOEM_"^^ . "0376"^^ . "https://github.com/information-artifact-ontology/IAO/issues/"^^ . . "https://togoid.dbcls.jp/#"^^ . . . "evan@epatters.org" . "data transformation" . "Database of Complete Genome Homologous Genes Families" . "https://www.datanator.info/metabolite/$1"^^ . "CHMO, the chemical methods ontology, describes methods used to"^^ . . "000072"^^ . . "occupational medicine" . "biomedical science" . . . . "hannele.laivuori@helsinki.fi" . . . . "hl7.v3codesystem" . . "http://www.loc.gov/premis/rdf/v3/"^^ . "^\\d+$"^^ . . "^CHEMBL\\d+$"^^ . . . . . "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^ . . . . "false"^^ . . . . . "NCBI Orthologs" . . . "zenodo.record" . . . "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"^^ . "ndfrt" . "obo" . . . "terms approved for use by BODC to describe the measurement units for data held in its repositories."^^ . . . "false"^^ . "https://morpheus.gitlab.io/models/"^^ . . "lschriml@som.umaryland.edu" . . . . "Ontology of Zebrafish Experimental Conditions"^^ . . . . . . . . . "gtuco.btuco@gmail.com" . . "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . "genetics" . . "chemical" . "Contributor Role Ontology" . . "Terminology of Anatomy of Human Embryology" . . . . "embryo" . "hoso" . . . "https://cropontology.org/rdf/CO_324:"^^ . . . . "ontology" . . "ontology" . "MEROPS Entry" . . "true"^^ . "itis" . . . "100810"^^ . . . . "protein" . "false"^^ . . . . . . . "The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for bacteria and archaea sources linked to their associated set of biosynthetic gene clusters (BGCs)."^^ . . "molecules" . "https://www.dpvweb.net/dpv/showdpv/?dpvno=$1"^^ . "https://scicrunch.org/resolver/RRID:$1_$2" . . . "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."^^ . . . . "environmental science" . . "genome" . "https://metacyc.org/META/NEW-IMAGE?object=$1"^^ . "ontology" . "http://purl.obolibrary.org/obo/OOSTT_"^^ . "Oryzabase Gene" . . "Histidinol dehydrogenase (EC 1.1.1.23)"^^ . . . "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."^^ . . "true"^^ . "scopus.publication" . "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" . . . . . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"^^ . . . "YeTFasCo" . "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . . . . . "ontology" . . "strain" . . "EDDA Study Designs Taxonomy" . . . . "MRA-253"^^ . . . . . . . . . "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."^^ . . "false"^^ . . . "A type for entries in the Bioregistry's metaregistry." . . . "has responsible" . . "MycoBrowser marinum" . . . . "true"^^ . "aallen@ascl.net" . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . "botany" . . "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1"^^ . "http://purl.obolibrary.org/obo/OBCI_"^^ . . . "druzinsk@uic.edu" . "Xenbase" . . "sequence" . . . "KIM Education Level" . "^\\d+$"^^ . "International Standard Serial Number" . "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)"^^ . . . "KEGG_DRUG_GROUP" . "http://www.ontology-of-units-of-measure.org/resource/om-2/"^^ . "tigrfam" . . . "Rachael P. Huntley" . . . . . . . "http://purl.obolibrary.org/obo/LIPRO_$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."^^ . . . . . "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . . "biology" . . . . "http://rs.tdwg.org/ontology/voc/TaxonRank#$1"^^ . . "agriculture" . . "ontology" . . . "scop.sunid" . "ontology" . . . . . . . . . . "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"^^ . . . "https://www.iedb.org/receptor/"^^ . . "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."^^ . "classification" . . . . . . . . . "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."^^ . . "false"^^ . . . . . . . . . . . . . "https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/$1"^^ . . . . "morphology" . . . "http://leafsnap.com/species/$1/"^^ . . _:Ne763fe65e2c8492a9dc145ee4037ff0d "Jonathan Bard" . "false"^^ . . "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."^^ . . . "nutritional science" . . . . . . "disease" . . . "https://www.thaiclinicaltrials.org/show/$1"^^ . "unipathway" . "food" . "interaction" . "http://purl.obolibrary.org/obo/DRON_$1"^^ . . . . . "CASGEN" . . "146421"^^ . . "false"^^ . "obo" . . . . . . . "false"^^ . . "vfdb.gene" . . . . "https://www.e-cyanobacterium.org/bcs/entity/$1"^^ . "HL7 V2 Code System" . . . "LOTUS Initiative for Open Natural Products Research" . . "0001157"^^ . . . "Sumir Pandit" . . . . . . "A representation of the variety of methods used to make clinical and phenotype measurements."^^ . . . . "false"^^ . . "neurondb" . "biomedical science" . . . . "small molecule" . "false"^^ . "metnetdb" . . "PELNAW"^^ . "4DN" . "oridb.sacch" . . . . "education level" . "DrugBank" . "Protocol for Web Description Resources (POWDER) Schema" . . "D053716"^^ . . "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically."^^ . "jaxmice" . "183"^^ . . "6000122"^^ . "A curated list by Sage Bionetworks of external resources that are automatically linked on Synapse.org and affiliated data portals" . . . "virology" . . . "https://www.brenda-enzymes.de/ligand.php?brenda_group_id="^^ . . . "flybase" . "INSPIRE theme register" . . . . "rbca.jackson@gmail.com" . . "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]"^^ . . . . . . . . "phylogenetics" . . . . . . "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."^^ . . "https://w3id.org/semapv/vocab/$1"^^ . "0000052"^^ . . . . . . . . . "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"^^ . . "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."^^ . . . "Ontology for Immune Epitopes" . . . . "http://purl.obolibrary.org/obo/OMP_$1"^^ . . . "Zebrafish developmental stages ontology" . . . "1"^^ . . . "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)."^^ . "0000001"^^ . "ybradford@zfin.org" . "https://www.cellosaurus.org/CVCL_"^^ . . . "https://cellxgene.cziscience.com/collections/"^^ . "Gene"^^ . . "false"^^ . "ontology" . . . . . . "0000512"^^ . . . . . "Scientific Evidence and Provenance Information Ontology" . "https://www.authorea.com/users/$1"^^ . . . . . . . "Evaluation and Report Language" . . . . "https://www.ebi.ac.uk/metagenomics/projects/"^^ . "subject agnostic" . "Allotrope Merged Ontology Suite"^^ . "obo" . "co_341" . "scientist" . "dce" . . "hssp" . "WikiGenes" . "classification" . . . . . . "Curation of Neurodegeneration Supporting Ontology" . . . "http://localhost/plosthes.2017-1#"^^ . "https://www.webofscience.com/wos/author/record/$1"^^ . "nfdi4dso" . "pdb.ligand" . "biomedical science" . . . "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"^^ . . "^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$"^^ . . "Human developmental anatomy, abstract version" . . "fideo" . . . "^\\d+$"^^ . . "false"^^ . . . . "Pocketome" . "cryptodb" . . . "ontology" . "^\\d{7}$"^^ . . . "rdfa" . . . . . "http://purl.obolibrary.org/obo/NIF_CELL_$1"^^ . . . . . . . "data schema" . "false"^^ . "genetics" . "Laia Subirats" . "true"^^ . "xhv" . . . . "https://catalog.integbio.jp/dbcatalog/en/record/"^^ . "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."^^ . . "chemical" . "004435"^^ . "hc.trial" . "Gerhard Mayer" . "NCBIGene" . "FOOD00020"^^ . "Cell line collections (Providers)"^^ . . . _:Nb5631ff21e9f4f0d986745314038884d "NLM Customer Service" . . "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."^^ . . . "1"^^ . . "condition" . "https://flybase.org/reports/FBrf$1"^^ . . "metascience" . . "ontology" . . . "dpv" . . "esldb" . . . "false"^^ . . . . . . _:N3e266efc844a4720a554e4b284b0e9de "kasschau@cgrb.oregonstate.edu" . . . . . "https://hub.docker.com/r/"^^ . . . "life science" . . "https://www.mavedb.org/#/experiments/urn:mavedb:"^^ . . . "FunderRegistry" . "Interactions are SupraBank's way to collect information about experiments that describe the binding interaction between molecules. The form for creating an interaction enables you to list all experimental conditions. An interaction is similar to an entry in a table in your scientific publication, but providing machine readable comprehensive information. (from homepage)"^^ . "KEGG_PATHWAY" . . "false"^^ . . . . "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id="^^ . . . "metadata" . . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . . . "2381/12775"^^ . . "Properties in DBPedia."^^ . "Infectious Disease Ontology" . . . . "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." . . . "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]"^^ . . . . "Kathryn Dumschott" . . "nlx.mol" . . "https://i.uestc.edu.cn/AACDB/details.php?id=$1"^^ . . . . "http://purl.obolibrary.org/obo/AAO_"^^ . "PhosphoSite Site Group" . . . . "cdpd" . . . . . "InformAll Allergenic Food Database" . "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein."^^ . . . "Computer Retrieval of Information on Science Projects Thesaurus" . . . . "false"^^ . . . "natural language processing" . . . . . . "^\\d{7}$"^^ . "402558626"^^ . "https://www.genedb.org/gene/$1"^^ . . . "(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."^^ . "false"^^ . "ICD10WHO" . . . . . "IntAct protein interaction" . . . "YAL001C"^^ . . . . . . "An Educational and Career-Oriented Recommendation Ontology" . . "ontology" . . "proglyc" . . "phenomics" . . "sensor data" . "topics" . . "2d-page" . . . . "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." . . . "cellxgene.collection" . . . "kblin@biosustain.dtu.dk" . . . "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . . . . "GiardiaDB" . . . . . . . "https://legacy.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . "dwudwary@lbl.gov" . "gene" . "PharmGKB pathway" . "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"^^ . "false"^^ . . . . . . "interaction" . "2-s2.0-0030770923"^^ . . "Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation."^^ . . "pspub" . "0000091"^^ . . . . "physiology" . "Selventa Complexes" . . . . "CL000025"^^ . . . . "http://xmlns.com/wot/0.1/"^^ . . "^S\\w+(\\.)?\\w+(\\.)?$"^^ . . "gwascentral.study" . "ALA"^^ . . . . . . . . "Elizabeth Arnaud" . _:Nff095911261b4b07a1c6079c6f0175ce . . "life science" . . "Semantic Web Applications in Neuromedicine" . "14362"^^ . "James Alastair McLaughlin" . "https://bioregistry.io/imgt.primerdb:"^^ . "false"^^ . . . "ato" . . . "false"^^ . "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."^^ . "Homologous Vertebrate Genes Database" . "joshua.adam.klein@gmail.com" . "false"^^ . "geographic location" . . . "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . . _:N593c178482fa4d9297fdf9d7014db005 "icd@who.int" . . "genbase" . "http://erop.inbi.ras.ru/result2.php?PepName=$1"^^ . "1"^^ . "GWAS Central Study" . . "microbe-host interaction phenotype" . "^H\\d\\.\\d{2}\\.\\d{2}\\.\\d\\.\\d{5}$"^^ . . . . . "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1"^^ . . . "kristian.axelsen@sib.swiss" . . "false"^^ . "agrovoc" . "ner" . . . "LINCS Data" . . . . "0000632"^^ . "CHEMBL3559721"^^ . . "obo" . "gmd.gcms" . . . "493771"^^ . . "International Clinical Trials Registry Platform" . . . "PMID" . "natural science" . . . "computational biology" . . "centrally registered identifier" . . . "schaefec@mail.nih.gov" . . . . . "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors."^^ . . . "r3d100014165" . "eric.sid@nih.gov" . "Brachiaria ontology" . . . . "obo" . "true"^^ . . . . . . . . . . . . "Canadian Drug Product Database" . "HOSAPI0399"^^ . "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories."^^ . "^\\d+$"^^ . . . "physiology" . . . "false"^^ . . . "enzyme" . . . . . "47419"^^ . "^\\d{7}$"^^ . . . _:Ncffc3b856e93458fb7ad9ae74fb39b2e "Pance Panov" . "false"^^ . . . . . . . . . . . . "ontology" . "phenotype" . . . "^\\d+$"^^ . . "chemistry" . . . "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . . . . "https://www.icd10data.com/search?s="^^ . . "ASTD" . "false"^^ . . . "dpbo" . "http://purl.org/nemo/competence#$1"^^ . . "http://w3id.org/kim/schulfaecher/"^^ . . "The data cube vocabulary" . . "ProtoNet ProteinCard" . . . . . "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family="^^ . . "EDAM Ontology" . . "BitterDB Compound" . . "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^ . "http://purl.obolibrary.org/obo/MS_$1"^^ . "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names."^^ . . . . . . . "85163"^^ . "biocuration" . . "^\\d{9}$"^^ . "436154da-bcf1-4130-9c8b-120ff9a888f2"^^ . . "false"^^ . "http://purl.obolibrary.org/obo/OBA_$1"^^ . . . "genome" . . "life science" . "genomics" . . "gene prediction" . "0000400"^^ . . "biocyc" . . . . . . . . "food" . . "An ontologization of Public Library of Science (PLOS) journal keywords and topics. It's not clear how the IDs correspond to the actual pages. Appears in ADCAD."^^ . "astd" . . . "true"^^ . "false"^^ . . . . "ontology and terminology" . "^\\w+$"^^ . . "Small Angle Scattering Biological Data Bank" . . . . "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1"^^ . . "biomedical science" . . . . . "65"^^ . "^DDB\\d+$"^^ . "false"^^ . "Assigns identifiers to knowledge graphs (KGs) that are used and/or maintained within any NFDI consortium."^^ . . "https://redoxibase.toulouse.inrae.fr/display_perox/view_perox/"^^ . . "true"^^ . . . . . . . . . . "registry" . "http://www.w3.org/2003/06/sw-vocab-status/ns#$1"^^ . . "false"^^ . "ontology" . . "bcrj" . . . . . . . "infectious" . "000009"^^ . "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$"^^ . _:Nd64ff50fbeeb4373853e6b7314155a9c "ncithesaurus@mail.nih.gov" . . . "CDC2"^^ . "Vlado Dancik" . . . . . "germline" . "0107180"^^ . . . . . "https://data.chembiosys.de/projects/$1"^^ . "https://www.datenportal.bmbf.de/portal/de/$1.html"^^ . . "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."^^ . . . . "obo" . . "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^ . . . . . . . . "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."^^ . . . . . . "pathobiochemistry" . "cthoyt"^^ . "false"^^ . . . . . "00000000001"^^ . "life science" . . . . . "depod@embl.de" . "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"^^ . . . . . . "ccle" . . "life science" . . "1801.012"^^ . . "https://images.endlessforms.info/collection/$1"^^ . . . . . "tgbugs@gmail.com" . . . "obo" . . "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^ . "nlp" . "knockout" . . . . "structrual bioinformatics" . . "disease course" . "An ontology of prokaryotic phenotypic and metabolic characters"^^ . "hoganwr@gmail.com" . . "^[A-Z0-9]+$"^^ . "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"^^ . . . "Sean May" . "http://www.ifomis.org/bfo/1.1/snap#"^^ . "false"^^ . . "taxonomic classification" . "Friend of a Friend" . . "qtl" . "P0DP23"^^ . . . . . . . "gomfid" . . "https://omia.org/phene/omia:"^^ . "BCRC Strain Collection Catalog" . "http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2" . "false"^^ . "http://purl.obolibrary.org/obo/FBcv_$1"^^ . "obo" . . "https://disprot.org/"^^ . . . . "https://www.sharkipedia.org/trends/"^^ . "apaonto" . . "title"^^ . . "gramene.qtl" . . . . . . "https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1"^^ . . . "Social Behavior in insects"^^ . "mouse embryonic stem cell line" . . "medicine" . . . . . . . . . . "protein" . . "pephub" . . "funding agencies" . . . "https://abrc.osu.edu/stocks/number/SALK_"^^ . . . . "http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?winid=1&recid=$1"^^ . . "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . . . . . . "^[1-9]\\d*$"^^ . . . . . "clinical trials" . "https://glytoucan.org/Structures/Glycans/"^^ . . "ontology" . "0000564"^^ . . "jrsmith@mcw.edu" . "false"^^ . . . . . "^[A-Za-z0-9-]+$"^^ . . . "joel.richardson@jax.org" . . . "https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/$1"^^ . "obo" . "https://psskb.org/motif/card/$1"^^ . "false"^^ . "obo" . . "markley@nmrfam.wisc.edu" . . "false"^^ . . "false"^^ . . "pubchem.classification" . . . . . . . . . . . . . "http://purl.obolibrary.org/obo/T4FS_"^^ . "A collaborative project intended to create an encyclopedia documenting all living species known to science"^^ . . "chemical" . . "NIF Dysfunction" . . "Rfam database of RNA families" . . . _:Nc47ec4ead5d14c2ca67e8fa44e0b94d8 "Laura Molloy" . "^\\d{7}$"^^ . . . "http://purl.obolibrary.org/obo/IDOMAL_$1"^^ . . "false"^^ . . "https://doulix.com/constructs/"^^ . . . . "upheno" . . "https://biopragmatics.github.io/providers/schem/"^^ . . . "http://purl.obolibrary.org/obo/FBcv_"^^ . . . . "worldavatar.compchem" . . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$"^^ . . . "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)."^^ . . . . "^DP\\d{5}$"^^ . "hoelzel" . . "http://purl.obolibrary.org/obo/TRANS_$1"^^ . "false"^^ . . . "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1"^^ . . . . . . . "Tetrahymena Genome Database" . . . "github" . "^CHEMBL\\d+$"^^ . "iuphar.ligand" . . . . "bioinformatics" . . . "mobio" . "0001079"^^ . "cultured cell line" . . "^[0-9a-fA-F]{32}$"^^ . . . . . . . "life science" . . . . "This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]"^^ . . "A project in the nmrXiv"^^ . . "NIF Standard Ontology: Neurolex" . . "cog.category" . "false"^^ . "^\\d{7}$"^^ . . "Software Package Data Exchange License" . "false"^^ . "false"^^ . . "false"^^ . . . . . . "OMIM" . . "spar" . "false"^^ . . "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."^^ . . "^KGR\\d+$"^^ . . "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an="^^ . "damion_dooley@sfu.ca" . "false"^^ . . "eo" . "true"^^ . "An ontology of minimum information regarding potential drug-drug interaction information."^^ . "https://mite.bioinformatics.nl/repository/$1"^^ . "inbred" . "wos.work" . "botany" . "ena.embl" . . "false"^^ . . . "molmovdb" . . . . . "ZINC1084"^^ . . "http://www.marinespecies.org/aphia.php?p=taxdetails&id="^^ . "DrugBank" . . . . . . . . "ontology" . . "https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema="^^ . "http://emmo.info/emmo/cif-core#$1"^^ . . . . . . "pathway" . "^[a-z0-9]{5}$"^^ . . "virology" . . "^\\d+$"^^ . "false"^^ . . . . . . . . . . . "false"^^ . . . . . "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^ . "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^ . . "^(\\w+)?\\d+$"^^ . "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome."^^ . . . . . . . . "false"^^ . "^\\d{7}$"^^ . "fetal fibroblast" . "http://viroligo.okstate.edu/main.php?vid="^^ . "resource metadata" . "http://purl.obolibrary.org/obo/NCRO_"^^ . . . . . . . "6"^^ . "https://europepmc.org/article/AGR/$1"^^ . "cell" . "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . . "An ICD-11 code is a standardized alphanumeric identifier used to classify and document diseases, conditions, and health-related issues for global healthcare and statistical purposes."^^ . . . . . . . "Marie-Angélique Laporte" . . "drugs" . . . . . "structure" . . . . "nmr" . . . . . . "https://modeldb.science/modellist/$1"^^ . . . "^\\d{7}$"^^ . "co_357" . "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."^^ . "biotop" . . . . "genome" . . . . . . . . . "^\\d+$"^^ . . "snap" . "GR_QTL" . . . . . "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . . . . . "Role Ontology" . "Blue Brain Project's published data as knowledge graphs and Web Studios."^^ . . . . . . . "An ontology of core ecological entities" . . . "^IHW\\d+$"^^ . "http://wodaklab.org/iRefWeb/interaction/show/"^^ . "Korean Cell Line Bank" . . . . "false"^^ . . . . "protein" . . . . . "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."^^ . . . "genome" . . . . . "eugenes" . . . "^\\d+$"^^ . "obo" . . "GL50803_102438"^^ . "^\\d+$"^^ . "Chemical Methods Ontology" . . . "^\\d{7}$"^^ . . . "ontology" . . . "irct" . . . . . . "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^ . . . . . . . . "Concepts for encoding bibliometric information"^^ . "^\\d+$"^^ . "http://stormo.wustl.edu/ScerTF/details/"^^ . . . . "https://github.com/monarch-initiative/mondo/issues/$1"^^ . "mieg@ncbi.nlm.nih.gov" . "genome" . "fish" . . "https://www.authorea.com/users/"^^ . . . "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid="^^ . "taxonomy" . . "David.Linke@catalysis.de" . "Resource" . . . . "G77500AY"^^ . . . . "MC" . "taxonomic classification" . . "Philippe.Lemercier@sib.swiss" . "The Amphioxus Development and Anatomy Ontology" . "TGME49_053730"^^ . "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place."^^ . . . . . "^TF\\w+$"^^ . . . . "bioinformatics" . . "false"^^ . . . . "http://purl.obolibrary.org/obo/CDAO_"^^ . . . "chempro.target" . . . "gexo" . "International Standard Classification of Education, 1997 Edition" . "^\\d{7}$"^^ . "Yeast Metabolome Database" . . . "273"^^ . . . . "life science" . . . . . . "Dialnet journal ID" . . "A hierarchical classification of congenital heart disease"^^ . . . . . . "gene" . . "jmg11@cam.ac.uk" . . . "academy" . . "developed by ICARDA - Dec 2018"^^ . "53504"^^ . . . . . "brain" . "scoro" . . . . . "kalpanap@ebi.ac.uk" . . . . . . . . . "d1id" . . "Lattes Platform number" . "Michal Linial" . "wos.researcher" . . . . . "culture" . . . "vgnc" . . . . "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^ . "life science" . . . "fungi" . "evm" . . . . . . . . . . . "pruitt@ncbi.nlm.nih.gov" . "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information."^^ . "life science" . . . "cardiovascular disease" . . . . . . . . "Gs0000008"^^ . "comparative genomics" . "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$"^^ . . . "rs11603840"^^ . . . . "ontology" . . . "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."^^ . . "systems biology" . . . "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"^^ . . . "^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$"^^ . . "https://drks.de/search/en/trial/$1"^^ . . . "https://w3id.org/information-resource-registry/"^^ . "Online Dictionary"^^ . "genomics" . . "^\\d+$"^^ . "suprabank.solvent" . . . "^\\d+$"^^ . . . "sty" . "https://cropontology.org/rdf/CO_348:"^^ . "25011"^^ . . "false"^^ . "true"^^ . . . "CohesinDB - cohesin-related chromatin loop" . . . . "HOMD Sequence Metainformation" . . "genome-wide association study" . "^[A-Z0-9]+$"^^ . "developmental biology" . . "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)"^^ . . . "small molecule" . . . . "Sigma Aldrich" . . . . . _:N680b661fb12648a886d0881f4fabc9fc "gregg@greggkellogg.net" . . "heart" . "gene" . . . "The localization and quantitation atlas of the yeast proteome" . . . . . "0000618"^^ . "KNApSAcK" . . "https://mediadive.dsmz.de/medium/"^^ . . . "1.1.1.1"^^ . . "EndlessForms Studio Image" . "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"^^ . . . "true"^^ . . . . . "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1"^^ . . . . "life science" . "Encyclopedia of Life" . "^\\d+$"^^ . . . . "MarDB includes all sequenced marine microbial genomes regardless of level of completeness."^^ . "disease phenotype" . "pdbe" . . . "^\\S+$"^^ . "false"^^ . . . . "false"^^ . "^\\d{7}$"^^ . . . "mouse" . "https://w3id.org/linkml/"^^ . . "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^ . . . . "12345"^^ . . . . . "pharmacology" . . . . . . . . . . . "http://purl.obolibrary.org/obo/GO_"^^ . . . . "false"^^ . "CAE46076"^^ . . . . "genome" . . . . "false"^^ . . "^NONHSAG\\d{5}$"^^ . . "0000041"^^ . . _:Nab3f592f14fe401faf7eb3b4f40c6466 "First DataBank Customer Support" . . . "knowledge graph" . . . . . . . "https://bioregistry.io/cadsr:"^^ . . . . . "true"^^ . . "co_327" . . . . . . "NXPFA" . "false"^^ . . . "mmdb" . . "schemaorg" . . . "KGR1"^^ . . "YBR125c"^^ . "https://ieeexplore.ieee.org/document/$1"^^ . . "^[1-9]\\d{0,5}$"^^ . . . . . . "false"^^ . . "46946"^^ . . "Nicolas Terrapon" . "SNOWMEDCT_US" . "katy@indiana.edu" . . . . "A download link for the given resource" . "bioportal" . . . "0000003"^^ . "NIF Standard Ontology: Chemical" . . "https://www.cellrepo.com/repositories/"^^ . . "subject agnostic" . . . . . _:Nea3693d03c2b40ebbbc21a04344079c1 "guqiong@mail.sysu.edu.cn" . . . "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."^^ . . "Keahi Kaʻiwalani Adolpho" . . . "RSNA Informatics RadLex" . . "The Artificial Intelligence Ontology" . . . "NBR016799"^^ . . . . . . _:Nbca27589757542ff9d0e528d8fc11cf5 . . . . . . . . "w3c rec" . . . "FBcv" . . . . "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)."^^ . . "sisu" . . . . . "HBB"^^ . . . "An ontology of predicates for actions in SIOC"^^ . . . "^SD\\d+$"^^ . "DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects."^^ . . . . . "peff" . "collagenmutdb" . . . . "vertebrate" . "BioData Catalyst" . "https://depmap.org/portal/cell_line/$1"^^ . . . "https://www.holofooddata.org/animal/"^^ . . . "false"^^ . . "http://purl.obolibrary.org/obo/CL_"^^ . . "LIPID_MAPS_class" . "RCSB_PDB" . _:Nea47939e040d4b03980219bf4c045c9a "David J. McLaughlin" . . "http://www.isni.org/isni/"^^ . . "phenology" . "Danielle Thierry-Mieg" . . "metabolite" . . "BioAssay Ontology" . . . "systems biology" . . . . "0000001"^^ . . . . "^PRI\\d*$"^^ . . "entrez" . . "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^ . "^HGVM\\d+$"^^ . "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"^^ . . . . "gene" . "0010015"^^ . . "https://proteinensemble.org/"^^ . . "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"^^ . "http://purl.obolibrary.org/obo/STATO_$1"^^ . "obo" . . . "^[A-Za-z0-9_]+([A-Za-z0-9_\\.]+[A-Za-z0-9_]+)?@[\\d\\w\\.\\-]+[0-9a-z]+$"^^ . . "neuroscience" . . . . . . . . . "Health Canada Drug Identification Number" . "http://pax-db.org/#!protein/"^^ . . "nbrc" . "0000001"^^ . "http://purl.obolibrary.org/obo/OVAE_"^^ . . "90901"^^ . . . . . "https://purl.brain-bican.org/ontology/dmbao/DMBA_$1"^^ . . "^\\d{7}$"^^ . "0000091"^^ . . . "nawrocke@ncbi.nlm.nih.gov" . . . "false"^^ . . . . . "structure" . . . . . . "^[1-9]\\d*$"^^ . . . . . "75121530"^^ . . . . . "C. elegans ORFeome cloning project" . "447860"^^ . "true"^^ . "http://purl.obolibrary.org/obo/GSSO_"^^ . "^\\w+$"^^ . . . . . . "^[AEP]-\\w{4}-\\d+$"^^ . . . . "Arun Prasad Pandurangan" . "Dawood B. Dudekula" . "http://purl.obolibrary.org/obo/BCGO_$1"^^ . . . "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule="^^ . . "false"^^ . "rna" . . "MeSH 2012" . . . . "life science" . . . "devtox" . . "pylebail@rennes.inra.fr" . . . "https://www.inaturalist.org/observations/"^^ . "population genetics" . . "http://zfin.org/"^^ . "false"^^ . . "nutritional science" . "^C?\\d+$"^^ . . "metaregistry" . "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."^^ . . . "UPISO" . . . . . . "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."^^ . . "^\\d+$"^^ . . . . "catalogs" . . . . . "An ontology of commonly encountered and/or high level Drosophila phenotypes."^^ . . . . "protein" . . . "141"^^ . . "zmp@ebi.ac.uk" . . . . . "life science" . "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."^^ . "fr" . . . "hpo" . . "obo" . . . . "cancer" . . . "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id="^^ . "true"^^ . . . . . . "http://w3id.org/nkos/$1"^^ . . . . . . . . . . . . . "protein" . "^\\d{5}$"^^ . . "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . . . "ehdaa2" . . . . . . . "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials."^^ . "https://www.ebi.ac.uk/metagenomics/genomes/"^^ . "false"^^ . "ontology" . . . "http://www.depod.bioss.uni-freiburg.de/showp.php?gene="^^ . . "^[a-z]+(\\..*?)?$"^^ . "1710"^^ . "01625"^^ . "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id="^^ . "biomedical science" . . "^Y[A-Z]{2}\\d+[CW]$"^^ . . . . . . "https://bioregistry.io/pocketome:"^^ . . . . . "bibliography" . . . . "genome" . . . . . . . . . . "https://bioregistry.io/hssp:"^^ . . "https://bioregistry.io/resolve/github/issue/"^^ . . . . . . "kaggle" . "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1"^^ . . . "eagle-i resource ontology" . . "centrally registered identifier" . . "^[A-Z_0-9]+$"^^ . "0061106995455595"^^ . . . "drug discovery" . . . "http://purl.obolibrary.org/obo/PSO_"^^ . "false"^^ . "Stemcell Knowledge and Information Portal" . "HPA000698"^^ . . . . . . . "genetics" . . . . "http://w3id.org/openeduhub/vocabs/educationalLevel/"^^ . "https://bacdive.dsmz.de/strain/$1"^^ . "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . . "false"^^ . "http://purl.obolibrary.org/obo/GENEPIO_"^^ . . . . . "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."^^ . . . . . "Endogenous Regulatory OligoPeptide knowledgebase-Moscow" . . "systems biology" . "A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum."^^ . . . "Hathi Trust Digital Library" . . . . "false"^^ . "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^ . "https://www.gbif.org/species/"^^ . "microbe-host interaction phenotype" . . "M0001"^^ . "3hB06"^^ . . . . "obo" . . . . . . . . . "COEXISTENCE - Thesaurus of intersectionality and decolonial issues: black studies, gender, sexuality and feminist studies"^^ . . "1046"^^ . . . . "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^ . . . "^\\d+$"^^ . . "biolink" . "^\\d+$"^^ . "https://www.ncbi.nlm.nih.gov/gene/$1/ortholog"^^ . . . . "http://purl.obolibrary.org/obo/NBO_$1"^^ . "Rat Genome Database qTL" . "open science" . "http://purl.obolibrary.org/obo/RBO_"^^ . . . . . "A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research.\n\nRadLex provides the foundation for vital data resources used in radiology:\n\n- The LOINC/RSNA Radiology Playbook\n- RadElement Common Data Elements\n-RadReport Radiology Reporting Templates\n\nThe development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project."^^ . "usageNote"^^ . "mark@gersteinlab.org" . "German Archaeological Institute Thesaurus" . . . . . . "false"^^ . . "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . "life science" . . . "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee."^^ . . . "false"^^ . "natural language processing" . . . . "expression" . "earthcube.swl" . "humanities" . . "false"^^ . "0004"^^ . "false"^^ . "go.chemical" . "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."^^ . . "nfdi" . "Online Mendelian Inheritance in Man" . "Brassica ontology" . "protein" . . . "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"^^ . "maglott@ncbi.nlm.nih.gov" . "https://bioregistry.io/flybrain.ndb:"^^ . . "AB" . . "http://purl.obolibrary.org/obo/BMONT_"^^ . . . "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^ . . . . "http://zinc15.docking.org/substances/"^^ . "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u"^^ . . . "33607"^^ . . "animal organ development" . . . . "gainesville.core" . "epidemiology" . "ontology" . . . "drug metabolism" . "MatrixDB Association" . "http://www.w3.org/ns/sosa/$1"^^ . "Q47475003"^^ . "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="^^ . "https://cellxgene.cziscience.com/e/$1"^^ . "MediaDive Ingredient" . . . . . . . . "http://vocab.nerc.ac.uk/collection/P06/current/"^^ . "^[0-9]*\\.*[0-9]*$"^^ . "^\\d+$"^^ . . . "Yongqunh He" . . "Identifiers for synthetic binding protein-target complexes, detailing their components, 3D structures and docking statistics"^^ . "Lentil ontology" . "Federica Quaglia" . . "david.lynn@flinders.edu.au" . "Cell line collections (Providers)"^^ . . . . . . . "grassbase" . . "agriculture" . "sioc.argument" . . . . . "false"^^ . . . . "mesh.2012" . "microbial ecology" . . . . "protege" . . . . . . . "Amanda Hicks" . "Hsa-Let-7-P2a3"^^ . "ThermoFisher is a life sciences supply vendor."^^ . . . "life science" . "https://flybase.org/reports/FBrf"^^ . "01N50ZZ"^^ . "^\\d{7}$"^^ . . "Erik.Segerdell@cchmc.org" . "GM17027"^^ . "annethessen@gmail.com" . "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."^^ . . . "false"^^ . . . . "dna" . . "TC" . "gene" . . "http://purl.obolibrary.org/obo/HAO_"^^ . . . "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)" . . . "5fde96bdc5f1aa9ff0cce18a"^^ . "ontology" . . "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-"^^ . "obo" . . "false"^^ . "reecehart@gmail.com" . "Abdomen"^^ . . . . . . "FAO/WHO_standards" . . . . "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."^^ . . "http://purl.obolibrary.org/obo/AGRO_$1"^^ . . . . . _:N28f417fe9b3c44bc93409fd79fad1d81 . "haiiu@dtu.dk" . "false"^^ . . . . . "ontology" . "http://edamontology.org/data_$1"^^ . . . . . . . "^\\d+$"^^ . . "false"^^ . . "http://rdfs.org/sioc/ns#$1"^^ . . . . . "false"^^ . "Gramene Gene" . "Plant Stress Ontology" . "false"^^ . "life science" . . "grid" . "RiceNetDB Compound" . . . . . . . . "^\\d{4}\\-\\d{6}\\-\\d{2}$"^^ . "https://cropontology.org/rdf/CO_340:"^^ . . . . . "http://purl.bioontology.org/ontology/NDDF/"^^ . . "classification" . "biomodels.vocabulary" . "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^ . . . "Egon Willighagen" . . "anatomy" . "health science" . . "ontology" . . "Ruth Duerr" . . "health science" . "https://www.thermofisher.com/antibody/product/"^^ . . . . . . . . . "https://www.kazusa.or.jp/huge/gfpage/$1"^^ . "software and information systems" . "BRIP1"^^ . . . "CLPUB00496"^^ . . . "false"^^ . . . . _:N3b2e5a75e65c4b6ebb253a66b8a9073c "cellsemantics@gmail.com" . . "https://hub.docker.com/u/"^^ . . "vdrc" . . . "rateRule"^^ . . . . . . . "amphibiaweb.species" . . . . . . . . "false"^^ . "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"^^ . . . "5359"^^ . "frederic.bastian@unil.ch" . . . "Tim Vandermeersch" . . "chemical entity" . "gfrishkoff@gsu.edu" . . "^EGA[SCPNRXZDBF][0-9]{11}$"^^ . "https://w3id.org/faircookbook/$1"^^ . . . . . . . . "http://www.genome.jp/dbget-bin/www_bget?ec:"^^ . "YOR172W_571.0"^^ . . "The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories.\n\nThe Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).\n\nThere are few notable resources providing access to the Enzyme Nomenclature:\n\n
WebsiteHomepageNotes
ExplorEnzhttps://www.enzyme-database.orgThis is the resource officially recommended by IUBMB
IUBMB (via by Queen Mary)https://iubmb.qmul.ac.uk/enzymeThis is a web-based version of the 1992 publication.
IntEnzhttps://www.ebi.ac.uk/intenzShutdown in 2024
ExPaSyhttps://enzyme.expasy.org
EnzymePortalhttps://www.ebi.ac.uk/enzymeportal
"^^ . "http://purl.uniprot.org/isoforms/$1"^^ . "google.patent" . "^\\d(\\d|\\w)$"^^ . "https://www.phenxtoolkit.org/protocols/view/"^^ . . "https://guolab.wchscu.cn/AnimalTFDB4//#/family_summary/TF/"^^ . "proteins" . . "ontology" . . . . "9789211613865"^^ . . . . . "gmd.ref" . . . . "obo" . . . . . . "https://emea.discoverx.com/catalog/$1"^^ . "P00024"^^ . . "chemistry" . . "KEGG Reaction Class" . . "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/)."^^ . . . . "http://www.orpha.net/ORDO/Orphanet_"^^ . "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . "NCBI_GeneID" . . "MEDRA" . "Chen Yang" . "https://gitlab.com/"^^ . . . . . "NCBI Protein" . _:N5f25bcb1b0db421f830a0cc3fcc06c6d "Marc Wick" . . . . . . . . "reaction data" . "co_323" . . . . . . "false"^^ . . "http://purl.obolibrary.org/obo/ADO_$1"^^ . . "http://topdb.enzim.hu/?m=show&id="^^ . "https://bioregistry.io/gmd:"^^ . . . . . . . . "Illumina Probe Identifier" . "https://data.chembiosys.de/publications/$1"^^ . "molecular_function" . . . . . . "https://europepmc.org/article/ppr/"^^ . . . "false"^^ . . . . "ChEMBL" . . "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific."^^ . "Ontology of Vaccine Adverse Events" . . . "life science" . . . . "^\\d{7}$"^^ . . . . . . . . . "00000000"^^ . . . . . "https://w3id.org/gaidet/"^^ . "fly" . . "^\\w{2,3}(-\\w+)?$"^^ . . . . "http://purl.obolibrary.org/obo/MMO_"^^ . "tissue" . . . . . . . . . . "Discourse Elements Ontology" . . "drug" . . "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . "false"^^ . . . . "^\\d+$"^^ . "^\\d{11}$"^^ . "Global Biodata Coalition - Global Core Biodata Resources" . . . . . . . "000004"^^ . . "false"^^ . "false"^^ . . . "ontology" . . . "false"^^ . "sider.drug" . "subject agnostic" . "DI-04240"^^ . . "false"^^ . . . . "Dynamic Ecological Information Management System - Site and dataset registry" . . . . "false"^^ . "metabolomics" . "https://bio.liclab.net/diabetesOmicdb/RNA-seq?sampleId=$1"^^ . "Continuous Automated Model Evaluation" . . . "civic.aid" . . "SwissProt" . . . "datasubs@ebi.ac.uk" . . "Enabling and Unlocking Biology in the Open" . "^MGYP\\d{12}$"^^ . . . "metascience" . "https://www.thermofisher.com/antibody/product/$1"^^ . "genomics" . . . "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^ . . "http://purl.org/spar/pro/$1"^^ . . . . . . . "true"^^ . "false"^^ . "^\\d+$"^^ . . "molecular neuroscience" . . "0000124"^^ . "0001109"^^ . "http://purl.obolibrary.org/obo/CRO_"^^ . "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."^^ . . . . . "bioactivities" . . . "https://www.ebi.ac.uk/ega/datasets/$1"^^ . "http://purl.obolibrary.org/obo/SLSO_$1"^^ . . "stitch" . . . "genomics" . . "28"^^ . "salk" . "http://purl.org/spar/scoro/$1"^^ . . . . . . . "false"^^ . . "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?"^^ . . . "^[AEP]-\\w{4}-\\d+$"^^ . . . . . . "SNOMEDCT_US_2023_03_01" . "^MTBL[CS]\\d+$"^^ . "metanetx.compartment" . . . . . . "quantitative genetics" . . "false"^^ . . . . "false"^^ . . . "expression data" . . . "One of the 23 stages of embryo development"^^ . . "irgsp" . "SUBSET_SIREN" . . . . . . . "https://protists.ensembl.org/id/"^^ . . "ontology and terminology" . . "http://substrate.burnham.org/protein/annotation/$1/html"^^ . . "false"^^ . . "narcis.fernandez@gmail.com" . . "http://addictovocab.org/ADDICTO_"^^ . "https://www.ebi.ac.uk/chembl/id_lookup/"^^ . . "small molecule" . . . . . "asap" . "tkg" . . "^cpd\\d+$"^^ . "false"^^ . . "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."^^ . "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."^^ . "disdriv" . . "ontology" . "maxneal@gmail.com" . "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID="^^ . "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1"^^ . "aireland@lbl.gov" . "false"^^ . "researcher" . . . . "biology" . "https://www-is.biotoul.fr/scripts/ficheIS.php?name="^^ . . . "6978836"^^ . . . . . "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"^^ . . "troy_pells@yahoo.ca" . "admin@envipath.org" . . . "false"^^ . . "research" . "https://www.ebi.ac.uk/ena/browser/view/"^^ . "ontology" . . "Jörg Waitelonis" . . . . . "^\\d+$"^^ . . . "German University Subject Classification System" . . . . . . . . "protein" . . . "false"^^ . . "false"^^ . . "J0705A10"^^ . . "false"^^ . . . . . "pharmgkb.pathways" . . . . . "subject agnostic" . . . . "https://bitbucket.org/"^^ . "http://purl.obolibrary.org/obo/WBbt_"^^ . . . . . "http://zbw.eu/stw/thsys/"^^ . "https://www.checklistbank.org/dataset/$1"^^ . "https://ssbd.riken.jp/database/dataset/"^^ . . "FooDB compound" . "Data Object Service" . _:Ne8f59032a90d4fe18933465e973bd258 "Tom Brennan" . "F45.21"^^ . . . . "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"^^ . . . . "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes."^^ . . "^CLPUB\\d+$"^^ . "A model in the ChemBioSys data platform"^^ . . "Publisher short codes appearin in the NLM Catalog."^^ . . . "ontology" . . . . . "amh"^^ . . "siren" . . "hgnc.genegroup" . . "proteomics" . "false"^^ . . . . . "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?"^^ . "Bryce Mecum" . "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . "allele" . . . . . . . . . . . . "https://lccn.loc.gov/"^^ . . . "false"^^ . . . . . . . "schalk@unf.edu" . "false"^^ . "c0001"^^ . . "EncryptedDocument"^^ . . "true"^^ . . "Human Chromosome Ontology" . . "gene" . . . "life cycle stage" . . . . . "biomedical science" . . . . . . "false"^^ . . "https://bioregistry.io/cldb:"^^ . . "materials informatics" . . . "1968"^^ . . . . "life science" . . . . "GlycoPOST" . . . "http://thebiogrid.org/$1"^^ . . "health" . . . "funcbase.yeast" . . . . . "stato" . . . . . "chemical" . "ontology" . . "^D\\d+$"^^ . "genome" . . "true"^^ . . "SupraBank Additive" . . "^[\\w\\-:,]{3,64}$"^^ . . "DBSALT001211"^^ . . . "http://purl.obolibrary.org/obo/ECAO_$1"^^ . . . "IUPAC Compendium of Analytical Nomenclature (Orange Book)" . "^[A-Z]+[0-9]+(\\.\\d+)?$"^^ . "qtldb" . . . "false"^^ . "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."^^ . "http://purl.obolibrary.org/obo/MMO_$1"^^ . . . . . . . . "false"^^ . . . . "bams" . . "An ontology to capture confidence information about annotations."^^ . . "false"^^ . . "fbcv" . . "Drug Target Ontology" . "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . "^(c|k)\\d{7}$"^^ . . "https://www.uniprot.org/proteomes/$1"^^ . "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . . "interaction" . . "dna" . "obo" . "Chemical Information Ontology" . . "false"^^ . . "has canonical" . "life science" . "false"^^ . . "dg.6vts" . . . . . . "Paul Schofield" . "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon."^^ . . . . . . . "0000190"^^ . "PDB ligand" . "Indications and other conditions in drugbank"^^ . . . . . "http://www.arachnoserver.org/toxincard.html?id="^^ . . "^[1-9]\\d{0,6}$"^^ . . "silva.taxon" . "true"^^ . . "https://graphics.endlessforms.info/unit?id=$1"^^ . . "economics" . . "https://registry.dome-ml.org/review/"^^ . "life science" . . "biology" . "https://pubseed.theseed.org/SubsysEditor.cgi?page=FunctionalRolePage&fr="^^ . . . "pathway" . "This specification contains a framework for representing pointers - entities that permit identifying a portion or segment of a piece of content - making use of the Resource Description Framework (RDF). It also describes a number of specific types of pointers that permit portions of a document to be referred to in different ways. When referring to a specific part of, say, a piece of web content, it is useful to be able to have a consistent manner by which to refer to a particular segment of a web document, to have a variety of ways by which to refer to that same segment, and to make the reference robust in the face of changes to that document. This specification is part of the Evaluation And Report Language (EARL) but can be reused in other contexts too. [from homepage]"^^ . . . "genome" . . "https://www.echa.europa.eu/information-on-chemicals/ec-inventory/-/dislist/details/$1"^^ . "Metabolic Network Exchange Database" . . . . . "https://fungi.ensembl.org/id/"^^ . "^(MAM\\d{5}\\w)|(MAR\\d{5})$"^^ . . "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"^^ . . "NCBI Gene" . . "^BE\\d{7}$"^^ . . . . . . . . . . . . "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."^^ . . "Rhiannon Cameron" . . . . "https://biopragmatics.github.io/providers/icepo/$1"^^ . . . "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1"^^ . . . "hivreagentprogram" . "false"^^ . . "false"^^ . "genome" . . . "https://www.ncbi.nlm.nih.gov/bioproject/?term="^^ . _:N649959919c924cc49fc032c5ce78f634 "kpetersen@who.int" . "data identity and mapping" . . "0002058"^^ . . . . "Identifiers repesent antimicrobial peptides in the Data Repository of Antimicrobial Peptides (DRAMP) database which is an open-access, manually curated database of antimicrobial peptides (AMPs)."^^ . "Wikidata" . . "oryzabase.stage" . "classification" . . . . "subject agnostic" . "00042"^^ . . . . . "ontology" . . . . "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."^^ . . _:N37a28bb55fee4da4bdbcdc1655f4cbe2 . _:N4654dbf5c0074a959f1cf5467bab33e1 "J.Bard@ed.ac.uk" . . . . "morbidity" . . "amphx" . . "10.2.1.1.3"^^ . . . . . "miR-1"^^ . . "https://lincs.hms.harvard.edu/db/datasets/"^^ . "Crystallographic Information Framework" . "genetic" . "true"^^ . "protein" . . "https://cbcb.cdutcm.edu.cn/AGD/plant/details/?id=$1"^^ . . . . . "murine" . . . "595"^^ . . . . . . . "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."^^ . . . . . "http://purl.obolibrary.org/obo/MS_"^^ . "false"^^ . . "false"^^ . . . . . "bfo" . . "balhoff@renci.org" . . "humanities" . . . . . . "strain" . . . . "Document Components Ontology" . "gene family" . . . . . . "false"^^ . "00000021"^^ . . "A-GEOD-50"^^ . "emsl.project" . . . . "civic.therapy" . . . . . "false"^^ . . . "obo" . "https://w3id.org/bervo/BERVO_$1"^^ . . . . "^rs\\d+$"^^ . . . . "http://www.kegg.jp/entry/$1"^^ . . "openwemi" . "zp" . . . . "false"^^ . . . . "62"^^ . "EUCTR" . . . . "medical biotechnology" . . . "Integrated Taxonomic Information System" . "false"^^ . . "co_335" . "thomas@luetteke-online.de" . "ontology" . "090803"^^ . "false"^^ . "^[1-9]\\d*$"^^ . . . . "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."^^ . "human" . . . . "^\\d+$"^^ . . . "chembiosys.strain" . "marine biology" . . "moid" . . "^ENSG\\d{11}$"^^ . "dentistry" . . . . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid="^^ . . "MMsINC" . "AutDB" . . . "The new national clinical trials registry of the Netherlands"^^ . "https://ordb.biotech.ttu.edu/ORDB/Data/$1"^^ . . . . . . . "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."^^ . "CFc000239295"^^ . . . . "genomics" . "ontology" . . "alternative splicing" . "ontology" . . "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . "environmental science" . . "nbo" . . "A application driven Epilepsy Ontology with official terms from the ILAE."^^ . "International Molecular Exchange" . . . "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam="^^ . . "uniprot/swiss-prot" . "false"^^ . "aceview.worm" . "^.+$"^^ . . "molecular entity" . . . . . "experimental measurement" . . . . . "isSupplementedBy"^^ . "gene" . . . . . "zhenyang@fudan.edu.cn" . "phylogenomics" . "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."^^ . . . "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."^^ . . . . "CALIPHO Group Ontology of Human Anatomy" . "74"^^ . . . "irefweb" . . . "101"^^ . . . . "https://www.isrctn.com/"^^ . "https://signor.uniroma2.it/relation_result.php?id="^^ . . "https://physics.nist.gov/cgi-bin/cuu/Value?$1"^^ . "^ANF\\d{5}$"^^ . . . . "https://www.bgee.org/gene/"^^ . . . . . . . . "nathan.baker@pnnl.gov" . "curies"^^ . . . . . "protein" . "Functional Requirements for Bibliographic Records" . "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."^^ . . "^\\d{7}$"^^ . . "ExAC Variant" . . . . "BitterDB Receptor" . . . . . "obo" . . "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases."^^ . . "nlx" . "12DICHLORETHDEG-PWY"^^ . . "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."^^ . "Ryuichiro Nakato" . . . . "agriculture" . . "https://biosimulations.org/projects/$1"^^ . . "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId="^^ . . . "wuhui@ibcas.ac.cn" . . . . . . . . "PubChem_Compound_CID" . . . . "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name="^^ . . "Etienne Posthumus" . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/TAHE_$1"^^ . "http://database.deepsolar.space:18080/dbs/nlfff/$1"^^ . . . . . "protein" . . . . "life science" . . . . "false"^^ . . "^\\d{7}$"^^ . . "frbr" . . . . . . "chembiosys.model" . "ontology" . . . . . . . . "NCI Drug Dictionary ID" . "Intrinsically Disordered proteins with Extensive Annotations and Literature" . . "obo" . . "plant phenotypes and traits" . . . _:Nfa934ac069554083883f6a0e265c393c "helpdesk@cropontology-curationtool.org" . . . "rapdb.transcript" . . . . "^\\d{16}$"^^ . "model" . "TogoID" . . "false"^^ . "International Protein Index" . "false"^^ . "00000011-a"^^ . "glytoucan" . . . . "false"^^ . "^\\d+$"^^ . . "disorder" . . . "life science" . "61"^^ . "^DB\\d{5}$"^^ . . "false"^^ . . . . . . . "http://darcsite.genzentrum.lmu.de/darc/view.php?id="^^ . . . . "PomBase" . "false"^^ . . "Clinical Trials Information System" . . . . "false"^^ . . "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"^^ . . "NXP" . . "^[1-9]\\d*$"^^ . . . . "Biological Imaging Methods Ontology" . "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"^^ . . . . . . . . "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId="^^ . "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata."^^ . . . . . "CropMRepository" . "life science" . "gene expression" . "Software Package Data Exchange RDF Vocabulary" . . . . "life science" . . . . "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments."^^ . "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$"^^ . "LGCEDe-S-000002244"^^ . "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . "false"^^ . . . . "Maciej.Antczak@cs.put.poznan.pl" . . . . "imr" . . "Alberto Traverso" . "https://smid-db.org/smid/"^^ . "AURKA"^^ . . "glycosciences.db" . "Wikidata Property" . . "false"^^ . "ArachnoServer" . . . . . . "phenotype" . . . . . "http://purl.obolibrary.org/obo/NIF_CELL_"^^ . . "yoh@dartmouth.edu" . . . . . . "life science" . "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . . "ASPL0000349247"^^ . . . . "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."^^ . . "hj@uestc.edu.cn" . . "faseb list" . "http://www.phosphosite.org/siteAction.do?id=$1"^^ . "physiology" . . . "MNXR101574"^^ . "pgx" . . "arthit@gmail.com" . . "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1"^^ . "ontology" . "protein" . "Contains identifiers for human small nucleolar RNAs (snoRNAs) from snoDB, an interactive database of human small nucleolar RNAs (snoRNAs) that includes up-to-date information on snoRNA features, genomic location, conservation, host gene, snoRNA–RNA targets and snoRNA abundance and provides links to other resources."^^ . . . . . "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" . "The Prescription of Drugs Ontology" . . "http://purl.obolibrary.org/obo/SEP_"^^ . . . "true"^^ . "false"^^ . . "trans" . "rat" . "semantic web" . . . . . . . "https://web.expasy.org/abcd/ABCD_"^^ . "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)?$"^^ . . "false"^^ . . "clinvar.record" . . "35742"^^ . . . . "holofood.animal" . . . "education level" . "188"^^ . . . . "http://purl.obolibrary.org/obo/KISAO_"^^ . "edam.topic" . . "CIViC gene" . . "false"^^ . . . . . "http://purl.obolibrary.org/obo/COVOC_$1"^^ . . . . "maaya.m466@gmail.com" . . "true"^^ . "sheepqtldb" . . "Ontologized MIABIS" . . . . . . . . . . "ecoliwiki" . . "Observational Medical Outcomes Partnership" . "ecyano.experiment" . . "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database."^^ . "false"^^ . . . "habronattus" . . . . "Minimum Information about a Biosynthetic Gene Cluster data repository" . "ontology" . "ensembl.protist" . "mirtarbase" . . . . . "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM="^^ . . . . . . "serhii.nazarovets@gmail.com" . . . "metabolomics" . "false"^^ . . . "https://euclinicaltrials.eu/app/#/view/"^^ . . . "^\\d{7}$"^^ . . . "EntrezGene" . "frbrer" . . . "^\\d+$"^^ . . "biomedical science" . . . "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^ . . . . "https://bioregistry.io/gabi:"^^ . . "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$"^^ . "OBOE Standard" . . . "human nucleolar rna" . . . "false"^^ . . "NAD%20biosynthesis"^^ . . "MGnify Analysis" . . . . "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity."^^ . "Donna R. Maglott" . . "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . "biopragmatics/bioregistry"^^ . . . . "ontology" . . "classification" . . "http://purl.obolibrary.org/obo/XAO_$1"^^ . . . . . "MarCat" . . "ChemPro is a database of chemoproteomic probes. This prefix provides identifiers for human proteins that interact with chemoproteomic probes."^^ . "fsnp" . . . "^\\w\\d{4}\\w\\d{2}(\\-[35])?$"^^ . "gene" . . . . "Compluyeast-2D-DB" . . . . . . "http://purl.obolibrary.org/obo/ONS_"^^ . "drosophila" . "false"^^ . . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id="^^ . "subject agnostic" . . "food security" . . . . . . "http://purl.obolibrary.org/obo/FBdv_$1"^^ . _:Nfc27c32c9dc74e128242d584b391a2ec . . . "functional magnetic resonance imaging" . . . "biomedical science" . "https://cropontology.org/rdf/CO_334:"^^ . "Quinoa Ontology" . . . . . . . . . . . . "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^ . . . . . . "728"^^ . . . . . . "^(STUDY|FILE|DATASET)\\d+$"^^ . "^\\d{7}$"^^ . . "http://ddinter.scbdd.com/ddinter/interact/"^^ . "bbtp" . . "https://nf.synapse.org/Explore/Tools/DetailsPage?resourceId="^^ . "^HIT\\d{9}(\\.\\d+)?$"^^ . . . "small molecule" . "http://purl.org/gc/"^^ . . "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."^^ . "norine" . . . . . "http://purl.obolibrary.org/obo/CVDO_"^^ . . "ACTRN12623000498695"^^ . . . . . . "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^ . "recombinant inbred rat" . "stap" . . "metadata standardization" . "c3abdc60-49f1-49db-81fe-863b7dbb21d3"^^ . "research project" . "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."^^ . "obo" . . . "Daniel.Kahn@toulouse.inra.fr" . . "fluticasone"^^ . "false"^^ . . . . "http://purl.obolibrary.org/obo/LOGGERHEAD_"^^ . . "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."^^ . . "https://www.proteomicsdb.org/#human/proteinDetails/$1"^^ . "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"^^ . . "rexo" . . . "1433C_TOBAC_1_252"^^ . . "https://archive.softwareheritage.org/browse/swh:"^^ . "false"^^ . . "HIP000030660"^^ . . . . . . "Identifiers for lipid-protein interactions, including details about protein functions, protein families, lipid classifications, lipid-protein binding affinities, membrane association type, and atomic structures."^^ . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . "true"^^ . . "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . . "bdsc" . . "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1"^^ . "false"^^ . . . "protein" . . "https://w3id.org/oc/corpus/"^^ . . . . "MESHD" . "BindingDB" . . "^\\d+$"^^ . . "linkml" . "Darren A. Natale" . "false"^^ . . "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^ . . . "SNOMEDCT_US_2022_12_31" . . "MGD" . . "ChemBioSys Assay" . "^[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}$"^^ . . . . "jrct" . . . . "Overview of Medical Research in the Netherlands" . . "jRCTs041220087"^^ . . "The Bioinorganic Motif Database" . . . . . "false"^^ . "Nisha Sharma" . . . . . . "matrixdb.association" . "^\\d+$"^^ . "^\\d{8}$"^^ . . "Karen Eilbeck" . "small molecule" . . "false"^^ . "cp" . "genotype" . "obo" . "false"^^ . "imgt.hla" . "0000295"^^ . . "^DP\\d{5}r\\d{3}$"^^ . . . . . . "buccal_gland"^^ . . . . . "sjbrown@ksu.edu" . . _:Nf7c00a8535ea4cf3857a950c86008370 . . . . . . "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . . "nlx.func" . . . "bcgo" . . "2679240"^^ . . . "sbalu@ebi.ac.uk" . . . . "David Eisenberg" . . "https://chemkg.github.io/chemrof/"^^ . . . . "Jennifer L Harrow" . _:N4654dbf5c0074a959f1cf5467bab33e1 . . . . "EST database maintained at the NCBI." . . "75"^^ . "neuroscience" . . . . . "cdd" . "biology" . . "A structured controlled vocabulary for the anatomy of fungi."^^ . "^\\d{7}$"^^ . . "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^ . . . . . "ARP-1513"^^ . . . . "mclarkson@uky.edu" . . "Physiome Model Repository workspace" . "coral.como" . "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . . . "http://www.hprd.org/protein/$1"^^ . . "^[0-9a-f\\-]+$"^^ . "https://schema.org/$1"^^ . . . "co_324" . . "DrugBank Metabolite" . . "neurodegeneration" . . "has URI pattern" . "w3c rec" . . . "false"^^ . . "evolution" . "classification" . . . . . "false"^^ . . "OncoMX Dataset" . . . . . . . . "life science" . . . . . . . . . "ecogene" . "sequence" . . . "Christine.Pourcel@u-psud.fr" . . . . . "http://ecoportal.lifewatch.eu" . . "obo" . . . . . "https://www.ebi.ac.uk/pdbsum/"^^ . "^\\d{5}$"^^ . . "false"^^ . . . . "ontology" . "http://purl.obolibrary.org/obo/CIDO_$1"^^ . "descriptor" . . "https://w3id.org/mixs/$1"^^ . . "http://ciliate.org/index.php/feature/details/"^^ . "Veterinary Substances DataBase" . . . "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^ . "diapriid@gmail.com" . "^FCB\\d{3}$"^^ . . . "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . "002368"^^ . . "http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1"^^ . . . . "https://bioregistry.io/leafsnap:"^^ . . . . "Alvin Walker" . . . . "10046"^^ . . . . "true"^^ . . "true"^^ . . "KEGG DRUG" . . "false"^^ . "genetic variant" . . . . . "erm" . "Valerie Wood" . . . . . "Sustainable Development Goals Interface Ontology" . . "Protein and Associated NucleotideDomains with Inferred Trees" . . . "false"^^ . "biology" . . "^\\d+$"^^ . . . . . "false"^^ . "life science" . . . . . . . "https://biopragmatics.github.io/providers/scomp/$1"^^ . . . "open educational resources" . . . . . . . . "Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars."^^ . "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id="^^ . . "miapa" . . . . . . . . . "help@emdatabank.org" . "ontology" . . "ncbi.gc" . "taxonomy" . "AC00963334"^^ . . "^[0-9A-Za-z_-]+$"^^ . . . . . . . . "false"^^ . . . . . . . "https://cropontology.org/rdf/CO_346:"^^ . "huang@southalabama.edu" . "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."^^ . . . . . . "811"^^ . "region" . "obo" . . . . "Sensor, Observation, Sample, and Actuator Ontology" . . . . . . . . "ontology" . "AphidBase Transcript" . . "civic.molecularprofile" . . "false"^^ . "biomedical science" . . . . . . . . "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry."^^ . . . "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$"^^ . "MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a data repository and associated data standard designed to describe biosynthetic gene clusters involved in the production of specialized metabolites. It also stores data on measured biological activities and links to other resources such as NCBI, NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and training dataset for machine learning."^^ . "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."^^ . . . "virology" . . . . . . "obo" . . "obo" . . . . "unigene" . "false"^^ . . . . . "mao" . "ivdb" . . . . "phenotype" . . . _:Nfe756a5fb0a64141bd9927ac3b82174b "albertgoldfain@gmail.com" . . "https://easychair.org/cfp/$1"^^ . . . "http://bigg.ucsd.edu/models/$1"^^ . . . . . _:Nc565f4c724574369978f4501b9fa42de "edd@usefulinc.com" . . . . . . "DataNode"^^ . "EAWAG Biocatalysis/Biodegradation Database rule" . "https://go.drugbank.com/indications/"^^ . "Sanger Cell Model Passports" . . . . . . . . "^\\d{7}$"^^ . . . . "https://www.ebi.ac.uk/thornton-srv/m-csa/search/?s="^^ . . . . "Human developmental anatomy, abstract" . . "https://ssbd.riken.jp/database/project/$1"^^ . . "false"^^ . "data transformation" . "Richard Boyce" . . . . "^\\d+$"^^ . "plant phenotypes and traits" . "gsso" . . . "alberto.traverso@maastro.nl" . . "false"^^ . "snp" . . . "3ae4ddfc175d768af5526a010bfe95aa"^^ . . "bioinformatics" . . "Pieter Mestdagh" . "https://www.storedb.org/store_v3/study.jsp?studyId=$1"^^ . . . . . "A classification system for the subject matter of works of art, originating from work from Henri van de Waal in the 1940."^^ . . "health" . . . . . "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)."^^ . . . . . . . . . "https://repeatsdb.org/structure/$1"^^ . "http://purl.obolibrary.org/obo/RS_$1"^^ . . "https://www.ncbi.nlm.nih.gov/dbvar/variants/"^^ . "https://knowledge.lonza.com/cell?id="^^ . . . "doco" . . . "estdab" . . "http://purl.obolibrary.org/obo/CHEBI_$1"^^ . . . . . "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . "gene" . . . "http://purl.obolibrary.org/obo/YPO_$1"^^ . "Anne Morgat" . . "https://cropontology.org/rdf/CO_357:"^^ . . "0000255"^^ . . . . . . . "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"^^ . . . "arXiv" . . . . . "http://purl.obolibrary.org/obo/CIO_$1"^^ . "UniProtKB-SubCell" . "http://synbip.idrblab.net/data/scaffold/details/$1"^^ . . "doap" . "assay" . . . . . . . "^\\d+$"^^ . "snp500cancer" . "https://www.aapc.com/codes/cpt-codes/$1"^^ . . . . "mgnifyprotein" . "pencehe@oneonta.edu" . . "OntoRXN" . "proteomics" . . . "biodiversity" . . . . _:N515931ddac9c47b8aaf50c9b43ffa491 . . "^\\d{7}$"^^ . "2966"^^ . "http://purl.obolibrary.org/obo/EHDAA2_$1"^^ . "drug interaction" . "humanities" . . . . . . "false"^^ . . . . "A dictionary of named properties and classes for Software Package Data Exchange (SPDX) - an open standard for communicating software bill of material information, including components, licenses, copyrights, and security references. SPDX reduces redundant work by providing a common format for companies and communities to share important data, thereby streamlining and improving compliance. [from homepage]"^^ . . . . . . "NucleaRDB" . "electronic health record" . . . . . . "metlin" . . . . "https://ega-archive.org/identifiers/"^^ . . . . "1000000"^^ . "https://purl.brain-bican.org/ontology/dmbao/DMBA_"^^ . . "false"^^ . "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id="^^ . . . "iobc" . "identifier for an author at the Social Science Research Network"^^ . . "VMH Gene" . . "ConfIDent Event" . "^GCST\\d{6}\\d*$"^^ . . . . . . "http://purl.obolibrary.org/obo/SPD_"^^ . . . . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . "A person" . "https://gdo.endlessforms.info/view/classes?uuid=GDO_"^^ . "https://ocid.ontochem.com/prefname?ocid=$1"^^ . "Marilyn Safran" . . "https://medical-data-models.org/forms/"^^ . . . "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code="^^ . . "100E"^^ . . . "https://www.alzforum.org/mutations/$1"^^ . . . . . . "keilbeck@genetics.utah.edu" . . . . . . . . . "0000003"^^ . . . . "Echinobase" . . . . "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships."^^ . "gene" . . "ontology" . . . "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$"^^ . "false"^^ . "An ontology representing the gross anatomy of Drosophila melanogaster."^^ . "pato" . "classification" . . _:N089183192451472da39f43d990695286 . . . "medicine" . "QJ51RV02"^^ . . . "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."^^ . "obo" . "SCC111"^^ . . "^\\d{7}$"^^ . . "00000014"^^ . . . . . . . . . . . . . . "https://gnss-metadata.eu/MOID/"^^ . "http://www.rcsb.org/ligand/$1"^^ . . . "https://pdc.cancer.gov/pdc/study/"^^ . . . . "BM0456"^^ . . "1915"^^ . . . . . . . "Secondary Metabolism Collaboratory - taxon" . . . . . . . . "http://www.bind.ca/Action?identifier=bindid&idsearch="^^ . "life science" . . . . . . . "person" . "http://rs.tdwg.org/ontology/voc/TaxonRank#"^^ . "false"^^ . . . "https://www.iedb.org/mhc/"^^ . . "AP00378"^^ . . . . _:N813950d1e49e4c18a5f90f70a007da2a . "disorders" . "Conrad L Schoch" . "database" . "enzymatic reaction" . "rxnorm" . "taxonomy" . . . "false"^^ . . "ontology" . . "life science" . "https://inspire.ec.europa.eu/theme/"^^ . . . . . "obo" . "https://lattes.cnpq.br/"^^ . "^\\d+$"^^ . . "molecule" . "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."^^ . _:N3c26ef7ec133462e85e04ed7ddf135d2 "register@clinicaltrials.gov" . "false"^^ . "lincs.data" . . "Radiation Biology Ontology" . "Darwin Core Terms" . . . . "Regulation of Transcription"^^ . . "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1"^^ . . . . . "drugbank.category" . "http://purl.obolibrary.org/obo/PATO_$1"^^ . . . . . . "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."^^ . "1178"^^ . "https://web.www.healthdatagateway.org/dataset/$1"^^ . _:N2d5072dd9d104290839761e23aeca8f0 "Marc Wick" . "bgee.stage" . . . "jt6@sanger.ac.uk" . "subject agnostic" . . . . . . . . "Name Reaction Ontology" . "spbase" . . "https://www.uniprot.org/database/" . . "yeastintron" . . . "pkarp@ai.sri.com" . "data analysis" . . "false"^^ . "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^ . . . "developmental biology" . . . . "false"^^ . "5HT3Arano"^^ . . "CIViC Molecular Profile" . "false"^^ . . . . . . "MMP02954345.1"^^ . "0000728"^^ . . . "false"^^ . "https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/$1"^^ . "0000001"^^ . "https://bionumbers.hms.harvard.edu/bionumber.aspx?id="^^ . "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . . "MGnify Sample" . "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"^^ . . . . "genetics" . . . . . . . "ontology" . "protein" . . "Europe PMC Preprints" . . . . "^\\d+$"^^ . "https://dandiarchive.org/dandiset/$1"^^ . . "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid="^^ . "^PA\\d+$"^^ . "novus" . . . _:N47ce5820433f4be091a64739ee3dc645 "João Paulo A. Almeida" . . . "elements" . . . "dockerhub.repo" . . . . . "protein acetylation" . . "HoloFood animal" . . . . . "Histopathology Ontology" . . . "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^ . "https://giardiadb.org/giardiadb/app/record/gene/"^^ . . . . . "FullySpecifiedAtom"^^ . "jgraybeal@stanford.edu" . "refseq" . . . . "https://mediadive.dsmz.de/solutions/"^^ . . . "Surjeet Kumar Arya" . "http://cutdb.burnham.org/relation/show/$1"^^ . "MultiCellDS Digital Cell Line" . . "gene" . "false"^^ . "VEG-03D"^^ . . . "http://biohackathon.org/resource/faldo#"^^ . "1251"^^ . . _:N3e266efc844a4720a554e4b284b0e9de "Kristin D. Kasschau" . . . . "ontology" . "false"^^ . . . . "false"^^ . "Ramasubbu Sankararamakrishnan" . . . "false"^^ . . . . . "true"^^ . "http://purl.obolibrary.org/obo/NGBO_"^^ . . "^\\d+$"^^ . "^\\d+$"^^ . . "osa-miR446"^^ . "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"^^ . . . . . . "health science" . "phenotype" . . "false"^^ . "false"^^ . . "00100005"^^ . . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"^^ . . "NCI Pathway Interaction Database: Pathway" . "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."^^ . . . . . . . . . . "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals."^^ . "false"^^ . "HEPRO is an ontology of informational entities and processes related to health procedures and health activities."^^ . "live animal" . . . . . . . . "identifier for an educational organization issued by the UK Register of Learning Providers"^^ . "true"^^ . _:N28f417fe9b3c44bc93409fd79fad1d81 "heinrich.herre@imise.uni-leipzig.de" . "Event (INOH pathway ontology)" . . "http://purl.obolibrary.org/obo/$1_$2" . . "Carbohydrate Active EnZYmes" . "kuiper@bio.ntnu.no" . "plant phenotypes and traits" . . . "^.+$"^^ . "^\\d{7}$"^^ . . . . "rrid" . . . "http://hpc-bioinformatics.cineca.it/fusion/cell_line/"^^ . . . . . . "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName="^^ . . . . "version control" . . . "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . . . "biology" . . . . . . "ontology and terminology" . . "ontology" . . . "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID="^^ . "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases"^^ . . . . . . . . "false"^^ . "DBPedia Resource" . . . "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$"^^ . . . "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^ . "false"^^ . . "COSMIC Gene" . . "https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail?id=$1"^^ . . "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$"^^ . . . "protein" . . . . . . . . . "life science" . "pharmacological family classification" . "endlessforms.graphic" . . "false"^^ . "^[A-Z0-9]+$"^^ . "anatomy" . "cvdo" . . "functional genomics" . . "^[0-9]+$"^^ . . . . "http://purl.obolibrary.org/obo/CMO_$1"^^ . . . . "^\\d{5,}$"^^ . "false"^^ . "molecular biology" . . . . . . "ychai@usc.edu" . "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)"^^ . . . . . "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."^^ . "epawaste" . . "digital curation" . "assay" . "bartoc" . "food" . . "http://cdb.iso.org/lg/$1"^^ . . . "regulation" . . "assay" . "Margaret R. Woodhouse" . "ontology" . "https://uts.nlm.nih.gov/uts/umls/vocabulary/MTH/$1"^^ . . "classification" . . . . . . "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . . . "Daniel W Udwary" . . "^\\w+$"^^ . "sequence" . . "AB016785"^^ . . "sayers@ncbi.nlm.nih.gov" . . "Ada Hamosh" . . . . "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."^^ . . . . "vario" . . "http://purl.obolibrary.org/obo/VO_$1"^^ . "microbiology" . . . "0000041"^^ . "Yaroslav Halchenko" . . "t4fs" . "data management" . "EP0311"^^ . . . . "preclinical studies" . . . "false"^^ . "Jeremy Zucker" . . . "M94112"^^ . "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id="^^ . . . "true"^^ . . . . "n2"^^ . . . "sebastien.moretti@sib.swiss" . . "phenomics" . . "R-ACH-1120024"^^ . "health science" . . . "uniprot.mnemonic" . . . "1"^^ . . . . "MolBiC Cell Line" . . . . . . "gold standard" . . "monosaccharides" . . "https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail?id="^^ . . . . . . . "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . "SM0000020"^^ . "true"^^ . . . . . . . "^[A-Za-z0-9]+$"^^ . . . . "biomedical science" . . "LigandBox" . . . . . "biomedical science" . . . "MeSH" . . . . "isced2011" . . "This controlled vocabulary contains terms to describe the mechanism of action for a chemical-target interaction. The terms can be retrieved from ACTION_TYPE table in ChEMBL's SQL dump and are used to annotate the DRUG_MECHANISM table. Because these aren't really identifiers, they are transformed by lowercasing and replacing spaces with dashes to form 'identifiers'. The pattern in the Bioregistry record contains an enumeration of the 33 allowed values as of ChEMBL v35."^^ . "false"^^ . . . . . . . . . "true"^^ . . . . . "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$"^^ . . . "false"^^ . . . "Cell line collections (Providers)"^^ . . "life science" . . . "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities."^^ . . . . "oslc" . . . . . . . . . . "false"^^ . . . "AGR" . . . . . . "https://id.loc.gov/vocabulary/relators/"^^ . . . "75"^^ . "Conference Ontology" . . . . "DRKS00031815"^^ . "ontology" . . . . . . . . "http://purl.obolibrary.org/obo/COB_$1"^^ . "http://www.w3.org/ns/shacl#"^^ . "false"^^ . . "false"^^ . "anatomy" . "obo" . "mutation" . "false"^^ . . "htn" . . "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . "genome" . . . . "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."^^ . "created"^^ . . . . "false"^^ . . "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^ . . . . . "vfb" . . "cog" . "drugs" . "KIM School Subjects" . "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://lincs.hms.harvard.edu/db/sm/$1"^^ . . . "agriculture" . . . "Harry Caufield" . "metamodel" . . . . . . "^\\d+$"^^ . . "http://cdb.iso.org/lg/"^^ . . . . . . . "regulation" . . . . . "false"^^ . . "Frédéric Bastian" . . . . "WBls" . "http://bigg.ucsd.edu/compartments/$1"^^ . "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^ . "data classification" . "giardiadb" . . "1426686"^^ . . . . . . . "The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the animal semantic space correspond to animals that samples in the database are obtained from."^^ . . . . . "false"^^ . . . "obo" . . . "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . . "proteomics" . . . "jecfa" . . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1"^^ . "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$"^^ . . "0000205"^^ . . . . . "Mouse gross anatomy and development, timed" . . . "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."^^ . . . . "ctd.disease" . "disorder" . "UniProt" . . "illumina.probe" . "wormpep" . . . . . "241889"^^ . . "false"^^ . . . . "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#"^^ . "mcro" . . "ecosystem science" . . "false"^^ . "false"^^ . . . . "pathway" . . . . "CABI Digital Library" . . "inaturalist.taxon" . . . "0000319"^^ . . "rna" . "false"^^ . . . . . "https://gateway.eubopen.org/compound/$1"^^ . . "false"^^ . "classification" . . "genome" . . "life science" . . . . . . . "http://www.alzgene.org/geneoverview.asp?geneid="^^ . . . . "3"^^ . "A RDF vocabulary for OER content on the web."^^ . . . . . "false"^^ . . "DepMap Cell Lines" . "false"^^ . "^rx[0-9]{5}$"^^ . . . "^rs\\d+$"^^ . "genome" . . "DBG2 Introns" . . . "John Beverly" . "^\\d+$"^^ . "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1"^^ . "pfbaldi@uci.edu" . "epidemiology" . "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."^^ . "medicine" . . . "MHC Restriction Ontology" . "false"^^ . . . . "vw253@cam.ac.uk" . "sivaram.arabandi@gmail.com" . . "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"^^ . . . "LNC" . . . . . "geonames.feature" . "hhe@ebi.ac.uk" . "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."^^ . . "registry" . . . . . . . "Fyler" . . "http://www.ontobee.org/ontology/$1" . . . . "9001411"^^ . . . . . "drug discovery" . "genome" . "http://purl.obolibrary.org/obo/ECTO_$1"^^ . . "ST000900"^^ . . "orpha" . "https://www.ebi.ac.uk/ena/browser/view/"^^ . "false"^^ . . "https://molbic.idrblab.net/data/compound/details/"^^ . . . . . . . "false"^^ . "slctr" . "47"^^ . . "mass spectrum" . "fair" . "Identifiers represent experimental tools and resources for neurofibromatosis (NF) research in the NF Data Portal Tools catalog."^^ . "agriculture" . "ontology" . . "The Science Data Discovery Ontology (sddo) is being developed to provide a semantic foundation for the discovery of information managed by NASA's Science Mission Directorate. This information spans many scientific disciplines, fields and subfields, including heliophysics, earth science, planetary science, astrophysics, biology, astrobiology, and physical science. [from repository]"^^ . "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."^^ . "daml.pt" . . "ontology" . "http://lisanwanglab.org/DASHR/entry/$1"^^ . "^\\d{6}$"^^ . . . . . . "ontology" . "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."^^ . "spd" . "Gwen Frishkoff" . . "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . "7499841"^^ . . . . . . . . . . . . . "Oryzabase Stage" . "genomics" . . "cell" . . . . . . . . . "http://purl.obolibrary.org/obo/TGMA_"^^ . . _:N660a55a7ed6a461481924dd0b463a5f0 "Unknown" . . . . "one" . "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"^^ . "ontology" . "agriculture" . . . . . . _:N6835ccee24b84375ab1206252243e893 "Michael Lincoln" . "diseases" . . . "^CDBL00\\d{6}$"^^ . . "^[0-9a-z_:\\.-]+$"^^ . "pathway" . . . . . "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"^^ . . . . . . "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^ . "^\\d{7}$"^^ . "Pathguide contains information about 325 biological related resources and molecular interaction related resources."^^ . . . . "Jeffrey A. Detras" . . . "gene name" . "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"^^ . . "http://multicellds.org/MultiCellDB/"^^ . . "http://purl.obolibrary.org/obo/COLAO_$1"^^ . . . . "life science" . . "phenotype" . "https://foodb.ca/foods/$1"^^ . . . . . . . . . . . "molmedb" . "mirte" . . "false"^^ . "co_322" . . . . . . "https://purl.org/nfdi4plants/ontology/dpbo/DPBO_"^^ . "^\\d{7}$"^^ . . . . "http://data.loterre.fr/ark:/67375/N9J$1"^^ . . "false"^^ . "Chris Mungall" . . . . . . "statistics" . . . . . "2842"^^ . "https://smc.jgi.doe.gov/sources/"^^ . . . . "gard" . "false"^^ . . . . . . "vaccine" . "epidemiology" . "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"^^ . "nort3314"^^ . "false"^^ . . . "Fabrice Legeai" . . . . "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."^^ . "An issue on the Information Artifact Ontology GitHub issue tracker"^^ . "genomics" . . "wikidata" . "https://flybase.org/reports/$1"^^ . "SNOMEDCT_US_2021_07_31" . . . "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . "http://purl.obolibrary.org/obo/FBbi_"^^ . "false"^^ . . "asteraceaegd.genome" . . . . . "protein" . "false"^^ . "KEGG Module" . . "5ede4273-b26c-4ea4-adb7-3ce294ab3397"^^ . "http://purl.obolibrary.org/obo/APOLLO_SV_"^^ . "gtr.condition" . . . . . . . . "redfly" . . . "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."^^ . . . . . . "observations" . "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."^^ . . . . . "dev.ga4ghdos" . . "^RCV\\d+(\\.\\d+)?$"^^ . . "https://isbnsearch.org/isbn/$1"^^ . . . . "model" . _:N515931ddac9c47b8aaf50c9b43ffa491 "hq@HL7.org" . . "true"^^ . "biomarker" . "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"^^ . . . . . "https://civicdb.org/links/evidence/$1"^^ . . . . . "protein" . . "chemical" . "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."^^ . "kegg.brite" . . "http://geneontology.org/" . . "whole plant development stage" . "https://www.re3data.org/repository/$1"^^ . . . "rdf" . "structure" . . "ontologies" . . . "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$"^^ . "phismith@buffalo.edu" . . . "Metabolic Atlas Reaction" . "100101"^^ . . "iedb.receptor" . "^\\d+$"^^ . . . . . . . . . . . . "ToxoDB" . _:N649959919c924cc49fc032c5ce78f634 . "MONDO Issue Tracker" . . . "psychology" . . "Pan African Clinical Trials Registry" . . . . "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . "false"^^ . . "https://jrct.niph.go.jp/en-latest-detail/"^^ . "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"^^ . . "Jesualdo Tomás Fernández-Breis" . "GWAS Central Marker" . "cell biology" . . . "ECGOntology" . . "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."^^ . "ontology" . "BlastRules (identifiers starting with the “NBR” prefix) are a type of evidence for functional classification of proteins based on BLAST (Basic Local Alignment Search Tool). A BlastRule consists of one or more 'model' proteins with known biological function, and BLAST identity and coverage cutoffs. Any protein aligning to a model protein above the cutoffs is considered a BlastRule hit. [from homepage]"^^ . . "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^ . . "millipore" . "https://mycobrowser.epfl.ch/genes/$1"^^ . . . . "http://purl.obolibrary.org/obo/MAT_"^^ . . . "obo" . . . . "false"^^ . . . "natural product" . . "pkdb" . . . "^ITMCTR\\d+$"^^ . . "dna" . . . "Fengcheng Li" . "development" . "https://glottolog.org/resource/languoid/id/"^^ . "Tobias Schulze" . . . "https://www.metabolome-express.org/datasetview.php?datasetid="^^ . . . . . . . . . . . "ontology" . "^\\d+$"^^ . . "NCITm" . . . . "Store DB" . "true"^^ . . "http://bio2rdf.org/affymetrix:$1"^^ . "A combination of an ISBN and local unique identifier for articles and other published works. Please see the [Wikipedia page](https://en.wikipedia.org/wiki/Publisher_Item_Identifier) for a detailed explanation. Some PIIs are used as the local identifiers in DOIs, such as https://doi.org/10.1136/S0003-4967(24)38620-0."^^ . . . "glygen" . . . . "google.book" . "https://cropontology.org/rdf/CO_370:$1"^^ . . . . . "obo" . . "U.S. Education Level Vocabulary" . "DOCiD" . . . . . . . . "Sequence types and features ontology" . "false"^^ . "false"^^ . "nfdi.kgi" . "https://precision.fda.gov/uniisearch/srs/unii/$1"^^ . "knowledge and information systems" . . . . . "false"^^ . "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id="^^ . . . . . . "gene" . . . . . . . . . . . "4DNESWX1J3QU"^^ . . "Jennifer C. Giron" . . "false"^^ . "bibliometrics" . . . . . . . . "https://web.archive.org/web/1/https://www.semion.io/Author/$1"^^ . . "https://biopragmatics.github.io/providers/cemo/"^^ . "http://www.narcis.nl/publication/RecordID/"^^ . . . "span" . . . . . . . . "anatomy" . . . "false"^^ . "false"^^ . . "0001191"^^ . "PANTHER Pathway Component" . "life sciences" . "Abdelmoneim Amer Desouki" . . . . . . . . "EndlessForms Studio Library" . "ATTC" . . "img.gene" . "mf" . "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term="^^ . . . . . . . "10.1621/vwN2g2HaX3"^^ . . "Citlalli Mejía-Almonte" . "http://exac.broadinstitute.org/transcript/"^^ . "https://publons.com/publon/"^^ . . "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1"^^ . "Bernd Müller" . . . . "eccode" . . "obo" . "paxdb.protein" . . "false"^^ . "http://purl.obolibrary.org/obo/XAO_"^^ . "https://www.xenbase.org/entry/"^^ . . . "A database-specific registry supporting curation in the Gene Ontology"^^ . "Taxonomic rank vocabulary" . "Human Reference Atlas Common Coordinate Framework Ontology" . . . "false"^^ . . . . . "true"^^ . "chemistry" . . "protein" . "^EBI\\-[0-9]+$"^^ . "systems biology" . . "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\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."^^ . . "phylogenetics" . . "phenotype" . "false"^^ . "^[0-9]{9}$"^^ . . "008893080"^^ . "https://www.biosino.org/rdbsb/bioparts_detail/$1"^^ . . . . . . . . "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1"^^ . . . . . "David S. Wishart" . . . "^[a-z0-9]{32,32}$"^^ . . "disease" . "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."^^ . . "http://www.case.edu/EpilepsyOntology.owl#$1"^^ . "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^ . "^r\\d+$"^^ . . . "identifier of an article in Dialnet"^^ . . . "Animal Trait Ontology for Livestock" . "NIF Standard Ontology: Digital Resources" . . _:N865029bd78814e35a1b703c468976221 . . . . "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code="^^ . . . . "004126"^^ . . "false"^^ . . . "JMChandonia@lbl.gov" . "https://deims.org/taxonomy/term/"^^ . "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID="^^ . . "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^ . "http://www.sasbdb.org/data/$1"^^ . . . "Niclas Karlsson" . "obo" . . . . . . . "absd" . "https://dgrc.bio.indiana.edu/product/View?product=$1"^^ . . . . . . . "false"^^ . "omics" . . . . . . . . . . . "metadata" . "assay" . "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes."^^ . . . "^[A-Z0-9]{4}$"^^ . . "^\\d{7}$"^^ . . . . . "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types."^^ . . "^\\d+$"^^ . . "Biological Expression Language" . . "https://omia.org/variant/omia.variant:"^^ . . . . . . "true"^^ . . "stri"^^ . "https://fairsharing.org/users/"^^ . "http://purl.org/dc/elements/1.1/$1"^^ . "biochemistry" . "nmrXiv compound" . . "Database of homology-derived secondary structure of proteins" . "general & upper" . "ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc."^^ . "grsdb" . . "false"^^ . "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^ . . . . . "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1"^^ . "http://purl.obolibrary.org/obo/FYPO_$1"^^ . "MT"^^ . "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."^^ . . . "http://polytraits.lifewatchgreece.eu/traitspublic_traitdefinitions.php#$1"^^ . . . _:Nd8d641a7ff3047728eaeb8c847a7e158 . "https://bioregistry.io/wicell:"^^ . "^\\d{7}$"^^ . . "The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects."^^ . "https://www.ensembl.org/id/"^^ . _:N922423823a164071873c18cd0da554a3 "nospam@iandavis.com" . . . "Aquatic Sciences and Fisheries Information System" . "false"^^ . "biomedical science" . . . . . . . . . "FooDB Food" . . . "compound" . . "Relator terms and their associated codes designate the relationship between an agent and a bibliographic resource."^^ . . . "ontology" . . . . "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id="^^ . "flowrepository" . "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia' prefix is used for phenes, either across species (omia:001000) or in a specific species (omia:001000-9615)"^^ . . . "false"^^ . . . "bertram@helix.mgh.harvard.edu" . . . . "napdi" . . . "false"^^ . . . . . "cohesindb.binding" . . "https://www.checklistbank.org/dataset/"^^ . . "https://rubygems.org/gems/$1"^^ . . . "false"^^ . . "A vocabulary describing licenses for data and code"^^ . . . . . . . "phenotype" . "https://purl.org/ontology/modalia#"^^ . . "Food Classification and Description System (from FSA Food Type identifiers)" . . "^\\d{7}$"^^ . . "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."^^ . . "environmental science" . . "https://gateway.eubopen.org/compound/"^^ . "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology."^^ . "life sciences" . . . "joerg.waitelonis@fiz-karlsruhe.de" . . . . . . "^\\d{7}$"^^ . . "http://rssf.i2bc.paris-saclay.fr/NAPP/Niveau2.php?specie="^^ . "true"^^ . . . . . . . . . "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId="^^ . . "http://purl.obolibrary.org/obo/VBO_$1"^^ . "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . . "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^ . . . "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . . . "biological regulation" . "https://istransbase.scbdd.com/database/trans/$1"^^ . . . "Learning Resource Metadata Innovation Terms" . . "false"^^ . . . "nanoparticle" . . . "biodiversity" . "rna" . . . . . . . "false"^^ . "data management" . "Ontology about the gross anatomy of the C. elegans"^^ . . . "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . "jgoll@emmes.com" . . "false"^^ . "false"^^ . "dome" . "structure" . "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."^^ . . . . "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 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."^^ . . . . . . . . . "Val Wood" . . . . . . . "NIH RePORTER" . . . . . . . . "Cube db" . . "cd00400"^^ . "false"^^ . . "^\\d{7}$"^^ . . . . "Mouse Developmental Anatomy Ontology with Theiler Stage" . "EOL Secretariat" . "SILVA Taxon" . "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . . "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data."^^ . . . . . . "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . "The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample."^^ . "Human Disease Ontology" . . . . "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results)."^^ . . "false"^^ . . "genetics" . "mpjensen@buffalo.edu" . "https://w3id.org/kim/isced-2011/level"^^ . . "structure" . . . "false"^^ . . . "http://www.w3.org/2003/01/geo/wgs84_pos#"^^ . "ihw" . "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . "http://purl.obolibrary.org/obo/UBERON_"^^ . "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q="^^ . "small molecule" . . _:N1cd40c152ac54ccf9674b630f1e1c5ff . . . . . . "The Genetic Testing Registry 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."^^ . . . . "https://www.phenxtoolkit.org/protocols/view/$1"^^ . . . . . "^\\d{4}$"^^ . . . . . . . "https://isbnsearch.org/isbn/"^^ . . . "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."^^ . "ontology" . . "Judith A Blake" . "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web."^^ . "false"^^ . . . . . . . "^\\d+$"^^ . . . "SABIO-RK EC Record" . "panther.pthcmp" . "life science" . . . . . "drosophila" . "false"^^ . . . "jax" . . "disease" . "PubMed ID" . . . . . . "false"^^ . . . "Neuroscience Multi-Omic BRAIN Initiative Data" . . "cmo" . "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$"^^ . . . "ontology" . . . . . . "false"^^ . "ontology" . . "^\\d{7}$"^^ . "j.detras@cgiar.org" . . . . "stem cell" . . . "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]"^^ . . . "http://rdfs.org/sioc/argument#$1"^^ . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . "Vertebrate Breed Ontology Issue Tracker" . . . "competence" . . "false"^^ . . . . "knowledge and information systems" . . . . . . "protein trap" . . . "ERM00000044"^^ . . "Carissa Park" . . . . . "ukprn" . . "BAO" . "http://data.loterre.fr/ark:/67375/N9J"^^ . "false"^^ . . "approved drug" . . . . . . . . "https://www.w3.org/2009/pointers#$1"^^ . "life science" . . _:Nedbc275e04954fc697a3f356038185e2 . . . "https://www.cellbiolabs.com/search?keywords="^^ . "gfo" . . "Stewart Thomas Cole" . . . . "life science" . . . "Yuki Yamagata" . . . "^(ZINC)?\\d+$"^^ . . . . . . . . "Plant Trait Ontology" . . . . "obo" . "software function" . . "13"^^ . "synbip.bts" . "1001"^^ . "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://func.mshri.on.ca/human/genes/list_functional_scores/"^^ . . . . . . . . . . . "https://bioregistry.io/ppdb:"^^ . "enhancer" . . . "Alzheimer's Disease Ontology" . . "^CNP\\d{7}(\\.\\d+)?$"^^ . "genome" . . "https://bioregistry.io/$1:$2" . "chemistry" . . . "cmedigue@genoscope.cns.fr" . . "dc06de9f-dd3a-4f28-b58f-b01b5ae72ab8"^^ . "P00747__P07355"^^ . "ndf-rt" . . "life science" . . . . "0000983"^^ . . . "https://www.storedb.org/?"^^ . . . "^\\d+$"^^ . . . . . . . "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"^^ . "nbn" . . . "structure" . . . . . . "^EGAD\\d{11}$"^^ . . . . . "http://purl.obolibrary.org/obo/MIRNAO_"^^ . . . "protein" . "journal" . . . . . . . . . "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^ . . "false"^^ . "nickf@ebi.ac.uk" . . "MycoBrowser smegmatis" . "^(?:\\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+)?)$"^^ . "Zhen Yang" . . . . "regulation of gene expression" . . "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."^^ . . . . . . "biochemistry" . "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . . "drug" . . "Rahuman Sheriff" . . "sequence feature" . . "https://osdr.nasa.gov/bio/repo/data/studies/"^^ . "communication science" . . . . "disease" . . "http://uri.neuinfo.org/nif/nifstd/sao$1"^^ . . "http://purl.obolibrary.org/obo/HsapDv_$1"^^ . "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"^^ . . "https://bbp.epfl.ch/nexus/web/studios/public/"^^ . "dai.thesauri" . . . "http://www.w3.org/2003/g/data-view#"^^ . . . . "bibliometrics" . "FaceBase Data Repository" . "Donny Winston" . "^\\d+$"^^ . . . . . "true"^^ . . . "Melanie Courtot" . . . "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"^^ . . "https://www.wormbase.org/species/c_elegans/rnai/$1"^^ . . . "^\\d{7}$"^^ . . . . "http://purl.obolibrary.org/obo/XPO_$1"^^ . . . . . . "Zhiliang Hu" . . . "elisa-kits" . . "transcriptomics" . "true"^^ . "gene group" . "Representation of languages"^^ . "RXN-14904"^^ . "metabolomics" . . . . "fionamcc@arizona.edu" . "M77F7JM"^^ . "UBPROP" . "gene" . . . . . . . "true"^^ . . "https://thebiogrid.org/interaction/"^^ . "Stefan Günther" . . . . . . "UPI000000000A"^^ . . . . "false"^^ . . . . . "reactions" . "info@daniel-marschall.de" . . . . . "Selventa legacy chemical namespace used with the Biological Expression Language"^^ . "true"^^ . "Time Ontology in OWL" . . "229233"^^ . . . "IUPHAR family" . . . "hms.lincs.compound" . . . . "0000000"^^ . . . . "http://dbpedia.org/property/$1"^^ . "false"^^ . . . . . "DataPLANT Biology Ontology" . "http://www.wikidata.org/entity/"^^ . . "GenBase" . . . . . "https://proteinensemble.org/$1"^^ . . . . "false"^^ . . . "https://cropontology.org/rdf/CO_322:$1"^^ . . . "0000123"^^ . . . . "centrally registered identifier" . . . "Ontology of units of Measure" . "Synthetic Binding Protein Protein Scaffold" . . . _:Nce41d6177596475ca307007440dd9504 . "ISO Object Identifier" . "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^ . "https://depmap.org/portal/cell_line/"^^ . . . . "obo" . . . . "0000049"^^ . . . "agriculture" . "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . . "The DOME registry is a curated set of papers related to machine learning methods in biology, each with its own unique DOME identifier."^^ . . "http://www.whocc.no/atcvet/atcvet_index/?code="^^ . "false"^^ . . . . "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid="^^ . . . . . . . "false"^^ . . "anatomy" . . . "983"^^ . . "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$"^^ . . . "https://bioregistry.io/resolve/github/issue/$1"^^ . "vcard" . . . "0000108"^^ . . "multicellds.cell_line" . "obo" . . . . . . . "resource metadata" . . . . "https://absd.pasteur.cloud/antibody/$1"^^ . "^\\d+$"^^ . "^\\w+$"^^ . "validatordb" . "nikkaji" . "^EUB\\d{7}$"^^ . . "0000639"^^ . "seed.role" . "life science" . "Anatomical Entity Ontology" . "Soybean Trait Dictionary in template v5 - IITA - July 2015"^^ . . "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$"^^ . . "https://www.arabidopsis.org/locus?accession=$1"^^ . . . . "synbip.pss" . "taxonomic classification" . . . . . "genomics" . . . "https://registry.bio2kg.org/resource/$1" . "stefan.schulz@medunigraz.at" . "aism" . . . "infectious disease medicine" . "Addiction Ontology" . . . . . "prov" . . "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."^^ . "https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code=$1"^^ . . "false"^^ . "The NFDI4Culture portal offers all content as Linked Open Data over this RESTful API. The API implements the Hydra-Specification of the W3C Hydra Community Group. The semantic description of this API can be retrieved by clients via the Hydra documentation file (JSON). Each metadata record offered via this API can also be retrieved in one of following machine-readable LOD serializations. The API is the basis for the Culture Research Information Graph, which together with the Culture Research Data Graph forms the [Culture Knowledge Graph](https://nfdi4culture.de/services/details/culture-knowledge-graph.html) (for more details see [this presentation](https://doi.org/10.5281/zenodo.7748740)) (from homepage)."^^ . "eukaryota" . "casent0106247"^^ . . . . . "sempav_voc" . _:N47b8474538d9407cb8dfc4a0f5ea868c . . . . "AntiFam is a database of spurious protein families that have been removed from Pfam due to incorrect hidden Markov model prediction."^^ . . . "Identifiers for epitopes, which are the specific parts of antigens recognized by the immune system."^^ . "https://cthoyt.com/evr/$1"^^ . . . . . . . . . "umls" . . . "ontology" . . . "040000"^^ . . . "kevin.boske@sagebase.org" . . "chemical" . . "topalis@imbb.forth.gr" . . . . . . . . . "CASID" . "^[A-Za-z-0-9_]+(\\@)?$"^^ . "^[0-9]+$"^^ . . . . . "dggr" . "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."^^ . "P3DB Protein" . "false"^^ . . . . . . . "biomedical science" . "http://spdx.org/rdf/terms#"^^ . "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."^^ . . "geonames" . "life science" . . . "false"^^ . . "gene" . . "false"^^ . "Terence D. Murphy" . . "false"^^ . . "matt@tislab.org" . "http://addgene.org/"^^ . . . "https://www.gwascentral.org/study/"^^ . "http://crdd.osdd.net/servers/virsirnadb/record.php?details="^^ . . . . "electronic health record" . . "taxonomic classification" . "phosphosite.protein" . . . "AcknowledgementCondition"^^ . . "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."^^ . _:N089183192451472da39f43d990695286 "helpdesk@eionet.europa.eu" . "cell lines" . . "EMLSAT00000003403"^^ . "resource metadata" . . . "MicrosporidiaDB" . . . . . . "chemistry" . . . . . . . "medicine" . "AOPWiki (Key Event Relationship)" . "dialnet.book" . . . . "A pull request in any public repository on GitHub."^^ . . "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."^^ . . "PA146123006"^^ . . . . . "molecular interaction" . . "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^ . . "kim.schulfaecher" . _:Na6e5ebb17d90415f947106893f425627 "evoc@sanbi.ac.za" . "ai10e-kctd13b"^^ . "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp="^^ . "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."^^ . . . . "oers" . "^(([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]+)$"^^ . . "Collagen Mutation Database" . . . . "Panorama Public" . "mgnifystudy" . . . . "hinv.protein" . . . . . . . . "ontology" . "false"^^ . "true"^^ . "2GC4"^^ . . "ArrayGroup"^^ . "0000002"^^ . . . . . . . . . "https://query.biodeep.cn/metabolite/"^^ . . . . . "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments."^^ . . "http://www.orpha.net/ORDO/Orphanet_$1"^^ . . "4390079"^^ . . . . . . . . "http://www.w3.org/2003/11/swrl#"^^ . "phenotype" . . "Andrew G. McArthur" . . "^\\d{7}$"^^ . "hamap" . "RepeatsDB Protein" . . "http://purl.obolibrary.org/obo/PCL_$1"^^ . "gemet.concept" . . . . . . . . . "https://coconut.naturalproducts.net/compound/coconut_id/$1"^^ . . . . . . . . . "whimar@ohsu.edu" . . . "^\\d+$"^^ . "life science" . . . "metadata" . . . . "kushida@biosciencedbc.jp" . . . "structure" . . . "http://purl.uniprot.org/core/$1"^^ . "https://rnaloops.cs.put.poznan.pl/search/details/"^^ . "false"^^ . . . . . "^1\\d{4}-\\d{3}$"^^ . . . . . "biology" . . . . . . . "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."^^ . "afpo" . . . "^T3\\d+$"^^ . "false"^^ . "dblp.author" . . . "http://purl.obolibrary.org/obo/PDRO_"^^ . _:N5fbd5c8934874ef48a5d69134f51c9a6 "Cynthia.Hake@cms.hhs.gov" . . . "false"^^ . . "aop.stressor" . . . . . . "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."^^ . . "https://www.metanetx.org/equa_info/$1"^^ . "unique academic work identifier assigned in Scopus bibliographic database"^^ . . "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id="^^ . "Database of validation results for ligands and non-standard residues in the Protein Data Bank."^^ . . . "Cryo Electron Microscopy ontology" . . "https://ieeexplore.ieee.org/document/"^^ . "molecular entity" . "false"^^ . . . "false"^^ . "hospital" . "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . . . . . "http://cor.esipfed.org/ont/earthcube/MOLA_"^^ . . "^\\w+(\\.\\d+)?$"^^ . "biodiversity" . "false"^^ . "https://w3id.org/lehrplan/ontology/LP_$1"^^ . . . "ontology" . "taxon" . . . . . . "https://reporter.nih.gov/project-details/"^^ . . . "receptome.family" . . "Q42"^^ . "cancer" . . . . "laml_tcga_pub"^^ . . "^casent\\d+(\\-D\\d+)?$"^^ . . "sequence variant" . . . "UPC04349"^^ . "262393"^^ . "Gazetteer" . . "Tarcisio Mendes de Farias" . . "bioimaging" . . . "false"^^ . "false"^^ . . "https://www.findacode.com/code.php?set=ICD10PCS&c="^^ . "neurophysiology" . . . . "http://www.fairsharing.org/ontology/subject/SRAO_$1"^^ . "https://ssrn.com/author=$1"^^ . "population genetics" . . "omics" . "brenda.ligand" . . . . . "beiresources" . "4b848c342a4f4abc871bdf8a09a60807"^^ . . "miriam.resource" . . "proteomics" . "^(Gi|Gc)\\d+$"^^ . . . . . . . . . . . "dna" . "1cukA01"^^ . . "false"^^ . . . . "zeco" . . "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."^^ . "67"^^ . . "bfo11span" . . . . "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster="^^ . "9002859"^^ . "developmental biology" . "liz.allen@f1000.com" . "WBPhenotype" . . . "pubmed" . . . . . "single cell" . . "false"^^ . . "false"^^ . . . "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."^^ . "false"^^ . . . . . . . . "174"^^ . "98127"^^ . . . . . "https://search.dalia.education/items/"^^ . . . . "http://www.gramene.org/db/genes/search_gene?acc="^^ . . . . "pdbsum" . . . . . . "jmedina@ebi.ac.uk" . . . . . "https://rubygems.org/gems/"^^ . "ontology" . "true"^^ . . . . . . . . "oers" . "croissant" . . . . "Vertebrate Breed Ontology" . "^\\d+$"^^ . "ontology" . "scopus.eid" . . . "metabolomics" . . . . . . . . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/EHDA_"^^ . "http://www.antweb.org/specimen.do?name=$1"^^ . "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam="^^ . . "^[0-9]+$"^^ . "fossilworks.taxon" . "101775319"^^ . . . "HD+118-001"^^ . . . . . . . . . "CohesinDB gene" . . . . "life science" . "Anton I Petrov" . "false"^^ . "HemOnc Terminology" . . "false"^^ . . "The Experimental Measurements, Purposes, and Treatments ontologY (EMPTY) is a structured vocabulary designed to capture and standardize the scientific reasoning behind experimental measurements. It addresses a critical gap in existing metadata standards, which primarily focus on technical specifications rather than scientific intent. The ontology provides a common language to express why a measurement was taken and the conceptual conditions under which it should be interpreted. By focusing on experimental purposes and treatments, EMPTY is designed to significantly improve the findability, interoperability, and reusability of scientific data. This enables researchers to discover relevant datasets for meta-analyses and cross-disciplinary research based on shared scientific goals. (from https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2753)"^^ . . . . "C6155"^^ . . "Angela Kranz" . . . . . "0000139"^^ . "signaling-gateway" . "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId="^^ . "https://books.google.com/books?id="^^ . . . "nextdb" . . "false"^^ . . . . "ontology" . "https://fedirect.toolforge.org/?id=$1"^^ . "tissue" . _:N851ebc0692b14a7b8f922a0351f3d2c5 "Kirk Hess" . . . "http://purl.obolibrary.org/obo/COVIDO_"^^ . . . . "UniPathway Compound" . . . "metaproteomics" . . "allyson.lister@oerc.ox.ac.uk" . . "A publication in the ChemBioSys data platform"^^ . . . . "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB."^^ . . . "false"^^ . "unists" . . . "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . . . "^\\d+$"^^ . . "life science" . "secondary_attack_rate"^^ . . . . . . . . "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:"^^ . . . . . . "false"^^ . . . . "false"^^ . . . . . . "myco.lepra" . . . . "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value="^^ . . "true"^^ . . "ontology" . . . "en-GB"^^ . . "Ensembl Bacteria" . "agriculture" . . . "SwissLipid" . "neurology" . . . "https://cropontology.org/rdf/CO_337:$1"^^ . . . "mutation" . "false"^^ . "https://neurovault.org/images/"^^ . "ogms" . . . "https://nsrrc.missouri.edu/nsrrc$1info/"^^ . . . . . "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task="^^ . . . . . . . . . . . . "human health" . . . . "drugbankv4.target" . "Nathan Edwards" . . . "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . . . . "Pavel Hobza" . . . "A controlled vocabulary to support the study of transcription in the primate brain"^^ . . . "PharmacoDB Tissues" . . . . . . . . . . "4dn.biosource" . "https://gtdb.ecogenomic.org/tree?r=$1"^^ . . . "protozoan" . . . . . . . . . . "ChEMBL tissue" . . . "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."^^ . . "biostudies" . "http://purl.uniprot.org/uniprot/"^^ . . . . "http://purl.obolibrary.org/obo/DC_CL_$1"^^ . "gpmdb" . "^\\d{7}$"^^ . "Joel Richardson" . "Database of protein-protein complexes" . "https://www.uniprot.org/diseases/"^^ . . . "infection process" . . . "neuromorpho" . . "intenz" . . . "pid.pathway" . "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$"^^ . . . "small molecule" . "Miguel A. Fortuna" . "medicine" . . . . "false"^^ . . . "sequence motif" . . . . . . "drug" . . . "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object="^^ . . . . _:N2697be6d126c450087aa40ec95d3632f . . . . . "https://go.drugbank.com/drugs/$1"^^ . . "0000004"^^ . . . . "1000003"^^ . . . . . . "chembiosys.investigation" . "caloha" . . "taxonomy" . . . . . . "structural biology" . . . "http://www.proglycprot.org/detail.aspx?ProId=$1"^^ . . . "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."^^ . . . "Identifiers for chemicals used as buffers"^^ . . . . . . "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."^^ . . . . . "Molecule role (INOH Protein name/family name ontology)" . . . . . "functional genomics" . . . "81d0ea69a9ab134f6ba68314e982171a367d3ab739c85c5ba49701dd02170ed3"^^ . "license" . "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."^^ . . . . . "Chinese Biological Abstracts" . "gene" . "http://www.w3.org/ns/odrl/2/"^^ . "https://id.loc.gov/authorities/$1"^^ . "https://datacommons.org/browser/$1"^^ . . . "NERC Vocabulary Server" . "false"^^ . . . . . . "false"^^ . . "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID="^^ . . . . "false"^^ . "interaction" . "^[A-Za-z0-9]+$"^^ . . "ontology" . "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]"^^ . "http://purl.bioontology.org/ontology/VANDF/"^^ . . . "ensembl.bacteria" . "mutant" . "https://www.pgscatalog.org/pgs/$1"^^ . "http://www.ontobee.org/" . "EC_CODE" . . . "ApiDB_PlasmoDB" . . . . . "gemet.group" . "d4e2515"^^ . . "pharmacodb.dataset" . . "128011350"^^ . "0e39569d-ff81-4b78-9c34-b07309504d80"^^ . . . . . . . "plant cell biology" . "alteration" . "biology" . . "101"^^ . . "^[0-9]+$"^^ . "NIF Standard Ontology: Investigations" . . "Cluster of orthologous genes" . . "identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829"^^ . . . . . . "false"^^ . . . . . . "4776"^^ . . "cellular component" . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . "OriDB Schizosaccharomyces" . . . "genome" . "ontology" . . . "2555646"^^ . "Antibody Registry" . . . . . "subject agnostic" . "bodc.unit" . . "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"^^ . . . "false"^^ . "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . . . "pmr" . . . "anzctr" . . . "life science" . . . . . "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^ . . . "elspeth@genenames.org" . . "hemonc" . "life science" . "ark" . "https://resolver.api.identifiers.org/resolveMirId/$1"^^ . "YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes."^^ . . . "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"^^ . "Property"^^ . . . "rna" . . . "https://cellmodelpassports.sanger.ac.uk/passports/"^^ . . . . . "blood" . . . . . . . . . "sperm" . . . "0000025"^^ . "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms."^^ . "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"^^ . . . "0807.4956v1"^^ . . . "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . "emi" . . . . "Zebrafish Information Network Gene" . . . . "http://purl.org/spar/pro/"^^ . "phenotype" . "https://prefix.zazuko.com/" . "sphn" . . "^\\d+$"^^ . . . . "https://repeatsdb.org/structure/"^^ . . "fungorum" . . . "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id="^^ . "civic.disease" . . . . "subject agnostic" . "This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from )" . "false"^^ . "false"^^ . _:N06309e1c65044b28b236eb3decc182be "takatter@dbcls.rois.ac.jp" . . "metabolomics" . "Vocabulary used in the RDF representation of SBML models."^^ . . . "https://metazoa.ensembl.org/id/$1"^^ . . "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers."^^ . . . "^\\d{6}$"^^ . . . . . . . . . "The SAGE Social Science Thesaurus is a multidisciplinary vocabulary of the most important concepts in the social sciences. SAGE uses this vocabulary as its principal keyword vocabulary for automated tagging of content on SAGE Knowledge and SAGE Research Methods. You are welcome to browse, download, use and transform the vocabulary for any non-commercial purpose.\n\nThe majority of concepts in the thesaurus have been mined from headwords in SAGE encyclopedias and other reference works. Relationships between concepts have been inferred from implicit structures in those works, for example subject indexes and readers' guides. As such, the thesaurus is a structured representation of what the editors of those reference works consider to be the most important concepts in the social sciences.\n\nAdditional scraping work has extracted and structured concept-specific metadata, such as dates (for events and people) and definitions. In addition to broader-narrower relationships, concepts are grouped by type: concepts, people, organizations, events, methods, theories or laws."^^ . . "fishbase" . . "https://lincs.hms.harvard.edu/db/datasets/$1"^^ . . . . . . . "Medical Action Ontology" . "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"^^ . "life science" . "tsrnadisease" . "The first number is the chapter then the remainder are subsections."^^ . . "anatomy" . . "http://purl.obolibrary.org/obo/VT_$1"^^ . . . . . . "http://purl.obolibrary.org/obo/NGBO_$1"^^ . . . . . . . "Immune Epitope Database Assays" . "An ontology covering the taxonomy of teleosts (bony fish)"^^ . . . . . . . . . . . . . . . . . . . . . . . . . . . . "yperez@ebi.ac.uk" . "https://bioregistry.io/treebase:"^^ . "Annotated Regulatory Binding Sites" . "ieee.document" . "biomedical science" . . . "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^ . . "^\\d{5}$"^^ . "GeoNames" . "false"^^ . "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . . "http://purl.org/spar/cito/"^^ . . . . "Developing Mouse Brain Atlas" . . "^\\d+$"^^ . . . . . . "Hadi Quesneville" . . "Dynamic Ecological Information Management System - Site and Dataset Registry - Network" . . . . "false"^^ . . "ontology" . . "http://cegg.unige.ch/orthodb/results?searchtext="^^ . "The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]"^^ . "0116"^^ . "false"^^ . . "false"^^ . . . "NCBI PubChem database of bioassay records" . . "^\\d{6}(-\\d+)?$"^^ . . . . "eea2b5c6-48d1-4612-957e-585783b3c7bb"^^ . . . . . . "Cell line collections (Providers)"^^ . . . . . . . "epidemiology" . . . . "https://gdo.endlessforms.info/view/classes?uuid=GDO_$1"^^ . "false"^^ . . "samuel.friedman@cammlab.org" . "teresa.k.attwood@manchester.ac.uk" . "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1"^^ . . "life cycle" . "H-InvDb Transcript" . . . . "false"^^ . . "https://cropontology.org/rdf/CO_343:$1"^^ . . "dct" . . . . . . . "violinId" . . . "AspGD Protein" . . . . "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."^^ . . "Proteomics Identification Database Ontology" . . . . "planp" . . . . . . . "EDAM Operation" . . . "http://www.t3db.org/toxins/$1"^^ . . . . "life science" . "NIHhESC-10-0083"^^ . "^bt\\d+$"^^ . "false"^^ . "false"^^ . . "PTHR12345"^^ . "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."^^ . . . . "24801"^^ . "trait" . "false"^^ . . "Fossilworks Journal" . "ontology" . "^\\d+$"^^ . "http://data.europa.eu/esco/skill/$1"^^ . . "https://www.re3data.org/repository/"^^ . . . . "rna" . . . "m.a.laporte@cgiar.org" . . "transcriptomics" . . . "CALM1"^^ . . . . . . "0000140"^^ . . . . . . . "kim.hochschulfaechersystematik" . . "true"^^ . . . . . . . . "ontology" . . . . . "https://cropontology.org/rdf/CO_360:"^^ . . "minid" . . . . "biro" . . . . . . . "scancerrna" . "^\\d{7}$"^^ . . . "nlx.br" . "phenotype" . . "Genetic and Rare Diseases Information Center" . . . "NEPOMUK Contact Ontology describes contact information, common in many places on the desktop. It evolved from the VCARD specification (RFC 2426) and has been inspired by the Vcard Ontology by Renato Ianella. The scope of NCO is much broader though. This document gives an overview of the classes, properties and intended use cases of the NCO ontology. (from homepage)"^^ . . "false"^^ . . "education" . . . . "Ioannis Xenarios" . "https://images.endlessforms.info/collection/"^^ . . . "Cell line collections (Providers)"^^ . . "Adnan Malik" . . "false"^^ . . . "ribonucleic acid" . . . . . "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"^^ . "computational biology" . . . . "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . . . . . . . "small molecule" . . . . . . . . . . "Activity Streams" . . "icd11.code" . "false"^^ . . . . "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."^^ . "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."^^ . . "https://suprabank.org/solvents/$1"^^ . . . "false"^^ . . . "https://commonchemistry.cas.org/detail?cas_rn=$1"^^ . . . "The Protocol for Web Description Resources (POWDER) allows metadata to be associated with groups of resources such as those found on a Web site. Its main 'unit of information' is the Description Resource (DR), one or more of which are contained in a POWDER document. Processing such a document yields RDF triples describing the resources that are within the scope of the DRs. POWDER documents are written in XML and have relatively loose semantics, however, a GRDDL transform, associated with the root namespace, renders the data in RDF/OWL with more formal semantics. [from homepage]"^^ . . . "protein" . . "hescriva@obs-banyuls.fr" . "synbip.epitope" . . "http://www.w3.org/ns/ssn/systems/$1"^^ . . "ontology" . . . . . . . "^\\d{7}$"^^ . "SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes.\n\nIt assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed."^^ . . . . . . "https://cropontology.org/rdf/CO_347:$1"^^ . _:Nea47939e040d4b03980219bf4c045c9a "davem@umn.edu" . "data management" . . "http://www.w3.org/ns/shex#"^^ . "clyh" . . "Philipp Bucher" . . . . "http://www.cathdb.info/cathnode/$1"^^ . . . "Nalika Palayoor" . . . . . . "preprints" . . . . "http://purl.obolibrary.org/obo/MPATH_"^^ . "false"^^ . "Genome Aggregation Database" . . . "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."^^ . . "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr="^^ . "snctp" . "ontology" . "imaging" . . "http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1"^^ . . "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.\n\nThe API can be accessed [here](https://goldbook.iupac.org/pages/api)"^^ . "protein" . . "^CL\\d+$"^^ . "^\\d{7}$"^^ . "https://www.wormbase.org/db/seq/protein?name="^^ . "^\\d+$"^^ . . "https://www.ncbi.nlm.nih.gov/nuccore/"^^ . "https://model.geneontology.org/"^^ . . "false"^^ . . "NLXRES" . . . . . . "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."^^ . "^AA\\d{4}$"^^ . . . . "Name-to-Thing" . . . . . "ITMCTR2023000002"^^ . . . . . "Scientific Information Retrieval and Exchange Network" . "^[0-9A-Za-z\\-.\\+]+$"^^ . . "http://bioportal.bioontology.org/ontologies/"^^ . . "imp10873"^^ . "21157"^^ . . . . "hsapdv" . . "BioSimulators" . . "https://uniresolver.io/#did:"^^ . "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1"^^ . . "https://cropontology.org/rdf/CO_350:$1"^^ . . "Creative Biolabs Protein provides identifiers for protein-related entities, including therapeutic proteins, proteolytic enzymes, antibody-like scaffold proteins, soluble T cell receptors, and tetramers."^^ . . . . . "model organism" . . . "GWAS Catalog" . . . . . . . . "http://www.kdbirp.aiddlab.com/detail/$1"^^ . "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies."^^ . . . . . "general & upper" . . . . "http://solgenomics.net/phenome/locus_display.pl?locus_id="^^ . . . "false"^^ . "kegg.rclass" . "virsi1909"^^ . "PR00001"^^ . . . "PubChem Substance ID (SID)" . . "https://medical-data-models.org/forms/$1"^^ . . . "molecular entity" . "false"^^ . "bioinformatics" . _:Nee88b7db3bb94ad38302a3495582d71e . . . . . "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"^^ . . . "biodiversity" . "small molecule" . . . . . "histology" . . . "0000390"^^ . . . "PROV Namespace" . . . "Vaccine Ontology" . . . . "AddexBio cell line products" . . . "https://www.re3data.org/repository/$1" . . . "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^ . . . "0000080"^^ . . . "false"^^ . "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . . "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."^^ . . "storedb.dataset" . . . . . "Gramene Reference" . . "false"^^ . "https://nztcs.org.nz/nztcs-species/$1"^^ . . . . . . . . "^\\d{6,7}$"^^ . "false"^^ . . . "life science" . . "false"^^ . "http://purl.org/ejp-rd/vocabulary/$1"^^ . . "002804"^^ . . "000320401"^^ . . _:N9756a95d55d04316b98ac063b1e03879 "custserv@nlm.nih.gov" . "https://www.nextprot.org/term/FA-"^^ . . . . "nlm.publisher" . "491187"^^ . "https://www.emsl.pnnl.gov/project/"^^ . . "autdb" . . "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."^^ . "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id="^^ . . . . "translation_language"^^ . "https://cellxgene.cziscience.com/e/"^^ . . . . . "mirTarBase" . . . . . . "Terminology for Description of Dynamics" . "nstd102"^^ . . "alan.bridge@sib.swiss" . . . . "0005452"^^ . . "4000027"^^ . "software engineering" . . . . . "Contains identifiers of cohesin-related chromatin loops from CohesinDB. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. Each identifier represents a single cohesin-related chromatin loop. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information."^^ . . "http://purl.obolibrary.org/obo/AEO_"^^ . . "FDA Application" . "http://www.pharmgkb.org/gene/$1"^^ . . "deficiency" . . . . . . . . . "JWS Online" . . . . "Fungal Nomenclature and Species Bank" . "toni.gabaldon@crg.eu" . . . . "cl3603"^^ . . . . . "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."^^ . . "false"^^ . "https://scicrunch.org/resolver/RRID:BCBC_"^^ . . "https://swissmodel.expasy.org/repository/uniprot/"^^ . . . . . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"^^ . "aBq"^^ . "spa"^^ . . . . . . "0000411"^^ . . "e0333"^^ . "http://ctdbase.org/detail.go?type=gene&acc=$1"^^ . "identifier of an entry in the NCI Drug Dictionary"^^ . . "Vincent Robert" . "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^ . . . . "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^ . "preclinical studies" . . "6VDC956"^^ . . . "AC119"^^ . . "mutation" . "protein" . . . . "hgnc" . "true"^^ . . . . . . . . . . "http://purl.obolibrary.org/obo/HEPRO_$1"^^ . . . . . . . "Daniel Schober" . "bcio" . "614"^^ . . "registry" . "https://scholar.google.com/citations?user="^^ . "NCBI Genetic Code" . . . . . . . . . . "^[A-Z]C\\d{1,3}$"^^ . . . "Ontology of Adverse Events" . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information."^^ . . . "http://purl.obolibrary.org/obo/VariO_"^^ . "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)."^^ . "Functional Genome Annotations with Transcriptional Activities" . "mdl" . . . . . "0000984"^^ . "ChemBioSys Model" . . "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."^^ . "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^ . . . . "phenotype" . . . "false"^^ . "relationships" . "https://www.gwascentral.org/phenotype/$1"^^ . . "http://genomics.senescence.info/diet/details.php?id="^^ . . "https://www.metanetx.org/comp_info/$1"^^ . . "0000712_1"^^ . "metadata" . . "SIGNOR-252737"^^ . . "Supplier of mice for research purposes. [from RRID]"^^ . . "Pathway ontology" . . "genome" . . "false"^^ . . "fisheries science" . "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^ . . . . . . . . "false"^^ . "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers."^^ . "haendel@ohsu.edu" . . "webelements" . . . . . . . . _:N1cd40c152ac54ccf9674b630f1e1c5ff "psidev-gps-dev@lists.sourceforge.net" . . . "https://nmrxiv.org/project/"^^ . . . "mesh.vocab" . . . . . "psychiatry" . "SugarBind" . "SED-ML model format" . "Xeni Kechagioglou" . _:Nb7e85f58056b4253a68baea08ef24c12 "wbug@ncmir.ucsd.edu" . "ecto" . . . . "^\\d+$"^^ . . "^\\d+$"^^ . "^\\d+$"^^ . . . "false"^^ . . . . "^PR[0-9]{6}$"^^ . . . . "SNOMED_CT" . . "^\\d{7}$"^^ . "International Standard Classification of Education, 2013 Edition" . "https://tools.ietf.org/rfc/rfc"^^ . "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019"^^ . . "Creative Biolabs antibody" . . . . . . . "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."^^ . "kegg.drug" . . "https://geneontology.org/GO_REF/$1"^^ . . . . "Uberon Property" . "cthoyt@gmail.com" . "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved."^^ . . "ClinGen Curation" . . "10531"^^ . "https://biopragmatics.github.io/providers/uniprot.ptm/"^^ . "viaf" . . . "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id="^^ . "^\\d{7}$"^^ . "An anatomical and developmental ontology for cephalopods"^^ . "LCL-2085"^^ . . . "kcris" . . "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology."^^ . . . "^[A-Z0-9]{4}\\.[A-Z0-9]{2}$"^^ . "https://www.ebi.ac.uk/intact/interaction/$1"^^ . . "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115="^^ . "medicine" . "Wikidata Entity" . . "http://purl.obolibrary.org/obo/CDAO_$1"^^ . . . . "NCBI Gene Expression Omnibus" . "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^ . . "FB" . "U001388"^^ . . "Allergy"^^ . . "false"^^ . . "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . "zbw.stw" . . . . . "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$"^^ . "data management" . . "EDAM Data" . "registry" . . "molecular biology" . . . "HMS Library of Integrated Network-based Cellular Signatures Antibodies" . . . "BioNumbers" . . . . "https://gold.jgi.doe.gov/resolver?id=$1"^^ . . "zhengj2007@gmail.com" . . . . . . . . . . . . . "http://purl.obolibrary.org/obo/OHMI_"^^ . "protein" . . . "obo" . "https://cropontology.org/rdf/CO_350:"^^ . . . . "life science" . . . . "license" . . "17254"^^ . . "stock" . "^[A-Za-z_0-9]+$"^^ . . "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump"^^ . . . . . . . "OpenCitations Meta Identifier" . "FlyBase" . "^[a-f0-9]{64}$"^^ . . . "http://purl.obolibrary.org/obo/SDDO_"^^ . "101"^^ . "https://www.chemspider.com/search?params="^^ . "phylogenetics" . . "mycobank" . _:N42478bbb417140eca19797e06830d29a "FALDO group" . . . . "phenolexplorer" . "1693"^^ . "false"^^ . . . "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information."^^ . "http://purl.bioontology.org/ontology/VANDF/$1"^^ . . . . "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . . . . . "http://purl.obolibrary.org/obo/SCDO_"^^ . "unesco.thesaurus" . . "lucas.leclere@obs-banyuls.fr" . . "https://www.uniprot.org/journals/$1"^^ . . . . . . . "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . "03yrm5c26"^^ . . "https://data.4dnucleome.org/experiment-set-replicates/"^^ . "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID="^^ . "scopus" . "false"^^ . "cto" . "https://cropontology.org/rdf/CO_323:$1"^^ . . . . "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . . . . . . . . . . "metabolomics" . "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^ . . "https://civicdb.org/links/assertions/"^^ . . . "https://vocab.nerc.ac.uk/collection/$1"^^ . . . . . . "false"^^ . . . "ontology" . . . . . . . . . . _:N06309e1c65044b28b236eb3decc182be . . "false"^^ . "rnacentral" . "SNOMEDCT_2020_03_01" . . "life science" . "Platynereis Developmental Stages" . . . . . "0000101"^^ . . . . . . . "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . . . "p3db.protein" . "http://purl.obolibrary.org/obo/RBO_$1"^^ . "false"^^ . . . "anatomy" . "Katy Börner" . . "true"^^ . . . "IST028"^^ . . "0000024"^^ . . . "medical informatics" . . . . . . . . . "KESTREL Ontology" . "pancreatic islet function" . . . "grin.taxonomy" . . "pharmacology" . . . "^\\d{7}$"^^ . "morbidity" . "false"^^ . . . "vectorbase" . . . . . . . . . "https://hub.docker.com/r/$1"^^ . . . . . . "https://www.geonames.org/"^^ . "obo" . "http://www.w3.org/ns/odrl/2/$1"^^ . . . . "cido" . . "GPST000024"^^ . . . "National Swine Resource and Research Center" . . "SWEETRealm" . . . . . . "Representing Content in RDF" . "M00002"^^ . "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . . . . "subject agnostic" . "jstor" . "probesanddrugs" . . "Erik Segerdell" . . "KEGG LIGAND" . "Gregory Landrum" . . "merops.clan" . . . . "structural biology" . . "CompoundEquivalence"^^ . . "clingen.curation" . "Locus Reference Genomic" . . "false"^^ . . "CTD Chemical" . . . . . "PMCID" . . "false"^^ . . "phenotype" . . "Ontology for computer aided process engineering" . . . . . "http://data.crossref.org/fundingdata/funder/10.13039/"^^ . . "carlo.ravagli@novartis.com" . "COVID-19 Surveillance Ontology" . . "Chan Zuckerberg CELLxGENE Collection" . . "work" . "2244"^^ . "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all."^^ . . . "^\\d{7}$"^^ . . . . "http://cgsc.biology.yale.edu/Site.php?ID="^^ . . . . . "4.2.78"^^ . "https://bioregistry.io/clingen.affiliation:"^^ . . "ontology" . . . "^[A-Z]+$"^^ . "emaps" . . "http://homosaurus.org/terms/"^^ . . . . . "Evidence and Conclusion Ontology" . . "NIST Chemistry WebBook" . . "01467"^^ . . "qtl" . "Franziska B. Grieder" . . . "https://www.hipsci.org/#/lines/$1"^^ . "50583"^^ . . . . "obo" . . . . "LNCipedia" . . "^\\d{4,6}$"^^ . . . "https://biomedit.ch/rdf/sphn-ontology/sphn#"^^ . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"^^ . . "genomics" . "https://awi.cuhk.edu.cn/dbAMP/information.php?db=dbamp_"^^ . "https://ieeexplore.ieee.org/author/"^^ . . . . . "ali.syed@kaust.edu.sa" . "PWY-1042"^^ . . "https://cropontology.org/rdf/CO_327:"^^ . "subject agnostic" . . . . "https://ssrn.com/author="^^ . . . "gene" . "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI."^^ . . . "false"^^ . "false"^^ . "senso" . . . "Simplified Upper Level Ontology" . "obo" . "pharmacogenomics" . "DragonDB Locus" . "National Bibliography Number" . "protein" . "go" . "giacomo.lanza@ptb.de" . . . "false"^^ . . . "EY223054.1"^^ . "neurofibromatosis" . "https://ibdc.dbtindia.gov.in/icpd/study-view-home/"^^ . . . "https://w3id.org/nfdi4cat/voc4cat_"^^ . . "judith.blake@jax.org" . "46"^^ . . "centrally registered identifier" . . "dbr" . "virology" . . . . "data retrieval" . . . . "life science" . . "^\\d{5}$"^^ . . . . . . "https://bioregistry.io/n2t:"^^ . . . . "protein" . "vbrc" . . "^[A-Za-z_0-9]+$"^^ . . . . . "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available."^^ . . "ontology" . . . _:N06309e1c65044b28b236eb3decc182be "Terue Takatsuki" . "https://purl.dataone.org/odo/SALMON_"^^ . . . . . "^\\d+$"^^ . . . . "biodeep" . . . "Blue Brain Project Topological sampling Knowledge Graph" . "beck@ncbi.nlm.nih.gov" . . . "tctr" . "data science" . . . "https://purl.dataone.org/odo/ADCAD_"^^ . . "http://www.jstor.org/stable/"^^ . . . . . . . . . . . . . "mr"^^ . . . . . . . . "obo" . _:N4f631ee049f94c9eba4ffad22d749de6 "Pat Brooks" . "Unified Phenotype Ontology" . . "glida.gpcr" . . . . . . . . . . "PA448710"^^ . . . . "algorithm" . "false"^^ . . "^\\d{7}$"^^ . "^\\w+$"^^ . "The official list of MIME types, now renamed to media types"^^ . . . "CutDB" . . . "sciflection" . . "http://classyfire.wishartlab.com/tax_nodes/C"^^ . . "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."^^ . . . . . . . . . "^([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])$"^^ . . . . . . "https://w3id.org/babelon/$1"^^ . "publisher" . . "genetics" . . . "compound" . . . . . . "obo" . "0000001"^^ . . "atc" . "fairsharing.user" . "https://www.storedb.org/store_v3/study.jsp?studyId="^^ . . "dctypes" . "COG Pathways" . . "https://odc-sci.org/data/$1"^^ . . "false"^^ . . "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name="^^ . "http://uri.neuinfo.org/nif/nifstd/nlx_chem_"^^ . "BEI_Resources" . . . . . . "https://data.chembiosys.de/assays/"^^ . "medicine" . "00001"^^ . . . . . "ontology" . "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did="^^ . . . . . . "^BGC\\d{7}$"^^ . . "clinvar.submitter" . . . . . "true"^^ . . . "^[A-Z0-9*:]+$"^^ . . . "false"^^ . . . . . . . "DataCite Ontology" . . . . . . . "taxonomic classification" . "ontology" . "inspire.theme" . . . . "rnavdb" . . . "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."^^ . . . "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"^^ . "Salmon Ontology" . . "biomedical science" . "ontology" . . . . . . . "Integrated Genomic Resources of human Cell Lines for Identification" . . "ontology" . . . "false"^^ . "duo" . "life cycle stage" . . . . . . . "https://www.ebi.ac.uk/ols4/ontologies/$1" . . "food" . "oryzabase.mutant" . . "http://func.mshri.on.ca/yeast/genes/list_functional_scores/"^^ . "coriell" . . "TreeHub" . . "ncbibook" . "ProDom" . . "63189"^^ . . . . . "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . "life science" . "http://dramp.cpu-bioinfor.org/browse/All_Information.php?id="^^ . . . . "http://streptomedb.vm.uni-freiburg.de:8000/streptomedb/get_drugcard/"^^ . . "https://id.loc.gov/vocabulary/languages/"^^ . . "An issue on the Vertebrate Breed Ontology GitHub issue tracker"^^ . . . . . "false"^^ . . . . "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code="^^ . . . . . "KEGG Enzyme" . "http://synbip.idrblab.net/data/sbp-target-complex/details/"^^ . "phenotype" . "Open Researcher and Contributor" . . . . "tdwg.taxonrank" . . . . . "https://www.icd10data.com/search?s=$1"^^ . "^\\d+$"^^ . "seed.reaction" . . "Peter D'Eustachio" . . "Allan Spradling" . "biochemistry" . . . "function" . . . "false"^^ . . "https://go.drugbank.com/bio_entities/"^^ . "phebert@uoguelph.ca" . . "https://www.webelements.com/$1"^^ . . . . "eol" . "chenyangnutrition@gmail.com" . . "genome" . . . "nomen" . . "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . . . "^\\d+$"^^ . . . "natural science" . . "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"^^ . . . "ontology" . . "http://purl.obolibrary.org/obo/ZECO_$1"^^ . . . . "chemistry" . . "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"^^ . . . "^\\d+$"^^ . . "experimental measurement" . . . "genetics" . . "phenotype" . "Agronomy Vocabulary" . . . "NIF Standard Ontology: Subcellular Entities" . . . "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^ . "linkContext"^^ . "tol.webproj" . "model organism database" . "pancreatic development" . "CRISP" . . . . . "^\\d{7}$"^^ . "disease" . . . "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."^^ . . "lncbook" . . "http://purl.obolibrary.org/obo/MICRO_"^^ . . . . . "experimental measurement" . . . . "http://www.w3.org/ns/adms#"^^ . . "2404"^^ . . . . "http://purl.obolibrary.org/obo/FIX_"^^ . . "http://www.ifomis.org/bfo/1.1/snap#$1"^^ . . . . "Drosophila Phenotype Ontology" . . . . . "classification" . . "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^ . "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1"^^ . . . . . "http://www.candidagenome.org/cgi-bin/locus.pl?dbid="^^ . . "https://data.4dnucleome.org/biosources/"^^ . "Epilepsy Ontology" . "^\\d{3}$"^^ . "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^ . "ximbio" . . "https://www.webofscience.com/wos/woscc/full-record/WOS:$1"^^ . . "sdap" . . "ontology" . . . "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome."^^ . . . . "https://w3id.org/semapv/vocab/"^^ . "Eukaryotic Linear Motif Resource" . "Database of Genomic Structural Variation - Variant" . "wikidata" . "insdc.sra" . "true"^^ . "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries."^^ . . . . "anatomy" . . "swo" . . . "https://www.facebase.org/data/record/#1/isa:dataset/accession="^^ . "seaver@anl.gov" . "^\\d{7}$"^^ . "https://ngdc.cncb.ac.cn/lncbook/gene?geneid="^^ . "false"^^ . . . . "cell types" . . . "cultured cell" . "The Data Model Language Controlled Vocabulary was created for NSF's EarthCube Program's Resource Registry. At this point it merely lists a few of the languages used by data model resources in the registry."^^ . . "somatic" . . . "mw.study" . "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" . "^activator|agonist|allosteric-antagonist|antagonist|antisense-inhibitor|binding-agent|blocker|chelating-agent|cross-linking-agent|degrader|disrupting-agent|exogenous-gene|exogenous-protein|hydrolytic-enzyme|inhibitor|inverse-agonist|methylating-agent|modulator|negative-allosteric-modulator|negative-modulator|opener|other|oxidative-enzyme|partial-agonist|positive-allosteric-modulator|positive-modulator|proteolytic-enzyme|reducing-agent|releasing-agent|rnai-inhibitor|sequestering-agent|stabiliser|substrate|vaccine-antigen$"^^ . . . "http://purl.obolibrary.org/obo/MC_"^^ . . . . . . . "Jennifer C. Girón" . . . . . "false"^^ . . . "^\\d{7}$"^^ . "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data."^^ . . . "http://avis.princeton.edu/pixie/viewgraph.php?graphID="^^ . "The Drug-Drug Interactions Ontology" . "^EG\\d+$"^^ . . "false"^^ . "https://www.ncbi.nlm.nih.gov/books/$1"^^ . "uniprot.resource" . . . "ontology" . . . . . "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."^^ . . . . "andrea.perego@jrc.ec.europa.eu" . . . "Aromatic"^^ . . . . "cellular" . "GlycoMapsDB" . . . . "https://www.nwo.nl/en/projects/$1"^^ . . "biomedical science" . . "systems biology" . . "WBRNAi00086878"^^ . . . . . "false"^^ . . . . . . . . . . . "http://www.molmovdb.org/cgi-bin/morph.cgi?ID="^^ . "false"^^ . . "sébastien Aubourg" . . . . "NOR00681"^^ . . "events" . . . . . "SNOMEDCT_2010_1_31" . . "The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners."^^ . . . "^\\d{7}$"^^ . "false"^^ . . . . . "MMSL_CODE" . . "762"^^ . . . . . "metabolights" . "Bibliographic Framework Initiative Vocabulary" . "dr.sebastian.koehler@gmail.com" . . . "NUI" . "radiology" . . . . . . "https://rrid.site" . "hospital" . . . . . . . . "false"^^ . . . "OnlineJournal"^^ . . . . . . . . . "false"^^ . "tag"^^ . "^\\d+$"^^ . "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO)."^^ . . "HGNC_GROUP" . . . . "https://bykdb.lyon.inserm.fr/data/html/annotated/$1.html"^^ . . "software"^^ . . . "http://classyfire.wishartlab.com/tax_nodes/C$1"^^ . . "https://fcs-free.org/fcs-database?"^^ . . . "1018"^^ . . . . . . "false"^^ . . . . . "GARD" . "policy" . "rr@uga.edu" . "epidemiology" . . . . "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id="^^ . "ISTransbase is a highly reliable and accessible database that focuses on inhibitors and substrates of drug transporters, offering a wealth of vital information encompassing experimental methods, transport parameters, and references."^^ . . . . "false"^^ . "^\\d{7}$"^^ . . . "rbrinkman@bccrc.ca" . "https://www.ribocentre.org/docs/$1"^^ . "life science" . . . "false"^^ . . . . "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs."^^ . . _:N649959919c924cc49fc032c5ce78f634 "Kim Petersen" . . "http://scop.berkeley.edu/sid=$1"^^ . "drks" . . "false"^^ . . . "^\\d+$"^^ . . "https://www.kegg.jp/entry/"^^ . . _:Ne3b81e66109543bd8b5f1e698db02f0c . "ecology" . . . "stoeckrt@pcbi.upenn.edu" . "eVOC mouse development stage" . . "forest management" . . "gold standard" . . . "315.1"^^ . . . . "8000221"^^ . . . . . . "williams.antony@epa.gov" . . . "structure" . . . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . . "pictar" . . . . . . . . "agriculture" . . . . . . . "glycomics" . . . . . "The data model underlying lexvo"^^ . . . "vjenkins@morgan.harvard.edu" . "An ontology demonstrating rich ontology for rubber extrusion."^^ . "http://purl.obolibrary.org/obo/NCIT_$1"^^ . . "SNOMEDCTCT_2019_03_01" . "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . . "http://www.humanproteomemap.org/protein.php?hpm_id=$1"^^ . . "true"^^ . . . "dommino" . "false"^^ . "https://services.scicrunch.io/sparc/drs/v1/package/$1"^^ . . . "https://glytoucan.org/Structures/Glycans/$1"^^ . . . . "false"^^ . "molecular chemistry" . . . . . . . . "268"^^ . . . . "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . . . "person" . . . . "false"^^ . . "false"^^ . . . . "rna" . . "cell_biolabs" . "iceberg.ice" . . "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#"^^ . . "13GS"^^ . "5282"^^ . . . "A Semantic Web Rule Language Combining OWL and RuleML" . "ontology" . . "mouse" . . . . . "http://purl.bioontology.org/ontology/IDODEN_$1"^^ . . "virus" . "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id="^^ . . "https://nfdi.fiz-karlsruhe.de/ontology/NFDI_"^^ . . "antibodyregistry" . . . . "life science" . . . . . . . . . . . . . . "ontology" . . "protein complex" . . . . . . . "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^ . . "iECABU_c1320"^^ . "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id="^^ . . . . "sgd" . "bacmap.biog" . . "syn" . . "^\\d{7}$"^^ . "agriculture" . . . . . "fabio" . . . . . "http://www.wikidata.org/entity/"^^ . . "false"^^ . . . "ontology" . "mineromero2901@ciencias.unam.mx" . "baoym@big.ac.cn" . "pwo" . . . "Mouse pathology ontology" . . . . "data identity and mapping" . . "natural product" . . . . "rscheuermann@jcvi.org" . "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."^^ . "phenotype" . "^\\d+$"^^ . . . "phenomics" . "SUPERFAMILY" . "https://www.langual.org/langual_thesaurus.asp?termid=$1"^^ . "biomedical science" . . "Vertebrate Taxonomy Ontology" . "soil science" . "plant phenotypes and traits" . . . "metabolomics" . . . "https://db.idrblab.net/ttd/data/target/details/$1"^^ . "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^ . "msigdb" . . . "GeneDB" . "hom" . "^NBK\\d+$"^^ . . . . "taxrank" . "debio" . "David Starns" . . . . . "false"^^ . . . . . . "embryonic stem cell line" . "person" . "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia."^^ . . "http://www.w3.org/2006/vcard/ns#"^^ . . "0000001"^^ . . "^TS-\\d{4}$"^^ . . . . "obo" . . "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion."^^ . "nih initiative" . . . "false"^^ . . . . "life science" . "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/"^^ . . . "^MGYA\\d+$"^^ . "http://www.ubio.org/browser/details.php?namebankID="^^ . "gene" . . . . . "^\\d+$"^^ . "true"^^ . . "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"^^ . . . "structural biology" . "^EBI\\-[0-9]+$"^^ . "ramirez@macn.gov.ar" . "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."^^ . . . _:Nce41d6177596475ca307007440dd9504 "julie@igbmc.u-strasbg.fr" . "pathway" . . . . . . . . . "PD000596"^^ . . . . . . . "10015919"^^ . . "23"^^ . "5fce9b7300001250"^^ . "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc."^^ . "joanne.kamens@addgene.org" . . . "iNaturalist User" . . "phytozome.locus" . . . "DrugBank Drug Category" . . "binding site" . . . . "false"^^ . "ontology" . "false"^^ . "https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/detailed_view/$1"^^ . . . . "Dengue Fever Ontology" . . . . "study design" . . . "blast" . "expression" . "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"^^ . . . . . "false"^^ . . . "http://purl.obolibrary.org/obo/PLO_$1"^^ . "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . . "vmc" . . "stefan.guenther@pharmazie.uni-freiburg.de" . . "genome" . . . "false"^^ . "Joe Flack" . "^\\d+\\w?$"^^ . "anne.morgat@sib.swiss" . . _:Ndb1e5a981dc841498d6b55b7a3393cac "info@who.int" . . . . "Robert Court" . . . . . "health science" . . . "Recommendation Ontology" . "Melek Chaouch" . "Patricia Siguier" . . "https://fairsharing.org/" . . . "Bio-Pesticides DataBase" . "http://w3id.org/nfdi4ing/metadata4ing#"^^ . . "lagonzalezmo@unal.edu.co" . . . . . "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."^^ . . . . . . "po" . . "^\\d+$"^^ . . . . . "https://www.bgee.org/gene/$1"^^ . "false"^^ . . . . . . . . "http://purl.obolibrary.org/obo/VIDO_$1"^^ . . . . . . "bbkg" . "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'."^^ . "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^ . "^\\d{7}$"^^ . "enzymology" . "Coronavirus Infectious Disease Ontology" . . . . . . . "^MMP\\d+.\\d+$"^^ . . . "Information for ligands in the BRENDA database."^^ . . "http://cor.esipfed.org/ont/earthcube/MOLA_$1"^^ . . . . "disease" . "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^ . . . . . "Clinical measurement ontology" . "genes" . . "Frederic Bastian" . . "food" . . "biomedical science" . . . "Jeff Beck" . "genomics" . . "Plant Ontology" . . . "life science" . "true"^^ . "mathematics" . "PROSITE" . . . "https://www.fisheries.noaa.gov/species/$1"^^ . . "false"^^ . . . . "fair" . "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)."^^ . . "A vocabulary describing subjects taught in German primary and secondary school (not university/hochschulen), such as German, math, and art."^^ . "https://ordb.biotech.ttu.edu/OdorDB/Data/"^^ . . . . . "false"^^ . . "false"^^ . . . . . . "ictv" . "67035"^^ . "PA131"^^ . . "preclinical studies" . . "Mouse adult gross anatomy" . "robert.hoehndorf@kaust.edu.sa" . . . "vbase2" . . . . . . . "https://ec.europa.eu/esco/lod/static/model.html#$1"^^ . "ChemBioSys Publication" . "International repository of Adverse Outcome Pathways."^^ . . "bsu:BSU01340"^^ . "Search Tool for Interactions of Chemicals" . "^C\\d+$"^^ . . . . . "iedb.assay" . . . . . "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"^^ . . . "obo" . "https://bioregistry.io/vsdb:"^^ . "Ambrose Carr" . . . . "bido" . . . . . . . . "10020.2"^^ . . "post-translational protein modification" . . "Babelon" . . "taxonomy" . "HIT000195363"^^ . "Maryann Elizabeth Martone" . "The hu.MAP integrates several large scale protein interaction datasets to obtain a comprehensive view of protein complexes."^^ . . "Alayne Cuzick" . . . . "634515043"^^ . . "false"^^ . . . . . "https://www.perkinelmer.com/searchresult?searchName="^^ . . . . . "microbiology" . . . "Medical Dictionary for Regulatory Activities" . "0000062"^^ . . . "dbamp" . . "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . "false"^^ . . . . . "European Science Vocabulary Ontology" . . "metabolomics" . . . . . "false"^^ . "Metabolomics Workbench Project" . . . . . "A0A009HB13"^^ . "phenotype" . "Andrea Jacobs" . . . . . . . "false"^^ . . . "000000012281955X"^^ . . . "ecacc" . . . . "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."^^ . . "http://purl.obolibrary.org/obo/ZFS_$1"^^ . . . "alfred" . "http://uri.neuinfo.org/nif/nifstd/nlx_res_"^^ . . . "mauno.vihinen@med.lu.se" . "preclinical studies" . "Probability Distribution Ontology" . "miRNEST" . . . . "StoreDB Study" . "cell biology" . . . . . "https://cropontology.org/rdf/CO_358:$1"^^ . "Mass spectrometry ontology" . . . "^K[0-9]+$"^^ . "false"^^ . "protein" . . . . . "time" . "Ontology of standardized units"^^ . . "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."^^ . "EC-CODE" . "SNOMEDCT_US_2015_03_01" . "http://www.w3.org/ns/activitystreams#$1"^^ . . . . . . "medicine" . . . . . . . "virology" . . . . . . "27223"^^ . . . "https://biopragmatics.github.io/providers/sfam/$1"^^ . . . . "UniProtKB" . "murphyte@ncbi.nlm.nih.gov" . . . "bugbase.expt" . . "https://go.drugbank.com/salts/$1"^^ . . . . "Carlo Ravagli" . . . "units" . . "Genome assembly database - INSDC accessions" . . . _:N3c26ef7ec133462e85e04ed7ddf135d2 . . "Images used as reference"^^ . . . . . . . . . . "http://purl.obolibrary.org/obo/EMPTY_"^^ . "obo" . "deepak.unni3@gmail.com" . . . . "^\\w+$"^^ . . "false"^^ . . "false"^^ . "scop.sccs" . . . . . . . "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . "alpha.tom.kodamullil@scai.fraunhofer.de" . "br/0601"^^ . . "^\\d+$"^^ . "sample" . . . "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests."^^ . "European Science Vocabulary (EuroSciVoc) is the taxonomy of fields of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with fields of science categories extracted from CORDIS content through a semi-automatic process developed with Natural Language Processing (NLP) techniques. (from homepage)"^^ . . . . . "dragondb.locus" . . . . "false"^^ . "ISA1083-2"^^ . . . "nmrxiv.compound" . "^\\d+$"^^ . . . . "434"^^ . . . "false"^^ . . . . . . "Permission"^^ . "danbri@w3.org" . . . . "obo" . . "Predicates that are used to construct the GESIS Knowledge Graph, a bibliometrics KG."^^ . . . "Vital Sign Ontology" . . "http://www.yeastract.com/view.php?existing=locus&orfname="^^ . "ovae" . "http://vbrc.org/gene_detail.asp?gene_id="^^ . . "https://togoid.dbcls.jp/#$1" . . "probonto" . . "http://purl.obolibrary.org/obo/OBIB_"^^ . "plant phenotypes and traits" . . "evolutionary biology" . . . . . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . . . . . "genome" . "nemo" . . "Metabolic Atlas" . . "20090602"^^ . . . . "medicine" . . "ontology" . "prediction" . . "^\\w+(\\.)?(\\d+)?$"^^ . . "Rv1908c"^^ . . "http://emmo.info/emmo#EMMO_$1"^^ . . "protein" . . . . . . . . . "http://purl.obolibrary.org/obo/SO_"^^ . . "https://purl.brain-bican.org/ontology/hbao/HBA_"^^ . . "false"^^ . "MF_01400"^^ . . "Victoria K. Jenkins" . . . . . "http://purl.obolibrary.org/obo/TAHH_"^^ . . . "https://civicdb.org/links/drugs/$1"^^ . . . . . . . "life science" . . "Ryan Brinkman" . "ClinVar Submission" . . . "https://creativecommons.org/ns#$1"^^ . . "^\\d{7}$"^^ . . . . . . . . . . "maize" . . . . . . . . . . . "https://cropontology.org/rdf/CO_327:$1"^^ . . . . . . . "070886"^^ . "asfis" . . . . "A unit of a vector graphic for an anatomical entity useful for biological and biomedical informatics applications."^^ . "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=$1"^^ . "mass spectrum" . "omo" . . . . . "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."^^ . "https://w3id.org/kim/license/$1"^^ . "20"^^ . "^\\d{7}$"^^ . "false"^^ . . "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid="^^ . "91"^^ . . . . "annotation" . . "chemistry" . "agaedigk@cmh.edu" . . "genetics" . . . . "ontology" . "https://www.arabidopsis.org/servlets/TairObject?type=locus&name="^^ . . . "rna" . . . . "^\\d{7}$"^^ . . . . "diagnosis" . . . . . . . . . . "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. "^^ . . . "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)"^^ . . . . "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."^^ . . "false"^^ . . . . "merckindex.reaction" . . . . . "Daniel Sonenshine" . "https://images.endlessforms.info/image/"^^ . "odc.sci" . . . "NIF Standard Ontology: Cell Types" . . . . . . . "Nucleotide Sequence Database" . . . "Informed Consent Ontology" . "European Commission Participant Identification Code (PIC)" . . "ctri" . . "education level" . . . . . "https://biopragmatics.github.io/providers/cemo/$1"^^ . "humap" . "researchgate.profile" . "false"^^ . "Acre"^^ . "mouse strain" . "false"^^ . . . . . "dwishart@ualberta.ca" . . . "CTD Gene" . . . "The HuBMAP donors dataset contains demographic and clinical metadata for individuals who donated tissue samples. Each donor has a unique identifier used to link them to their associated tissue samples and derived experimental data."^^ . . . . . . . . . . . "^\\d{6}$"^^ . "false"^^ . "0000038"^^ . . "global health" . . . "https://cropontology.org/rdf/CO_339:"^^ . "life science" . . "false"^^ . . . . . . . . . . "https://github.com/semanticchemistry/semanticchemistry" . "pathway" . "NFDI Core Ontology" . "false"^^ . . _:N94c2ea8167254c9a89ccab8a27c6161e . . . . "https://www.deciphergenomics.org/syndrome/"^^ . . "http://www.wikidata.org/entity/$1" . . "food" . "ontology" . "false"^^ . . . . "Dataset"^^ . . . . . "society" . . . . . "quality" . . . . . . "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$"^^ . . . . . "false"^^ . . "182"^^ . . "COSMIC Cell Lines" . . . "lozana.rossenova@tib.eu" . . "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"^^ . "Library of Congress Resource Types Scheme" . . . "false"^^ . . "https://www.ebi.ac.uk/biostudies/studies/"^^ . "UniProt Resource" . "Semantic Resource Types Vocabulary" . "false"^^ . . . . . "ontology" . "0004486"^^ . . . . . . "false"^^ . . "^NX_\\w+$"^^ . "patrice.buche@inrae.fr" . "false"^^ . . "MeDRA" . . . . "NX_O00165"^^ . "^\\d+$"^^ . . . . "Item"^^ . "dlxb" . . . . "Colin Batchelor" . . "gabdank@stanford.edu" . "^[1-9]\\d*$"^^ . . . . "obo" . . "spar" . . "^fdd\\d+$"^^ . "false"^^ . . "pfr" . "http://www.pharmgkb.org/drug/"^^ . . . "small molecule" . "cellular_component" . . . "false"^^ . "arrayexpress" . . . . . . . . . "shoshana@sickkids.ca" . "Molbase" . . "property" . "jws" . "^T\\d{3}$"^^ . . "nembase" . "Todd M Lowe" . "genetics" . "biomedical science" . "90806"^^ . . . "51"^^ . "https://www.ncbi.nlm.nih.gov/research/cog/pathway/"^^ . . . . . . . "biomedical science" . . . "cherry@genome.stanford.edu" . . "py.vandenbussche@gmail.com" . . . . . . . . . . . "Pathogen Transmission Ontology" . . "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . . . . . "https://registry.identifiers.org/registry/$1" . "evidence" . . . . . . . . . . . "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images."^^ . "assays" . . "https://proteininformationresource.org/cgi-bin/resid?id=$1"^^ . "http://purl.obolibrary.org/obo/FYPO_"^^ . . . . . "reaction" . . "100"^^ . . "John G Tate" . . "Foods in FooDB"^^ . . "A subspace of Metabolic Atlas for reactions."^^ . . . . "hilmar.lapp@duke.edu" . . "Vaccine administered code set" . . "Collection"^^ . "UniProt Subcellular Locations" . "genetics" . "https://pubchem.ncbi.nlm.nih.gov/compound/$1"^^ . . . . "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)."^^ . "health science" . . . . . "false"^^ . . . . . . "violinnet" . . . . . "CoVoc Coronavirus Vocabulary" . . . _:N37a28bb55fee4da4bdbcdc1655f4cbe2 "Alex Skrenchuk" . . . "alzforum.mutation" . . . "sourceDateStart"^^ . . . . . . . "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"^^ . . . . . . "Célia Michotey" . "The LifeWatch ERIC repository of semantic resources for the ecological domain." . "vsao" . "false"^^ . . . _:N737c82f1d18947caa3d2c88fd2aea61d . . "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. "^^ . . "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."^^ . . "false"^^ . . . "genome" . . . . "Marc_Ciriello@hms.harvard.edu" . "genecards.gene" . "https://cstr.cn/"^^ . . . . "11084"^^ . "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."^^ . . . "Mathias Brochhausen" . "false"^^ . . . "http://www.innatedb.ca/getGeneCard.do?id="^^ . . . . "bindingdb" . . . "https://w3id.org/kim/isced-1997/level$1"^^ . "^\\w+$"^^ . . "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^ . "agriculture" . "mondo" . . "chemical" . . . "toxoplasma" . "https://openalex.org/$1"^^ . "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"^^ . . . "119514"^^ . . . "developmental biology" . "subject agnostic" . . "false"^^ . . "text mining" . . "Structural Database of Allergenic Proteins" . "Machine-readable Cataloging (MARC) List for Languages" . . "false"^^ . "pass2" . . . . . . . . . . . . . . . . . . "meshUID" . . . "Sébastien Moretti" . "microbiome" . . . "https://identifiers.org/$1:$2" . . "cutg" . . "do" . . "TR0000001"^^ . . "terms4FAIRskills" . . . . "^\\d+$"^^ . . . . . "^\\w+$"^^ . . "hgvs" . "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^ . . "Database of Sequence Tagged Sites" . . "^EP\\d{4}$"^^ . . "LexicalMatching"^^ . . "jla1@sanger.ac.uk" . "false"^^ . "biomedical science" . "https://github.com/prefixcommons/biocontext" . . . "0000199"^^ . . . . . "Selventa legacy disease namespace used with the Biological Expression Language"^^ . "false"^^ . . . . . "biomedical science" . . . "molecular microbiology" . . . . . . . "false"^^ . . . . "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."^^ . "false"^^ . . . . . "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . . . "unpd" . "physiology" . . . . . . "ARBA00000001"^^ . "00000099"^^ . "oa" . . "ncbidrs" . "Bgee family" . . . "^\\d+$"^^ . . "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata."^^ . . . "https://www.ebi.ac.uk/chembl/target/inspect/"^^ . "Identifiers for specific experimental assays that serve as evidence for immune-related studies."^^ . . . "54"^^ . . . . . "Feature Annotation Location Description Ontology" . . "dashr" . . . . . . . "life science" . "health sciences" . "http://www.semanticdesktop.org/ontologies/2007/08/15/nao#$1"^^ . . . . "Q-2958"^^ . . . "false"^^ . . . "http://ctdbase.org/detail.go?type=disease&db=MESH&acc="^^ . . . "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . . . "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."^^ . "ensembl.fungi" . "Assists in resolving data across cloud resources."^^ . . . . "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^ . "protein" . "rebase" . . . . "fbql" . "ontology" . "false"^^ . . . "A repository of software packages written in PHP."^^ . . "UniProt journal" . "scicrunch" . "primary health care" . "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."^^ . "data retrieval" . "SitEx" . . . . . . . "echobase" . "PTM" . "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"^^ . . . "https://bioregistry.io/pesticides:"^^ . . . "hms.lincs.antibody" . . "Conserved Domain Database at NCBI" . "chemistry" . . . "https://w3id.org/reproduceme#"^^ . "Jeffrey Wong" . "nmrXiv project" . . . "false"^^ . "^WP\\d{1,5}(\\_r\\d+)?$"^^ . . "Ximbio" . "false"^^ . "Glycan Naming and Subsumption Ontology" . "Rhea reaction" . . "lynn.schriml@gmail.com" . "Teleost taxonomy ontology" . . . "^\\w+$"^^ . . . . . "http://purl.obolibrary.org/obo/EPO_$1"^^ . . . . "botany" . "anatomy" . . . . "mpath" . "anatomy" . . . "^\\d{7}$"^^ . "Q0VCA6"^^ . . . . "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid="^^ . "https://lincs.hms.harvard.edu/db/cells/"^^ . "occ" . "3dmet" . "unit" . . "http://purl.obolibrary.org/obo/TXPO_$1"^^ . "cgrove@caltech.edu" . "Performance Summary Display Ontology" . . "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . . . . "Tiffany J. Callahan" . . . "gene family" . . . . "false"^^ . "roberts@neb.com" . "genome" . "cst.antibody" . . . "https://lincs.hms.harvard.edu/db/antibodies/"^^ . . . . . . "developmental biology" . "Richard H. Scheuermann" . . . . "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^ . . "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . "disease" . . . . . . . . "Nathan Baker" . . "issn" . "^\\d{7}$"^^ . . "^\\d+$"^^ . . . "GXA Gene" . "ontology" . "NONCODE v4 Transcript" . . . . "chemfont.ontology" . "SNHG3"^^ . "linguistics" . "Insect Cell Line Database" . "surjeet.arya@uky.edu" . "morbidity" . "^\\w+_?\\d+(.\\d+)?$"^^ . . "animal husbandry" . . "BIOMD0000000048"^^ . . . . "false"^^ . . . "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"^^ . "hco" . . "https://osdr.nasa.gov/bio/repo/data/payloads/"^^ . . . . "Nicolas Le Novere" . "https://w3id.org/sulo/"^^ . . . . . . "bio.tools" . . . . . . . "nepomuk.pimo" . . "pazar" . . . . . "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID="^^ . . "https://www.plantplus.cn/treehub/tree/"^^ . . "false"^^ . . . . "knowledge and information systems" . . . . "CONSO00010"^^ . "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker."^^ . . . "CID" . "fabrice.legeai@rennes.inra.fr" . . . . "false"^^ . . . . "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q="^^ . . . . "epigenetics" . "^\\d+$"^^ . "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^ . "SubtiWiki" . "^\\d+$"^^ . . "Regulation of Gene Expression"^^ . "true"^^ . . "https://rapdb.dna.affrc.go.jp/locus/?name="^^ . . . "dbest" . "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)."^^ . "pgs" . . . . . . . _:N1f4a0c25aeec4f6ebb4e66593f74a4e2 "bao@miamiedu.onmicrosoft.com" . . . . . "Microbial Conditions Ontology is an ontology..."^^ . . . "astronomy and astrophysics" . . . "phenomics" . . . . "http://rdfs.org/sioc/swan#$1"^^ . . "Yi Zhao" . . . . . . "davidos@ebi.ac.uk" . . . . . . . "http://data.europa.eu/8mn/euroscivoc/"^^ . . "Silvio Tosatto" . "UniChem compound" . . . "arc"^^ . . . "false"^^ . . . . "aaeA"^^ . "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://purl.brain-bican.org/ontology/dhbao/DHBA_"^^ . "false"^^ . "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . . . "https://biokb.lcsb.uni.lu/fact/"^^ . . "0000001"^^ . . . "http://www.molbase.com/en/index.php?app=search&search_keyword="^^ . . . . "http://bacmap.wishartlab.com/organisms/$1"^^ . . . . . . . "https://datanator.info/reaction/$1"^^ . . . . "http://www.weizmann.ac.il/molgen/loqate/gene/view/"^^ . . . . . . . . . "https://fairsharing.org/$1"^^ . . . "832"^^ . . . "arachnoserver" . . . . "https://www.ebi.ac.uk/thornton-srv/m-csa/search/?s=$1"^^ . . _:N4a37364fe53a4e4d92048112b84cc3d0 . . . . _:N813950d1e49e4c18a5f90f70a007da2a "usha@molecularconnections.com" . . "co_320" . "Melissa D Clarkson" . . "https://bioregistry.io/dragondb.locus:"^^ . "EB0170"^^ . "lei" . "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information."^^ . "The RNA Modification Database" . "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus="^^ . "https://biopragmatics.github.io/debio/"^^ . . . "ValidatorDB" . . . . "RAP-DB Locus" . "SNOMEDCT_US_2018_09_01" . "https://www.kaggle.com/"^^ . "SBML RDF Vocabulary" . "false"^^ . "biomaterial manufacture" . . . "false"^^ . "https://bioregistry.io/p3db.site:"^^ . "https://bioschemas.org/profiles/"^^ . . "dsm-iv" . . . "abdelmoneim.desouki@tu-darmstadt.de" . . . . . . "false"^^ . . . . . "https://bioregistry.io/loop:"^^ . . "^\\d+$"^^ . . . "http://www.radiomics.org/RO/$1"^^ . . "European Mouse Mutant Archive" . "false"^^ . "person" . . "http://wodaklab.org/iRefWeb/interaction/show/$1"^^ . _:N7d8ef3b598314e69805b74e833189665 . . . . . . "ontology" . . . . . "SCancerRNA" . . . "https://cropontology.org/rdf/CO_323:"^^ . . "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."^^ . "true"^^ . . . . . . "WoRMS-ID for taxa" . "http://purl.obolibrary.org/obo/HABRONATTUS_"^^ . "7345"^^ . . . . . "PiroplasmaDB" . . . "animal genetics" . "https://www.ebi.ac.uk/ols4" . . . "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)."^^ . . "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . . . . . . . "Toby J Gibson" . "false"^^ . . . "http://purl.obolibrary.org/obo/CDNO_"^^ . "http://purl.org/ASN/scheme/ASNEducationLevel/$1"^^ . . . . . . "0001056"^^ . . "video resource" . "^[\\w-]+$"^^ . . . "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"^^ . "datanator.metabolite" . "http://purl.obolibrary.org/obo/DERMO_$1"^^ . . . . "chemistry" . . . . . . . . . "false"^^ . . "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"^^ . . "genetics" . . . . . . . "http://open-services.net/ns/core#$1"^^ . . "http://rs.tdwg.org/dwc/terms/$1"^^ . . "https://docid.africapidalliance.org/docid/$1"^^ . . . . . . . . . . "life science" . "transcript" . . "obo" . "https://www.webelements.com/"^^ . "0000032"^^ . "https://discover.pennsieve.io/package/"^^ . "nucleotide" . . . . . . "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^ . . "EMAPA_RETIRED" . . . "0000003"^^ . . "Cancer Data Standards Registry and Repository" . "jiezhen@med.umich.edu" . . "http://purl.org/spar/biro/"^^ . . "^\\d+$"^^ . . "Transport Systems Tracker" . "http://purl.obolibrary.org/obo/CMF_$1"^^ . . "false"^^ . "1000000"^^ . . . "mathias.uhlen@scilifelab.se" . . "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . . . "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."^^ . "Identifiers for space-related data from experiments that investigate biological and health responses of terrestrial life to spaceflight"^^ . . . . . . "bridgedb" . "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^ . . "ontology" . "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1"^^ . "false"^^ . . "registry" . . "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment."^^ . . . . "lewis.geer@nih.gov" . . "sael" . "BacDive" . "kupo" . . . "aftol.category" . "MLCommons Association" . . "ontology" . "frapo" . . . "Wojciech M. Karlowski" . . . . . "life science" . . . . . "0000001"^^ . . "0000208"^^ . "Physico-chemical methods and properties" . . "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . . . "false"^^ . . "^RPCEC\\d+$"^^ . "^\\d+$"^^ . . . . . . . . . . . . . . . "Integrated Canine Data Commons" . "https://cropontology.org/rdf/CO_346:$1"^^ . . "obo" . "GPCR Natural Variants database" . . . "Cell line collections (Providers)"^^ . . . "brettolivier@gmail.com" . . . "phenomics" . . . . . "lipro" . . "Ontology of Biological and Clinical Statistics" . "ontology" . "http://purl.obolibrary.org/obo/DRON_"^^ . . . . . . . . "genetics" . . . "study design" . . "BioSample" . "regulation" . . "https://embryology.med.unsw.edu.au/embryology/index.php/Carnegie_Stages#Stage_$1"^^ . . . . "expression data" . . . . . . "^\\d{1,7}$"^^ . "obo" . "ecology" . . "umls.mth" . . . . . . "ICD9CM_2006" . "Scholia Registry" . . . . "^\\d+$"^^ . . . . . "DTXSID7032004"^^ . "qualityOfObservation"^^ . . "true"^^ . "immunology" . "ontology" . "database management" . . . . . . "phenotype" . . . . "000000001"^^ . . _:Nb039f65249c74fabb39262758d9cba60 "lars.juhl.jensen@cpr.ku.dk" . "0000000"^^ . . . . . . . . "nucleotide" . . . "https://osdr.nasa.gov/bio/repo/data/missions/"^^ . . "ontology" . . "https://www.merriam-webster.com/dictionary/"^^ . "biochemistry" . . . "false"^^ . . "false"^^ . . "https://www.mavedb.org/#/experiments/urn:mavedb:$1"^^ . . "false"^^ . "Database portal containing replicate experiments of different assays and samples"^^ . . . . "^PS\\d{5}$"^^ . . . . . . . . . . "itiswebmaster@itis.gov" . "DiabetesOmic is a multi-omics database designed to collect and analyze transcriptional regulatory information across five high-throughput sequencing modalities, including ChIP-seq, RNA-seq, ATAC-seq, scATAC-seq, and scRNA-seq. This database's identifiers each represent a single sample. It contains clinical complication annotations including diabetic nephropathy, retinopathy, and atherosclerosis to enhance translational relevance. It enables the identification of disease-associated regulatory elements, epigenetic modifications, and cell type-specific molecular signatures, providing valuable insights into the molecular mechanisms of diabetes and its complications."^^ . . . . . . "false"^^ . . . . "false"^^ . . . . . . "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3"^^ . "ClinVar Submitter" . . . . . . . . "http://www.vbase2.org/vgene.php?id=$1"^^ . "https://osdr.nasa.gov/bio/repo/data/hardware/"^^ . "https://licebase.org/?q=$1"^^ . "^\\d{7}$"^^ . . "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"^^ . . . "salamander" . . . "idoo" . . . "sperm" . . "omrse" . . . . . . "project" . . . "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology" . . . . "WB_REF" . . . "bervo" . . "false"^^ . . "^[1-9]\\d*$"^^ . "nasc" . "PicTar" . . "echinobase" . . . "An investigation in the ChemBioSys data platform"^^ . . . "http://purl.obolibrary.org/obo/MPATH_$1"^^ . "Cell line databases/resources"^^ . . . "MolBiC Protein" . . "nuclear magnetic resonance spectroscopy" . . . . . . . . "bibframe" . "false"^^ . . "researcher" . . . . "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."^^ . . . "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id="^^ . "BioLegend" . . "false"^^ . . "false"^^ . . . "http://www.informatics.jax.org/accession/MGI:$1"^^ . . . "One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]"^^ . . . "BeAn 70563"^^ . . . . "false"^^ . . . "^\\d+$"^^ . "Japan Collection of Microorganisms" . . . . "te" . . . "The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,000 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information and communication technology and, increasingly, environmental science. [from homepage]"^^ . "tricdb" . . . . "http://www.w3.org/ns/prov#$1"^^ . . "GlycomeDB" . . "biological_process" . "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."^^ . . . . "http://purl.dataone.org/odo/ECSO_"^^ . . . . "O08709"^^ . . "homd.seq" . "Michelle Giglio" . . . . . "epidemiology" . . "false"^^ . . . "Maize gross anatomy" . . "cell biology" . "biosimulations" . . . . "epidemiology" . . . . . . . . . "life science" . "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"^^ . . "iceberg.element" . "National Microbiome Data Collaborative" . . . . . "ruili.huang@nih.gov" . . . "life science" . . . "^\\d+$"^^ . "6200"^^ . "life science" . "MSMEG_3769"^^ . "0000389"^^ . "0001410"^^ . . . . . . "inbred rat strain" . "glottolog" . "sabiork.reaction" . "ontology" . "DBLP author ID" . "102l"^^ . . "sioc.actions" . . "gene" . . . . "ontology" . . . . . . "AntiBodies Chemically Defined database" . "bibliography" . "ontology" . . "http://www.cellresource.cn/cellsearch.aspx?sc=1&where="^^ . "Jennifer Smith" . "uniprot.db" . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid="^^ . . . "behavior" . . . "SR0000178"^^ . . . . "b.gyori@northeastern.edu" . . . "rec" . "false"^^ . "Human Induced Pluripotent Stem Cells Initiative" . "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."^^ . . "CAID" . . "bioinformatics" . "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid="^^ . "European Union Publications Office dataset" . . . . "0000001"^^ . "https://lattes.cnpq.br/$1"^^ . . . . . . . . . . "Genome assembly database - RefSeq accessions" . . . . "0003"^^ . . "A vendor of antibodies and other biologics"^^ . . . . "transgenic" . . "life science" . . . "bioinformatics" . . "genotyping" . . . . . "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . "http://purl.obolibrary.org/obo/CLYH_"^^ . . "A set of guides on implementing various processes within hospitals or healthcare systems."^^ . . "regulation" . . . . . . . . "^AT[1-5]G\\d{5}(\\.\\d+)?$"^^ . "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code="^^ . "hmsl_id" . "^SIGNOR-\\d+$"^^ . . . . . . . "maya.schuldiner@weizmann.ac.il" . . . "true"^^ . . . . . "http://www.case.edu/EpilepsyOntology.owl#"^^ . . . "hcpcs" . . . . . . . . "tbreddy@lbl.gov" . "gdc" . "michall@cc.huji.ac.il" . "^\\d{7}$"^^ . . "subject agnostic" . "resource metadata" . . . . . . "repository" . "https://data.chembiosys.de/tags/$1"^^ . . "^[A-Z-a-z0-9]+$"^^ . "81944ba1-81d0-436e-8552-33d77a27834b"^^ . . "http://www.gramene.org/db/protein/protein_search?protein_id=$1"^^ . . . "false"^^ . . . . . "foodb" . . "false"^^ . . . . "bs" . "contributor roles" . "^[1-9][0-9]{1,6}$"^^ . "metabolomics" . "MatrixDB" . "drug interaction" . . "40565"^^ . "computational biology" . . . . . . . "OENC205"^^ . . . "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."^^ . "false"^^ . . . "john.garavelli@ebi.ac.uk" . . . . . . "https://www.deciphergenomics.org/syndrome/$1"^^ . "false"^^ . . "metadata" . "SNOMEDCT_US_2023_02_28" . . . . "0000127"^^ . "NCIThesaurus" . . "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."^^ . "false"^^ . . . . "life science" . . . . . "tair.locus" . . . "hcvdb" . . . . "The identifier for an observation in iNaturalist"^^ . . . . . . . "false"^^ . . . . . "Mouse Brain Atlas" . . . "false"^^ . . . . "https://horizondiscovery.com/en/search?searchterm=$1"^^ . "nucc.taxonomy" . . "ontology" . . "Google Books" . . "Omar Harb" . . "https://pubchem.ncbi.nlm.nih.gov/element/"^^ . "rdo" . "zfa" . . . "complexportal" . "ontology" . "http://europepmc.org/articles/"^^ . "codata.rdmt" . . . . . . . "Chemical Component Dictionary" . "This mini-ontology contains classes and instances for each version of the licenses that are commonly used in software projects, particularly open source software projects. The URI's for each are the canonical URI's for that license (where they exist)."^^ . "protein" . . . . "false"^^ . . "geology" . "kim.hcrt" . "linguist.gold" . . . . . . "dna" . "http://www.bind.ca/Action?identifier=bindid&idsearch=$1"^^ . . . . "genetics" . "http://pombe.oridb.org/details.php?id="^^ . "Duration"^^ . "anatomy" . "https://datacommons.org/browser/"^^ . . "genomics" . "protein" . "ChemPro Probe" . . . . "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available."^^ . "gnd" . "premis" . "The Virus Infectious Disease Ontology" . "protein" . "0000109"^^ . . . "dna" . "Cell Signaling Technology Pathways" . . "ontology" . . "expression" . "activityBoundOf"^^ . . . "nanotechnology" . . . . . . . . . "graingenes.reference" . . "Claudia Tredup" . . "The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. It uses the language of visual communication, illustration, and technical drawing. The GDO is rooted in the Basic Formal Ontology (BFO) and uses several classes from the Information Entity Ontology of the Common Core Ontologies as a mid-level ontology. [from https://gdo.endlessforms.info/about]"^^ . "Cell line collections (Providers)"^^ . . "discoverx" . "false"^^ . "C. Robin Buell" . "gene" . "^LGCEDe-S-\\d{9}$"^^ . . "comparative genomics" . . "datf" . . . . . . . "http://purl.obolibrary.org/obo/EMAP_"^^ . . "lbo" . "https://registry.identifiers.org/registry/$1"^^ . "^\\d+$"^^ . "false"^^ . . . . . "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1"^^ . . . "http://dictybase.org/gene/$1"^^ . . . "false"^^ . "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis."^^ . "https://deims.org/locations/"^^ . . . "secretariat@eol.org" . . "cryopreserved" . . "genome" . "life science" . . . "mvx" . "CNCB Genome Warehouse" . "anatomy" . "experimental plant" . "faseb list" . "biodiversity" . . "^\\d{7}$"^^ . . "ChEMBL Compound" . . "protein" . "Gene Expression Analysis Resource" . . . . . . . "publons.publication" . "^GPM\\d+$"^^ . . "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene."^^ . . . . "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine."^^ . . "http://purl.obolibrary.org/obo/GAZ_"^^ . "Aspergillus Genome Database" . "0000138"^^ . "^\\d+$"^^ . "EBI-2307691"^^ . "Mark Jensen" . . . "^[1-9]\\d*$"^^ . "chembl.compound" . . . . . . . . . . "gene" . "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^ . . . . . . "StoreDB Dataset" . . . . "82"^^ . . "Matthias Samwald" . . "Li7"^^ . . "loggerhead" . "ontology" . "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . . "^\\d+$"^^ . . "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist="^^ . "false"^^ . "http://purl.obolibrary.org/obo/PROPREO_"^^ . "md.tyers@umontreal.ca" . "person" . "botany" . "785"^^ . . . "http://purl.obolibrary.org/obo/ZEA_"^^ . . "^[EL]D[SG]-\\d+$"^^ . . . . . . . . . . "John Graybeal" . . "biofactoid" . . . "linguist" . . . . "disease model" . . . . . . . . . "Anatomical Therapeutic Chemical Vetinary" . . . . "http://lincsportal.ccs.miami.edu/cells/#/view/$1"^^ . . . "false"^^ . . . "true"^^ . . "A structured controlled vocabulary used for various aspects of annotation by FlyBase."^^ . . "computer science" . . . _:N83343f3eac114bfabaf9d0c12d45d92f "Pierre Sprumont" . . . . "obo" . "false"^^ . "https://www.arraymap.org/pgx:"^^ . "https://www.uniprot.org/uniprotkb/"^^ . "http://www.pharmgkb.org/disease/$1"^^ . "Cell line databases/resources"^^ . . "https://www.fao.org/fishery/en/species/"^^ . . "deims.dataset" . "false"^^ . . . . . "https://bioregistry.io/d1id:"^^ . "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$"^^ . . "insdc.gcf" . . . "gxa.expt" . "fibroblast" . . "^\\d{7}$"^^ . . . . . "W2741809807"^^ . "Identifiers for molecules in SupraBank"^^ . . . . "Animal Genome Cattle QTL" . "Gert Vriend" . . . "^\\d{7}$"^^ . "^ps\\d+$"^^ . . . . . . "dbvar.variants" . "true"^^ . "http://purl.obolibrary.org/obo/kestrelo_"^^ . . . . "Zebrafish Phenotype Ontology" . . . "https://www.merckmillipore.com/catalogue/item/"^^ . . "false"^^ . . "^\\d{7}$"^^ . . . "^(cl|tum)\\d+$"^^ . "https://cropontology.org/rdf/CO_360:$1"^^ . . . "anatomy" . . "NPC139585"^^ . "Alicia Clum" . . . . . . . . . "http://www.xmetdb.org/xmetdb/protocol/"^^ . "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$"^^ . "HUMAN0000001"^^ . "^tgv[0-9]+$"^^ . . . . . . . "^\\d+$"^^ . . "0100010"^^ . "catalogs" . . . . . . "http://champ-project.org/images/ontology/cao.owl#CAO_"^^ . . . "pennsieve" . . . . "https://pephub.databio.org/$1"^^ . "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books."^^ . . . "false"^^ . "classification" . "Imke Tammen" . . . . . "ontology" . "Rodent Unidentified Gene-Encoded Large Proteins" . . "amalik@ebi.ac.uk" . "Proteoform Atlas" . "life science" . . "585"^^ . "owl" . "^\\d+$"^^ . . "http://unite.ut.ee/bl_forw.php?nimi="^^ . "nsrrc" . "slm" . "tngb" . . . . . . . "http://www.geneontology.org/formats/oboInOwl#"^^ . "small molecule" . . . "aspgd.locus" . "biocatalogue.service" . . "TAIR Protein" . "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."^^ . . "co_339" . _:Ne763fe65e2c8492a9dc145ee4037ff0d "J.Bard@ed.ac.uk" . . . . "obo" . . "https://scicrunch.org/resolver/RRID:IMSR_TAC_$1"^^ . . . . "Orthology Ontology" . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . "CN970821"^^ . . . "http://purl.obolibrary.org/obo/CHEBI_"^^ . . . . "metagenomics" . . "^\\d+$"^^ . "drosophilidae" . . . . . . "obo" . "publishing" . "https://flybase.org/reports/FBtc"^^ . . "Psychology Ontology" . . . "Occupation Ontology" . . . . . "RO_proposed_relation" . . "^\\w+_COVID19_[-\\w]+$"^^ . . "http://purl.obolibrary.org/obo/MF_$1"^^ . "cell" . . . "false"^^ . "^\\d+$"^^ . "SNOMEDCT_US_2018_03_01" . . "false"^^ . . . "false"^^ . . . . "ontology" . . . . . "Charles Tapley Hoyt" . . "reagent" . "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]"^^ . . . "life science" . "1484"^^ . . . . . "https://bcrj.org.br/pesquisa/?search=$1"^^ . "LOC_Os02g13300"^^ . "false"^^ . . . "dbvar.studies" . "Elementary Multiperspective Material Ontology" . . "^\\d{7}$"^^ . "false"^^ . "https://www.uniprot.org/tissues/$1"^^ . . "https://glyconavi.org/hub/?id="^^ . . . . . "http://purl.obolibrary.org/obo/CHIRO_$1"^^ . "https://dandiarchive.org/dandiset/"^^ . "0002350"^^ . "https://www.glycoepitope.jp/epitopes/$1"^^ . . . . "http://purl.org/spar/bido/$1"^^ . "Relation Ontology" . "000001"^^ . . . . . "subject agnostic" . . . . . . . . . "http://repository.topdownproteomics.org/proteoforms/"^^ . "LK99"^^ . "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. "^^ . "biochemistry" . . "false"^^ . "https://www.drugbank.ca/categories/"^^ . "anatomy" . "subject agnostic" . . . . . "http://purl.obolibrary.org/obo/HANCESTRO_"^^ . "disprot" . "^\\d+$"^^ . . . "metacyc.pathway" . "Immune Epitope Database MHC Restrictions" . "genomics" . "phenotype" . _:N42cc44321cb54e62b72732e52a61041c . "fcsfree" . . . . . . . "researcher" . "^\\d+$"^^ . "obo" . . . "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1"^^ . . . . . . "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA="^^ . "Common Access to Biological Resources and Information Project" . "life science" . . . "genetics" . . . . . . . "false"^^ . . "https://www.worldcat.org/oclc/"^^ . . "false"^^ . . . . . . "false"^^ . . . . . "P136"^^ . "https://omim.org/MIM:"^^ . . . . . . "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."^^ . "http://purl.obolibrary.org/obo/OGSF_$1"^^ . . "http://purl.obolibrary.org/obo/ZFS_"^^ . . "domainIncludes"^^ . . . . . . . . . . "^\\d{6}$"^^ . "false"^^ . "false"^^ . "mmsinc" . . "International Genome Sample Resource" . "Minimal set of terms for anatomy"^^ . . . . . . . "uniprot.arba" . . "deims.location" . . . . . _:N89147f83abed402a8bbc6aa743fcf60b . . _:N813950d1e49e4c18a5f90f70a007da2a "Usha Mahadevan" . . . . "co_343" . . "Microarray experimental conditions" . . "http://purl.obolibrary.org/obo/FIDEO_"^^ . . . "disease" . "MEDIGUE Claudine" . . . . . "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1"^^ . "http://purl.obolibrary.org/obo/OMP_"^^ . "00000532"^^ . . . "protein"^^ . . . . . . "false"^^ . . . . . "w3c rec" . "https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_$1"^^ . . . "developmental biology" . "bioinformatics" . "http://purl.obolibrary.org/obo/DINTO_"^^ . . . . . "cell lines" . . "codelink" . . . . . "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound="^^ . "https://progenetix.org/services/ids/"^^ . "https://www.omicsdi.org/dataset/massive/$1"^^ . . . . "interaction" . . . "NCT" . . . . . "emotion process" . . . . . . . "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"^^ . . . . "LDS-1110"^^ . "rliningt@sfu.ca" . "http://purl.obolibrary.org/obo/RO_$1"^^ . "true"^^ . "http://purl.obolibrary.org/obo/LEPAO_"^^ . "Academic Event Ontology" . . "ped.ensemble" . "http://synbip.idrblab.net/data/sbp/details/"^^ . "tair.protein" . . "enviPath" . "iNaturalist Observation" . . "^r\\d+$"^^ . . . "https://registry.identifiers.org/registry?query=MIR:"^^ . . "mlc" . . . . . . . . . . . . "cls" . . "false"^^ . "A strain in the ChemBioSys data platform"^^ . . "pina" . . . "BastianFromm@gmail.com" . "http://ensembl.org/glossary/ENSGLOSSARY_"^^ . "OMA Protein" . "rex" . . "disorders" . . . "http://purl.obolibrary.org/obo/VSMO_$1"^^ . "ESCO Ontology" . "rvita@liai.org" . "CPD-10330"^^ . "Synthetic Binding Proteins Binding Target" . "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . "term_status"^^ . . . "structural biochemistry" . . "discipline" . "false"^^ . . . . . "^\\d{7}$"^^ . . "http://rdfs.org/sioc/services#"^^ . . "Chinese Clinical Trial Registry" . . "A german-language glossary provides you with definitions of the terms used in the portal in the fields of education, science, research and innovation and is updated regularly."^^ . . . "^\\d{7}$"^^ . "gene" . . . . . "frbr" . "rbk" . "device" . "https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/org-details/$1"^^ . . "eolife" . . . "disease" . . "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch."^^ . . . . . . "http://gmd.mpimp-golm.mpg.de/Analytes/"^^ . . . "obo" . . . . "adam@burnham.org" . "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use." . "medicine" . "false"^^ . "person" . "life cycle stage" . . "true"^^ . "ArrayExpress Platform" . . . "Brendan MacLean" . . . . . . . . "mfo" . "PRJDB3"^^ . . "0002005"^^ . . . . "^[A-Za-z]+$"^^ . . . "https://go.drugbank.com/drugs/"^^ . . . "http://purl.obolibrary.org/obo/OGMS_"^^ . . . "unit" . "https://osdr.nasa.gov/bio/repo/data/subjects/"^^ . "false"^^ . "cellosaurus.resource" . "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."^^ . . "nmr" . . . "Ramona Walls" . . . "Measurement method ontology" . "mass spectrum" . "false"^^ . . "false"^^ . . . "https://oid-base.com/get/"^^ . "rat model" . . . "false"^^ . "false"^^ . "comparative genomics" . . . "protein" . "false"^^ . . "Eric W. Sayers" . . . . "1h68"^^ . . "Integrated Chemical Environment - Chemical data" . "https://www.kegg.jp/pathway/$1"^^ . . . _:N5a29923746d74e12b425843c144a6e90 "pbrooks@hcfa.gov" . . . "https://reactome.org/content/detail/"^^ . "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . . . . "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."^^ . . "Cell line databases/resources"^^ . "true"^^ . "Wormpep" . "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." . "https://cropontology.org/rdf/CO_321:"^^ . "ev:E00032"^^ . . . . "false"^^ . . . . . . . . "false"^^ . . . . "^[a-z0-9]+:[A-Za-z0-9.\\-:]+$"^^ . . . . . "http://www.coloncanceratlas.org/search_cell_line?cell_line="^^ . . "^A(N|O)\\d+-\\d+$"^^ . . . . . "https://w3id.org/sulo/$1"^^ . "https://deims.org/networks/$1"^^ . . . . . "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . . "false"^^ . . . . . . . . . "https://ordb.biotech.ttu.edu/OdorDB/Data/$1"^^ . "psskb" . . . . . "false"^^ . . "person" . . "Next Generation Biobanking Ontology" . "Emmanuel Guiderdoni" . "https://units-of-measurement.org/$1"^^ . . . "false"^^ . . "Identifiers represent antimicrobial peptides in the Database of Antimicrobial Peptides (dbAMP) which is an open-access, manually curated database of antimicrobial peptides (AMPs)."^^ . . . . "false"^^ . "http://ecoportal.lifewatch.eu/ontologies/$1" . "^\\d{7}$"^^ . "Authorea author ID" . . "chictr" . . "faseb list" . "Stian Soiland-Reyes" . . "https://www.kegg.jp/entry/$1"^^ . . . "humap3" . . "chickenqtldb" . "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org"^^ . . "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^ . . . "genome" . . . . "viralzone" . . . . "https://www.ncbi.nlm.nih.gov/datasets/genome/"^^ . . . . . . "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . . "louis@imbb.forth.gr" . . . . . . . . . . . "S6"^^ . . "anatomy" . "3000045"^^ . . . "Resource Description Framework" . . "false"^^ . . . "ontology" . . . . "false"^^ . . . "so" . . "fetus" . . . . . . . "^.+$"^^ . . . "obo" . . . "^CTRI/\\d{4}/\\d{2,3}/\\d+$"^^ . . . "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors"^^ . . . . "pharmgkb.gene" . "^(\\d+)|(\\w+)$"^^ . "https://onderzoekmetmensen.nl/en/trial/"^^ . "obo" . . "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID="^^ . "ChEMBL_ID" . . . . . . . . "Sequence Read Archive" . "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^ . . . . . . . "^JCGG-STR\\d{6}$"^^ . "virus" . . . . "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line"^^ . . . . . . "biology" . . "The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]"^^ . . . "biomedical science" . "false"^^ . . "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . . "spar" . "https://merckindex.rsc.org/monographs/"^^ . "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . "https://ec.europa.eu/esco/lod/static/model.html#"^^ . "hagr.genage" . . "02dacc42-ea46-48fb-a4df-7a875d801086"^^ . . . "obo" . . . . "experimentally determined" . . . . . "^\\d+$"^^ . "http://viaf.org/viaf/"^^ . "pathology" . . "NIAID ChemDB ID" . . . . . . . "sioc.quote" . "Bio-MINDER Tissue Database" . . "^MSMEG\\w+$"^^ . . . . _:Nf7c39b4a52e24a1c9bd5e05e15b5c7c5 . . . . "kegg.glycan" . "^\\d{7}$"^^ . . . . "Crop Ontology Curation Tool" . "http://foodb.ca/compounds/$1"^^ . . . "developmental biology" . . "oryzabase.reference" . . . "UP" . . "The pattern for identifiers in the given resource" . "atsushi.yoshiki@riken.jp" . . "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . . "System capabilities, operating ranges, and survival ranges ontology" . "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1"^^ . . "^[0-9a-f\\-]+$"^^ . . "ontology" . "conference" . "molecular chemistry" . "fish" . "life science" . "http://www.bioinfo.org/NONCODEv4/show_gene.php?id="^^ . "false"^^ . . "^\\d{7}$"^^ . "^\\d{7}$"^^ . . . . "false"^^ . "Fababean ontology" . . "http://igsn.org/"^^ . . . "https://nmrxiv.org/sample/$1"^^ . "^\\d+$"^^ . . . "CellBank Australia" . . "life science" . . . "life science" . . . . "00000101"^^ . "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . "https://www.ebi.ac.uk/arrayexpress/arrays/$1"^^ . . "life science" . . "https://www.ebi.ac.uk/gwas/studies/"^^ . . . "Uniprot ID" . "VHOG_RETIRED" . "babelon" . . . "developmental biology" . . . . . "https://data.chembiosys.de/investigations/"^^ . . . . . "false"^^ . . . . "0000000"^^ . . . . . . . . "false"^^ . "umbbd.reaction" . . . "31253.11.sciencedb.j00001.00123"^^ . . "Archival Resource Key" . "MMP3888430"^^ . . . . . . . . "http://w3id.org/nfdi4ing/metadata4ing#$1"^^ . "^[0-9][A-Za-z0-9]{3}$"^^ . "glenn.king@imb.uq.edu.au" . . . . . "knowledge representation" . . "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . . "117395"^^ . . "046-19"^^ . "https://www.webofscience.com/wos/woscc/full-record/WOS:"^^ . . . "apo" . "FuncBase Human" . . "^[a-z0-9\\-]+$"^^ . . . "lincs.protein" . . "genomics" . . "anatomy" . . . . "computer science" . "cell lines" . . . "biocuration" . . . "false"^^ . . "Cell Markers Ontology" . . "ontology" . . . "hello@vivekkrish.com" . "Minoru Kanehisa" . "oarcs" . . . . "ontology" . . "false"^^ . . . . "metadata standardization" . "https://crates.io/crates/"^^ . . . . . "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1"^^ . . . . . "biomedical science" . . "^\\d{7}$"^^ . . . "false"^^ . . . "omics" . "timrobertson100@gmail.com" . . "The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library's holdings in LocatorPlus, NLM's online public access catalog, are also provided. [from homepage]"^^ . . . "http://www.scancerrna.com/toDetail?id="^^ . "cell biology" . . . . "life science" . . "t3db" . "false"^^ . . . _:N749c18c21fcc4173a73a708a383c810a "Frédérick Giasson" . "VIVO Ontology" . . . . . . "phylogeny" . . "https://biodolphin.chemistry.gatech.edu/detail/"^^ . . "preclinical studies" . . "^\\d+$"^^ . . "The digital content format descriptions accessible here provide specific information about individual formats and their characteristics. Each description provides moderately detailed information and citations. Planned for inclusion are a wide variety of formats: file formats, file-format classes, bitstream structures and encodings, and the mechanisms used to compress files or bitstreams. Inclusion of a description for a format does not imply that the format is preferred or acceptable for Library of Congress collections. [from homepage]"^^ . . "false"^^ . "massbank" . . . . . . "^\\d+$"^^ . . . . . . . . "annika.jahnke-bornemann@uni-hamburg.de" . "http://purl.obolibrary.org/obo/PSDO_$1"^^ . . . . . . . . "ontology" . "http://www.daml.org/2003/01/periodictable/PeriodicTable#"^^ . "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^ . . . "00000"^^ . . . "Plant Experimental Conditions Ontology" . "Jennifer R Smith" . . . . . "genome" . . . . "The UNESCO Thesaurus is a controlled and structured list of terms used in subject analysis and retrieval of documents and publications in the fields of education, culture, natural sciences, social and human sciences, communication and information. Continuously enriched and updated, its multidisciplinary terminology reflects the evolution of UNESCO's programmes and activities. [from homepage]"^^ . "protein" . . . . . . "false"^^ . "Semion author ID (archived)" . . . . "Biological Magnetic Resonance Data Bank" . . "true"^^ . "James McLaughlin" . . "dna" . "https://www.kegg.jp/entry/"^^ . "PANTHER Pathway" . "schema" . . "http://purl.obolibrary.org/obo/VIBSO_"^^ . . . . "interaction" . "food" . "Pierre Baldi" . . . . . . . . . . . "catalogs" . . "http://igsn.org/$1"^^ . . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . "PubMed" . . . . "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid="^^ . . . "subject agnostic" . "^ARBA\\d+$"^^ . . . "Allotrope Merged Ontology Suite" . . "life science" . "1691753"^^ . . "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L"^^ . . . . "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."^^ . . . . "http://www.proteinmodelportal.org/query/uniprot/$1"^^ . "Cell Version Control Repository" . "pmr.workspace" . . "multicellds.collection" . . "http://purl.obolibrary.org/obo/MRO_"^^ . . . . . . . . . "gene" . . "obo" . . "hdr" . . . . . "protein" . . "Antoine Danchin" . . "genomics" . . . . . . "https://www.cropontology.org" . . . . . "^\\d{7}$"^^ . . "umbbd.compound" . . "http://biocyc.org/getid?id="^^ . . . . . . "wujm@bjmu.edu.cn" . "colao" . . . "scomp" . . "stefanie.seltmann@ibmt.fraunhofer.de" . . "^\\d{7}$"^^ . "UMR7315"^^ . . "prints" . "StoreDB File" . . "NIF Cell" . . . . "false"^^ . "door" . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1"^^ . . . "data management" . . . . . . "Yang Chai" . . . _:Nf1e1ab922e6f4149b4c3fddb86110c0d "custserv@nlm.nih.gov" . "ontology" . . "Vienna Drosophila Resource Center" . . . . "genomics" . . . "ontology" . . . "structure" . . . "^[a-zA-Z0-9_\\.]+$"^^ . "preclinical studies" . . . . . . "Teri E Klein" . "^\\d{7}$"^^ . "ModelDB concept" . . . . "Maria Taboada" . "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web."^^ . "bcrc" . . "ML0224"^^ . "Personal Information Model" . . . . . . . . "0000435"^^ . . . "265912"^^ . . . "knowledge and information systems" . . "http://data.food.gov.uk/codes/foodtype/id/"^^ . . "academy" . . "false"^^ . "antibody" . . "false"^^ . . . . "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^ . . . . "https://chemprosquare.idrblab.net/data/competitor/details/"^^ . "ontology" . . "^PA\\d+$"^^ . . "mouse" . "false"^^ . . . "false"^^ . "REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs)."^^ . "Studies in dbVar."^^ . . . _:Ne763fe65e2c8492a9dc145ee4037ff0d . . "false"^^ . "RiceNetDB Reaction" . "345201101230312003"^^ . . . . . . . . . . "drc.filenumber" . . "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" . "fbsp" . . . . . . "Basic Register of Thesauri, Ontologies & Classifications" . . . . "IPD-IMGT/HLA" . "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1"^^ . . "co_326" . . . "Tanya Barrett" . "Redistributor of bilogics and biomedical supplies"^^ . . . "FAIRSharing" . . . . "false"^^ . . . . . "^LDPC\\d+$"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"^^ . "http://purl.obolibrary.org/obo/FBbt_$1"^^ . . . . . . "omx.dataset" . . . . . "^\\d+$"^^ . "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . "^\\d+$"^^ . . . . . . . . "^\\d+$"^^ . "Maude Pupin" . . "false"^^ . . "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no="^^ . "Adverse Event Reporting Ontology" . "subcellular compartment" . . . "false"^^ . . . . . . . "^\\d{7}$"^^ . . "systems biology" . "http://rdfs.org/sioc/types#$1"^^ . . "Relations in GEMET"^^ . "ontology" . . . . . . . "classification" . . . . "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^ . . . . "alzgene" . . . . "IPR016380"^^ . "beta-carotene"^^ . . . "ktk@netlabs.org" . . . . "NCit" . . . "Nicolas Le Novère" . . "molecular dynamics" . "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"^^ . . . "preclinical studies" . "charprot" . . . "GenBank" . . "Nanbyo Disease Ontology" . . "taxonomy" . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$"^^ . . . . . . "false"^^ . "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"^^ . . . "RE" . . . . . . . "false"^^ . . . . "https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code="^^ . . . "metascience" . "false"^^ . . . . . . "app-d678n-tottori"^^ . "false"^^ . . . . "Variable"^^ . . . "false"^^ . "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."^^ . "false"^^ . . . "https://biomarkerkb.org/biomarker/$1"^^ . . . . . "biorxiv" . . "health science" . . . . . "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes."^^ . "http://purl.obolibrary.org/obo/EPO_"^^ . . . . . "false"^^ . . . . "Yiming Bao" . . . "The PIMO Ontology can be used to express Personal Information Models of individuals. It is based on RDF and NRL, the NEPOMUK Representational Language and other Semantic Web ontologies. This document describes the principle elements of the language and how to use them. (from homepage)"^^ . . . . . . . . . "false"^^ . . . . "^\\d{7}$"^^ . "Pascale Gaudet" . "false"^^ . "OECD Harmonised Templates" . . "Mihail Anton" . . "Ontology for Avida digital evolution platform" . "DI" . . . "A vocabulary and ontology repository for agronomy and related domains." . . . "HOSO is an ontology of informational entities and processes related to healthcare organizations and services."^^ . . "oma.protein" . . . . "simon.harding@igmm.ed.ac.uk" . . "nje5@georgetown.edu" . . "false"^^ . . "proteomics" . . . . . "Japan Consortium for Glycobiology and Glycotechnology Database" . "^\\d+$"^^ . "microbial" . . "Der Thesaurus enthält Vokabular zu allen ökonomischen Themenstellungen: über 6.000 Schlagwörter und über 28.000 zusätzliche Synonyme als Zugangshilfe, um individuelle Formulierungen bei der Suche aufzufangen. Auch Fachbegriffe aus benachbarten Bereichen wie z.B. Recht, Soziologie oder Politik sowie Geobegriffe sind dort zu finden. Wenn Sie Schlagwörter aus diesem Vokabular auswählen, können Sie sicher sein Treffer zu erhalten, die zu dem gewünschten Sachgebiet passen. [from homepage]"^^ . . "Cell line databases/resources"^^ . . "life science" . . . "false"^^ . . "Polygenic Score Catalog" . . "true"^^ . . "https://w3id.org/linkml/$1"^^ . . . . "methods" . . . . "jason.stajich@ucr.edu" . "^NPC\\d+$"^^ . . . "false"^^ . . "Reproductive and behavioural traits of both adult and larval stages, as well as information on environmental preferences and a few morphological traits."^^ . . "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1"^^ . "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^ . . . "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."^^ . "false"^^ . . . "http://uri.neuinfo.org/nif/nifstd/oen_$1"^^ . "ribonucleic acid" . . . "http://www.kegg.jp/entry/$1"^^ . . . . . "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."^^ . . . "http://www.w3.org/2006/vcard/ns#$1"^^ . "false"^^ . "^\\d{7}$"^^ . "NLXQUAL" . . "1"^^ . "^\\d+$"^^ . . "ResearchGate profile ID" . "https://bioregistry.io/phosphopoint.kinase:"^^ . . . "SIGNOR-C41"^^ . . "phenomics" . "http://id.loc.gov/ontologies/bibframe/"^^ . . "https://www.ncbi.nlm.nih.gov/snp/"^^ . . . . "life science" . . "NIST Chemistry WebBook" . . . "pier.buttigieg@awi.de" . . . "161671"^^ . "exmo" . . . . . . "ontology and terminology" . . . . . . . . "aging" . . . "genomics" . "https://mediadive.dsmz.de/solutions/$1"^^ . . . . . "Cell Line Database" . . . . "dragondb.protein" . . . . "bgee.gene" . . "http://www.humanproteomemap.org/protein.php?hpm_id="^^ . . . . . . . "noncodev4.gene" . "metagenomics" . "Geographical Entity Ontology" . . . . "http://www.w3.org/ns/dcat#"^^ . "protein" . "genome" . . "olivier@nlm.nih.gov" . . . . . . . "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."^^ . "http://purl.obolibrary.org/obo/UO_"^^ . "Collection" . . . . . . . . . . . "wosid" . . . "miRBase mature miRNA" . . . "entiminae@gmail.com" . "COMe" . "dc.terms" . "PharmGKB Drug" . "small molecule" . . . . . "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1"^^ . . . . . "wicell" . . . . . . "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."^^ . . "bigg.reaction" . . . . "bioinformatics" . . "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."^^ . . . "56305849200"^^ . . "suzia@stanford.edu" . . . "chromosome structure variation" . "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^ . "https://bioregistry.io/resolve/github/pull/"^^ . . . . . . "http://virtualflybrain.org/reports/$1"^^ . . . "ENCSR163RYW"^^ . "false"^^ . . "^\\d+$"^^ . . . . "false"^^ . "ontology" . . "false"^^ . . . . . . _:N0435ca59d05d421ab77b24c1658c8f42 "The World Health Organization" . "^\\d+$"^^ . . . . "ontology" . . "https://en.wiktionary.org/wiki/"^^ . "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource"^^ . . "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid="^^ . . "09200010"^^ . "https://www.flymine.org/flymine/report/ChromosomeBand/"^^ . . "^\\d{7}$"^^ . . "A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc."^^ . "https://www.grid.ac/institutes/$1"^^ . . . "drugs" . "assay" . "Pier Luigi Buttigieg" . . "https://data.chembiosys.de/models/$1"^^ . . "40592-R001-100"^^ . "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . "1868"^^ . . . . . "biomedical science" . "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"^^ . "false"^^ . "PeptideAtlas Dataset" . . "https://portal.hubmapconsortium.org/browse/donor/$1"^^ . . "omics" . "mt002305"^^ . "bioschemas" . . . "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees."^^ . . . . "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID="^^ . . . . . "homologene" . . . . "Sorghum TDv5 - Oct 2019"^^ . . . "ENVO" . "embryo" . "^\\d+$"^^ . . . . . "school subject" . . "^SLCTR/\\d{4}/\\d+$"^^ . . . . . "http://sweetontology.net/matrMineral/$1"^^ . . . . "Cell line collections (Providers)"^^ . "ontology" . . . "Authenticus ID" . "has provider formatter" . . . . . . "http://www.w3.org/ns/rdfa#"^^ . "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . "European Nucleotide Archive" . . "plant" . . "The International Standard Book Number (ISBN) is for identifying printed books."^^ . "ontology" . . . . . . . "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."^^ . . . "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.tcdb.org/search/result.php?tc="^^ . . . . . . . . "microbiology" . . "Indian Crop Phenome Database Project" . . . . . . "life science" . . "interaction" . . "scop.sun" . . . "life science" . . . . . . . . . . "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."^^ . . . . . . "http://purl.obolibrary.org/obo/CIDO_"^^ . "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."^^ . "http://purl.obolibrary.org/obo/TO_"^^ . . . "ontology" . . "IPR" . "emmo.cif" . . . . . . . . "obo" . "rna" . "evolutionary biology" . "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^ . . "SKOS-Thes: An extension to SKOS based on the ISO 25964 data model. The ISO 25964 standard, published in 2011, covers all aspects of developing thesauri and setting up mappings across vocabularies to encourage high quality information retrieval across networked resources. [from https://www.dublincore.org/specifications/skos-thes/]"^^ . "^\\d+$"^^ . . . . "true"^^ . "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1"^^ . . . . "^\\d{7}$"^^ . . . . "ontology" . "^\\d\\w+$"^^ . . . . . . . "true"^^ . . . . . "Ontology for Nutritional Studies" . . . . . . . . . . . "https://vocab.lternet.edu/vocab/vocab/index.php?tema="^^ . . "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology."^^ . . . . "https://www.re3data.org" . . "National Center for Biotechnology Information Registry" . . . . . . . "VIRsiRNA" . . . "^CHEMBL\\d+$"^^ . . . "http://purl.org/spar/c4o/$1"^^ . . . . "protein" . . . . "Alistair Miles" . . . . . . . . . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . . "PIRSF000100"^^ . "^TIGR\\d+$"^^ . "ksdrew@uic.edu" . "Antibody-Antigen Complex Database" . . "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID="^^ . . . "^\\d{7}$"^^ . . "true"^^ . "^[A-Z]-[0-9A-Z]{3}-[0-9A-Z]{3}$"^^ . . "21877"^^ . "https://fairsharing.org/organisations/$1"^^ . "false"^^ . . "false"^^ . "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^ . . . "obo" . "^\\d+$"^^ . . . . . . . "http://www.imgt.org/ligmdb/view?id=$1"^^ . . . . "false"^^ . . "https://bioregistry.io/geonames.feature:"^^ . . "https://envipath.org/package/$1"^^ . "https://fcs-free.org/fcs-database?$1"^^ . "false"^^ . "gene" . . . . . . "ontology" . "Haruki Nakamura" . . "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." . . "nci.drug" . "http://scicrunch.org/resolver/SCR_$1"^^ . . . "false"^^ . . "Rosa2"^^ . . . "BacMap Map" . . . . . "true"^^ . . . . . . "4779"^^ . "smart" . . . . . . "ontology" . . . "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^ . . "Registry of Toxic Effects of Chemical Substances" . . . . "nmrXiv sample" . "https://nfdi.fiz-karlsruhe.de/nfdi4dso/"^^ . . . "Since the introduction of ISO 639-3 in 2007, access to language information has increased tremendously. The code set initially adopted as ISO639-3:2007 was based on a harmonization of ISO 639-2 with the code set of SIL’s Ethnologue 15th edition and languages from Linguist List to form a comprehensive set of code elements for world languages. SIL International, the Language Coding Agency for 639-3, relies on the contributions of linguists, language coding experts, and language users around the world to maintain and improve the code set through the change request process defined in the ISO 639 standard. [from homepage]"^^ . "https://www.jax.org/strain/"^^ . "ID in osf.io"^^ . . . . . . . . . "gene" . . . . . . . "^\\d+$"^^ . . . "HL7 V3 Code System" . "Database of RNA Junctions and Kissing loop Structures" . . . . "false"^^ . . "https://www.chemfont.ca/chemicals/"^^ . . . . . . . "https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid="^^ . "265"^^ . "chemical biology" . "http://purl.obolibrary.org/obo/CEPH_$1"^^ . "Human Cell Atlas Ontology" . . . . . . "ontology" . "0000066"^^ . . . . . "Zach Landis-Lewis" . "transcriptomics" . . "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$"^^ . "false"^^ . . . . . "http://purl.obolibrary.org/obo/LEPAO_$1"^^ . "BD1a05-A-A-IPM1"^^ . . . . "0045310"^^ . . "eukaryotic" . . . . . "^\\d{8}$"^^ . "Sensitive Data Ontology" . "Dutch Research Council file numbers are used for approved grants."^^ . . . "0000111"^^ . "1199"^^ . . . "obo" . . . "https://www.holofooddata.org/sample/$1"^^ . . . . "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."^^ . "Ontology for Biobanking" . . . "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . "cell line" . "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks."^^ . "genomics" . "icepo" . "dna" . "Assertion"^^ . "swissregulon" . . . "stn" . "functional genomics" . "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]"^^ . "https://ngdc.cncb.ac.cn/lncbook/gene?geneid=$1"^^ . . . . . . . . "https://www.ebi.ac.uk/ega/studies/$1"^^ . . "knowledge and information systems" . . "lrmi" . "false"^^ . . "https://ligandbook.org/package/"^^ . "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites)."^^ . "^\\d{7}$"^^ . . "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession="^^ . . . . "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$"^^ . . . "Christoph Wohner" . . . . "Semantically-Interlinked Online Communities Types Ontology" . . . "Paula Duek Roggli" . "chemistry" . "eukaryotic Subcellular Localization database" . . . . "http://www.w3.org/ns/rdfa#$1"^^ . "^[0-9\\-_]+$"^^ . . "biochemistry" . "http://purl.org/biotop/biotop.owl#"^^ . "obo" . . . . . . . "ENSG00000026508"^^ . . . . . . "false"^^ . "http://purl.obolibrary.org/obo/MOBIO_$1"^^ . . . . . . . "plant" . "https://gitlab.com/$1"^^ . "https://www.emsl.pnnl.gov/project/$1"^^ . . . "https://health-products.canada.ca/dpd-bdpp/info?lang=eng&code=$1"^^ . . "https://gpcrdb.org/protein/"^^ . . "0000947"^^ . "https://www.mlcommons.org/mlc-id/$1"^^ . . . . "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"^^ . . "drug" . . "Chromosome Ontology" . . "https://n2t.net/$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."^^ . . . "NCI2004_11_17" . . . . "CAA71118.1"^^ . . "KIM License" . "false"^^ . . . "peptideatlas" . "http://purl.obolibrary.org/obo/XPO_"^^ . . . "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."^^ . . "sequence" . . . "computational chemistry" . . _:N445027b9bb704cde95d8a87f75403aa4 "Animal Diversity Web technical staff" . "false"^^ . "60141"^^ . "Matteo Guenci" . "pactr" . "http://www.w3.org/ns/activitystreams#"^^ . . "http://www.hgmd.cf.ac.uk/ac/gene.php?gene="^^ . "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."^^ . . . . . "comparative genomics" . "https://drugs.ncats.io/drug/"^^ . . "SCTID" . "data retrieval" . . . . . . . . . . "false"^^ . . . . . "PSI-MOD" . . . . . . . . . . "population genetics" . . . "BiGG Model" . . "false"^^ . "obo" . . "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession="^^ . . . . . . . . "2.7.1.1"^^ . . . "Reference"^^ . "web of things" . "false"^^ . . "drug discovery" . . . "Pierre-Yves Vandenbussche" . _:N445027b9bb704cde95d8a87f75403aa4 "adw_geeks@umich.edu" . . "alternative_term"^^ . . . "https://pubseed.theseed.org/SubsysEditor.cgi?page=ShowSubsystem&subsystem=$1"^^ . . . "false"^^ . "BRENDA Ligand Group" . "comparative genomics" . . "Joao Pedro de Magalhaes" . "compound" . . . . "http://www.bindingdb.org/rwd/entry/"^^ . "Luis A. Gonzalez-Montana" . . "http://purl.obolibrary.org/obo/PSDO_"^^ . "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^ . "nb2018006591"^^ . . . . . "15543"^^ . "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"^^ . "http://purl.unep.org/sdg/SDGIO_$1"^^ . . . . . . "Ontology Lookup Service" . "dsm-v" . . . . . . . . "https://cryptodb.org/cryptodb/app/record/gene/"^^ . "https://ferr.gulab.org.cn/browse/"^^ . "gwascentral.phenotype" . . . . . "dylan.mcgagh@magd.ox.ac.uk" . . . . . "NCBI Taxonomy" . . "protein" . . . . . . . "behavior" . . "uniprot.journal" . . . . "Publons publication" . . . . . "https://www.nextprot.org/term/FA-$1"^^ . "ontology" . "CLV_MEL_PAP_1"^^ . "publishing" . . . . . "true"^^ . "https://reactome.org/content/detail/$1"^^ . . . . . "ygyingli@ncsu.edu" . . "false"^^ . . "Human BioMolecular Atlas Program Dataset" . . "false"^^ . "genome" . . . "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules."^^ . . "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^ . "5601141"^^ . "false"^^ . . . . . . "structure" . "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . . . "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#"^^ . . "An ontology supporting data modeling in WikiPathways"^^ . . . . . "GFAM" . . "Addgene Plasmid Repository" . . . "http://www.cathdb.info/domain/"^^ . . . . . . . "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . . . . . . . "security" . . . . "F001"^^ . "ro" . . "^\\w+$"^^ . "Human ancestry ontology for the NHGRI GWAS Catalog"^^ . "^\\d+$"^^ . "false"^^ . "K"^^ . "Golm Metabolome Database Analyte" . "Ontology of Arthropod Circulatory Systems" . . . . . "Cell line collections"^^ . . "true"^^ . "An ontology for description of concepts in the nutritional studies domain."^^ . "10090-chr10qC"^^ . "false"^^ . "https://thebiogrid.org/interaction/$1"^^ . "sh" . "life cycle stage" . . "structure" . . "false"^^ . . . . . . "https://www.rhea-db.org/rhea/"^^ . . . "life science" . "^\\d+$"^^ . "https://www.ensembl.org/id/$1"^^ . . . . . "Functional annotations of genomes for studying gene regulation, with a primary focus on cis-regulatory elements (CREs) such as promoters and enhancers."^^ . . . . "false"^^ . . . . . . . "https://www.probes-drugs.org/compound/"^^ . . . . . . . "v.robert@wi.knaw.nl" . . . . "RNA Virus Database" . "^\\d+$"^^ . . . "https://www.npmjs.com/package/$1"^^ . . "https://www.alliancegenome.org/accession/$1"^^ . . . . "^\\d+$"^^ . . . . . . . . . "A nomenclatural ontology for biological names" . "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)"^^ . . . "methods" . . . . "dbmhc" . "biominder" . . "map" . . "https://www.biorxiv.org/content/10.1101/"^^ . "InterPro" . "neuroscience" . "Global Natural Products Social Molecular Networking Task" . "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id="^^ . . . . "Open Science Framework ID" . . "mw.project" . . "creativebiolabs.protein" . "https://nrid.nii.ac.jp/ja/nrid/10000$1"^^ . . . . "xenbase" . . . "biomedical science" . "false"^^ . . . "https://w3id.org/faircookbook/"^^ . . "Jaime Huerta-Cepas" . . . . . . "http://purl.obolibrary.org/obo/SOPHARM_$1"^^ . . "https://biomodels.net/vocab/idot.rdf#$1"^^ . "0000598"^^ . . . . "http://www-bionet.sscc.ru/sitex/index.php?siteid="^^ . . . . . . . . "Identifiers for immune receptors, representing receptor complexes or groups studied for their interactions with antigens or epitopes."^^ . . "00000003"^^ . . . "^\\d+$"^^ . . . . . . . . "TaxonomyID" . . "protein" . "dendrology" . "gmd.analyte" . "publication" . . "false"^^ . "10004892"^^ . . . . "ftp://hgdownload.cse.ucsc.edu/goldenPath/"^^ . "pathway" . . "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology."^^ . . . . . . "A vocabulary of argumentation predicates for SIOC"^^ . . "phenotype" . . . . . . . . . . "http://hawaii.eagle-i.net/i/$1"^^ . "clinical studies" . "false"^^ . . "^\\d{7}$"^^ . "^\\d+$"^^ . "^\\d{5}$"^^ . . . . . . . "biology" . "biomedical science" . . . . . . "true"^^ . . . "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."^^ . . "European Paediatric Cardiac Codes" . . "hpiwowar@gmail.com" . "structure" . "false"^^ . . . "BN000065"^^ . . . "false"^^ . . . "skills" . . . "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . . "Yosef Shiloh" . . . . . . "0000006"^^ . . . "Narcis Fernandez-Fuentes" . "http://purl.obolibrary.org/obo/CIO_"^^ . . . "https://www.ebi.ac.uk/ega/datasets/"^^ . "obo" . . . . . "http://synbip.idrblab.net/data/bts/details/$1"^^ . . . "NONHSAT000001"^^ . "0000196"^^ . "false"^^ . . . . . . . . . "http://purl.bioontology.org/ontology/HCPCS/$1"^^ . . . "InChI" . "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc="^^ . . . . . "mhb120@gmail.com" . "NLXMOL" . . "pathway" . "false"^^ . . "^\\d+$"^^ . "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."^^ . "Swiss National Clinical Trials Portal" . . . . . "structure" . . . . . . . . "https://fairsharing.org/$1" . "^(data|topic|operation|format)\\_\\d{4}$"^^ . "social science" . . . . . "dalia.oer" . . "Cellular Microscopy Phenotype Ontology" . . . "CHEMBL3307800"^^ . "1948"^^ . "life science" . . . "phosphopoint.kinase" . . . "Georgeta Bordea" . "The Digital Object Identifier System is for identifying content objects in the digital environment."^^ . . . . . . "obo" . "^[0-9a-zA-Z]{8}$"^^ . . . "0001114"^^ . . . "false"^^ . . "false"^^ . "false"^^ . "http://www.pseudomonas.com/feature/show/?locus_tag="^^ . "gene" . . . "Linda Reha-Krantz" . . "rna-protein interactions" . . "obo" . . "esco.isco" . . . . . . . . . . . . "utrdb" . "sfam" . . . "EcoLexicon" . "https://biomarkerkb.org/canonical/"^^ . . . . . . . "AOPWiki (Key Event)" . "https://www.ebi.ac.uk/metagenomics/proteins/$1"^^ . "DBMET02292"^^ . . . . "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."^^ . "Prefix Commons" . . . . . "Instrument"^^ . "https://bioregistry.io/polbase:"^^ . . . . "https://doi.org/$1"^^ . "education level" . . "false"^^ . . . "DrugBank Salts" . . "HGNC gene family" . . "General Formal Ontology" . . "FBbi" . . . . "1a24"^^ . . . . . "ontology" . . . "bacterin-toxoid" . "true"^^ . "http://www.phosphosite.org/proteinAction.do?id=$1"^^ . . "http://purl.obolibrary.org/obo/STATO_"^^ . "false"^^ . "https://viralzone.expasy.org/$1"^^ . . "chemical entity" . "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1"^^ . . "sdbs" . . . "CHEBI"^^ . . . . . "metadata" . . . "Docker Hub repository" . "http://id.loc.gov/vocabulary/resourceTypes/"^^ . . . "^8\\d{4}$"^^ . "identifier of an author in Dialnet"^^ . "ICD-10" . _:N173b76cb92df4b748c1e838498a75183 "zimmerly@ucalgary.ca" . . "false"^^ . . . . . "go.ref" . . . . "0000000"^^ . . "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC="^^ . "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."^^ . "2008-005144-16"^^ . . "GlycoNAVI" . . . "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code="^^ . . . "torsten.schwede@unibas.ch" . . "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."^^ . "Livestock Product Trait Ontology" . . "false"^^ . . "Molecular Modeling Database" . "false"^^ . "genome" . "false"^^ . . "semantic web" . . "Gary Bader" . . . . . . . "worms" . "189"^^ . . . . "DICOM Controlled Terminology"^^ . "^\\d{8}$"^^ . "false"^^ . "https://aopwiki.org/stressors/$1"^^ . . . "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."^^ . . . . . . . . . . . . . . . "Job Dekker" . . . "AS000060"^^ . . . . . . . . . . "cheminformatics" . . "false"^^ . "false"^^ . "Association-Rule-Based Annotator" . . "Michael Feolo" . _:N5fb757cbe6c640f5932a18d812860cd9 "J.Bard@ed.ac.uk" . . "http://xmlns.com/wot/0.1/$1"^^ . . "hsa-let-7a"^^ . "true"^^ . . "^PA\\w+$"^^ . _:Nf7c39b4a52e24a1c9bd5e05e15b5c7c5 "PhenX Admin" . . "This resource provides identifiers for listed hazardous wastes which are substances explicitly identified due to their potential harm to human health and the environment. These are categorized into four groups (F, K, P, and U) based on specific criteria, such as their source or inherent properties."^^ . "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^ . . . . . . "Wikipedia" . . . "machine learning" . . . . "false"^^ . "famplex" . . . . "^\\d+$"^^ . "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^ . "Provenance, Authoring, and Versioning Vocabulary" . "obo" . . . . . . "craniofacial phenotype" . "^\\d{7}$"^^ . _:Nba63b9197e1b4f7d9250736af3631bbb "NLM Customer Service" . . . . "nicolas.maillet@pasteur.fr" . . "ontology" . . . . "https://deims.org/networks/"^^ . . "machine learning" . "C063233"^^ . "grin" . "^HMDB\\d+$"^^ . "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/"^^ . _:N6321c68bb95043c780afe7f03dba1a5c . . . "^[A-Z][a-z][0-9]+$"^^ . . . . . . . . "Ioannis.Xenarios@unil.ch" . . . . . "oct 2016"^^ . . . "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."^^ . . . "^\\d{6}$"^^ . "rna secondary structure" . . . . . . . . . "AU124"^^ . _:N5d925c954f78444c8cfe40526902d06f "curator@inoh.org" . . "flymine.chromosome" . "^\\w+$"^^ . "Stephen Randal Voss" . "ModelDB" . . . "http://purl.obolibrary.org/obo/EMPTY_$1"^^ . . . . "biology" . "RBR-6qvdftm"^^ . . "antibodies" . . . "false"^^ . "d.e.starns@liv.ac.uk" . . . . . . "http://purl.org/spar/pwo/$1"^^ . . . "developmental biology" . . . . "ontology" . . . "genetics" . . . . "RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project."^^ . "PDBeChem" . . . . . "^[a-z0-9-_.]+$"^^ . . . "plant genetics" . "Mouse Developmental Anatomy Ontology" . "vipr" . "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id="^^ . . . . . "biology" . "ICEberg cis-integrative and mobilizable element" . . "sioc.types" . "https://pb.apf.edu.au/phenbank/strain.html?id="^^ . . . . . "functional genomics" . "https://www.devtox.org/nomenclature/ml_manus.php?mno=$1"^^ . "GnpIS" . "^\\d+$"^^ . . . . "traits" . "protein" . "A vector graphic for an anatomical entity useful for biological and biomedical informatics applications."^^ . . . . . . . . . . "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."^^ . . . . "Sylvain V Costes" . "biology" . . . . "disease" . . "ontology" . "http://purl.obolibrary.org/obo/OBCS_$1"^^ . "Environmental Molecular Sciences Laboratory Project" . . . "^c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y$"^^ . "vendor" . "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/"^^ . "pathway" . . . "pocketome" . . "biomedical science" . . . . . . . "false"^^ . "biology" . "ma" . "Sharkipedia Trait" . . "false"^^ . "Semantically-Interlinked Online Communities Access Ontology" . . . . "false"^^ . . . . . "life science" . "^\\d{8}$"^^ . "false"^^ . . . . . "0000423"^^ . . "false"^^ . "0000086"^^ . . . . . . "datacommons" . "inhand" . . . . "^NCT\\d{8}$"^^ . . "virology" . . "http://purl.obolibrary.org/obo/MONDO_$1"^^ . "Richard Scheuermann" . . . "^\\d+$"^^ . "^\\d+$"^^ . . . "false"^^ . "https://osdr.nasa.gov/bio/repo/data/payloads/$1"^^ . "neuronames" . "behavior" . "false"^^ . . "false"^^ . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"^^ . . . "https://sed-ml.org/urns.html#language:"^^ . "false"^^ . "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . "cst.pathway" . . . . . . . "liujianghua@usc.edu.cn" . . . . "^MGYS\\d{8}$"^^ . . "https://w3id.org/aio/"^^ . "^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$"^^ . . . "drug" . . "^\\w+$"^^ . "DUO is an ontology which represent data use conditions."^^ . . . "1122888"^^ . . . "adcad" . . . . . . . . . . "http://purl.obolibrary.org/obo/CVDO_$1"^^ . "^CP\\d+$"^^ . . . "^\\d{7}$"^^ . "https://www.enzyme-database.org/query.php?ec=$1"^^ . "http://www.ebi.ac.uk/efo/EFO_"^^ . . . "true"^^ . "Sumir H Pandit" . "http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?winid=1&recid="^^ . . . "ontology" . "2019-08-03_00000089_1"^^ . "dgrc" . "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0="^^ . "phenotype" . "euroscivoc" . "1017"^^ . . . "A UUID for a community indexed in the Data Liteacy Alliance (DALIA) web application"^^ . "br/1"^^ . . . "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."^^ . . . "ebf69ca24298b28b2361e7d43eb52d6c"^^ . _:N5d925c954f78444c8cfe40526902d06f . . "molecular" . . "United States Patent and Trademark Office" . . . "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . . "kinetics" . "nhcdr" . "An ontology of qualifications, distinctions, and certifications that uses the Phenotype And Trait Ontology term quality (PATO:0000001) as a root term."^^ . . . "OMIA variants" . . . . . . "foodb.food" . . . "false"^^ . "Sue Bello" . "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)."^^ . "genetics" . . "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."^^ . . . "0001000"^^ . "false"^^ . . . "http://ddinter.scbdd.com/ddinter/drug-detail/$1"^^ . "botany" . . . "A repository of software packages written in Ruby."^^ . . . . "SEED Reactions" . . . . . . "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . "https://datalab.rwth-aachen.de/MINDER/resource/"^^ . "^[0-9]{4}$"^^ . "narcis" . . "https://www.disprot.org/idpo/IDPO:"^^ . "http://purl.obolibrary.org/obo/ENVO_"^^ . . "phenomics" . . "false"^^ . "Japan Chemical Substance Dictionary" . . . . "^\\d+$"^^ . "21552"^^ . "obo" . . "false"^^ . . . "epso" . . "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"^^ . . . "^TTHERM\\_\\d+$"^^ . . "false"^^ . . "STUDY1040"^^ . "biomedical science" . "https://ssrn.com/abstract="^^ . "http://terminology.hl7.org/CodeSystem/v2-"^^ . "simon.harding@ed.ac.uk" . "fly" . "bioresource" . . . . . . . "5277619"^^ . . . . . . . . . "co_340" . . "agriculture" . "Jesper Friis" . . . . . . "wdrs" . . . . . "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. " . . . "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)."^^ . . . "ArrayMap" . . . "Vertebrate Homologous Organ Group Ontology" . . . . "^\\d{7}$"^^ . . "educational resource" . . . "genome" . . . "ontology" . "187021"^^ . "pain medicine" . . . "cpt" . . "false"^^ . "http://www.alzgene.org/geneoverview.asp?geneid=$1"^^ . . . "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"^^ . . . . "false"^^ . "https://www.encodeproject.org/$1"^^ . . _:Nff095911261b4b07a1c6079c6f0175ce "LOINC Support" . "Web Annotation Ontology" . . "The pre-IND tracking number for submissions to the FDA"^^ . "The European Genome-phenome Archive (EGA) is a global network for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Jointly managed by the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre for Genomic Regulation (CRG) in Barcelona."^^ . . . "JCOIN" . . . "^\\d{6}$"^^ . . "11"^^ . . "56586"^^ . "false"^^ . "KW-1273"^^ . "false"^^ . "https://lobid.org/gnd/"^^ . . . "cell biology" . "political science" . . . "pns12@hermes.cam.ac.uk" . . "microbial" . "http://multicellds.org/MultiCellDB/"^^ . . . . . "AgroPortal" . "^[a-z]{3}-[a-km-z0-9]{7}$"^^ . . "natural history" . "Reaxys" . "TIGR00010"^^ . . . . . "Dataset"^^ . . "fema" . . . . "https://lincs.hms.harvard.edu/db/proteins/"^^ . . "https://biocomputeobject.org/BCO_"^^ . . . "false"^^ . "phenotype" . "https://w3id.org/seo#$1"^^ . . . "Idan Gabdank" . . . . . . . . . . . . . . . . . . "MobiDB is a database of protein disorder and mobility annotations."^^ . "DEF"^^ . "botany" . . "false"^^ . "Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications."^^ . "splash" . . . . . "health science" . "Human Oral Microbiome Database" . "genetic" . . . . "microarray" . "Minimum Information about a Tailoring Enzyme data repository" . . . "LNCRNADB" . . "Kalpana Panneerselvam" . . . . . . "http://www.antweb.org/specimen.do?name="^^ . . . "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."^^ . "phenotype" . . . . . . . "false"^^ . . . . . . "nfdi4culture.cto" . . . "kim.lp" . . "protein" . "ZFA description."^^ . "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."^^ . "life science" . . . _:N5b03584c81674192b841994dd3875efa "Natalie L Catlett" . . "18"^^ . . . . "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."^^ . . "botany" . "16S rRNA gene database" . . . . . . . "NONCODE v3" . . . . . "iceberg.ime" . . . "false"^^ . . "ontology" . . . "SIDER Drug" . "mcourtot@gmail.com" . "gene" . "taxonomy" . "true"^^ . . . "ricenetdb.protein" . "151022"^^ . "http://purl.obolibrary.org/obo/SDDO_$1"^^ . "4D Nucleome Data Portal Biosource" . . . "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas="^^ . "PREMIS 3 Ontology" . . . . . . "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."^^ . . . . . "Ontology of Biological Attributes" . "https://w3id.org/nfdi4cat/voc4cat_$1"^^ . . . "structure" . . "MM00040"^^ . "false"^^ . . . . . . . . . . . . . . . . "^\\d{7}$"^^ . . . . _:Ndaeb335c10e4454b92d1360067e4b4c2 "WikiData Support" . . . . . . . "Saccharomyces Genome Database" . . . "https://bioregistry.io/metaregistry/go/$1"^^ . . "anatomy" . "ForwardStrandPosition"^^ . . "uberon"^^ . . "^r3d\\d{9,9}$"^^ . "morphology" . "false"^^ . "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"^^ . . "https://www.ebi.ac.uk/intact/search?query="^^ . . . . . . "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language."^^ . . . . . . . "http://scop.berkeley.edu/sid="^^ . . . "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\"."^^ . . . . . "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . "http://zfin.org/$1"^^ . . "https://bio.tools/"^^ . . . . . . "rna" . "structure" . . . . . . . . . . . . . . "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^ . "^\\d+$"^^ . . . . . . "Golm Metabolome Database" . "COG Categories" . . . . . . "protein" . "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1"^^ . . . "trnadbce" . . . . . "https://web.archive.org/web/1/https://www.semion.io/Author/"^^ . "false"^^ . "TriTrypDB" . . . . "false"^^ . "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"^^ . "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/"^^ . "guiderdoni@cirad.fr" . . "false"^^ . "https://www.kew.org/data/grasses-db/www/$1"^^ . . . . . . . "^OSD-\\d+$"^^ . "DB-0174" . . . . . . "http://purl.obolibrary.org/obo/AEON_$1"^^ . . . . . . . . . "FMA_RETIRED" . . . . . . . "gocc" . "http://arabidopsis.info/StockInfo?NASC_id="^^ . . "sonami@riken.jp" . . . . . "health science" . "pathway" . "https://integbio.jp/en/" . "enzyme" . . . "http://purl.uniprot.org/annotation/VAR_$1"^^ . . . "clinicaltrials" . . . . . . "SoyBase" . . . . . . . . . . . . "false"^^ . . "The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR."^^ . "http://webapps2.ucalgary.ca/~