BIND Biomolecular Interaction Network Database bind ^\d+$ BIND is a database of protein-protein interactions. This data-resource is not open-access. false urn:miriam:bind http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id http://www.bind.ca/ Unleashed Informatics Canada ChEBI chebi ^CHEBI:\d+$ Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. true http://www.ebi.ac.uk/chebi/ urn:miriam:obo.chebi http://purl.obolibrary.org/obo/CHEBI http://identifiers.org/chebi/ http://identifiers.org/obo.chebi/ urn:miriam:chebi metabolite chemical ontology ols http://www.ebi.ac.uk/ols/ontologies/chebi/terms?obo_id=$id CHEBI:36927 http://www.ebi.ac.uk/ols/ontologies/chebi European Bioinformatics Institute, Hinxton, Cambridge UK ebi http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 http://www.ebi.ac.uk/chebi/ European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/CHEBI/$id CHEBI:36927 http://bioportal.bioontology.org/ontologies/CHEBI National Center for Biomedical Ontology, Stanford USA Ensembl ensembl ^((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ 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. false urn:miriam:ensembl http://www.ensembl.org/ sequence genome nucleotide eukaryotic http://useast.ensembl.org/id/$id ENSG00000139618 http://useast.ensembl.org/ USA http://uswest.ensembl.org/id/$id ENSG00000139618 http://uswest.ensembl.org/ USA ebi http://www.ensembl.org/id/$id ENSG00000139618 http://www.ensembl.org/ Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge UK http://asia.ensembl.org/id/$id ENSG00000139618 http://asia.ensembl.org/ Singapore Enzyme Nomenclature Enzyme Classification EC EC code ec-code ec ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. false http://www.ec-code.org/ urn:lsid:ec-code.org http://www.ebi.ac.uk/IntEnz/ urn:miriam:ec-code taxonomy enzyme protein classification expasy http://enzyme.expasy.org/EC/$id 1.1.1.1 http://enzyme.expasy.org/ Swiss Institute of Bioinformatics Switzerland intenz http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id 1.1.1.1 http://www.ebi.ac.uk/intenz/ European Bioinformatics Institute, Hinxton, Cambridge UK expenz http://www.enzyme-database.org/query.php?ec=$id 1.1.1.1 http://www.enzyme-database.org/ Trinity College, Dublin Ireland http://www.genome.jp/dbget-bin/www_bget?ec:$id 1.1.1.1 http://www.genome.jp/dbget-bin/www_bfind?enzyme Kyoto University Bioinformatics Center Japan UniProt Knowledgebase UniProtKB/Swiss-Prot UniProtKB Protein Knowledgebase UniProt-TrEMBL UniProt/TrEMBL UniProt uniprot ^([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+)?$ 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. false urn:miriam:uniprot urn:lsid:uniprot.org urn:lsid:uniprot.org:uniprot http://www.uniprot.org/ http://identifiers.org/uniprot/ protein sequence http://www.pir.uniprot.org/cgi-bin/upEntry?id=$id P62158 http://www.pir.uniprot.org/ Georgetown University USA http://us.expasy.org/uniprot/$id P62158 http://www.expasy.uniprot.org/ Swiss Institute of Bioinformatics Switzerland http://purl.uniprot.org/uniprot/$id P0DP23 http://www.uniprot.org/ UniProt Consortium ebi http://www.ebi.uniprot.org/entry/$id P62158 http://www.ebi.uniprot.org/ European Bioinformatics Institute, Hinxton, Cambridge UK http://www.uniprot.org/uniprot/$id P0DP23 http://www.uniprot.org/ UniProt Consortium USA, UK and Switzerland ncbi http://www.ncbi.nlm.nih.gov/protein/$id P0DP23 http://www.ncbi.nlm.nih.gov/protein/ National Center for Biotechnology Information (NCBI) USA Taxonomy NEWT NCBI taxonomy taxonomy taxon ^\d+$ The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. false http://purl.obolibrary.org/obo/NCBITaxon http://www.uniprot.org/taxonomy/ urn:miriam:taxonomy http://bio2rdf.org/taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/ http://identifiers.org/taxonomy/ http://www.taxonomy.org/ taxonomy ols http://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?short_form=NCBITaxon_$id 9606 http://www.ebi.ac.uk/ols/ontologies/ncbitaxon/ European Bioinformatics Institute, Hinxton, Cambridge UK http://purl.uniprot.org/taxonomy/$id 9606 http://www.uniprot.org/taxonomy/ UniProt Consortium USA, UK and Switzerland ncbi http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$id 9606 http://www.ncbi.nlm.nih.gov/Taxonomy/ National Center for Biotechnology Information (NCBI) USA ebi http://www.ebi.ac.uk/ena/data/view/Taxon:$id 9606 http://www.ebi.ac.uk/ena/ European Bioinformatics Institute, Hinxton, Cambridge UK http://taxonomy.bio2rdf.org/describe/?url=http://bio2rdf.org/taxonomy:$id 9606 http://taxonomy.bio2rdf.org/fct/ Bio2RDF.org bptl http://purl.bioontology.org/ontology/NCBITAXON/$id 9606 http://bioportal.bioontology.org/ontologies/NCBITAXON National Center for Biomedical Ontology, Stanford USA BioModels Database BioModels biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. false http://bio2rdf.org/biomodels http://identifiers.org/biomodels.db/ http://www.ebi.ac.uk/biomodels/ urn:miriam:biomodels.db model http://cu.biomodels.bio2rdf.org/describe/?url=http://bio2rdf.org/biomodels:$id BIOMD0000000048 http://cu.biomodels.bio2rdf.org/fct/ Bio2RDF.org ebi http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 http://www.ebi.ac.uk/biomodels/ European Bioinformatics Institute, Hinxton, Cambridge UK http://biomodels.caltech.edu/$id BIOMD0000000048 http://biomodels.caltech.edu/ California Institute of Technology USA MIRIAM Registry collection MIRIAM Resources MIRIAM miriam.collection ^MIR:000\d{5}$ MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. false http://biomodels.net/MIRIAM/ urn:miriam:miriam.datatype urn:miriam:miriam http://www.biomodels.net/MIRIAM/ urn:miriam:miriam.collection registry ebi http://www.ebi.ac.uk/miriam/main/$id MIR:00000008 http://www.ebi.ac.uk/miriam/ European Bioinformatics Institute, Hinxton, Cambridge UK ICD icd ^[A-Z]\d+(\.[-\d+])?$ The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. false http://www.who.int/classifications/icd/ urn:miriam:icd taxonomy disease http://apps.who.int/classifications/icd10/browse/2010/en#/$id C34 http://www.who.int/classifications/icd/en/ German Institute of Medical Documentation and Information Germany IntAct intact ^EBI\-[0-9]+$ IntAct provides a freely available, open source database system and analysis tools for protein interaction data. false urn:miriam:intact http://www.ebi.ac.uk/intact/ protein interaction ebi http://www.ebi.ac.uk/intact/interaction/$id EBI-2307691 http://www.ebi.ac.uk/intact/ European Bioinformatics Institute, Hinxton, Cambridge UK InterPro interpro ^IPR\d{6}$ InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. false http://purl.uniprot.org/interpro/ http://identifiers.org/interpro/ http://www.ebi.ac.uk/interpro/ http://bio2rdf.org/interpro urn:miriam:interpro protein domain ebi http://www.ebi.ac.uk/interpro/entry/$id IPR000100 http://www.ebi.ac.uk/interpro/ European Bioinformatics Institute, Hinxton, Cambridge UK http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$id IPR000100 http://interpro.bio2rdf.org/fct/ Bio2RDF.org KEGG Pathway KEGG kegg.pathway ^\w{2,4}\d{5}$ KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. false urn:miriam:kegg.pathway http://www.genome.jp/kegg/pathway/ pathway http://www.kegg.jp/entry/$id hsa00620 http://www.genome.jp/kegg/pathway.html Kyoto University Bioinformatics Center Japan KEGG Compound KEGG kegg.compound ^C\d+$ KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. false http://www.genome.jp/kegg/compound/ urn:miriam:kegg.compound chemical metabolite structure http://www.kegg.jp/entry/$id C12345 http://www.genome.jp/kegg/ligand.html Kyoto University Bioinformatics Center Japan KEGG Reaction KEGG kegg.reaction ^R\d+$ KEGG reaction contains our knowledge on the universe of reactions that are relevant to life. false http://www.genome.jp/kegg/reaction/ urn:miriam:kegg.reaction reaction http://www.kegg.jp/entry/$id R00100 http://www.genome.jp/kegg/reaction/ Kyoto University Bioinformatics Center Japan PubMed pubmed pmid ^\d+$ PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. false urn:miriam:pubmed http://www.pubmed.gov/ http://identifiers.org/pubmed/ http://linkedlifedata.com/resource/pubmed/id/ http://www.ncbi.nlm.nih.gov/PubMed/ http://bio2rdf.org/pubmed bibliography http://ukpmc.ac.uk/abstract/MED/$id 16333295 http://ukpmc.ac.uk/ UKPMC Funders Group UK ncbi http://www.ncbi.nlm.nih.gov/pubmed/$id 16333295 http://www.ncbi.nlm.nih.gov/PubMed/ National Center for Biotechnology Information (NCBI) USA ebi http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$id 16333295 http://www.ebi.ac.uk/citexplore/ European Bioinformatics Institute, Hinxton, Cambridge UK ebi http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:$id] 16333295 http://www.ebi.ac.uk/Databases/MEDLINE/medline.html European Bioinformatics Institute, Hinxton, Cambridge UK http://pubmed.bio2rdf.org/describe/?url=http://bio2rdf.org/pubmed:$id 23735196 http://pubmed.bio2rdf.org/fct Bio2RDF.org epmc http://europepmc.org/abstract/MED/$id 16333295 http://europepmc.org/ Europe PubMed Central partners UK hubmed http://www.hubmed.org/display.cgi?uids=$id 16333295 http://www.hubmed.org/ Alfred D. Eaton United Kingdom http://linkedlifedata.com/resource/pubmed/id/$id 23735196 http://linkedlifedata.com/ Linkedlifedata, Ontotext, Sofia Bulgaria OMIM Online Mendelian Inheritance in Man MIM Mendelian Inheritance in Man omim ^[*#+%^]?\d{6}$ Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. false http://bio2rdf.org/omim http://identifiers.org/omim/ http://www.ncbi.nlm.nih.gov/OMIM/ urn:miriam:omim disorder human phenotype http://omim.bio2rdf.org/describe/?url=http://bio2rdf.org/omim:$id 603903 http://omim.bio2rdf.org/fct Bio2RDF.org http://us-east.omim.org/entry/$id 603903 http://us-east.omim.org/ OMIM, Virgina USA ebi http://europe.omim.org/entry/$id 603903 http://europe.omim.org/ European Bioinformatics Institute, Hinxton, Cambridge UK http://mirror.omim.org/entry/$id 603903 http://mirror.omim.org/ Johns Hopkins University, Baltimore, Maryland USA http://omim.org/entry/$id 603903 http://omim.org/ Johns Hopkins University, Baltimore, Maryland USA PIRSF Protein Information Resource pirsf ^PIRSF\d{6}$ The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. false http://pir.georgetown.edu/pirsf/ urn:miriam:pirsf protein clustering http://pir.georgetown.edu/cgi-bin/ipcSF?id=$id PIRSF000100 http://pir.georgetown.edu/ Georgetown University Medical Center USA Reactome Reactome Stable ID reactome (^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$) The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology. false urn:miriam:reactome http://www.reactome.org/ pathway reaction human http://reactome.org/content/detail/$id R-HSA-201451 http://www.reactome.org/ Ontario Institute for Cancer Research, NYU Medical School, Cold Spring Harbor Laboratory and European Bioinformatics Institute Canada / USA / UK DOI Digital Object Identifier doi ^(doi\:)?\d{2}\.\d{4}.*$ The Digital Object Identifier System is for identifying content objects in the digital environment. false urn:miriam:doi http://www.doi.org/ bibliography http://doi.org/$id 10.1038/nbt1156 http://www.doi.org/ International DOI Foundation United Kingdom http://hdl.handle.net/$id 10.1038/nbt1156 http://www.handle.net/index.html Corporation for National Research Initiatives USA http://doai.io/$id 10.1038/nbt1156 http://doai.io/ CAPSH (Committee for the Accessibility of Publications in Sciences and Humanities), Paris France Protein Data Bank PDB pdb ^[0-9][A-Za-z0-9]{3}$ The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. false urn:miriam:pdb http://www.pdb.org/ structure protein pdbj http://pdbj.org/mine/summary/$id 2gc4 http://www.pdbj.org/ Institute for Protein Research, Osaka University Japan http://proteopedia.org/wiki/index.php/$id 2gc4 http://www.proteopedia.org/ Weizmann Institute of Science Israel pdbe http://www.pdbe.org/$id 2gc4 http://www.pdbe.org/ European Bioinformatics Institute, Hinxton, Cambridge UK rcsb http://www.rcsb.org/pdb/explore/explore.do?structureId=$id 2gc4 http://www.pdb.org/ Rutgers, The State University of New Jersey USA ebi http://www.ebi.ac.uk/pdbsum/$id 2gc4 http://www.ebi.ac.uk/pdbsum/ European Bioinformatics Institute, Hinxton, Cambridge UK CluSTr clustr ^[0-9A-Za-z]+:\d+:\d{1,5}(\.\d)?$ The CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons (Smith-Waterman) between protein sequences. false http://www.ebi.ac.uk/clustr/ urn:miriam:clustr protein clustering ebi http://www.ebi.ac.uk/clustr-srv/CCluster?interpro=yes&cluster_varid=$id HUMAN:55140:308.6 http://www.ebi.ac.uk/clustr/ European Bioinformatics Institute, Hinxton, Cambridge UK Gene Ontology GO go ^GO:\d{7}$ The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. true http://bio2rdf.org/go http://purl.obolibrary.org/obo/GO urn:miriam:go http://identifiers.org/obo.go/ urn:miriam:obo.go http://www.geneontology.org/ http://identifiers.org/go/ ontology http://www.bioinf.ebc.ee/EP/EP/GO/?Q=$id GO:0006915 http://ep.ebi.ac.uk/EP/GO/ European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/GO/$id GO:0006915 http://bioportal.bioontology.org/ontologies/GO National Center for Biomedical Ontology, Stanford USA http://www.pantherdb.org/panther/category.do?categoryAcc=$id GO:0000003 http://www.pantherdb.org/ Keck School of Medicine, University of Southern California USA quickgo http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 http://www.ebi.ac.uk/QuickGO/ European Bioinformatics Institute, Hinxton, Cambridge UK amigo http://amigo.geneontology.org/amigo/term/$id GO:0006915 http://amigo.geneontology.org/ The Gene Ontology Consortium USA ols http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id GO:0006915 http://www.ebi.ac.uk/ols/ontologies/go European Bioinformatics Institute, Hinxton, Cambridge UK http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/$id GO:0006915 http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/ Berkeley Bioinformatics Open-source Projects, Lawrence Berkeley National Lab, Berkeley, California USA http://www.informatics.jax.org/searches/GO.cgi?id=$id GO:0006915 http://www.informatics.jax.org/searches/GO_form.shtml The Jackson Laboratory USA SGD Saccharomyces Genome Database sgd ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$ The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. false http://www.yeastgenome.org/ http://identifiers.org/sgd/ urn:miriam:sgd http://bio2rdf.org/sgd eukaryotic nucleotide genome http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=$id S000028457 http://www.yeastgenome.org/ Stanford University USA http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$id S000006169 http://sgd.bio2rdf.org/fct Bio2RDF.org Systems Biology Ontology SBO sbo ^SBO:\d{7}$ 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. true http://www.biomodels.net/SBO/ http://identifiers.org/sbo/ urn:miriam:biomodels.sbo urn:miriam:obo.sbo urn:miriam:sbo http://biomodels.net/SBO/ ontology ols http://www.ebi.ac.uk/ols/ontologies/sbo/terms?obo_id=$id SBO:0000262 http://www.ebi.ac.uk/ols/ontologies/sbo European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/SBO/$id SBO:0000262 http://bioportal.bioontology.org/ontologies/SBO National Center for Biomedical Ontology, Stanford USA ebi http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 http://www.ebi.ac.uk/sbo/ European Bioinformatics Institute, Hinxton, Cambridge UK KEGG Drug KEGG kegg.drug ^D\d+$ KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. false http://www.genome.jp/kegg/drug/ urn:miriam:kegg.drug drug structure http://www.kegg.jp/entry/$id D00123 http://www.genome.jp/kegg/drug/ Kyoto University Bioinformatics Center Japan KEGG Glycan KEGG kegg.glycan ^G\d+$ 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. false urn:miriam:kegg.glycan http://www.genome.jp/kegg/glycan/ structure polysaccharide http://www.kegg.jp/entry/$id G00123 http://www.genome.jp/kegg/glycan/ Kyoto University Bioinformatics Center Japan WormBase wormbase ^(WBGene\d{8}|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references genes. false http://bio2rdf.org/wormbase http://www.wormbase.org/ http://identifiers.org/wormbase/ urn:miriam:wormbase genome expression protein nucleotide http://wormbase.sanger.ac.uk/db/gene/gene?name=$id;class=Gene WBGene00000001 http://wormbase.sanger.ac.uk/ Wellcome Trust Sanger Institute United Kingdom http://imbb.wormbase.org/db/gene/gene?name=$id;class=Gene WBGene00000001 http://imbb.wormbase.org/ Institute of Molecular Biology and Biotechnology Greece http://wormbase.bio2rdf.org/describe/?url=http://bio2rdf.org/wormbase:$id WBGene00000001 http://wormbase.bio2rdf.org/fct Bio2RDF.org http://crfb-3.univ-mrs.fr/db/gene/gene?name=$id;class=Gene WBGene00000001 http://crfb-3.univ-mrs.fr/ Marseille-Nice Genopole France http://caltech.wormbase.org/db/gene/gene?name=$id;class=Gene WBGene00000001 http://caltech.wormbase.org/ California Institute of Technology USA http://www.wormbase.org/db/gene/gene?name=$id;class=Gene WBGene00000001 http://www.wormbase.org/ Cold Spring Harbor Laboratory USA Pfam Protein Family Database pfam ^PF\d{5}$ The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. false urn:miriam:pfam http://pfam.org/ protein domain http://pfam.ccbb.re.kr/cgi-bin/getdesc?acc=$id PF01234 http://pfam.ccbb.re.kr/index.shtml Center for Computational Biology and Bioinformatics Korea http://pfam.sbc.su.se/family/$id PF01234 http://pfam.sbc.su.se/ Karolinska Institutet Sweden http://pfam.jouy.inra.fr/cgi-bin/getdesc?acc=$id PF01234 http://pfam.jouy.inra.fr/ Institut National de la Recherche Agronomique France http://pfam.janelia.org/family/$id PF01234 http://pfam.janelia.org/ Howard Hughes Medical Institute USA ebi http://pfam.xfam.org/family/$id PF01234 http://pfam.xfam.org/ European Bioinformatics Institute, Hinxton, Cambridge UK http://pfam.sanger.ac.uk/family/$id/ PF01234 http://pfam.sanger.ac.uk/ Wellcome Trust Sanger Institute United Kingdom Nucleotide Sequence Database INSDC GenBank NCBI nucleotide International Nucleotide Sequence Database Collaboration insdc ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. false http://www.insdc.org/ urn:miriam:insdc nucleotide sequence http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$id X58356 http://www.ddbj.nig.ac.jp/ DNA Data Bank of Japan, Mishima, Shizuoka Japan ebi http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+EntryPage+-e+[EMBL:$id]+-view+EmblEntry X58356 http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+EMBL European Bioinformatics Institute, Hinxton, Cambridge UK http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$id X58356 http://www.ncbi.nlm.nih.gov/Genbank/ National Center for Biotechnology Information (NCBI) USA ncbi http://www.ncbi.nlm.nih.gov/nuccore/$id X58356 http://www.ncbi.nlm.nih.gov/nuccore/ National Center for Biotechnology Information (NCBI) USA ebi http://www.ebi.ac.uk/ena/data/view/$id X58356 http://www.ebi.ac.uk/ena/ European Bioinformatics Institute, Hinxton, Cambridge UK FlyBase flybase ^FB\w{2}\d{7}$ FlyBase is the database of the Drosophila Genome Projects and of associated literature. false http://www.flybase.org/ urn:miriam:flybase eukaryotic nucleotide genome http://flybase.org/reports/$id.html FBgn0011293 http://flybase.org/ The FlyBase Consortium USA / United Kingdom Wormpep wormpep ^CE\d{5}$ Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. false http://www.wormpep.org/ urn:miriam:wormpep protein genome http://caltech.wormbase.org/db/seq/protein?name=$id CE28239 http://caltech.wormbase.org/db/seq/protein California Institute of Technology USA http://wormbase.sanger.ac.uk/db/seq/protein?name=WP:$id CE28239 http://wormbase.sanger.ac.uk/ Wellcome Trust Sanger Institute United Kingdom http://imbb.wormbase.org/db/seq/protein?name=$id CE28239 http://imbb.wormbase.org/db/seq/protein Institute of Molecular Biology and Biotechnology Greece http://www.wormbase.org/db/seq/protein?name=WP:$id CE28239 http://www.wormbase.org/db/seq/protein Cold Spring Harbor Laboratory USA http://crfb-3.univ-mrs.fr/db/seq/protein?name=$id CE28239 http://crfb-3.univ-mrs.fr/db/seq/protein Marseille-Nice Genopole France PROSITE prosite ^PS\d{5}$ PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. false http://www.prosite.org/ urn:miriam:prosite protein domain http://www.expasy.org/cgi-bin/get-prosite-entry?$id PS00001 http://www.expasy.org/prosite/ Swiss Institute of Bioinformatics (SIB) Switzerland expasy http://prosite.expasy.org/$id PS00001 http://www.expasy.org/prosite/ Swiss Institute of Bioinformatics (SIB) Switzerland PubChem-substance PubChem SID PubChem Substance pubchem.substance ^\d+$ 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. false http://www.pubchem.gov/substance/ urn:miriam:pubchem.substance chemical ncbi http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=$id 100101 http://pubchem.ncbi.nlm.nih.gov/ National Center for Biotechnology Information (NCBI) USA PubChem-compound PubChem CID PubChem Compound pubchem.compound ^\d+$ 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. false urn:miriam:pubchem.compound http://www.pubchem.gov/compound/ chemical structure metabolite ncbi http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=$id 100101 http://pubchem.ncbi.nlm.nih.gov/ National Center for Biotechnology Information (NCBI) USA arXiv arxiv ^(\w+(\-\w+)?(\.\w+)?/)?\d{4,7}(\.\d{4}(v\d+)?)?$ arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. false urn:miriam:arxiv urn:oai:arXiv.org http://arxiv.org/ bibliography http://arxiv.org/abs/$id 0807.4956v1 http://arxiv.org/ Cornell University USA ArrayExpress arrayexpress ^[AEP]-\w{4}-\d+$ 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. false http://arrayexpress.org/ urn:miriam:arrayexpress expression nucleotide microarray ebi http://www.ebi.ac.uk/arrayexpress/experiments/$id E-MEXP-1712 http://www.ebi.ac.uk/arrayexpress/ European Bioinformatics Institute, Hinxton, Cambridge UK Mouse Genome Database MGD Mouse Genome Informatics MGI mgi ^MGI:\d+$ 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. true http://mousegenome.org/ urn:miriam:mgd http://identifiers.org/mgd/ http://identifiers.org/mgi/ http://bio2rdf.org/mgi: urn:miriam:mgi phenotype expression sequence http://www.informatics.jax.org/accession/$id MGI:2442292 http://www.informatics.jax.org/ The Jackson Laboratory USA http://mgi.bio2rdf.org/describe/?url=http://bio2rdf.org/mgi:$id 2442292 http://mgi.bio2rdf.org/fct Bio2RDF.org SABIO-RK Reaction sabiork.reaction ^\d+$ SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. false http://sabio.villa-bosch.de/reaction/ urn:miriam:sabiork.reaction pathway reaction kinetics http://sabiork.h-its.org/newSearch?q=sabioreactionid:$id 75 http://sabiork.h-its.org/ Heidelberg Institute for Theoretical Studies (HITS gGmbH) Germany RefSeq refseq ^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?$ The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. false urn:miriam:refseq protein mammalian annotation sequence ncbi http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$id NP_012345 http://www.ncbi.nlm.nih.gov/projects/RefSeq/ NCBI, NIH, Bethesda, Maryland USA Transport Classification Database TCDB tcdb ^\d+\.[A-Z]\.\d+\.\d+\.\d+$ The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally. false urn:miriam:tcdb protein classification interaction http://www.tcdb.org/search/result.php?tc=$id 5.A.1.1.1 http://www.tcdb.org/ Division of Biological Sciences, UCSD USA UniParc uniparc ^UPI[A-F0-9]{10}$ The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases. false urn:miriam:uniparc protein http://www.uniprot.org/uniparc/$id UPI000000000A http://www.uniprot.org/uniparc/ UniProt Consortium USA, UK and Switzerland ebi http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$id UPI000000000A http://www.ebi.ac.uk/uniparc/ European Bioinformatics Institute, Hinxton, Cambridge UK MINT mint ^MINT\-\d{1,7}$ 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 urn:miriam:mint protein interaction ebi http://www.ebi.ac.uk/intact/query/interaction_id:$id MINT-7905142 http://www.ebi.ac.uk/intact/ European Bioinformatics Institute, Hinxton, Cambridge UK http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 http://mint.bio.uniroma2.it/mint/ University of Rome Tor Vergata, Rome Italy IPI International Protein Index ipi ^IPI\d{8}$ The International Protein Index (IPI) provides complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases false urn:miriam:ipi eukaryotic protein ebi http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ipi&id=$id&format=default&style=html IPI00000001 http://www.ebi.ac.uk/IPI European Bioinformatics Institute, Hinxton, Cambridge UK Database of Interacting Proteins DIP dip ^DIP(\:)?\-\d{1,}[ENXS]$ The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions false urn:miriam:dip interaction protein http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N http://dip.doe-mbi.ucla.edu/ UCLA USA Signaling Gateway SGMP AfCS UCSD Signaling Gateway Molecule Pages Signaling Gateway Molecule Pages UCSD - Molecule Pages signaling-gateway A\d{6}$ The Signaling Gateway provides information on mammalian proteins involved in cellular signaling. false urn:miriam:signaling-gateway protein mammalian http://www.signaling-gateway.org/molecule/query?afcsid=$id A001094 http://www.signaling-gateway.org/molecule UC San Diego USA RESID resid ^AA\d{4}$ The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. false urn:miriam:resid structure protein http://pir0.georgetown.edu/cgi-bin/resid?id=$id AA0001 http://pir0.georgetown.edu/resid/ Georgetown University Medical Center, Washington USA ebi http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 http://www.ebi.ac.uk/RESID/ European Bioinformatics Institute, Hinxton, Cambridge UK Rat Genome Database RGD rgd ^\d{4,7}$ Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes. false urn:miriam:rgd mammalian eukaryotic pathway gene phenotype nucleotide annotation genome sequence disease http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 http://rgd.mcw.edu/ Medical College of Wisconsin USA TAIR Protein tair.protein ^AASequence:\d{10}$ The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept false urn:miriam:tair.protein genome protein eukaryotic plant http://arabidopsis.org/servlets/TairObject?accession=$id AASequence:1009107926 http://arabidopsis.org/index.jsp Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR) USA TAIR Gene tair.gene ^Gene:\d{7}$ 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. false urn:miriam:tair.gene eukaryotic gene genome nucleotide plant http://arabidopsis.org/servlets/TairObject?accession=$id Gene:2200934 http://arabidopsis.org/index.jsp Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR) USA TAIR Locus tair.locus ^AT[1-5]G\d{5}$ The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS. false urn:miriam:tair.locus plant eukaryotic genome http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 http://arabidopsis.org/index.jsp Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR) USA HMDB Human Metabolome Database hmdb ^HMDB\d{5}$ 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. false urn:miriam:hmdb http://www.hmdb.ca/ chemical metabolite human http://www.hmdb.ca/metabolites/$id HMDB00001 http://www.hmdb.ca/ University of Alberta, Edmonton, AB Canada LIPID MAPS LMSD lipidmaps ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ 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. false urn:miriam:lipidmaps taxonomy structure lipid http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$id LMPR0102010012 http://www.lipidmaps.org University of California, San Diego USA PeptideAtlas peptideatlas ^PAp[0-9]{8}$ The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. false urn:miriam:peptideatlas mass spectrometry https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$id PAp00000009 http://www.peptideatlas.org/ Institute for Systems Biology, Seattle USA GEO Gene Expression Omnibus geo ^GDS\d+$ The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. false urn:miriam:geo microarray expression nucleotide ncbi http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=$id GDS1234 http://www.ncbi.nlm.nih.gov/geo/ National Center for Biotechnology Information (NCBI) USA Evidence Code Ontology ECO eco ECO:\d{7}$ Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. true http://identifiers.org/obo.eco/ urn:miriam:obo.eco urn:miriam:eco classification ols http://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=$id ECO:0000006 http://www.ebi.ac.uk/ols/ontologies/eco European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/ECO/$id ECO:0000006 http://bioportal.bioontology.org/ontologies/ECO National Center for Biomedical Ontology, Stanford USA Protein Modification Ontology PSI-MOD MOD mod ^MOD:\d{5} 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. true urn:miriam:mod urn:miriam:obo.psi-mod http://identifiers.org/mod/ urn:miriam:psimod http://identifiers.org/obo.psi-mod/ protein ontology bptl http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=$id MOD:00001 http://bioportal.bioontology.org/ontologies/PSIMOD National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=$id MOD:00001 http://www.ebi.ac.uk/ols/ontologies/mod European Bioinformatics Institute, Hinxton, Cambridge UK Saccharomyces genome database pathways sgd.pathways ^PWY\w{2}\-\d{3}$ Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). false urn:miriam:sgd.pathways genome pathway sequence http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$id PWY3O-214 http://pathway.yeastgenome.org/ SGD, Stanford University USA BioGRID biogrid ^\d+$ BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. false urn:miriam:biogrid protein gene interaction http://thebiogrid.org/$id 31623 http://thebiogrid.org/ Ontario Cancer Institute Canada MEROPS merops ^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3})$ The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. false urn:miriam:merops enzyme protein http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$id S01.001 http://merops.sanger.ac.uk/index.htm Wellcome Trust Sanger Institute United Kingdom PANTHER Family panther.family ^PTHR\d{5}(\:SF\d{1,3})?$ The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families. false urn:miriam:panther urn:miriam:panther.family gene http://www.pantherdb.org/panther/family.do?clsAccession=$id PTHR12345 http://www.pantherdb.org/ Keck School of Medicine, University of Southern California USA PRINTS SPRINT prints ^PR\d{5}$ PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. false urn:miriam:prints http://identifiers.org/prints/ urn:miriam:sprint protein domain http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$id&display_opts=Prints&category=None&queryform=false&regexpr=off PR00001 http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ University of Manchester United Kingdom Ligand Expo Ligand Depot ligandexpo ^(\w){3}$ Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. false urn:miriam:ligandexpo structure interaction http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$id&operation=ccid ABC http://ligand-expo.rcsb.org/ Rutgers, The State University of New Jersey USA rcsb http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$id&operation=ccid ABC http://ligand-depot.rutgers.edu/index.html Rutgers, The State University of New Jersey USA Aclame aclame ^mge:\d+$ ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. true urn:miriam:aclame gene http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=$id mge:2 http://aclame.ulb.ac.be/ Service de Conformation de Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles Belgium ISBN isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ The International Standard Book Number (ISBN) is for identifying printed books. false urn:miriam:isbn bibliography http://www.worldcat.org/isbn/$id 9781584885658 http://www.worldcat.org/ OCLC Online Computer Library Center, Inc. Ohio USA http://isbndb.com/search-all.html?kw=$id 9781584885658 http://isbndb.com/ ISNBdb project, San Gabriel, California USA PRIDE pride ^\d+$ 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. false urn:miriam:pride protein ebi http://www.ebi.ac.uk/pride/archive/assays/$id 1 http://www.ebi.ac.uk/pride/ European Bioinformatics Institute, Hinxton, Cambridge UK 3DMET 3dmet ^B\d{5}$ 3DMET is a database collecting three-dimensional structures of natural metabolites. false urn:miriam:3dmet chemical metabolite structure http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$id B00162 http://www.3dmet.dna.affrc.go.jp/ Bioinformatics Research Unit, National Institute of Agrobiological Sciences Japan FMA Foundational Model of Anatomy Ontology fma ^FMA:\d+$ The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. true http://identifiers.org/obo.fma/ urn:miriam:obo.fma urn:miriam:fma ontology bptl http://purl.bioontology.org/ontology/FMA_subset/$id FMA:67112 http://bioportal.bioontology.org/ontologies/FMA National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=$id FMA:67112 http://www.ebi.ac.uk/ols/ontologies/fma/ European Bioinformatics Institute, Hinxton, Cambridge UK MatrixDB matrixdb.association ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. false urn:miriam:matrixdb.association protein interaction polysaccharide lipid http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$id&class=Association P00747__P07355 http://matrixdb.univ-lyon1.fr/ Institut de Biologie et Chimie des Protéines, Lyon University France NCBI Gene Entrez Gene ncbigene ^\d+$ Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. false http://bio2rdf.org/ncbigene urn:miriam:ncbi.gene urn:miriam:entrez.gene http://identifiers.org/ncbigene/ urn:miriam:ncbigene gene genome sequence http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$id 100010 http://ncbigene.bio2rdf.org/fct Bio2RDF.org ncbi http://www.ncbi.nlm.nih.gov/gene/$id 100010 http://www.ncbi.nlm.nih.gov/gene National Center for Biotechnology Information (NCBI) USA KEGG Genes KEGG kegg.genes ^\w+:[\w\d\.-]*$ KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. false urn:miriam:kegg.genes http://www.genome.jp/kegg/genes/ gene http://www.kegg.jp/entry/$id syn:ssr3451 http://www.genome.jp/kegg/genes.html Kyoto University Bioinformatics Center Japan BRENDA brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. false urn:miriam:brenda enzyme http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$id 1.1.1.1 http://www.brenda-enzymes.org/ Technical University Braunschweig, Institute for Bioinformatics and Biochemistry Germany PubChem-bioassay pubchem.bioassay ^\d+$ 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 urn:miriam:pubchem.bioassay chemical ncbi http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$id 1018 http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay National Center for Biotechnology Information (NCBI) USA Pathway Commons pathwaycommons ^\d+$ Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. false urn:miriam:pathwaycommons pathway http://www.pathwaycommons.org/pc/record2.do?id=$id 485991 http://www.pathwaycommons.org/pc/ Memorial Sloan-Kettering Cancer Center USA HOVERGEN hovergen ^HBG\d+$ 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. false urn:miriam:hovergen gene http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$id&db=HOVERGEN HBG004341 http://pbil.univ-lyon1.fr/databases/hovergen.php Laboratoire de Biométrie, Génétique et Biologie des Populations France Melanoma Molecular Map Project Biomaps MMMP Biomaps biomaps ^\d+$ A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. false urn:miriam:mmmp:biomaps pathway http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$id 37 http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp Melanoma Molecular Map Project WikiPathways wikipathways WP\d{1,5}(\_r\d+)?$ WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style. All content is under the Creative Commons Attribution 3.0 Unported license. false urn:miriam:wikipathways pathway http://www.wikipathways.org/instance/$id WP100 http://www.wikipathways.org/ BiGCaT Bioinformatics (University of Maastricht) and Conklin Lab (UCSF). Holland and USA MACiE macie ^M\d{4}$ 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. false urn:miriam:macie enzyme classification ebi http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$id M0001 http://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html European Bioinformatics Institute, Hinxton, Cambridge UK miRBase Sequence mirbase MI\d{7} The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). false urn:miriam:mirbase sequence nucleotide http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=$id MI0000001 http://microrna.sanger.ac.uk/ University of Manchester and Wellcome Trust Sanger institute UK http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 http://www.mirbase.org/ Faculty of Life Sciences, University of Manchester UK ZFIN Gene zfin ZDB\-GENE\-\d+\-\d+ ZFIN serves as the zebrafish model organism database. This collection references gene information. false urn:miriam:zfin gene http://zfin.org/$id ZDB-GENE-041118-11 http://zfin.org Zebrafish Information Network, University of Oregon USA HGNC HUGO Gene Nomenclature Committee hgnc ^((HGNC|hgnc):)?\d{1,5}$ The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. false http://identifiers.org/hgnc/ http://bio2rdf.org/hgnc urn:miriam:hgnc gene human http://hgnc.bio2rdf.org/describe/?url=http://bio2rdf.org/$id hgnc:2674 http://hgnc.bio2rdf.org/fct Bio2RDF.org ebi http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$id 2674 http://www.genenames.org European Bioinformatics Institute, Hinxton, Cambridge UK Sequence Ontology Sequence Types and Features SO so ^SO:\d{7}$ The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. true http://identifiers.org/obo.so/ urn:miriam:obo.so urn:miriam:so DNA ontology bptl http://purl.bioontology.org/ontology/SO/$id SO:0000704 http://bioportal.bioontology.org/ontologies/SO National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=$id SO:0000704 http://www.ebi.ac.uk/ols/ontologies/so European Bioinformatics Institute, Hinxton, Cambridge UK http://www.sequenceontology.org/miso/current_release/term/$id SO:0000704 http://www.sequenceontology.org/ Department of Molecular and Cellular Biology, University of California, Berkeley USA Rhea rhea ^\d{5}$ Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed "spontaneous". false urn:miriam:rhea reaction http://www.rhea-db.org/reaction?id=$id 12345 http://www.rhea-db.org/ European Bioinformatics Institute and Swiss Institute of Bioinformatics UK Unipathway unipathway ^UPA\d{5}$ UniPathway is a manually curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway. false urn:miriam:unipathway pathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 http://www.grenoble.prabi.fr/obiwarehouse/unipathway Swiss Institute of Bioinformatics (SIB) and French National Institute for Research in Computer Science and Control Switzerland ChEMBL compound chembl.compound ^CHEMBL\d+$ 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. false http://identifiers.org/chembl.compound/ http://bio2rdf.org/chembl urn:miriam:chembl.compound metabolite chemical http://linkedchemistry.info/chembl/chemblid/$id CHEMBL308052 https://github.com/egonw/chembl.rdf Maastricht University The Netherlands ebi https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 https://www.ebi.ac.uk/chembldb/ European Bioinformatics Institute, Hinxton, Cambridge UK http://rdf.ebi.ac.uk/resource/chembl/molecule/$id CHEMBL308052 https://www.ebi.ac.uk/rdf/services/chembl/ European Bioinformatics Institute, Hinxton, Cambridge UK ChEMBL target chembl.target ^CHEMBL\d+$ 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. false urn:miriam:chembl.target protein ebi https://www.ebi.ac.uk/chembl/target/inspect/$id CHEMBL3467 https://www.ebi.ac.uk/chembldb/ European Bioinformatics Institute, Hinxton, Cambridge UK http://linkedchemistry.info/chembl/chemblid/$id CHEMBL3467 https://github.com/egonw/chembl.rdf Maastricht University The Netherlands http://rdf.ebi.ac.uk/resource/chembl/target/$id CHEMBL3467 http://rdf.ebi.ac.uk/resource/chembl/ European Bioinformatics Institute, Hinxton, Cambridge UK SABIO-RK Kinetic Record sabiork.kineticrecord ^\d+$ 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. false urn:miriam:sabiork.kineticrecord reaction kinetics http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$id 5046 http://sabiork.h-its.org/ Heidelberg Institute for Theoretical Studies (HITS gGmbH) Germany Ligand-Gated Ion Channel database LGICdb lgic ^\w+$ The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. false urn:miriam:lgic protein gene sequence ebi http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$id.php 5HT3Arano http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php European Bioinformatics Institute, Hinxton, Cambridge UK Anatomical Therapeutic Chemical ATC atc ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. false urn:miriam:atc classification drug http://www.whocc.no/atc_ddd_index/?code=$id A10BA02 http://www.whocc.no/atc_ddd_index/ World Health Organisation Switzerland PharmGKB Pathways pharmgkb.pathways ^PA\d+$ 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. PharmGKB 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 urn:miriam:pharmgkb.pathways pathway pharmacogenomics http://www.pharmgkb.org/pathway/$id PA146123006 http://www.pharmgkb.org/ Department of Genetics, School of Medicine, Stanford University, Stanford, California USA PharmGKB Disease pharmgkb.disease ^PA\d+$ 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. false urn:miriam:pharmgkb.disease pharmacogenomics http://www.pharmgkb.org/disease/$id PA447218 http://www.pharmgkb.org/ Department of Genetics, School of Medicine, Stanford University, Stanford, California USA PharmGKB Drug pharmgkb.drug ^PA\d+$ 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. false urn:miriam:pharmgkb.drug drug pharmacogenomics http://www.pharmgkb.org/drug/$id PA448710 http://www.pharmgkb.org/ Department of Genetics, School of Medicine, Stanford University, Stanford, California USA TTD Drug Therapeutic Target Database ttd.drug ^DAP\d+$ 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. false urn:miriam:ttd.drug drug structure http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$id DAP000773 http://bidd.nus.edu.sg/group/ttd/ttd.asp Computational Science Department, National University of Singapore Singapore TTD Target ttd.target ^TTDS\d+$ 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. false urn:miriam:ttd.target drug pathway http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$id TTDS00056 http://bidd.nus.edu.sg/group/ttd/ttd.asp Computational Science Department, National University of Singapore Singapore NeuronDB neurondb ^\d+$ 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. false urn:miriam:neurondb neuroscience http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$id 265 http://senselab.med.yale.edu/NeuronDB/ Yale University School of Medicine USA NeuroMorpho neuromorpho ^\w+$ NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. false urn:miriam:neuromorpho neuroscience http://neuromorpho.org/neuron_info.jsp?neuron_name=$id Rosa2 http://neuromorpho.org/index.jsp Krasnow Institute, Virginia USA ChemIDplus chemidplus ^\d+$ 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. false urn:miriam:chemidplus chemical structure http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id 000057272 http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp National Library of Medicine, Maryland USA BioSystems biosystems ^\d+$ The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. false urn:miriam:biosystems gene protein pathway ncbi http://www.ncbi.nlm.nih.gov/biosystems/$id 001 http://www.ncbi.nlm.nih.gov/biosystems/ National Center for Biotechnology Information (NCBI) USA CTD Chemical ctd.chemical ^[CD]\d+$ 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. false urn:miriam:ctd.chemical chemical pharmacogenomics http://ctdbase.org/detail.go?type=chem&acc=$id D001151 http://ctdbase.org/ The Mount Desert Island Biological Laboratory USA CTD Disease ctd.disease ^D\d+$ 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. false urn:miriam:ctd.disease pharmacogenomics disease http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$id D053716 http://ctdbase.org/ The Mount Desert Island Biological Laboratory USA CTD Gene ctd.gene ^\d+$ 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. false urn:miriam:ctd.gene gene pharmacogenomics http://ctdbase.org/detail.go?type=gene&acc=$id 101 http://ctdbase.org/ The Mount Desert Island Biological Laboratory USA BioNumbers bionumbers ^\d+$ BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. false urn:miriam:bionumbers registry http://www.bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=$id&ver=1 104674 http://www.bionumbers.hms.harvard.edu/search.aspx Weizmann Institute Israel DrugBank drugbank ^DB\d{5}$ The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. false http://identifiers.org/drugbank/ http://bio2rdf.org/drugbank urn:miriam:drugbank drug protein http://drugbank.bio2rdf.org/describe/?url=http://bio2rdf.org/drugbank:$id DB00001 http://drugbank.bio2rdf.org/fct/ Bio2RDF.org http://www.drugbank.ca/drugs/$id DB00001 http://www.drugbank.ca/ Departments of Computing Science & Biological Sciences, University of Alberta Canada T3DB Toxin and Toxin Target Database t3db ^T3D\d+$ Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. false urn:miriam:t3db protein drug http://www.t3db.org/toxins/$id T3D0001 http://www.t3db.org/ University of Alberta Canada Small Molecule Pathway Database SMPDB smpdb ^SMP\d{5}$ 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. false urn:miriam:smpdb chemical metabolite pathway human http://smpdb.ca/view/$id SMP00001 http://www.smpdb.ca/pathways University of Alberta, Edmonton, AB Canada PhosphoSite Protein PhosphoSitePlus phosphosite.protein ^\d{5}$ PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database. false urn:miriam:phosphosite urn:miriam:phosphosite.protein mammalian protein http://www.phosphosite.org/proteinAction.do?id=$id 12300 http://www.phosphosite.org/homeAction.do Cell Signaling Technology, Inc. USA GeneDB genedb ^[\w\d\.-]*$ GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. false urn:miriam:genedb sequence genome http://www.genedb.org/gene/$id Cj1536c http://www.genedb.org/ Pathogen Genomics, Sanger Institute and European Bioinformatics Institute UK TEDDY biomodels.teddy ^TEDDY_\d{7}$ The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. false urn:miriam:teddy urn:miriam:biomodels.teddy ontology bptl http://purl.bioontology.org/ontology/TEDDY/$id TEDDY_0000066 http://teddyontology.sourceforge.net/ National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/teddy/terms?short_form=$id TEDDY_0000066 http://www.ebi.ac.uk/ols/ontologies/teddy European Bioinformatics Institute, Hinxton, Cambridge UK KiSAO Kinetic Simulation Algorithm Ontology biomodels.kisao ^KISAO_\d+$ 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. false urn:miriam:biomodels.kisao ols http://www.ebi.ac.uk/ols/ontologies/kisao/terms?short_form=$id KISAO_0000057 http://www.ebi.ac.uk/ols/ontologies/kisao European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/KISAO/kisao:$id KISAO_0000057 http://bioportal.bioontology.org/ontologies/KISAO National Center for Biomedical Ontology, Stanford USA Molecular Interactions Ontology MI psimi ^MI:\d{4}$ The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. true urn:miriam:obo.mi urn:miriam:psimi http://identifiers.org/obo.mi/ ontology interaction protein bptl http://purl.bioontology.org/ontology/PPIO/$id MI:0308 http://bioportal.bioontology.org/ontologies/PPIO National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=$id MI:0308 http://www.ebi.ac.uk/ols/ontologies/mi European Bioinformatics Institute, Hinxton, Cambridge UK Cell Type Ontology Cell Ontology CL cl ^CL:\d{7}$ The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. true http://identifiers.org/obo.clo/ http://identifiers.org/cl/ urn:miriam:cl urn:miriam:obo.clo http://purl.obolibrary.org/obo/CL ontology bptl http://purl.bioontology.org/ontology/CL/$id CL:0000232 http://bioportal.bioontology.org/ontologies/CL National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=$id CL:0000232 http://www.ebi.ac.uk/ols/ontologies/cl European Bioinformatics Institute, Hinxton, Cambridge UK Brenda Tissue Ontology BTO bto ^BTO:\d{7}$ 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. true http://identifiers.org/obo.bto/ http://identifiers.org/bto/ urn:miriam:obo.bto urn:miriam:bto http://purl.obolibrary.org/obo/BTO ontology bptl http://purl.bioontology.org/ontology/BTO/$id BTO:0000146 http://bioportal.bioontology.org/ontologies/BTO National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=$id BTO:0000146 http://www.ebi.ac.uk/ols/ontologies/bto European Bioinformatics Institute, Hinxton, Cambridge UK PATO pato ^PATO:\d{7}$ PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. true http://purl.obolibrary.org/obo/PATO http://identifiers.org/obo.pato/ urn:miriam:obo.pato http://identifiers.org/pato/ urn:miriam:pato http://purl.org/obo/owl/PATO phenotype ontology bptl http://purl.bioontology.org/ontology/PATO/$id PATO:0001998 http://bioportal.bioontology.org/ontologies/PATO National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=$id PATO:0001998 http://www.ebi.ac.uk/ols/ontologies/pato European Bioinformatics Institute, Hinxton, Cambridge UK Chemical Component Dictionary PDB-CCD PDBeChem pdb-ccd ^\w{3}$ The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. false urn:miriam:pdb-ccd chemical classification ebi http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id AB0 http://www.ebi.ac.uk/pdbe-srv/pdbechem/ European Bioinformatics Institute, Hinxton, Cambridge UK GlycomeDB glycomedb ^\d+$ 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. false urn:miriam:glycomedb structure http://www.glycome-db.org/database/showStructure.action?glycomeId=$id 1 http://www.glycome-db.org/showMenu.action?major=database German Cancer Research Center, Heidelberg Germany LipidBank lipidbank ^\w+\d+$ LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. false urn:miriam:lipidbank lipid structure http://lipidbank.jp/cgi-bin/detail.cgi?id=$id BBA0001 http://lipidbank.jp/index.html Department of Computational Biology, University of Tokyo, Tokyo Japan KEGG Orthology KEGG kegg.orthology ^K\d+$ KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. false urn:miriam:kegg.orthology clustering pathway http://www.kegg.jp/entry/$id K00001 http://www.genome.jp/kegg/ko.html Department of Computational Biology, University of Tokyo, Tokyo Japan ProDom prodom ^PD\d+$ ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. false urn:miriam:prodom protein domain http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$id PD10000 http://prodom.prabi.fr/prodom/current/html/home.php Laboratoire des Interactions Plantes-Microorganismes, INRA/CNRS France SMART smart ^SM\d{5}$ The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures. false urn:miriam:smart protein domain gene http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 http://smart.embl-heidelberg.de/ EMBL, Heidelberg Germany Conserved Domain Database CDD cdd ^(cd)?\d{5}$ The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. false urn:miriam:cdd domain protein ncbi http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$id cd00400 http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd National Library of Medicine, National Institutes of Health, Maryland USA Relation Ontology ro ^RO_\d+{7}$ The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. false urn:miriam:ro urn:miriam:obo.ro http://identifiers.org/obo.ro/ ontology http://purl.obolibrary.org/obo/$id RO_0002533 http://obofoundry.org/ontology/ro.html University of Michigan Medical School (MI), Lawrence Berkeley National Laboratory (CA) and Science Commons (MA) USA http://www.obofoundry.org/ro/#$id OBO_REL:is_a http://www.obofoundry.org/ro/ Institute for Formal Ontology and Medical Information Science, Saarbrücken Germany ols http://www.ebi.ac.uk/ols/ontologies/ro/terms?short_form=$id RO_0002533 http://www.ebi.ac.uk/ols/ontologies/ro European Bioinformatics Institute, Hinxton, Cambridge UK Molecular Modeling Database MMDB Entrez Structure mmdb ^\d{1,5}$ The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. false urn:miriam:mmdb structure domain protein http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$id 50885 http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure National Library of Medicine, National Institutes of Health, Maryland USA IMEx imex ^IM-\d+(-?)(\d+?)$ 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. false urn:miriam:imex protein interaction https://imexcentral.org/icentral/imex/rec/$id IM-19210-3 http://www.ebi.ac.uk/intact/ European Bioinformatics Institute, Hinxton, Cambridge UK ebi http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$id IM-19210-3 http://www.imexconsortium.org/ European Bioinformatics Institute, Hinxton, Cambridge UK iRefWeb irefweb ^\d+$ iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived. false urn:miriam:irefweb interaction protein http://wodaklab.org/iRefWeb/interaction/show/$id 617102 http://wodaklab.org/iRefWeb/ Wodak Lab, Hospital for Sick Children, Toronto Canada Microbial Protein Interaction Database MPID mpid ^\d+$ The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. false urn:miriam:mpid interaction microbial protein http://www.jcvi.org/mpidb/experiment.php?interaction_id=$id 172 http://www.jcvi.org/mpidb/about.php J. Craig Venter Institute, Maryland USA ebi http://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$id 1776 http://www.ebi.ac.uk/intact/ European Bioinformatics Institute, Hinxton, Cambridge UK PhosphoSite Residue phosphosite.residue ^\d+$ PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence. false urn:miriam:phosphosite.residue http://www.phosphosite.org/siteAction.do?id=$id 2842 http://www.phosphosite.org/homeAction.do Cell Signaling Technology, Inc. USA NeuroLex BIRNLex NIFSTD neurolex ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$ The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). false urn:miriam:neurolex ontology neuroscience controlled vocabulary bptl http://purl.bioontology.org/ontology/BIRNLEX/$id birnlex_1672 http://bioportal.bioontology.org/ontologies/BIRNLEX National Center for Biomedical Ontology, Stanford USA http://www.neurolex.org/wiki/$id Birnlex_721 http://www.neurolex.org/wiki/Main_Page Department of Neuroscience, University of California, San Diego USA Ontology for Biomedical Investigations OBI obi (^OBI:\d{7}$)|(^OBI_\d{7}$) The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). false http://identifiers.org/obo.obi/ http://identifiers.org/obi/ urn:miriam:obi urn:miriam:obo.obi http://purl.obolibrary.org/obo/$id OBI_0000070 http://www.ontobee.org/ University of Michigan Medical School (MI), awrence Berkeley National Laboratory (CA) and Science Commons (MA) USA ols http://www.ebi.ac.uk/ols/ontologies/obi/terms?obo_id=$id OBI:0000070 http://www.ebi.ac.uk/ols/ontologies/obi European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/OBI/$id OBI:0000070 http://bioportal.bioontology.org/ontologies/OBI National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/beta/ontologies/obi/terms?obo_id=$id OBI:0000070 http://www.ebi.ac.uk/ols/beta/ontologies/obi European Bioinformatics Institute, Hinxton, Cambridge UK http://ashby.csail.mit.edu/cgi-bin/obiterm?ref=$id OBI:0000225 http://obi-ontology.org/page/Main_Page Massachusetts Institute of Technology (MIT) USA SABIO-RK EC Record SABIO-RK Enzyme Classification Record sabiork.ec ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$ SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. false urn:miriam:sabiork.ec kinetics enzyme classification http://sabiork.h-its.org/newSearch?q=ecnumber:$id 2.7.1.1 http://sabiork.h-its.org/ Heidelberg Institute for Theoretical Studies (HITS gGmbH) Germany Ontology of Physics for Biology OPB opb ^OPB_\d+$ The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. false urn:miriam:opb ontology bptl http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$id OPB_00573 http://bioportal.bioontology.org/ontologies/OPB National Center for Biomedical Ontology, Stanford USA JWS Online JWS jws ^\w+$ JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. false urn:miriam:jws model http://jjj.biochem.sun.ac.za/models/$id/ curien http://jjj.biochem.sun.ac.za/models/ Department of Biochemistry, Stellenbosch University South Africa http://jjj.mib.ac.uk/models/$id curien http://jjj.mib.ac.uk/index.html Manchester Interdisciplinary Biocentre, University of Manchester UK http://jjj.bio.vu.nl/models/$id/ curien http://jjj.bio.vu.nl/models/ University of Amsterdam Netherlands ModelDB modeldb ^\d+$ 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. false urn:miriam:modeldb model neuroscience http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$id 45539 http://senselab.med.yale.edu/ModelDB/ Yale University School of Medicine USA SubtiWiki subtiwiki ^BSU\d{5}$ 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. Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon. false urn:miriam:subtiwiki microbial gene genome protein http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page University of Göttingen, Department for General Microbiology Germany NCI Pathway Interaction Database: Pathway NCI-Nature Pathway Interaction Database PID NCI-Nature PID NCI_Nature NCI_Nature curated Pathway Interaction Database NCI-Nature Curated Data pid.pathway ^\w+$ 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. false urn:miriam:pid.pathway pathway human interaction http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$id pi3kcipathway http://pid.nci.nih.gov/ National Cancer Institute, Rockville, Maryland USA Database of Quantitative Cellular Signaling: Model DOQCS Model doqcs.model ^\d+$ 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. false urn:miriam:doqcs.model model http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$id 57 http://doqcs.ncbs.res.in/ National Centre for Biological Sciences, Bangalore India Database of Quantitative Cellular Signaling: Pathway DOQCS Pathway doqcs.pathway ^\d+$ The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. false urn:miriam:doqcs.pathway pathway http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$id 131 http://doqcs.ncbs.res.in/ National Centre for Biological Sciences, Bangalore India Unit Ontology UO uo ^UO:\d{7}? Ontology of standardized units true urn:miriam:uo http://purl.obolibrary.org/obo/UO urn:miriam:obo.unit urn:miriam:unit http://identifiers.org/unit/ http://identifiers.org/uo/ http://identifiers.org/obo.unit/ ontology bptl http://purl.bioontology.org/ontology/UO/$id UO:0000080 http://bioportal.bioontology.org/ontologies/UO National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=$id UO:0000080 http://www.ebi.ac.uk/ols/ontologies/uo European Bioinformatics Institute, Hinxton, Cambridge UK ClinicalTrials.gov NCT clinicaltrials ^NCT\d{8}$ ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries false http://identifiers.org/clinicaltrials/ urn:miriam:clinicaltrials http://bio2rdf.org/clinicaltrials pharmacogenomics human disease disorder http://clinicaltrials.bio2rdf.org/describe/?url=http://bio2rdf.org/clinicaltrials:$id NCT00222573 http://clinicaltrials.bio2rdf.org/fct Bio2RDF.org http://clinicaltrials.gov/ct2/show/$id NCT00222573 http://clinicaltrials.gov/ National Library of Medicine and ClinicalTrials.gov, Maryland USA ChemSpider chemspider ^\d+$ ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. false urn:miriam:chemspider chemical structure http://www.chemspider.com/Chemical-Structure.$id.html 56586 http://www.chemspider.com/ Royal Society of Chemistry, Cambridge UK NCIt National Cancer Institute Thesaurus NCI thesaurus ncit ^C\d+$ 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. false urn:miriam:ncit controlled vocabulary ontology http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$id C80519 http://ncit.nci.nih.gov/ National Cancer Institute, Center for Bioinformatics, Maryland USA BioCatalogue biocatalogue.service ^\d+$ 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. false urn:miriam:biocatalogue.service registry ebi https://www.biocatalogue.org/services/$id 614 http://www.biocatalogue.org/ European Bioinformatics Institute, Hinxton, Cambridge UK Protein Ontology pr ^PR\:\d+$ The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. true http://identifiers.org/obo.pr/ urn:miriam:obo.pr urn:miriam:pr protein ontology ols http://www.ebi.ac.uk/ols/ontologies/pr/terms?obo_id=$id PR:000000024 http://www.ebi.ac.uk/ols/ontologies/pr European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/PR/$id PR:000000024 http://bioportal.bioontology.org/ontologies/PR National Center for Biomedical Ontology, Stanford USA http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=$id PR:000000024 http://pir.georgetown.edu/pro/pro.shtml Georgetown University Medical Center, Washington USA OMIA Online Mendelian Inheritance in Animals omia ^\d+$ Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse). false urn:miriam:omia phenotype disorder http://omia.angis.org.au/$id/ 1000 http://omia.angis.org.au/ Reprogen, Faculty of Veterinary Science, University of Sydney Australia http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=omia&dopt=Detailed&list_uids=$id 1000 http://www.ncbi.nlm.nih.gov/sites/entrez?db=omia National Center for Biotechnology Information (NCBI) USA ChemBank chembank ^\d+$ ChemBank stores small molecule information, as well as measurements derived from cells and other biological assay systems treated with small molecules. false urn:miriam:chembank metabolite chemical http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$id 1000000 http://chembank.broadinstitute.org/ Broad Institute of Harvard and MIT, Cambridge, MA USA CSA Catalytic Site Atlas csa ^[0-9][A-Za-z0-9]{3}$ The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. false urn:miriam:csa protein structure ebi http://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$id 1a05 http://www.ebi.ac.uk/thornton-srv/databases/CSA/ European Bioinformatics Institute, Hinxton, Cambridge UK Candida Genome Database CGD cgd ^CAL\d{7}$ The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. false urn:miriam:cgd nucleotide genome eukaryotic http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$id CAL0003079 http://www.candidagenome.org/ Stanford University, USA AntWeb antweb ^casent\d+(\-D\d+)?$ AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. false urn:miriam:antweb classification http://www.antweb.org/specimen.do?name=$id casent0106247 http://www.antweb.org/ California Academy of Sciences, Goldengate Park, San Francisco USA PMC International PubMed Central PMCI pmc PMC\d+ PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature. false urn:miriam:pmc bibliography http://ukpmc.ac.uk/articles/$id PMC3084216 http://ukpmc.ac.uk/ UKPMC Funders Group UK ncbi http://www.ncbi.nlm.nih.gov/pmc/articles/$id/?tool=pubmed PMC3084216 http://www.ncbi.nlm.nih.gov/pmc/ NCBI USA epmc http://europepmc.org/articles/$id PMC3084216 http://europepmc.org/ Europe PubMed Central partners UK cpmc http://pubmedcentralcanada.ca/pmcc/articles/$id PMC3084216 http://pubmedcentralcanada.ca/pmcc Canadian Institute of Health, Ottawa Canada AmoebaDB amoebadb ^EDI_\d+$ 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. false urn:miriam:amoebadb eukaryotic http://amoebadb.org/amoeba/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id EDI_244000 http://amoebadb.org/amoeba/ Center for Tropical & Emerging Global Diseases, University of Georgia USA CryptoDB cryptodb ^\w+ CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. false urn:miriam:cryptodb genome eukaryotic http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id cgd7_230 http://cryptodb.org/cryptodb/ Center for Tropical & Emerging Global Diseases, University of Georgia USA PlasmoDB plasmodb ^\w+$ 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. false urn:miriam:plasmodb genome eukaryotic http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id PF11_0344 http://plasmodb.org/plasmo/ Center for Tropical & Emerging Global Diseases, University of Georgia USA GiardiaDB giardiadb ^\w+$ 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. false urn:miriam:giardiadb genome eukaryotic http://giardiadb.org/giardiadb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id GL50803_102438 http://giardiadb.org/giardiadb/ Center for Tropical & Emerging Global Diseases, University of Georgia USA MicrosporidiaDB microsporidia ^\w+$ 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. false urn:miriam:microsporidia genome eukaryotic http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id ECU03_0820i http://microsporidiadb.org/micro/ Center for Tropical & Emerging Global Diseases, University of Georgia USA ToxoDB toxoplasma ^\w+$ ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. false urn:miriam:toxoplasma eukaryotic genome http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id TGME49_053730 http://toxodb.org/toxo/ Center for Tropical & Emerging Global Diseases, University of Georgia USA TrichDB trichdb ^\w+$ TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. false urn:miriam:trichdb eukaryotic genome http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id TVAG_386080 http://trichdb.org/trichdb/ Center for Tropical & Emerging Global Diseases, University of Georgia USA TriTrypDB Kinetoplastid Genomics Resource tritrypdb ^\w+(\.)?\w+(\.)?\w+ TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. false urn:miriam:tritrypdb genome eukaryotic http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id Tb927.8.620 http://tritrypdb.org/tritrypdb/ Wellcome Trust Sanger Institute, Hinxton UK BDGP insertion DB BDGP gene disruption bdgp.insertion ^\w+$ BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. false urn:miriam:bdgp.insertion gene sequence http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$id KG09531 http://flypush.imgen.bcm.tmc.edu/pscreen/ Baylor College of Medicine, Texas USA BeetleBase beetlebase ^TC\d+$ BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. false urn:miriam:beetlebase classification http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$id TC010103 http://beetlebase.org/ Bioinformatics Center, Kansas State University USA BOLD Taxonomy bold.taxonomy ^\d+$ 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 urn:miriam:bold.taxonomy classification http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$id 27267 http://www.boldsystems.org/ Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario Canada dbEST Database of Expressed Sequence Tags NCBI EST dbest ^([A-Z]+)?\d+(\.\d+)?$ The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. false urn:miriam:dbest gene expression ebi http://www.ebi.ac.uk/ena/data/view/$id BP100000.1 http://www.ebi.ac.uk/ena European Bioinformatics Institute, Hinxton, Cambridge UK ncbi http://www.ncbi.nlm.nih.gov/nucest/$id BP100000 http://www.ncbi.nlm.nih.gov/nucest National Center for Biotechnology Information (NCBI) USA http://getentry.ddbj.nig.ac.jp/getentry/na/$id BP100000 http://www.ddbj.nig.ac.jp/ DNA Data Bank of Japan, Mishima, Shizuoka Japan dbProbe dbprobe ^\d+$ 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. false urn:miriam:dbprobe nucleotide ncbi http://www.ncbi.nlm.nih.gov/probe/?term=$id 1000000 http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe National Center for Biotechnology Information (NCBI) USA dbSNP dbsnp ^rs\d+$ The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. false urn:miriam:dbsnp gene nucleotide ncbi http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$id 121909098 http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp National Center for Biotechnology Information (NCBI) USA UniSTS dbSTS unists ^\d+$ UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. false urn:miriam:unists gene sequence ncbi http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$id 456789 http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists National Center for Biotechnology Information (NCBI) USA EcoGene ecogene ^EG\d+$ 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. false urn:miriam:ecogene genome microbial http://www.ecogene.org/gene/$id EG10173 http://ecogene.org/ Miller School of Medicine, University of Miami USA http://maxd.cs.purdue.edu:9455/geneInfo.php?eg_id=$id EG10173 http://maxd.cs.purdue.edu:9455 Purdue University USA GABI GABI PD gabi ^\w+$ GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. false urn:miriam:gabi plant gene genome http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$id&Mode=ShowBioObject 2679240 http://www.gabipd.org/ Max Planck Institute of Molecular Plant Physiology, Berlin Germany GreenGenes greengenes ^\d+$ A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. false urn:miriam:greengenes sequence http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$id 100000 http://greengenes.lbl.gov/ Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, California USA GRIN Plant Taxonomy GRIN Taxonomy for Plants Germplasm Resources Information Network Plant Taxonomy grin.taxonomy ^\d+$ GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. false urn:miriam:grin.taxonomy plant taxonomy http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$id 19333 http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en National Germplasm Resources Laboratory, Beltsville, Maryland USA H-InvDb Locus hinv.locus ^HIX\d{7}(\.\d+)?$ 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. false urn:miriam:hinv.locus human gene http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$id HIX0004394 http://h-invitational.jp/hinv/ahg-db/index.jsp BIRC, Tokyo Japan H-InvDb Transcript hinv.transcript ^HIT\d{9}(\.\d+)?$ H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view. false urn:miriam:hinv.transcript human expression http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$id HIT000195363 http://h-invitational.jp/hinv/ahg-db/index.jsp BIRC, Tokyo Japan H-InvDb Protein hinv.protein ^HIP\d{9}(\.\d+)?$ H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view. false urn:miriam:hinv.protein protein human http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$id HIP000030660 http://h-invitational.jp/hinv/ahg-db/index.jsp BIRC, Tokyo Japan HOMD Sequence Metainformation Human Oral Microbiome Database homd.seq ^SEQF\d+$ 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. false urn:miriam:homd.seq genome microbial http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$id SEQF1003 http://www.homd.org/index.php The Forsyth Institute, Boston USA HOMD Taxonomy homd.taxon ^\d+$ The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. false urn:miriam:homd.taxon microbial taxonomy http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$id&view=dynamic 811 http://www.homd.org/index.php The Forsyth Institute, Boston USA IRD Segment Sequence Influenza Research Database Segment ird.segment ^\w+(\_)?\d+(\.\d+)?$ 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). false urn:miriam:ird.segment gene protein http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$id CY077097 http://www.fludb.org/ Southwestern Medical Center, University of Texas, Dallas USA ISFinder Insertion Sequence Finder isfinder ^IS\w+(\-\d)?$ ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. false urn:miriam:isfinder gene sequence https://www-is.biotoul.fr/scripts/ficheIS.php?name=$id ISA1083-2 http://www-is.biotoul.fr/i Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, Toulouse France Japan Collection of Microorganisms JCM jcm ^\d+$ The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. false urn:miriam:jcm microbial strain http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$id 17254 http://www.jcm.riken.go.jp/ RIKEN BioResource Center, Ibaraki Japan Integrated Microbial Genomes Taxon IMG Taxon img.taxon ^\d+$ The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. false urn:miriam:img.taxon genome taxonomy http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$id 648028003 http://img.jgi.doe.gov/ Lawrence Berkeley National Laboratory, Berkeley USA Integrated Microbial Genomes Gene img.gene ^\d+$ The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. false urn:miriam:img.gene gene genome http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$id 638309541 http://img.jgi.doe.gov/ Lawrence Berkeley National Laboratory, Berkeley USA MaizeGDB Locus maizegdb.locus ^\d+$ MaizeGDB is the maize research community's central repository for genetics and genomics information. false urn:miriam:maizegdb.locus genome plant http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$id 25011 http://www.maizegdb.org/ Division of Plant Sciences, Missouri USA MycoBank mycobank ^\d+$ MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. false urn:miriam:mycobank classification http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$id 349124 http://www.mycobank.org/ CBS-KNAW Fungal Biodiversity Centre, Utrecht Netherlands NITE Biological Research Center Catalogue NBRC Catalogue nbrc ^\d+$ NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. false urn:miriam:nbrc strain microbial http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$id 00001234 http://www.nbrc.nite.go.jp/e/index.html National Institute of Technology Evaluation, Tokyo Japan Pseudomonas Genome Database PGD Pseudocap pseudomonas ^P\w+$ The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation. false urn:miriam:pseudomonas microbial protein gene http://v2.pseudomonas.com/getAnnotation.do?locusID=$id PSEEN0001 http://www.pseudomonas.com/ Simon Fraser University, British Columbia Canada Gramene protein gramene.protein ^\d+$ 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 proteins in Gramene. false urn:miriam:gramene.protein genome plant sequence expression http://www.gramene.org/db/protein/protein_search?protein_id=$id 78073 http://www.gramene.org/ Cold Spring Harbor Laboratory, New York USA Gramene genes gramene.gene ^GR\:\d+$ 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. false urn:miriam:gramene.gene genome gene plant http://www.gramene.org/db/genes/search_gene?acc=$id GR:0080039 http://www.gramene.org/ Cold Spring Harbor Laboratory, New York USA Gramene Taxonomy gramene.taxonomy ^GR\_tax\:\d+$ 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 taxonomic information in Gramene. false urn:miriam:gramene.taxonomy taxonomy plant http://www.gramene.org/db/ontology/search?id=$id GR_tax:013681 http://www.gramene.org/ Cold Spring Harbor Laboratory, New York USA Gramene QTL gramene.qtl ^\w+$ 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. false urn:miriam:gramene.qtl plant phenotype genome gene http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$id CQG5 http://www.gramene.org/ Cold Spring Harbor Laboratory, New York USA Sol Genomics Network SGN sgn ^\d+$ The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. false urn:miriam:sgn genome plant http://solgenomics.net/phenome/locus_display.pl?locus_id=$id 0001 http://solgenomics.net/ Boyce Thompson Institute for Plant Research, New York USA Xenbase xenbase ^(XB-GENE-)?\d+$ Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. false urn:miriam:xenbase expression genome http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=$id 922462 http://www.xenbase.org/ Department of Biological Sciences, University of Calgary, Alberta Canada BioPortal bioportal ^\d+$ 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. false urn:miriam:bioportal ontology registry bptl http://bioportal.bioontology.org/ontologies/$id 1046 http://bioportal.bioontology.org/ National Center for Biomedical Ontology, Stanford University USA MIRIAM Registry resource miriam.resource ^MIR:001\d{5}$ 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. false urn:miriam:miriam.resource ebi http://www.ebi.ac.uk/miriam/main/resources/$id MIR:00100005 http://www.ebi.ac.uk/miriam/ European Bioinformatics Institute, Hinxton, Cambridge UK EDAM Ontology EMBRACE Data and Methods Ontology edam ^(data|topic|operation|format)\_\d{4}$ 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). false http://edamontology.org/ urn:miriam:edam ontology ols http://www.ebi.ac.uk/ols/ontologies/edam/terms?short_form=$id data_1664 http://www.ebi.ac.uk/ols/ontologies/edam European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/EDAM/$id data_1664 http://bioportal.bioontology.org/ontologies/EDAM National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ontology-lookup/?termId=EDAM_data:$id 1664 http://www.ebi.ac.uk/ontology-lookup/ European Bioinformatics Institute, Hinxton, Cambridge UK Protein Model Database PMDB pmdb ^PM\d{7} The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. false urn:miriam:pmdb protein structure https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$id PM0012345 https://bioinformatics.cineca.it/PMDB/ CASPUR and Biocomputing group, Department of Biochemical Sciences, University of Rome, Rome Italy 2D-PAGE protein 2D-PAGE E. coli 2d-page.protein ^([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])$ 2DBase of Escherichia coli stores 2D polyacrylamide gel electrophoresis and mass spectrometry proteome data for E. coli. This collection references a subset of Uniprot, and contains general information about the protein record. false urn:miriam:2d-page.protein protein http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?ac=$id P39172 http://2dbase.techfak.uni-bielefeld.de/ Graduate School in Bioinformatics and Genome Research, University of Bielefeld, Germany AGD Ashbya Genome Database agd ^AGR\w+$ AGD 3.0 is a genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from the fungi Ashbya gossypii and Saccharomyces cerevisiae. false urn:miriam:agd nucleotide expression microarray http://agd.vital-it.ch/Ashbya_gossypii/geneview?gene=$id AGR144C http://agd.vital-it.ch/ Biozentrum der Universität Basel, Basel Switzerland ArachnoServer arachnoserver ^AS\d{6}$ ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. false urn:miriam:arachnoserver sequence structure drug http://www.arachnoserver.org/toxincard.html?id=$id AS000060 http://www.arachnoserver.org/ Institute for Molecular Bioscience, The University of Queensland, Brisbane Australia BioCyc biocyc ^[A-Z-0-9]+(?<!CHEBI)(\:)?[A-Za-z0-9+_.%-]+$ BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. false urn:miriam:biocyc chemical genome sequence reaction pathway http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX http://biocyc.org Bioinformatics Research Group, SRI International, California USA CAZy Carbohydrate-Active enzYmes cazy ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ 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. false urn:miriam:cazy polysaccharide classification http://www.cazy.org/$id.html GT10 http://www.cazy.org/ Architecture et Fonction des Macromolécules Biologiques, CNRS, Marseille France GOA Gene Ontology Annotation UniProtKB-GOA goa ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. false urn:miriam:goa http://identifiers.org/goa/ protein annotation ontology quickgo http://www.ebi.ac.uk/QuickGO/GProtein?ac=$id P12345 http://www.ebi.ac.uk/GOA/ European Bioinformatics Institute, Hinxton, Cambridge UK PaleoDB Paleobiology database paleodb ^\d+$ 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. false urn:miriam:paleodb taxonomy http://paleodb.geology.wisc.edu/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$id 83088 http://paleodb.geology.wisc.edu/ University of Wisconsin, Madison USA http://fossilworks.org/?a=taxonInfo&taxon_no=$id 83088 http://paleodb.org/ Macquarie University, Sydney Australia http://museumu03.museumwww.naturkundemuseum-berlin.de/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$id 83088 http://museumu03.museumwww.naturkundemuseum-berlin.de/ Museum für Naturkunde, Berlin Germany Compulyeast Compluyeast-2D-DB compulyeast ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. false urn:miriam:compulyeast protein http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$id O08709 http://compluyeast2dpage.dacya.ucm.es/ Department Microbiology II, Universidad Complutense Madrid, Madrid Spain DisProt disprot ^DP\d{5}$ The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. false urn:miriam:disprot protein structure http://www.disprot.org/$id DP00003 http://www.disprot.org/ Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis USA EchoBASE echobase ^EB\d+$ EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. false urn:miriam:echobase genome gene protein http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$id EB0170 http://www.york.ac.uk/ Department of Biology (Area 10), University of York, York UK eggNOG eggnog ^\w+$ eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). false urn:miriam:eggnog clustering gene http://eggnog.embl.de/cgi_bin/display_single_node.pl?node=$id veNOG12876 http://eggnog.embl.de/version_2/ European Molecular Biology Laboratory, Heidelberg Germany http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$id veNOG12876 http://eggnog.embl.de/version_3.0/ European Molecular Biology Laboratory, Heidelberg Germany Ensembl Bacteria Ensembl Genomes Bacteria ensembl.bacteria ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ 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. false urn:miriam:ensembl.bacteria nucleotide genome sequence ebi http://bacteria.ensembl.org/id/$id MU9_3181 http://bacteria.ensembl.org/ European Bioinformatics Institute, Hinxton, Cambridge UK Ensembl Protists Ensembl Genomes Protists ensembl.protist ^\w+$ 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. false urn:miriam:ensembl.protist sequence nucleotide genome ebi http://protists.ensembl.org/id/$id PFC0120w http://protists.ensembl.org European Bioinformatics Institute, Hinxton, Cambridge UK Ensembl Metazoa Ensembl Genomes Metazoa ensembl.metazoa ^\w+(\.)?\d+$ Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. false urn:miriam:ensembl.metazoa genome sequence nucleotide ebi http://metazoa.ensembl.org/id/$id FBtr0084214 http://metazoa.ensembl.org/ European Bioinformatics Institute, Hinxton, Cambridge UK Ensembl Plants Ensembl Genomes Plants ensembl.plant ^\w+(\.\d+)?(\.\d+)?$ Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. false urn:miriam:ensembl.plant nucleotide sequence genome ebi http://plants.ensembl.org/id/$id AT1G73965 http://plants.ensembl.org/ European Bioinformatics Institute, Hinxton, Cambridge UK Ensembl Fungi Ensembl Genomes Fungi ensembl.fungi ^[A-Z-a-z0-9]+$ 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. false urn:miriam:ensembl.fungi nucleotide genome sequence ebi http://fungi.ensembl.org/id/$id CADAFLAT00006211 http://fungi.ensembl.org/ European Bioinformatics Institute, Hinxton, Cambridge UK HCVDB euHCVDB hcvdb ^M\d{5}$ the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. false urn:miriam:hcvdb genome sequence https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$id M58335 http://euhcvdb.ibcp.fr/euHCVdb/ Institut de Biologie et Chimie des Protéines, CNRS, University of Lyon , Lyon-Gerland France Genatlas genatlas ^\w+$ GenAtlas is a database containing information on human genes, markers and phenotypes. false urn:miriam:genatlas human gene disorder http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$id HBB http://genatlas.medecine.univ-paris5.fr/ Paris Descartes University, Paris France CATH superfamily cath.superfamily ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. false urn:miriam:cath.superfamily structure classification protein http://www.cathdb.info/cathnode/$id 1.10.10.200 http://www.cathdb.info/ Institute of Structural and Molecular Biology, University College London United Kingdom CATH domain cath.domain ^\w+$ The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. false urn:miriam:cath.domain protein structure classification http://www.cathdb.info/domain/$id 1cukA01 http://www.cathdb.info/ Institute of Structural and Molecular Biology, University College London UK GeneFarm genefarm ^\d+$ GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. false urn:miriam:genefarm nucleotide genome expression sequence https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$id 4892 http://urgi.versailles.inra.fr/Genefarm/ Unité de Recherche en Génomique Végétale, Evry France GPCRDB G protein-coupled receptor database gpcrdb ^\w+$ 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 urn:miriam:gpcrdb protein http://www.gpcrdb.org/protein/$id/ RL3R1_HUMAN http://www.gpcrdb.org/ Radboud University Nijmegen Medical Centre, Nijmegen, Holland HOGENOM hogenom ^\w+$ HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. false urn:miriam:hogenom sequence classification http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$id HBG284870 http://pbil.univ-lyon1.fr/databases/hogenom/ Laboratoire de Biométrie et Biologie Evolutive, CNRS, Lyon France GeneTree Ensembl GeneTree genetree ^ENSGT\d+$ 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. false urn:miriam:genetree classification gene protein http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$id ENSGT00550000074763 http://www.ensembl.org/ Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge UK HSSP Homology-derived Structure of Proteins hssp ^\w{4}$ 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. false urn:miriam:hssp sequence protein clustering ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$id.hssp.bz2 102l ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/ Nijmegen Centre for Molecular Life Sciences, CMBI, Nijmegen Holland ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$id.hssp.bz2 102l http://swift.cmbi.kun.nl/swift/hssp/ Protein Design Group, European Molecular Biology Laboratory, Heidelberg Germany MycoBrowser tuberculosis TubercuList myco.tuber ^Rv\d{4}(A|B|c)?$ Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. false urn:miriam:myco.tuber sequence genome http://tuberculist.epfl.ch/quicksearch.php?gene+name=$id Rv1908c http://tuberculist.epfl.ch/ Global Health Institute, Lausanne Switzerland MycoBrowser leprae Leproma myco.lepra ^ML\w+$ 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. false urn:miriam:myco.lepra genome sequence http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$id ML0224 http://mycobrowser.epfl.ch/leprosy.html Global Health Institute, Lausanne Switzerland MycoBrowser marinum marinolist myco.marinum ^MMAR\_\d+$ Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. false urn:miriam:myco.marinum sequence genome http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$id MMAR_2462 http://mycobrowser.epfl.ch/marinolist.html Global Health Institute, Lausanne Switzerland MycoBrowser smegmatis smegmalist myco.smeg ^MSMEG\w+$ Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. false urn:miriam:myco.smeg genome sequence http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$id MSMEG_3769 http://mycobrowser.epfl.ch/smegmalist.html Global Health Institute, Lausanne Switzerland Orphanet Orpha orphanet ^\d+$ Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases. false http://bio2rdf.org/orphanet urn:miriam:orphanet http://identifiers.org/orphanet/ human disease drug http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:$id 85163 http://orphanet.bio2rdf.org/fct Bio2RDF.org http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$id 85163 http://www.orpha.net/consor/ Inserm, Hôpital Broussais, Paris France OrthoDB orthodb ^\w+$ OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups false urn:miriam:orthodb sequence eukaryotic protein http://cegg.unige.ch/orthodb/results?searchtext=$id Q9P0K8 http://cegg.unige.ch/orthodb4 Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, Geneva Switzerland Peroxibase peroxibase ^\d+$ Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. false urn:miriam:peroxibase sequence enzyme http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$id 5282 http://peroxibase.toulouse.inra.fr/ Department of Plant Biology, University of Geneva, Geneva Switzerland PhylomeDB phylomedb ^\w+$ PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins. false urn:miriam:phylomedb genome protein taxonomy http://phylomedb.org/?seqid=$id Phy000CLXM_RAT http://phylomedb.org/ Bioinformatics Department,Centro de Investigación Príncipe Felipe, Valencia Spain SubstrateDB PMAP substrateDB pmap.substratedb ^\d+$ 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. false urn:miriam:pmap.substratedb protein domain reaction http://substrate.burnham.org/protein/annotation/$id/html 1915 http://substrate.burnham.org/ The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, California USA CutDB PMAP cutDB pmap.cutdb ^\d+$ 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). false urn:miriam:pmap.cutdb protein domain reaction http://cutdb.burnham.org/relation/show/$id 25782 http://cutdb.burnham.org The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, California USA ProtClustDB Protein Clusters Database Entrez ProtClustDB protclustdb ^\w+$ 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. false urn:miriam:protclustdb clustering protein ncbi http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$id O80725 http://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters National Center for Biotechnology Information (NCBI) USA PMP Protein Model Portal pmp ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ 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. false urn:miriam:pmp structure protein http://www.proteinmodelportal.org/query/uniprot/$id Q0VCA6 http://www.proteinmodelportal.org/ Biozentrum, University of Basel, Basel Switzerland ProtoNet ProteinCard protonet.proteincard ^\d+$ ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. false urn:miriam:protonet.proteincard protein http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$id 16941567 http://www.protonet.cs.huji.ac.il/ Hebrew University, Jerusalem Israel ProtoNet Cluster protonet.cluster ^\d+$ ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information. false urn:miriam:protonet.cluster protein clustering classification http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$id 4349895 http://www.protonet.cs.huji.ac.il/ Hebrew University, Jerusalem Israel REBASE Restriction Enzyme Database rebase ^\d+$ REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. false urn:miriam:rebase reaction enzyme http://rebase.neb.com/rebase/enz/$id.html 101 http://rebase.neb.com/rebase/ New England Biolabs, Ipswich, Massachusetts USA SWISS-MODEL swiss-model ^\w+$ The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for sequences registered is SWISS-PROT. false urn:miriam:swiss-model protein structure http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 http://swissmodel.expasy.org/ Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel Switzerland VectorBase vectorbase ^\D{4}\d{6}(\-\D{2})?$ VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. false urn:miriam:vectorbase gene protein genome ebi https://www.vectorbase.org/search/site/$id?&site="Genome" ISCW007415 http://www.vectorbase.org/ European Bioinformatics Institute, Hinxton, Cambridge UK Human Disease Ontology DO doid ^DOID\:\d+$ The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. true urn:miriam:doid urn:miriam:obo.do http://identifiers.org/obo.do/ human ontology disease ols http://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=$id DOID:11337 http://www.ebi.ac.uk/ols/ontologies/doid European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/DOID/$id DOID:11337 http://bioportal.bioontology.org/ontologies/DOID National Center for Biomedical Ontology, Stanford University USA http://disease-ontology.org/term/$id DOID:11337 http://disease-ontology.org/ University of Maryland (Maryland) and Northwestern University (Illinois) USA Cell Cycle Ontology cco ^CCO\:\w+$ The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. true urn:miriam:cco ontology ols http://www.ebi.ac.uk/ontology-lookup/?termId=$id CCO:P0000023 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://bioportal.bioontology.org/ontologies/1507?p=terms&conceptid=$id CCO:P0000023 http://bioportal.bioontology.org/ National Center for Biomedical Ontology, Stanford USA miRBase mature sequence mirbase.mature MIMAT\d{7} The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. false urn:miriam:mirbase.mature sequence nucleotide http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 http://www.mirbase.org/ Faculty of Life Sciences, University of Manchester UK nextProt nextprot ^NX_\w+ neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases. false urn:miriam:nextprot human protein http://www.nextprot.org/db/entry/$id NX_O00165 http://www.nextprot.org/ Swiss Institute of Bioinformatics, Geneva Switzerland CAS CAS Number CASRN CAS Registry Number Chemical Abstracts Service cas ^\d{1,7}\-\d{2}\-\d$ CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. false urn:miriam:cas chemical structure http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=$id 50-00-0 http://www.ncbi.nlm.nih.gov/pccompound National Center for Biotechnology Information (NCBI) USA http://commonchemistry.org/ChemicalDetail.aspx?ref=$id 50-00-0 http://commonchemistry.org American Chemistry Society, Washington, DC USA KEGG Genome KEGG Organism KEGG kegg.genome ^(T0\d+|\w{3,5})$ KEGG Genome is a collection of organisms whose genomes have been completely sequenced. false urn:miriam:kegg.genome genome http://www.kegg.jp/entry/$id eco http://www.genome.jp/kegg/catalog/org_list.html Kyoto University Bioinformatics Center, Kyoto Japan KEGG Metagenome KEGG kegg.metagenome ^T3\d+$ The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. false urn:miriam:kegg.metagenome genome http://www.kegg.jp/entry/$id T30002 http://www.genome.jp/kegg/catalog/org_list3.html Kyoto University Bioinformatics Center, Kyoto Japan NARCIS National Academic Research and Collaborations Information System narcis ^oai\:cwi\.nl\:\d+$ NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. false urn:miriam:narcis bibliography http://oai.cwi.nl/oai?verb=GetRecord&metadataPrefix=nl_didl&identifier=oai:cwi.nl:$id oai:cwi.nl:4725 http://persistent-identifier.nl/ Dans, The Hague Holland http://www.narcis.nl/publication/RecordID/$id oai:cwi.nl:4725 http://www.narcis.nl/?Language=en NARCIS, Royal Netherlands Academy of Science and Arts Holland Japan Chemical Substance Dictionary jcsd ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). false urn:miriam:jcsd structure chemical http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$id J55.713G http://jglobal.jst.go.jp/en/ Japan Science and Technology Agency Japan Pathway Ontology pw ^PW:\d{7}$ The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions. true urn:miriam:obo.pw http://identifiers.org/obo.pw/ urn:miriam:pw ontology pathway human mammalian ols http://www.ebi.ac.uk/ols/ontologies/pw/terms?obo_id=$id PW:0000208 http://www.ebi.ac.uk/ols/ontologies/pw European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/PW/$id PW:0000208 http://bioportal.bioontology.org/ontologies/PW National Center for Biomedical Ontology, Stanford, California USA http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=$id PW:0000208 http://rgd.mcw.edu/rgdweb/ontology/search.html Medical College of Wisconsin, Wisconsin USA Sequence Read Archive insdc.sra ^[SED]R[APRSXZ]\d{7} The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database. false urn:miriam:insdc.sra sequence ncbi http://www.ncbi.nlm.nih.gov/sra/$id?&report=full SRX000007 http://www.ncbi.nlm.nih.gov/sra National Center for Biotechnology Information (NCBI) USA http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$id SRX000007 http://trace.ddbj.nig.ac.jp/dra/ DNA Data Bank of Japan, Mishima, Shizuoka Japan ebi http://www.ebi.ac.uk/ena/data/view/$id SRX000007 http://www.ebi.ac.uk/ena European Bioinformatics Institute, Hinxton, Cambridge UK ScerTF scretf ^\w+$ ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor. false urn:miriam:scretf nucleotide domain sequence http://stormo.wustl.edu/ScerTF/details/$id/ RSC3 http://stormo.wustl.edu/ScerTF/ Department of Genetics, Washington University Medical School, St Louis, Missouri USA PharmGKB Gene pharmgkb.gene ^PA\w+$ 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. false urn:miriam:pharmgkb.gene gene pharmacogenomics http://www.pharmgkb.org/gene/$id PA131 http://www.pharmgkb.org/ Department of Genetics, School of Medicine, Stanford University, Stanford, California USA miRNEST mirnest ^MNEST\d+$ miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. false urn:miriam:mirnest expression http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$id MNEST029358 http://rhesus.amu.edu.pl/mirnest/copy/ Institute of Molecular Biology, Adam Mickiewicz University, Poznan Poland NAPP Nucleic Acid Phylogenetic Profiling napp ^\d+$ NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. false urn:miriam:napp clustering nucleotide http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$id 351 http://napp.u-psud.fr/ Institut de Génétique et Microbiologie, UMR 8621, CNRS, Université Paris Sud, Paris France NONCODE v3 noncodev3 ^\d+$ NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. false urn:miriam:noncodev3 urn:miriam:noncode http://identifiers.org/noncode/ nucleotide expression http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$id 377550 http://www.noncode.org/ Bioinformatics Research Group, Chinese Academy of Sciences, Beijing China VIRsiRNA Virus siRNA database VIRsiRNAdb virsirna ^virsi\d+$ 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. false urn:miriam:virsirna nucleotide mammalian http://crdd.osdd.net/servers/virsirnadb/record.php?details=$id virsi1909 http://crdd.osdd.net/servers/virsirnadb Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India India ELM Eukaryotic Linear Motifs elm ^[A-Za-z_0-9]+$ 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. false urn:miriam:elm domain eukaryotic protein http://elm.eu.org/elms/elmPages/$id.html CLV_MEL_PAP_1 http://elm.eu.org/ Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg Germany MimoDB BDB Biopanning Data Bank Mimotope Database mimodb ^\d+$ MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. false urn:miriam:mimodb interaction protein http://immunet.cn/bdb/index.php/mimoset/$id 1 http://immunet.cn/bdb/ Key Laboratory for Neuroinformation of Ministry of Education, University of Electronic Science and Technology of China, Sichuan China SitEx sitex ^\d+$ 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. false urn:miriam:sitex structure sequence eukaryotic domain http://www-bionet.sscc.ru/sitex/index.php?siteid=$id 1000 http://www-bionet.sscc.ru/sitex/ Novosibirsk State University, Novosibirsk Russia BYKdb Bacterial protein tYrosine Kinase database bykdb ^[A-Z0-9]+$ The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. false urn:miriam:bykdb microbial domain sequence https://bykdb.ibcp.fr/data/html/annotated/$id.html A0A010GJI9 http://bykdb.ibcp.fr/BYKdb/ Unité Bases Moléculaires et Structurales des Systèmes Infectieux; CNRS - Université Claude Bernard, Lyon France Conoserver conoserver ^\d+$ ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. false urn:miriam:conoserver protein drug http://www.conoserver.org/?page=card&table=protein&id=$id 2639 http://www.conoserver.org/ Institute for Molecular Bioscience, The University of Queensland, Brisbane Australia TopFind topfind ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ 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. false urn:miriam:topfind domain protein http://clipserve.clip.ubc.ca/topfind/proteins/$id Q9UKQ2 http://clipserve.clip.ubc.ca/topfind Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver Canada MIPModDB mipmod ^\w+$ 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 urn:miriam:mipmod structure protein http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$id HOSAPI0399 http://bioinfo.iitk.ac.in/MIPModDB Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur India Cell Image Library The Cell: An Image Library-Cell Centered Database CIL The Cell: An Image Library-CCDB cellimage ^\d+$ The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. false urn:miriam:cellimage image library http://cellimagelibrary.org/images/$id 24801 http://cellimagelibrary.org/ American Society for Cell Biology, Bethesda, Maryland and The National Center for Microscopy and Imaging Research, San Diego, California USA COMBINE specifications combine.specifications ^\w+(\-|\.|\w)*$ 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 urn:miriam:combine.specifications ebi http://co.mbine.org/specifications/$id sbgn.er.level-1.version-1.2 http://co.mbine.org/standards/ European Bioinformatics Institute, Hinxton, Cambridge UK ZFIN Phenotype zfin.phenotype ^ZDB\-GEN0\-\d+\-\d+$ ZFIN serves as the zebrafish model organism database. This collection references the phenotypes observed for any given genotype. false urn:miriam:zfin.phenotype gene phenotype http://zfin.org/$id ZDB-GENO-980202-899 http://zfin.org Zebrafish Information Network, University of Oregon, USA USA ZFIN Expression zfin.expression ^ZDB\-GEN0\-\d+\-\d+$ ZFIN serves as the zebrafish model organism database. This collection references the set of expressed genes for any given genotype. false urn:miriam:zfin.expression gene expression http://zfin.org/$id ZDB-GENO-980202-899 http://zfin.org Zebrafish Information Network, University of Oregon, USA USA CABRI cabri ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. false urn:miriam:cabri microbial catalogue eukaryotic http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id] dsmz_mutz-id:ACC 291 http://www.cabri.org/ National Cancer Research Institute of Genova, Genova Italy http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id] dsmz_mutz-id:ACC 291 http://www.be.cabri.org/ BCCM, Brussels Belgium http://www.fr.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id] dsmz_mutz-id:ACC 291 http://www.fr.cabri.org/ nstitut Pasteur, Paris France CYGD cygd ^\w{2,3}\d{2,4}(\w)?$ The MIPS Comprehensive Yeast Genome Database (CYGD) provides information on the molecular structure and functional network of the entirely sequenced the budding yeast, Saccharomyces cerevisiae, as well as on related yeasts which are used for comparative analysis. false urn:miriam:cygd genome protein gene http://mips.gsf.de/genre/proj/yeast/singleGeneReport.html?entry=$id YFL039c http://mips.gsf.de/genre/proj/yeast/ Institute for Bioinformatics (MIPS) Germany http://pedant.helmholtz-muenchen.de/pedant3htmlview/pedant3view?Db=p3_p13838_Sac_cerev&Method=ReportGene&GeneticelemCode=$id YFL039c http://pedant.helmholtz-muenchen.de/pedant3htmlview/pedant3view?Method=start_method&Db=p3_p13838_Sac_cerev Biomax Informatics AG, Planegg Germany http://mips.helmholtz-muenchen.de/genre/proj/yeast/singleGeneReport.html?entry=$id YFL039c http://mips.helmholtz-muenchen.de/genre/proj/yeast/ Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, GmbH, Neuherberg Germany HUGE huge ^KIAA\d{4}$ The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. false urn:miriam:huge protein DNA http://www.kazusa.or.jp/huge/gfpage/$id/ KIAA0001 http://www.kazusa.or.jp/huge/ Kazusa DNA Research Institute, Chiba Japan BindingDB bindingDB ^\d+$ BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. false urn:miriam:bindingDB interaction protein drug http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$id 22360 http://www.bindingdb.org/bind/index.jsp Skaggs School of Pharmacy & Pharmaceutical Sciences, La Jolla, California USA STRING Search Tool for Retrieval of Interacting Genes/Proteins string ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$ STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. false urn:miriam:string protein interaction http://string-db.org/interactions/$id P53350 http://string-db.org/ European Molecular Biology Laboratory, Heidelberg Germany http://string.embl.de/interactions/$id P53350 http://string.embl.de/ European Molecular Biology Laboratory, Heidelberg Germany STITCH stitch ^\w{14}$ 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. false urn:miriam:stitch chemical protein interaction http://stitch.embl.de/interactions/$id BQJCRHHNABKAKU http://stitch.embl.de/ European Molecular Biology Laboratory, Heidelberg Germany Anatomical Therapeutic Chemical Vetinary atcvet ^Q[A-Z0-9]+$ 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. false urn:miriam:atcvet classification drug http://www.whocc.no/atcvet/atcvet_index/?code=$id QJ51RV02 http://www.whocc.no/atcvet/atcvet_index/ World Health Organisation Switzerland Phenol-Explorer phenolexplorer ^\d+$ 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. false urn:miriam:phenolexplorer chemical http://phenol-explorer.eu/foods/$id 75 http://www.phenol-explorer.eu/foods/ INRA and University of Alberta France and Canada SNOMED CT snomedct ^(\w+)?\d+$ SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc. false urn:miriam:snomedct controlled vocabulary http://www.snomedbrowser.com/Codes/Details/$id 284196006 http://www.snomedbrowser.com/ The Health Informatics Service, NHS, West Yorkshire UK http://vtsl.vetmed.vt.edu/TerminologyMgt/Browser/ISA.cfm?SCT_ConceptID=$id 284196006 http://vtsl.vetmed.vt.edu/ Virginia Maryland Regional College of Veterinary Medicine, Virginia USA http://unknown/$id 284196006 http://www.ihtsdo.org/snomed-ct/ IHTSDO, Copenhagen Denmark MeSH 2012 Medical Subject Headings 2012 mesh.2012 ^[A-Za-z0-9]+$ MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. false urn:miriam:mesh.2012 controlled vocabulary bptl http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=$id D018377 http://bioportal.bioontology.org/ National Center for Biomedical Ontology, Stanford University USA http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$id&view=expanded 17186 http://www.nlm.nih.gov/mesh/ U.S. National Library of Medicine, National Institute of Health, Maryland USA KnapSack knapsack ^C\d{8} Knapsack provides information on metabolites and the taxonomic class with which they are associated. false urn:miriam:knapsack metabolite http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$id C00000001 http://kanaya.aist-nara.ac.jp/KNApSAcK/ Nara Institute of Science and Technology Japan Canadian Drug Product Database DPD cdpd ^\d+$ 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). false urn:miriam:cdpd registry drug http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$id 63250 http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp Health Canada, Ottawa, Ontario Canada MassBank massbank ^[A-Z]{2}[A-Z0-9][0-9]{5}$ MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). false urn:miriam:massbank chemical metabolite mass spectrometry http://msbi.ipb-halle.de/MassBank/jsp/FwdRecord.jsp?id=$id PB000166 http://msbi.ipb-halle.de/MassBank/ The MassBank Consortium Germany http://www.massbank.jp/jsp/FwdRecord.jsp?id=$id PB000166 http://www.massbank.jp The MassBank Consortium Japan http://www.massbank.eu/MassBank/jsp/FwdRecord.jsp?id=$id PB000166 http://www.massbank.eu/ NORMAN Network and The MassBank Consortium Germany Golm Metabolome Database GMD gmd ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. false urn:miriam:gmd metabolite http://gmd.mpimp-golm.mpg.de/Metabolites/$id.aspx 68513255-fc44-4041-bc4b-4fd2fae7541d http://gmd.mpimp-golm.mpg.de/ Max Planck Institute of Molecular Plant Physiology, Potsdam Germany HomoloGene homologene ^\d+$ HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. false urn:miriam:homologene http://bio2rdf.org/homologene http://identifiers.org/homologene/ clustering eukaryotic gene ncbi http://www.ncbi.nlm.nih.gov/homologene/$id 1000 http://www.ncbi.nlm.nih.gov/homologene/ National Center for Biotechnology Information (NCBI) USA http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$id 1000 http://homologene.bio2rdf.org/fct Bio2RDF.org UM-BBD Compound University of Minnesota Biocatalysis/Biodegradation Database (Compound) umbbd.compound ^c\d+$ 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. false urn:miriam:umbbd.compound metabolite microbial http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$id c0001 http://umbbd.ethz.ch/ ETH, Zurich Switzerland http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=c&compID=$id c0001 http://umbbd.msi.umn.edu/index.html Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota USA ABS Annotated regulatory Binding Sites database abs ^A\d+$ The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. false urn:miriam:abs interaction gene http://genome.crg.es/datasets/abs2005/entries/$id.html A0014 http://genome.crg.es/datasets/abs2005/ Institut Municipal d'Investigaci&oacute; M&egrave;dica, Barcelona Spain APD Antimicrobial Peptide Database apd ^\d{5}$ The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. false urn:miriam:apd drug protein http://aps.unmc.edu/AP/database/query_output.php?ID=$id 01001 http://aps.unmc.edu/AP/ Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha USA ChemDB chemdb ^\d+$ 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. false urn:miriam:chemdb chemical http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$id 3966782 http://cdb.ics.uci.edu/ University of California, Irvine USA DPV DPVweb Description of Plant Viruses dpv ^\d+$ Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. false urn:miriam:dpv plant http://www.dpvweb.net/dpv/showdpv.php?dpvno=$id 100 http://www.dpvweb.net/ Plant-Pathogen Interactions Division, Wheat Pathogenesis Programme, Rothamsted Research Harpenden, Hertfordshire UK IUPHAR receptor International Union of Basic and Clinical Pharmacology IUPHAR-DB iuphar.receptor ^\d+$ The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. false urn:miriam:iuphar.receptor mammalian http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 101 http://www.guidetopharmacology.org/targets.jsp Centre for Cardiovascular Science, University of Edinburgh, Edinburgh UK Aceview Worm AceView WormGenes aceview.worm ^[a-z0-9-]+$ AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. false urn:miriam:aceview.worm eukaryotic gene ncbi http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$id aap-1 http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm National Center for Biotechnology Information (NCBI) USA ASAP asap ^[A-Za-z0-9-]+$ ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. false urn:miriam:asap microbial genome gene http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$id ABE-0009634 http://asap.ahabs.wisc.edu/asap/home.php Animal Health and Biomedical Sciences, University of Wisconsin, Madison USA ATCC American Type Culture Collection atcc ^\d+$ The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. false urn:miriam:atcc microbial eukaryotic catalogue http://www.lgcstandards-atcc.org/Products/All/$id.aspx 11303 http://www.atcc.org/ American Type Culture Collection, Manassas, Virginia USA BDGP EST Berkeley Drosophila Genome Project EST bdgp.est ^\w+(\.)?(\d+)?$ The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). false urn:miriam:bdgp.est eukaryotic expression ncbi http://www.ncbi.nlm.nih.gov/nucest/$id EY223054.1 http://www.ncbi.nlm.nih.gov/dbEST/index.html National Center for Biotechnology Information (NCBI) USA Dictybase Gene dictybase.gene ^DDB_G\d+$ The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. false urn:miriam:dictybase.gene gene plant http://dictybase.org/gene/$id DDB_G0267522 http://dictybase.org/ Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, Chicago, Illinois USA IMGT LIGM IMGT/LIGM-DB imgt.ligm ^M\d+$ 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. false urn:miriam:imgt.ligm immunogenetics mammalian http://www.imgt.org/ligmdb/view?id=$id M94112 http://www.imgt.org/ CNRS, Montpellier University, Montpellier France ebi http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+1fmSL1g8Xvs+-e+[IMGTLIGM:'$id'] M94112 http://www.ebi.ac.uk/imgt/ European Bioinformatics Institute, Hinxton, Cambridge UK http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$id'] M94112 http://genius.embnet.dkfz-heidelberg.de/ DKFZ TP3, Heidelberg Germany Worfdb Worm Orf DB worfdb ^\w+(\.\d+)? WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends). false urn:miriam:worfdb eukaryotic gene http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$id T01B6.1 http://worfdb.dfci.harvard.edu/ Center for Cancer Systems Biology, Harvard Medical School, Massachusetts USA NEXTDB Nematode Expression Pattern Database nextdb ^[A-Za-z0-9]+$ NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones. false urn:miriam:nextdb expression eukaryotic http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$id 6b1 http://nematode.lab.nig.ac.jp/ National Institute of Genetics, Shizuoka Japan Plant Genome Network pgn ^\d+$ The Plant Genome Network (PGN) is a resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. All data are directly derived from chromatograms with original and intermediate data stored in the database. false urn:miriam:pgn expression plant http://pgn.cornell.edu/unigene/unigene_assembly_contigs.pl?unigene_id=$id 196828 http://pgn.cornell.edu/ Cornell University, Ithaca, New York USA SoyBase soybase ^\w+(\-)?\w+(\-)?\w+$ SoyBase is a repository for curated genetics, genomics and related data resources for soybean. false urn:miriam:soybase gene plant http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$id BARC-013845-01256 http://soybase.org/ USDA-ARS-CICGRU, Iowa State University, Iowa USA HAMAP High-quality Automated and Manual Annotation of microbial Proteomes hamap ^MF_\d+$ 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. false urn:miriam:hamap microbial annotation http://hamap.expasy.org/unirule/$id MF_01400 http://hamap.expasy.org/ Swiss Institute of Bioinformatics, Geneva Switzerland Rouge Rodent Unidentified Gene-Encoded Large Proteins rouge ^m\w+$ The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. false urn:miriam:rouge mammalian protein gene http://www.kazusa.or.jp/rouge/gfpage/$id/ mKIAA4200 http://www.kazusa.or.jp/rouge/ Kazusa DNA Research Institute, Chiba Japan ArrayExpress Platform arrayexpress.platform ^[AEP]-\w{4}-\d+$ 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. false urn:miriam:arrayexpress.platform microarray ebi http://www.ebi.ac.uk/arrayexpress/arrays/$id A-GEOD-50 http://www.ebi.ac.uk/arrayexpress/ European Bioinformatics Institute, Hinxton, Cambridge UK CGSC Strain Coli Genetic Stock Center cgsc ^\d+$ The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. false urn:miriam:cgsc microbial strain http://cgsc.biology.yale.edu/Strain.php?ID=$id 11042 http://cgsc.biology.yale.edu/index.php Dept. of Molecular, Cellular, and Developmental Biology, Yale University, Conneticut USA COGs Clusters of Orthologous Groups cogs ^COG\d+$ Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. false urn:miriam:cogs protein clustering genome ncbi http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?$id COG0001 http://www.ncbi.nlm.nih.gov/COG/ National Center for Biotechnology Information (NCBI) USA DragonDB DNA dragondb.dna ^\d\w+$ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. false urn:miriam:dragondb.dna DNA plant http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id;class=DNA 3hB06 http://www.antirrhinum.net/ University of British Columbia, Vancouver Canada DragonDB Protein dragondb.protein ^\w+$ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. false urn:miriam:dragondb.protein plant protein http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id;class=Peptide AMDEFA http://www.antirrhinum.net/ University of British Columbia, Vancouver Canada DragonDB Locus dragondb.locus ^\w+$ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. false urn:miriam:dragondb.locus plant DNA http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id&amp;class=Locus DEF http://www.antirrhinum.net/ University of British Columbia, Vancouver Canada DragonDB Allele dragondb.allele ^\w+$ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. false urn:miriam:dragondb.allele gene plant http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id&amp;class=Allele cho http://www.antirrhinum.net/ University of British Columbia, Vancouver Canada ISSN issn ^\d{4}-\d{3}[\dX]$ 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 urn:miriam:issn bibliography https://catalog.loc.gov/vwebv/search?searchCode=STNO&searchArg=$id&searchType=1&recCount=25 0745-4570 http://catalog.loc.gov/webvoy.htm Library of Congress Online Catalogue, Washington DC USA MEROPS Family merops.family ^[SCTAGMNU]\d+$ The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. false urn:miriam:merops.family protein interaction enzyme http://merops.sanger.ac.uk/cgi-bin/famsum?family=$id S1 http://merops.sanger.ac.uk/index.htm Wellcome Trust Sanger Institute, Hinxton UK MGED Ontology MO mo ^\w+$ The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. false urn:miriam:mo ontology bptl http://purl.bioontology.org/ontology/MO/$id ArrayGroup http://bioportal.bioontology.org/ National Center for Biomedical Ontology, Stanford University USA ebi http://mged.sourceforge.net/ontologies/MGEDontology.php#$id ArrayGroup http://mged.sourceforge.net/ontologies/MGEDontology.php (Ontology Working Group), European Bioinformatics Institute, Hinxton, Cambridge UK NASC code The Nottingham Arabidopsis Stock Centre nasc ^(\w+)?\d+$ The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. false urn:miriam:nasc plant strain http://arabidopsis.info/StockInfo?NASC_id=$id N1899 http://arabidopsis.info/ The Nottingham Arabidopsis Stock Centre, University of Nottingham UK NIAEST niaest ^\w\d{4}\w\d{2}(\-[35])?$ A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones. false urn:miriam:niaest gene expression human http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$id J0705A10 http://lgsun.grc.nia.nih.gov/cDNA/ National Institute on Aging, NIH USA Pazar Transcription Factor Pazar Database pazar ^TF\w+$ 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. false urn:miriam:pazar protein DNA interaction http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$id TF0001053 http://www.pazar.info/ Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver Canada Plant Ontology PO po ^PO:\d+$ The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. true urn:miriam:po http://identifiers.org/po/ http://purl.obolibrary.org/obo/PO http://identifiers.org/obo.po/ urn:miriam:obo.po ontology plant amigo http://www.plantontology.org/amigo/go.cgi?view=details&query=$id PO:0009089 http://www.plantontology.org/ Cold Spring Harbor Laboratory, Cold Spring Harbor, New York USA bptl http://purl.bioontology.org/ontology/PO/$id PO:0009089 http://bioportal.bioontology.org/ontologies/PO National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/po/terms?obo_id=$id PO:0009089 http://www.ebi.ac.uk/ols/ontologies/po European Bioinformatics Institute, Hinxton, Cambridge UK RNA Modification Database RNAmods rnamods ^\d{3}$ The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. false urn:miriam:rnamods nucleotide http://mods.rna.albany.edu/mods/modifications/view/$id 101 http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm Department of Medicinal Chemistry and Department of Biochemistry, University of Utah, Salt Lake City, Utah USA Science Signaling Pathway-Independent Component sciencesignaling.pic ^CMC_\d+$ The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway independent component information. false urn:miriam:sciencesignaling.pic pathway http://stke.sciencemag.org/cgi/cm/stkecm;$id CMC_15493 http://stke.sciencemag.org/ Science Mag, Washington DC USA Science Signaling Pathway-Dependent Component sciencesignaling.pdc ^CMN_\d+$ The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway-dependent component information. false urn:miriam:sciencesignaling.pdc interaction http://stke.sciencemag.org/cgi/cm/stkecm;$id CMN_15494 http://stke.sciencemag.org/ Science Mag, Washington DC USA Science Signaling Pathway sciencesignaling.path ^CMP_\d+$ The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway information. false urn:miriam:sciencesignaling.path http://stke.sciencemag.org/cgi/cm/stkecm;$id CMP_18019 http://stke.sciencemag.org/ Science Mag, Washington DC USA TreeBASE treebase ^TB[1,2]?:[A-Z][a-z]?\d+$ 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. false urn:miriam:treebase clustering http://purl.org/phylo/treebase/phylows/study/$id?format=html TB2:S1000 http://treebase.org/ Phyloinformatics Research Foundation, Durham, North Carolina USA Tetrahymena Genome Database TGD tgd ^TTHERM\_\d+$ The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature. false urn:miriam:tgd genome sequence gene http://ciliate.org/index.php/feature/details/$id TTHERM_00648910 http://ciliate.org/index.php/ Department of Genetics, School of Medicine, Stanford University, Stanford, California USA CMR Gene Comprehensive Microbial Resource Gene Page cmr.gene ^\w+(\_)?\w+$ The Comprehensive Microbial Resource (CMR) contains annotation for all complete microbial genomes and allows for a wide variety of data retrievals. This collection refers to the Gene Page which provides information pertaining to a specific gene such as the Locus Name, Gene Symbol, Coordinates, DNA Molecule Name, and Gene Length. false urn:miriam:cmr.gene sequence gene http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=$id NTL15EF2281 http://cmr.jcvi.org/cgi-bin/CMR/CmrHomePage.cgi The Institute for Genomic Research, Rockville, Maryland USA TIGRFAMS tigrfam ^TIGR\d+$ TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. false urn:miriam:tigrfam clustering protein http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$id TIGR00010 http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi The Institute for Genomic Research, Rockville, Maryland USA Animal TFDB Family Animal Transcription Factor Database atfdb.family ^\w+$ The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. false urn:miriam:atfdb.family interaction protein DNA http://www.bioguo.org/AnimalTFDB/family.php?fam=$id CUT http://www.bioguo.org/AnimalTFDB/family_index.php Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan China IUPHAR family iuphar.family ^\d+$ The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. false urn:miriam:iuphar.family mammalian http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$id 78 http://www.guidetopharmacology.org/ International Union of Pharmacology, Edinburgh UK http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=$id 78 http://www.iuphar-db.org/ Centre for Cardiovascular Science, University of Edinburgh, Edinburgh UK DBG2 Introns Database for Bacterial Group II Introns dbg2introns ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ 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. false urn:miriam:dbg2introns DNA sequence http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$id Cu.me.I1 http://webapps2.ucalgary.ca/~groupii/ Department of Biological Sciences, University of Calgary, Calgary, Alberta Canada Spectral Database for Organic Compounds SDBS sdbs \d+$ The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra. false urn:miriam:sdbs mass spectrometry chemical http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$id 4544 http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi National Institute of Advanced Industrial Science and Technology (AIST) Japan Vbase2 vbase2 ^\w+$ The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. false urn:miriam:vbase2 immunogenetics sequence human http://www.vbase2.org/vgene.php?id=$id humIGHV025 http://www.vbase2.org/vbase2.php Department of Experimental Immunology, German Research Centre for Biotechnology, Braunschweig Germany SPIKE Map Signaling Pathways Integrated Knowledge Engine spike.map ^spike\d{5}$ 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. false urn:miriam:spike.map pathway http://www.cs.tau.ac.il/~spike/maps/$id.html spike00001 http://www.cs.tau.ac.il/~spike/ School of Computer Sciences and School of Medicine, Tel Aviv University Israel METLIN Metabolite and Tandem Mass Spectrometry Database metlin ^\d{4}$ 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. false urn:miriam:metlin metabolite mass spectrometry http://metlin.scripps.edu/metabo_info.php?molid=$id 1455 http://masspec.scripps.edu/ Scripps Research Institute, San Diego USA GeneCards genecards ^\w+$ The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. false urn:miriam:genecards human gene http://genecards_v3.hgc.jp/cgi-bin/carddisp.pl?gene=$id ABL1 http://genecards_v3.hgc.jp/ Human Genome Center, Institute of Medical Science, Univ of Tokyo Japan http://genecards.bii.a-star.edu.sg/cgi-bin/carddisp.pl?gene=$id ABL1 http://genecards.bii.a-star.edu.sg/ Bioinformatics Institute, A*STAR Singapore http://www.genecards.org/cgi-bin/carddisp.pl?gene=$id ABL1 http://www.genecards.org/ Department of Molecular Genetics, Weizmann Institute of Science, Rehovot Israel http://p570e70p1.ophid.utoronto.ca/genecards/cgi-bin/carddisp.pl?gene=$id ABL1 http://p570e70p1.ophid.utoronto.ca/genecards/index.php University Health Network, University of Toronoto, Toronto Canada http://genecards.bioinformatics.nl/cgi-bin/carddisp.pl?gene=$id ABL1 http://genecards.bioinformatics.nl/ Laboratory of Bioinformatics, Wageningen UR, Wageningen Holland http://bioinformatics.mdanderson.org/genecards/cgi-bin/carddisp.pl?gene=$id ABL1 http://bioinformatics.mdanderson.org/genecards/ Univ of Texas M.D. Anderson Cancer Center, Houston, Texas USA http://www6.unito.it/cards/cgi-bin/carddisp.pl?gene=$id ABL1 http://www6.unito.it/cards/ Dept. of Clinical and Biological Sciences , Univ of Torino Italy MMRRC Mutant Mouse Regional Resource Centers mmrrc ^\d+$ The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. false urn:miriam:mmrrc strain mammalian catalogue http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$id 70 http://www.mmrrc.org/ University of North Carolina USA UM-BBD Reaction University of Minnesota Biocatalysis/Biodegradation Database (Reaction) umbbd.reaction ^r\d+$ The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information. false urn:miriam:umbbd.reaction reaction microbial http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$id r0001 http://umbbd.ethz.ch/ ETH, Zurich Switzerland http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=$id r0001 http://umbbd.msi.umn.edu/index.html Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota USA UM-BBD Enzyme University of Minnesota Biocatalysis/Biodegradation Database (Enzyme) umbbd.enzyme ^e\d+$ 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. false urn:miriam:umbbd.enzyme microbial enzyme http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=$id e0333 http://umbbd.msi.umn.edu/index.html Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota USA http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$id e0333 http://umbbd.ethz.ch/ ETH, Zurich Switzerland UM-BBD Pathway University of Minnesota Biocatalysis/Biodegradation Database (Pathway) umbbd.pathway ^\w+$ 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 urn:miriam:umbbd.pathway pathway microbial http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$id ala http://umbbd.ethz.ch/ ETH, Zurich Switzerland http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=p&pathway_abbr=$id ala http://umbbd.msi.umn.edu/index.html Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota USA UM-BBD Biotransformation Rule umbbd.rule ^bt\d+$ 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. false urn:miriam:umbbd.rule reaction microbial http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$id bt0001 http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules ETH, Zurich Switzerland http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=$id bt0001 http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allrules Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota USA mirEX mirex ^\d+(\w+)?$ mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages. false urn:miriam:mirex gene expression plant http://comgen.pl/mirex1/?page=results/record&name=$id&exref=pp2a&limit=yes 165a http://comgen.pl/mirex/?page=home Institute of Molecular Biology, Adam Mickiewicz University, Poznan Poland Dictybase EST dictybase.est ^DDB\d+$ 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 urn:miriam:dictybase.est DNA sequence plant http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$id DDB0016567 http://dictybase.org/ Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, Chicago, Illinois USA IMGT HLA IPD IMGT/HLA imgt.hla ^[A-Z0-9*:]+$ 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. false urn:miriam:imgt.hla immunogenetics human ebi http://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$id A*01:01:01:01 http://www.ebi.ac.uk/imgt/hla/allele.html European Bioinformatics Institute, Hinxton, Cambridge UK Flystock Bloomington Drosophila Stock Center at Indiana University flystock ^\d+$ The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. false urn:miriam:flystock eukaryotic strain http://flystocks.bio.indiana.edu/Reports/$id.html 33159 http://flystocks.bio.indiana.edu/bloomhome.htm BDSC, Department of Biology, Indiana University, Bloomington USA OPM Orientations of Proteins in Membranes opm ^[0-9][A-Za-z0-9]{3}$ 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 urn:miriam:opm protein structure http://opm.phar.umich.edu/protein.php?pdbid=$id 1h68 http://opm.phar.umich.edu/ Department of Medicinal Chemistry, College of Pharmacy, University of Michigan USA Allergome allergome ^\d+$ Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. false urn:miriam:allergome human chemical http://www.allergome.org/script/dettaglio.php?id_molecule=$id 1948 http://www.allergome.org/ Center for Clinical and Experimental Allergology, Rome Italy PomBase pombase ^S\w+(\.)?\w+(\.)?$ PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. false urn:miriam:pombase nucleotide eukaryotic genome http://www.pombase.org/spombe/result/$id SPCC13B11.01 http://www.pombase.org/ Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge UK HPA Human Protein Atlas hpa ^ENSG\d{11}$ The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. false urn:miriam:hpa disease image library protein http://www.proteinatlas.org/$id ENSG00000026508 http://www.proteinatlas.org/ Department of Proteomics, School of Biotechnology, AlbaNova University Center, Stockholm Sweden JAX Mice jaxmice ^\d+$ JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory. false urn:miriam:jaxmice strain mammalian http://jaxmice.jax.org/strain/$id.html 005012 http://jaxmice.jax.org/ The Jackson Laboratory, Sacremento, California USA uBio NameBank Universal Biological Indexer and Organizer (NameBank) ubio.namebank ^\d+$ NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context. false urn:miriam:ubio.namebank taxonomy controlled vocabulary http://www.ubio.org/browser/details.php?namebankID=$id 2555646 http://www.ubio.org Marine Biological Laboratory, Woods Hole, Massachusetts USA YeTFasCo Yeast Transcription Factor Specificity Compendium yetfasco ^\w+\_\d+(\.\d+)?$ The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. false urn:miriam:yetfasco interaction eukaryotic gene http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$id YOR172W_571.0 http://yetfasco.ccbr.utoronto.ca/ Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto Canada TarBase tarbase ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)? TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used. false urn:miriam:tarbase interaction nucleotide gene http://diana.cslab.ece.ntua.gr/DianaToolsNew/index.php?r=tarbase/index&mirnas=$id hsa-let-7 http://diana.cslab.ece.ntua.gr/DianaToolsNew/index.php?r=tarbase IMIS Institute, Athena Research Center, Athens Greece http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$id hsa-let-7a-2-3p http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly Greece CharProt charprot ^CH_\d+$ CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. false urn:miriam:charprot annotation controlled vocabulary gene http://www.jcvi.org/charprotdb/index.cgi/view/$id CH_001923 http://www.jcvi.org/charprotdb J Craig Venter institute, Rockville, Maryland USA OMA Protein Orthologous MAtrix oma.protein ^[A-Z0-9]{5}\d+$ OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. false urn:miriam:oma.protein clustering protein http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$id HUMAN16963 http://omabrowser.org/cgi-bin/gateway.pl ETH Zurich, Computer Science, Zurich Switzerland OMA Group oma.grp ^[A-Z]+$ 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. false urn:miriam:oma.grp protein clustering http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$id LCSCCPN http://omabrowser.org/cgi-bin/gateway.pl ETH Zurich, Computer Science, Zurich Switzerland NCBI Protein ncbiprotein ^(\w+\d+(\.\d+)?)|(NP_\d+)$ The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. false urn:miriam:ncbiprotein protein sequence ncbi http://www.ncbi.nlm.nih.gov/protein/$id CAA71118.1 http://www.ncbi.nlm.nih.gov/protein National Center for Biotechnology Information (NCBI) USA GenPept protein genbank identifier genpept ^\w{3}\d{5}(\.\d+)?$ The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. false urn:miriam:genpept genome sequence protein ncbi http://www.ncbi.nlm.nih.gov/protein/$id?report=genpept CAA71118.1 http://www.ncbi.nlm.nih.gov/protein National Center for Biotechnology Information (NCBI) USA UniGene unigene ^\d+$ 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. false urn:miriam:unigene http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$id 4900 http://www.ncbi.nlm.nih.gov/unigene National Center for Biotechnology , Maryland USA BitterDB Receptor bitterdb.rec ^\d+$ BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. false urn:miriam:bitterdb.rec protein human chemical http://bitterdb.agri.huji.ac.il/Receptor.php?id=$id 1 http://bitterdb.agri.huji.ac.il/dbbitter.php The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot Israel BitterDB Compound bitterdb.cpd ^\d+$ 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 urn:miriam:bitterdb.cpd chemical human http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$id 46 http://bitterdb.agri.huji.ac.il/dbbitter.php The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot Israel BioProject bioproject ^PRJ[DEN][A-Z]\d+$ 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. false urn:miriam:bioproject annotation ncbi http://www.ncbi.nlm.nih.gov/bioproject?term=$id PRJDB3 http://www.ncbi.nlm.nih.gov/bioproject National Center for Biotechnology Information (NCBI) USA ebi http://www.ebi.ac.uk/ena/data/view/$id PRJDB3 http://www.ebi.ac.uk/ena/ European Bioinformatics Institute, Hinxton, Cambridge UK http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=$id PRJDB3 http://trace.ddbj.nig.ac.jp/bioproject/ DNA Data Bank of Japan, Shizuoka Japan BioSample BioSdn BioSDe biosample ^SAM[NED](\w)?\d+$ 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. false urn:miriam:biosample annotation ncbi http://www.ncbi.nlm.nih.gov/biosample?term=$id SAMN00000002 http://www.ncbi.nlm.nih.gov/biosample National Center for Biotechnology Information (NCBI) USA http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$id SAMD00005257 http://trace.ddbj.nig.ac.jp/biosample/ Institution DNA Data Bank of Japan, Shizuoka Japan ebi http://www.ebi.ac.uk/biosamples/sample/$id SAMEA2397676 http://www.ebi.ac.uk/biosamples/ European Bioinformatics Institute, Hinxton, Cambridge UK PiroplasmaDB piroplasma ^TA\d+$ PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. false urn:miriam:piroplasma eukaryotic genome http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id TA14985 http://piroplasmadb.org/ Center for Tropical &amp; Emerging Global Diseases, University of Georgia, Georgia USA Unite unite ^UDB\d{6}$ 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. false urn:miriam:unite nucleotide sequence http://unite.ut.ee/bl_forw.php?nimi=$id UDB000691 http://unite.ut.ee/ Institute of Botany, University of Tartu, Tartu Estonia NCIm NCI metathesaurus National Cancer Institute Metathesaurus ncim ^C\d+$ NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. false urn:miriam:ncim ontology controlled vocabulary http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$id C0026339 http://ncim.nci.nih.gov/ National Cancer Institute, Center for Bioinformatics, Maryland USA ProGlycProt proglyc ^[A-Z]C\d{1,3}$ 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. false urn:miriam:proglyc sequence protein http://www.proglycprot.org/detail.aspx?ProId=$id AC119 http://www.proglycprot.org/ Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh India PolBase polbase ^[A-Za-z-0-9]+$ Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity. false urn:miriam:polbase enzyme DNA https://polbase.neb.com/polymerases/$id#sequences 19-T4 http://polbase.neb.com/ New England Biolabs, Ipswich, Massachusetts USA NucleaRDB nuclearbd ^\w+\_\w+$ NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs. false urn:miriam:nuclearbd interaction sequence protein http://www.receptors.org/nucleardb/proteins/$id prgr_human http://www.receptors.org/nucleardb/ CMBI, Radboud University Nijmegen Medical Centre, Dreijenplein, Wageningen Holland SUPFAM SUPERFAMILY supfam ^\w+$ SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. false urn:miriam:supfam protein structure http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id SSF57615 http://supfam.org/SUPERFAMILY/ MRC Laboratory of Molecular Biology, Cambridge UK Rice Genome Annotation Project ricegap ^LOC\_Os\d{1,2}g\d{5}$ The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines. false urn:miriam:ricegap sequence genome http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$id LOC_Os02g13300 http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml The Institute for Genomic Research, Rockville, Maryland USA PINA Protein Interaction Network Analysis pina ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ 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 urn:miriam:pina interaction protein http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$id&showExtend=null Q13485 http://cbg.garvan.unsw.edu.au/pina/ Garvan Institute of Medical Research, Sydney Australia Tissue List tissuelist ^TS-\d{4}$ 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. false urn:miriam:tissuelist controlled vocabulary http://www.uniprot.org/tissues/$id TS-0285 http://www.uniprot.org/docs/tisslist.txt Swiss Institute of Bioinformatics (SIB), Geneva Switzerland BacMap Biography bacmap.biog ^\d+$ BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. false urn:miriam:bacmap.biog genome microbial http://bacmap.wishartlab.com/organisms/$id 1050 http://bacmap.wishartlab.com/ Department of Computing Science, Food and Nutritional Science, University of Alberta, Edmonton Canada HGNC Symbol HUGO Gene Nomenclature Committee Symbol hgnc.symbol ^[A-Za-z-0-9_]+(\@)?$ The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. false urn:miriam:hgnc.symbol human gene ebi http://www.genenames.org/cgi-bin/gene_symbol_report?match=$id DAPK1 http://www.genenames.org/ European Bioinformatics Institute, Hinxton, Cambridge UK PANTHER Pathway panther.pathway ^P\d{5}$ The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. false urn:miriam:panther.pathway http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$id P00024 http://www.pantherdb.org/ Keck School of Medicine, University of Southern California USA BioSharing biosharing ^bsg-\d{6}$ The web-based BioSharing 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. false urn:miriam:biosharing registry https://www.biosharing.org/$id bsg-000052 https://www.biosharing.org/ Oxford e-Research Centre, University of Oxford, Oxford UK FungiDB fungidb ^[A-Za-z_0-9]+$ 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 urn:miriam:fungidb gene genome http://fungidb.org/gene/$id CNBG_0001 http://FungiDB.org Department of Plant Pathology & Microbiology, University of California, Riverside, California USA DARC Database of Aligned Ribosomal Complexes darc ^\d+$ 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 urn:miriam:darc structure protein http://darcsite.genzentrum.lmu.de/darc/view.php?id=$id 1250 http://darcsite.genzentrum.lmu.de/darc/index.php Gene Center and Department for Biochemistry and Center for integrated Protein Science Munich, University of Munich, Munich Germany DRSC FlyRNAi Drosophila RNAi Screening Cente drsc ^DRSC\d+$ 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. false urn:miriam:drsc gene expression eukaryotic http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$id DRSC05221 http://flyrnai.org/ Department of Genetics, Harvard Medical School, Boston, Massachusetts USA OriDB Schizosaccharomyces oridb.schizo ^\d+$ 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. false urn:miriam:oridb.schizo eukaryotic genome http://pombe.oridb.org/details.php?id=$id 1 http://pombe.oridb.org/index.php Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham UK OriDB Saccharomyces oridb.sacch ^\d+$ OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae. false urn:miriam:oridb.sacch genome eukaryotic http://cerevisiae.oridb.org/details.php?id=$id 1 http://cerevisiae.oridb.org/index.php Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham UK PSCDB Protein Structural Change DataBase pscdb ^\d+$ 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 urn:miriam:pscdb structure interaction protein http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$id.html 051 http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku Japan SCOP Structural Classification of Proteins scop ^\d+$ The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes. false urn:miriam:scop structure protein classification http://scop.bic.nus.edu.sg/search.cgi?sunid=$id 47419 http://scop.bic.nus.edu.sg/ National University Singapore Singapore http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$id 47419 http://scop.mrc-lmb.cam.ac.uk/scop/ MRC Laboratory of Molecular Biology, Centre for Protein Engineering, Hills Road, Cambridge UK http://scop.berkeley.edu/sunid=$id 47419 http://scop.berkeley.edu/ University of California, Berkeley USA ENA Embl-Bank European Nucleotide Archive ena.embl ^[A-Z]+[0-9]+(\.\d+)?$ 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. false urn:miriam:ena.embl nucleotide sequence ebi http://www.ebi.ac.uk/ena/data/view/$id BN000065 http://www.ebi.ac.uk/ena/ European Bioinformatics Institute, Hinxton, Cambridge UK DOMMINO Database of Macromolecular Interactions dommino ^[0-9][A-Za-z0-9]{3}$ DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. false urn:miriam:dommino interaction protein http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$id 2GC4 http://dommino.org/ Informatics Institute and Department of Computer Science and Bond Life Science Center, University of Missouri, Columbia USA PANTHER Node panther.node ^PTN\d{9}$ 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. false urn:miriam:panther.node http://www.pantree.org/node/annotationNode.jsp?id=$id PTN000000026 http://pantree.org/ Keck School of Medicine, University of Southern California USA Consensus CDS CCDS ccds ^CCDS\d+\.\d+$ The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. false urn:miriam:ccds protein genome mammalian sequence ncbi http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$id CCDS13573.1 http://www.ncbi.nlm.nih.gov/CCDS/ National Center for Biotechnology Information (NCBI) USA Locus Reference Genomic LRG lrg ^LRG_\d+$ Locus Reference Genomic (LRG) provides identifiers to stable genomic DNA sequences for regions of the human genome, providing a recognized reference-sequence standard for reporting sequence variants. LRG is maintained by the NCBI and the European Bioinformatics Institute (EBI). false urn:miriam:lrg DNA genome sequence human http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id LRG_1 http://asia.ensembl.org/ Singapore http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id LRG_1 http://uswest.ensembl.org/ USA ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$id.xml LRG_1 http://www.lrg-sequence.org/ Department of Genetics, University of Leicester, Leicester UK http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id LRG_1 http://www.ensembl.org/ EnSembl, Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge UK http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id LRG_1 http://useast.ensembl.org/ USA HPRD Human Protein Reference Database hprd ^\d+$ The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. false urn:miriam:hprd human protein http://www.hprd.org/protein/$id 00001 http://www.hprd.org/ Institute of Bioinformatics, International Tech Park, Bangalore India GXA Gene Gene Expression Atlas Gene gxa.gene ^\w+$ 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. false urn:miriam:gxa.gene expression microarray gene ebi http://www.ebi.ac.uk/gxa/genes/$id AT4G01080 http://www.ebi.ac.uk/gxa/ European Bioinformatics Institute, Hinxton, Cambridge UK GXA Expt Gene Expression Atlas Experiment gxa.expt ^[AEP]-\w{4}-\d+$ The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. false urn:miriam:gxa.expt expression microarray ebi http://www.ebi.ac.uk/gxa/experiments/$id E-MTAB-2037 http://www.ebi.ac.uk/gxa/ European Bioinformatics Institute, Hinxton, Cambridge UK MetaboLights metabolights ^MTBLS\d+$ MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. false urn:miriam:metabolights metabolite ebi http://www.ebi.ac.uk/metabolights/$id MTBLS1 http://www.ebi.ac.uk/metabolights/ European Bioinformatics Institute, Hinxton, Cambridge UK National Bibliography Number NBN nbn ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$ The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. false urn:miriam:nbn bibliography http://nbn-resolving.org/resolver?identifier=$id&verb=redirect urn:nbn:fi:tkk-004781 http://nbn-resolving.org/resolve_urn.htm Deutsche Nationalbibliothek, Frankfurt Germany ORCID Open Researcher and Contributor ID orcid ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. false urn:miriam:orcid bibliography https://orcid.org/$id 0000-0002-6309-7327 http://orcid.org ORCID Inc, Bethesda, Mayrland USA InChI IUPAC International Chemical Identifier inchi ^InChI\=1S?\/[A-Za-z0-9]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/]+)*$ The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier. false urn:miriam:inchi chemical structure http://rdf.openmolecules.net/?$id InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 http://rdf.openmolecules.net/ BiGCaT, Department of Bioinformatics, Maastricht Netherlands ebi http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$id InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 http://www.ebi.ac.uk/chebi/ European Bioinformatics Institute, Hinxton, Cambridge UK http://webbook.nist.gov/cgi/cbook.cgi?$id InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 http://webbook.nist.gov/chemistry National Institute of Standards and Technology, Gaithersburg, Maryland USA http://www.chemspider.com/$id InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 http://www.chemspider.com/ Royal Society of Chemistry, Cambridge UK Wikipedia (En) wikipedia.en ^[A-Za-z-0-9_]+$ Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay. false urn:miriam:wikipedia.en encyclopedia http://en.wikipedia.org/wiki/$id SM_UB-81 http://en.wikipedia.org/wiki/Main_Page Wikimedia Foundation, San Francisco, California USA http://dbpedia.org/page/$id SM_UB-81 http://wiki.dbpedia.org/ OpenLink Software, Burlington, Massachusetts USA PhosphoPoint Kinase phosphopoint.kinase ^\w+$ 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. false urn:miriam:phosphopoint.kinase interaction protein human http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$id&drawing=0&sorting=0&kinome=1 AURKA http://kinase.bioinformatics.tw/ Department of Computer Science and Information Engineering, National Taiwan University Republic of China PhosphoPoint Phosphoprotein phosphopoint.protein ^\w+$ 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. false urn:miriam:phosphopoint.protein interaction protein human http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$id&drawing=0&sorting=0&kinome=0 AURKA http://kinase.bioinformatics.tw/ Department of Computer Science and Information Engineering, National Taiwan University Republic of China InChIKey hashed InChI inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. false urn:miriam:inchikey structure chemical http://www.chemspider.com/inchikey=$id RYYVLZVUVIJVGH-UHFFFAOYSA-N http://www.chemspider.com/ Royal Society of Chemistry, Cambridge UK http://cactus.nci.nih.gov/chemical/structure/$id/names RYYVLZVUVIJVGH-UHFFFAOYSA-N http://cactus.nci.nih.gov/chemical/structure National Cancer Institute, Rockville, Maryland USA UniProt Isoform UniProtKB Isoform uniprot.isoform ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$ The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information. false urn:miriam:uniprot.isoform sequence protein http://www.uniprot.org/uniprot/$id Q5BJF6-3 http://www.uniprot.org/ UniProt Consortium USA, UK and Switzerland http://purl.uniprot.org/uniprot/$id Q5BJF6-3 http://purl.uniprot.org/ UniProt Consortium USA, UK and Switzerland http://www.uniprot.org/uniparc/?query=$id Q5BJF6-3 http://www.uniprot.org/uniparc/ UniProt Consortium USA, UK and Switzerland KEGG Environ KEGG kegg.environ ^(ev\:)?E\d+$ 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. false urn:miriam:kegg.environ drug chemical http://www.kegg.jp/entry/$id ev:E00032 http://www.genome.jp/kegg/drug/environ.html Kyoto University Bioinformatics Center Japan CLDB Cell Line Data Base cldb ^(cl|tum)\d+$ The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. false urn:miriam:cldb catalogue strain mammalian http://bioinformatics.hsanmartino.it/hypercldb/$id.html cl3603 http://bioinformatics.hsanmartino.it/hypercldb/indexes.html Bioinformatics, Cell Bank, National Cancer Research Institute, Genova Italy Experimental Factor Ontology EFO efo ^\d{7}$ 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. false urn:miriam:efo http://identifiers.org/efo/ ontology bptl http://purl.bioontology.org/ontology/EFO/efo:EFO_$id 0004859 http://bioportal.bioontology.org/ontologies/EFO National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=EFO:$id 0004859 http://www.ebi.ac.uk/ols/ontologies/efo European Bioinformatics Institute, Hinxton, Cambridge UK ebi http://www.ebi.ac.uk/efo/EFO_$id 0004859 http://www.ebi.ac.uk/efo/ European Bioinformatics Institute, Hinxton, Cambridge UK HGMD Human Gene Mutation Database hgmd ^[A-Z_0-9]+$ 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 urn:miriam:hgmd human disease gene http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$id CALM1 http://www.hgmd.cf.ac.uk/ac/index.php Cardiff University, Cardiff Wales AphidBase Transcript aphidbase.transcript ^ACYPI\d{6}(-RA)?$ AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. false urn:miriam:aphidbase.transcript sequence genome http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$id ACYPI000159 http://www.aphidbase.com/aphidbase INRA UMR, Le Rheu France Affymetrix Probeset affy.probeset \d{4,}((_[asx])?_at)? An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration. false http://bio2rdf.org/affymetrix urn:miriam:affy.probeset http://identifiers.org/affy.probeset/ nucleotide genome http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$id 243002_at http://cu.affymetrix.bio2rdf.org/fct/ Bio2RDF.org https://www.affymetrix.com/LinkServlet?probeset=$id 243002_at http://www.affymetrix.com/ Affymetrix, Santa Clara, California USA TreeFam treefam ^\w{1,2}\d+$ 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. false urn:miriam:treefam http://www.treefam.org/family/$id TF101014 http://www.treefam.org/ Beijing Genomics Institute, Beijing China CAPS-DB caps ^\d+$ CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. false urn:miriam:caps protein structure domain http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$id 434 http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home Leeds Institute of Molecular Medicine, Section of Experimental Therapeutics, University of Leeds, Leeds UK Cube db cubedb ^[A-Za-z_0-9]+$ Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. false urn:miriam:cubedb human domain protein http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$id/ AKR http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html Bioinformatics Institute, Singapore China IDEAL Intrinsically Disordered proteins with Extensive Annotations and Literature ideal ^IID\d+$ 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. false urn:miriam:ideal protein http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/idealItem.php?id=$id IID00001 http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/ Faculty of Engineering, Maebashi Institute of Technology, Maebashi Japan STAP Statistical Torsional Angles Potentials of NMR stap ^[0-9][A-Za-z0-9]{3}$ STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). false urn:miriam:stap structure protein http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$id 1a24 http://psb.kobic.re.kr/STAP/refinement/ Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon South Korea Pocketome pocketome ^[A-Za-z_0-9]+ Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries. false urn:miriam:pocketome structure protein interaction http://www.pocketome.org/files/$id.html 1433C_TOBAC_1_252 http://www.pocketome.org/sfSearch.cgi?act=browseall UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, California USA GOLD genome gold.genome ^[Gi|Gc]\d+$ The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes. false urn:miriam:gold.genome genome registry http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$id Gi07796 http://www.genomesonline.org/cgi-bin/GOLD/index.cgi Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, California USA GOLD metadata gold.meta ^Gm\d+$ The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples. false urn:miriam:gold.meta annotation genome http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$id Gm00047 http://www.genomesonline.org/cgi-bin/GOLD/index.cgi Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, California USA BugBase Protocol bugbase.protocol ^\d+$ BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. false urn:miriam:bugbase.protocol microarray microbial expression http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$id&amp;action=view 67 http://bugs.sgul.ac.uk/E-BUGS Bacterial Microarray Group, St George's, University of London UK BugBase Expt bugbase.expt ^\d+$ BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. false urn:miriam:bugbase.expt microarray expression microbial http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$id&action=view 288 http://bugs.sgul.ac.uk/E-BUGS Bacterial Microarray Group, St George's, University of London UK Tree of Life tol ^\d+$ The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things. false urn:miriam:tol classification http://tolweb.org/$id 98034 http://tolweb.org/tree/ University of Arizona USA VariO Variation Ontology vario ^VariO:\d+$ The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. false urn:miriam:vario DNA protein ontology http://www.variationontology.org/cgi-bin/amivario/term-details.cgi?term=$id VariO:0294 http://www.variationontology.org/ Department of Experimental Medical Science, Lund University Sweden bptl http://purl.bioontology.org/ontology/VARIO/$id VariO:0294 http://bioportal.bioontology.org/ontologies/VARIO National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/vario/terms?obo_id=$id VariO:0294 http://www.ebi.ac.uk/ols/ontologies/vario European Bioinformatics Institute, Hinxton, Cambridge UK ViPR Strain Virus Pathogen Resource Strain vipr ^[A-Za-z 0-9]+$ 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. false urn:miriam:vipr viral strain http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$id&decorator=arena BeAn 70563 http://www.viprbrc.org/brc/home.do?decorator=vipr J. Craig Venter Institute, San Diego, California USA EPD Eukaryotic Promoter Database epd ^[A-Z-_0-9]+$ The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. false urn:miriam:epd sequence DNA eukaryotic expression ebi http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+1fmSL1hlE31+-e+[EPD:'$id'] TA_H3 http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-lib+EPD European Bioinformatics Institute, Hinxton, Cambridge UK http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$id TA_H3 http://epd.vital-it.ch/ Swiss Institute of Bioinformatics (SIB), Geneva Switzerland RFAM RNA Family Database rfam ^RF\d{5}$ 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. false urn:miriam:rfam domain nucleotide ebi http://rfam.xfam.org/family/$id RF00230 http://rfam.xfam.org/ European Bioinformatics Institute, Hinxton, Cambridge UK http://rfam.janelia.org/family/$id RF00230 http://janelia.org/ Janelia Farm Research Campus, Ashburn, Virginia USA http://rfam.sanger.ac.uk/family/$id RF00230 http://rfam.sanger.ac.uk/ Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK Fungal Barcode Fungal Barcode of Life FBOL International Fungal Working Group fbol ^\d+$ 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. false urn:miriam:fbol classification eukaryotic http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$id&Fields=All&ExactMatch=T 2224 http://www.fungalbarcoding.org/ Fungal Biodiversity Centre, Utrecht Netherlands AFTOL Assembling the Fungal Tree of Life aftol.taxonomy ^\d+$ The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. false urn:miriam:aftol.taxonomy http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$id 959 http://aftol.org/data.php Department of Plant Biology, University of Minnesota, Minnesota USA AspGD Locus Aspergillus Genome Database Locus aspgd.locus ^[A-Za-z_0-9]+$ 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. false urn:miriam:aspgd.locus http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$id ASPL0000349247 http://www.aspgd.org/ Department of Genetics, Stanford University Medical School, Stanford, California USA AspGD Protein aspgd.protein ^[A-Za-z_0-9]+$ The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information. false urn:miriam:aspgd.protein http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$id ASPL0000349247 http://www.aspgd.org/ Department of Genetics, Stanford University Medical School, Stanford, California USA DrugBank Target v3 drugbank.target ^\d+$ 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 3 of the database. false urn:miriam:drugbank.target protein interaction http://v3.drugbank.ca/molecules/$id?as=target 54 http://v3.drugbank.ca/ Departments of Computing Science, Biological Sciences, University of Alberta Canada AutDB Autism Database autdb ^[A-Z]+[A-Z-0-9]{2,}$ 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. false urn:miriam:autdb human disorder gene http://autism.mindspec.org/GeneDetail/$id ADA http://autism.mindspec.org/autdb/ MindSpec Inc., Fairfax, Virginia USA BacMap Map bacmap.map ^\w+(\_)?\d+(\.\d+)?$ BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. false urn:miriam:bacmap.map genome microbial http://bacmap.wishartlab.com/maps/$id/index.html AP011135 http://bacmap.wishartlab.com/ Department of Computing Science, Food and Nutritional Science, University of Alberta, Edmonton Canada Bgee family bgee.family ^(ENSFM|ENSGTV:)\d+$ Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. false urn:miriam:bgee.family gene expression clustering http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$id ENSFM00500000270089 http://bgee.unil.ch/bgee/bgee Swiss Institute of Bioinformatics, Lausanne Switzerland Bgee gene bgee.gene ^(ENS|FBgn)\w+$ Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression within anatomical structures within a species. false urn:miriam:bgee.gene expression gene http://bgee.unil.ch/bgee/bgee?page=gene&action=summary&gene_id=$id ENSDARG00000013057 http://bgee.unil.ch/bgee/bgee Swiss Institute of Bioinformatics, Lausanne Switzerland Bgee stage bgee.stage ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$ 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. false urn:miriam:bgee.stage gene expression http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$id&stage_children=on HsapDO:0000004 http://bgee.unil.ch/bgee/bgee Swiss Institute of Bioinformatics, Lausanne Switzerland Bgee organ bgee.organ ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$ 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. false urn:miriam:bgee.organ controlled vocabulary expression gene http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$id&organ_children=on EHDAA:2185 http://bgee.unil.ch/bgee/bgee Swiss Institute of Bioinformatics, Lausanne Switzerland BioCarta Pathway biocarta.pathway ^([hm]\_)?\w+Pathway$ BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. false urn:miriam:biocarta.pathway pathway image library http://cgap.nci.nih.gov/Pathways/BioCarta/$id h_aktPathway http://www.biocarta.com/ National Cancer Institute, Center for Bioinformatics, Maryland USA PANTHER Pathway Component panther.pthcmp ^G|P|U|C|S\d{5}$ The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation. false urn:miriam:panther.pthcmp classification pathway protein http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$id P00266 http://www.pantherdb.org/ Keck School of Medicine, University of Southern California USA Golm Metabolome Database Profile gmd.profile ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. false urn:miriam:gmd.profile assay metabolite http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$id 10b38aaf-b977-4950-85b8-f4775f66658d http://gmd.mpimp-golm.mpg.de/ Max Planck Institute of Molecular Plant Physiology, Potsdam Germany Golm Metabolome Database GC-MS spectra gmd.gcms ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 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. false urn:miriam:gmd.gcms mass spectrometry metabolite http://gmd.mpimp-golm.mpg.de/Spectrums/$id 53d583d8-40c6-40e1-9296-23f821cd77a5 http://gmd.mpimp-golm.mpg.de/ Max Planck Institute of Molecular Plant Physiology, Potsdam Germany Golm Metabolome Database Reference Substance gmd.ref ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. false urn:miriam:gmd.ref metabolite structure catalogue http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$id 8cf84adb-b4db-4807-ac98-0004247c35df http://gmd.mpimp-golm.mpg.de/ Max Planck Institute of Molecular Plant Physiology, Potsdam Germany Golm Metabolome Database Analyte gmd.analyte ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 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. false urn:miriam:gmd.analyte metabolite structure mass spectrometry http://gmd.mpimp-golm.mpg.de/Analytes/$id 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 http://gmd.mpimp-golm.mpg.de/ Max Planck Institute of Molecular Plant Physiology, Potsdam Germany IntAct Molecule intact.molecule ^EBI\-[0-9]+$ IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. false urn:miriam:intact.molecule protein interaction ebi http://www.ebi.ac.uk/intact/molecule/$id EBI-366083 http://www.ebi.ac.uk/intact/ European Bioinformatics Institute, Hinxton, Cambridge UK DEPOD human DEPhOsphorylation Database depod ^[A-Z0-9]+$ The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. false urn:miriam:depod structure human interaction http://www.koehnlab.de/depod/showp.php?gene=$id PTPN1 http://www.koehnlab.de/depod/ European Molecular Biology Laboratory EMBL, Heidelberg Germany Cell Signaling Technology Pathways cst ^[A-Za-z0-9_-]+$ Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. false urn:miriam:cst immunogenetics catalogue pathway http://www.cellsignal.com/reference/pathway/$id.html Akt_PKB http://www.cellsignal.com/pathways/index.html Cell Signaling Technology, Inc., Danvers, Massachusetts USA Cell Signaling Technology Antibody cst.ab ^\d+$ Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. false urn:miriam:cst.ab catalogue immunogenetics interaction http://www.cellsignal.com/products/$id.html 3305 http://www.cellsignal.com/catalog/index.html Cell Signaling Technology, Inc., Danvers, Massachusetts USA National Drug Code NDC ndc ^\d+\-\d+\-\d+ The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. false urn:miriam:ndc http://identifiers.org/ndc/ http://bio2rdf.org/ndc catalogue drug http://healthprovidersdata.com/hipaa/codes/NDC_$id.aspx 0002-1975 http://healthprovidersdata.com/ Health Providers Data, Fargo, North Dakota USA http://ndc.bio2rdf.org/describe/?url=http://bio2rdf.org/ndc:$id 0002-1975-61 http://ndc.bio2rdf.org/fct Bio2RDF.org http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$id 0002-1975-61 http://www.accessdata.fda.gov/scripts/cder/ndc/ U.S. Food and Drug Administration, Maryland USA Phytozome Locus phytozome.locus ^[A-Za-z0-9]+$ 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. false urn:miriam:phytozome.locus http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$id Glyma0021s00410 http://www.phytozome.net/ Joint Genome Institute, California, and the Center for Integrative Genomics, Lausanne USA and Switzerland SubtiList subtilist ^BG\d+$ SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList 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. false urn:miriam:subtilist http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$id BG11523 http://genolist.pasteur.fr/SubtiList/ Pasteur Institute, Paris France DailyMed dailymed ^[A-Za-z0-9-]+ DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read. false urn:miriam:dailymed drug catalogue http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=$id 8889bcd7-d0e9-434b-b09d-30132bd033b0 http://dailymed.nlm.nih.gov/dailymed/ U.S. National Library of Medicine, Bethesda, Maryland USA SIDER Drug Side Effect Resource sider.drug ^\d+$ 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. false urn:miriam:sider.drug phenotype drug http://sideeffects.embl.de/drugs/$id/ 2244 http://sideeffects.embl.de/ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg Germany SIDER Side Effect sider.effect ^C\d+$ SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER. false urn:miriam:sider.effect phenotype drug http://sideeffects.embl.de/se/$id/ C0017565 http://sideeffects.embl.de/ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg Germany WikiGenes wikigenes ^\d+$ WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process. false urn:miriam:wikigenes interaction disease gene http://www.wikigenes.org/e/gene/e/$id.html 3771877 http://www.wikigenes.org/ Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts USA Broad Fungal Genome Initiative Magnaporthe comparative genomics database broad ^S\d+$ 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. false urn:miriam:broad fungal disease genome http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$id S7000002168151102 http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ Broad Institute of MIT and Harvard, Cambridge, Massachuchetts USA Coriell Cell Repositories coriell ^[A-Z]{2}\d+$ 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. false urn:miriam:coriell human mammalian catalogue http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$id GM17027 http://ccr.coriell.org/ Coriell Institute for Medical Research, New Jersey USA CORUM corum ^\d+$ 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. false urn:miriam:corum protein mammalian http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=$id 100 http://mips.helmholtz-muenchen.de/genre/proj/corum/ Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum M&amp;uuml;nchen-German Research Center for Environmental Health, Neuherberg Germany COGs Function Clusters of Orthologous Groups Function cogs.function ^[A-Z]$ Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. This collection references functional groups. false urn:miriam:cogs.function protein clustering ncbi http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?fun=$id A http://www.ncbi.nlm.nih.gov/COG/ National Center for Biotechnology Information (NCBI) USA EcoliWiki ecoliwiki ^[A-Za-z0-9-]+$ 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. false urn:miriam:ecoliwiki microbial genome http://ecoliwiki.net/colipedia/index.php/$id:Gene aaeA http://ecoliwiki.net/colipedia/ Texas Agrilife Research, Texas A&amp;M University College Station USA Genome Properties genprop ^GenProp\d+$ The Genome Properties system captures key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties, expressed using controlled vocabulary, reflect gene content, phenotype, phylogeny and computational analyses. Additional properties are derived from curation, published reports and other forms of evidence. false urn:miriam:genprop microbial controlled vocabulary http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomePropDefinition.cgi?prop_acc=$id GenProp0151 http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomePropertiesHomePage.cgi J Craig Venter institute, Rockville, Maryland USA JSTOR Journal Storage jstor ^\d+$ 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. false urn:miriam:jstor bibliography http://www.jstor.org/stable/$id 3075966 http://www.jstor.org/ Ithaka Harbors, Inc., New York USA Mouse Adult Gross Anatomy ma ^MA:\d+$ A structured controlled vocabulary of the adult anatomy of the mouse (Mus) true urn:miriam:ma ontology ols http://www.ebi.ac.uk/ols/ontologies/ma/terms?obo_id=$id MA:0002502 http://www.ebi.ac.uk/ols/ontologies/ma European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/MA/$id MA:0002502 http://bioportal.bioontology.org/ontologies/MA National Center for Biomedical Ontology, Stanford USA http://www.informatics.jax.org/searches/AMA.cgi?id=$id MA:0002502 http://www.informatics.jax.org/ The Jackson Laboratory, Bar Harbor, Maine USA UBERON Uber Anatomy Ontology uberon ^UBERON\:\d+$ 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. true http://purl.obolibrary.org/obo/UBERON http://identifiers.org/uberon/ urn:miriam:uberon ontology ols http://www.ebi.ac.uk/ols/ontologies/uberon/terms?obo_id=$id UBERON:0008203 http://www.ebi.ac.uk/ols/ontologies/uberon European Bioinformatics Institute, Hinxton, Cambridge UK bptl http://purl.bioontology.org/ontology/UBERON/$id UBERON:0008203 http://bioportal.bioontology.org/ontologies/UBERON National Center for Biomedical Ontology, Stanford USA Unimod unimod ^\d+$ Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). false urn:miriam:unimod mass spectrometry protein http://www.unimod.org/modifications_view.php?editid1=$id 1200 http://www.unimod.org/ Matrix Science Ltd., London UK VBRC Viral Bioinformatics Resource Center vbrc ^\d+$ The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. false urn:miriam:vbrc genome viral http://vbrc.org/gene_detail.asp?gene_id=$id 35742 http://vbrc.org/ University of Alabama, Birmingham and the University of Victoria, British Columbia USA and Canada ViralZone viralzone ^\d+$ 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. false urn:miriam:viralzone viral image library http://viralzone.expasy.org/all_by_protein/$id.html 992 http://www.expasy.org/viralzone/ Swiss Institute of Bioinformatics, Centre Médical Universitaire, Geneva Switzerland Gene Ontology Reference GO reference collection go.ref ^GO_REF:\d{7}$ 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 urn:miriam:go.ref controlled vocabulary http://www.geneontology.org/cgi-bin/references.cgi#$id GO_REF:0000041 http://www.geneontology.org/cgi-bin/references.cgi The Gene Ontology Consortium USA Rat Genome Database qTL rgd.qtl ^\d+$ Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes. false urn:miriam:rgd.qtl gene phenotype http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$id 1354581 http://rgd.mcw.edu/ Medical College of Wisconsin, Milwaukee, Wisconsin USA Rat Genome Database strain rgd.strain ^\d+$ Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology. false urn:miriam:rgd.strain http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$id 5688061 http://rgd.mcw.edu/ Medical College of Wisconsin, Milwaukee, Wisconsin USA DOOR Database for prOkaryotic OpeRons door ^\d+$ DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. false urn:miriam:door http://csbl1.bmb.uga.edu/OperonDB/genedetail.php?id=$id 60101 http://csbl1.bmb.uga.edu/OperonDB/DOOR.php Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia USA Degradome Database degradome ^[AMCST][0-9x][0-9]$ 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 urn:miriam:degradome http://degradome.uniovi.es/cgi-bin/protease/$id Ax1 http://degradome.uniovi.es/ Departamento de Bioqu&amp;amp;iacute;mica y Biolog&amp;amp;iacute;a Molecular, Facultad de Medicina, Universidad de Oviedo Spain DBD Transcription Factor Database dbd ^\d+$ The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. false urn:miriam:dbd http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$id+cat:DBD 0045310 http://www.transcriptionfactor.org/ MRC Laboratory of Molecular Biology, Cambridge UK DATF Database of Arabidopsis transcription factors datf ^AT[1-5]G\d{5}(\.\d+)?$ DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. false urn:miriam:datf http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$id AT1G01030.1 http://datf.cbi.pku.edu.cn/ Center for Bioinformatics, Peking Peoples Republic of China. IUPHAR ligand iuphar.ligand ^\d+$ 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. false urn:miriam:iuphar.ligand http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1755 http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all Centre for Cardiovascular Science, University of Edinburgh, Edinburgh UK Molbase molbase ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. false urn:miriam:molbase http://www.molbase.com/en/index.php?app=search&search_keyword=$id 128796-39-4 http://www.molbase.com/ Chinese Academy of Sciences, Xuhui District Shanghai China YRC PDR Yeast Resource Center Public Data Repository yrcpdr ^\d+$ 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. false urn:miriam:yrcpdr http://yeastrc.org/pdr/viewProtein.do?id=$id 2673500 http://www.yeastrc.org/pdr/ Department of Biochemistry, University of Washington, Seattle USA Yeast Intron Database v3 yid ^[A-Z0-9]+$ The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]. false urn:miriam:yid DNA eukaryotic sequence http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$id SNR17A http://compbio.soe.ucsc.edu/yeast_introns.html Baskin School of Engineering, Center for Molecular Biology of RNA, University of California, Santa Cruz, California USA FuncBase Fly funcbase.fly ^\d+$ 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. false urn:miriam:funcbase.fly http://func.mshri.on.ca/fly/genes/list_functional_scores/$id 10194 http://func.mshri.on.ca/fly Harvard Medical School, Boston, Massachusetts USA FuncBase Human funcbase.human ^\d+$ 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 urn:miriam:funcbase.human http://func.mshri.on.ca/human/genes/list_functional_scores/$id 119514 http://func.mshri.on.ca/human/ Harvard Medical School, Boston, Massachusetts USA FuncBase Mouse funcbase.mouse ^\d+$ Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. false urn:miriam:funcbase.mouse http://func.mshri.on.ca/mouse/genes/list_functional_scores/$id 1351341 http://func.mshri.on.ca/mouse/ Harvard Medical School, Boston, Massachusetts USA FuncBase Yeast funcbase.yeast ^\d+$ Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. false urn:miriam:funcbase.yeast http://func.mshri.on.ca/yeast/genes/list_functional_scores/$id 2701 http://func.mshri.on.ca/yeast Harvard Medical School, Boston, Massachusetts USA YDPM Yeast Deletion Project and Proteomics of Mitochondria Database ydpm ^Y[A-Z]{2}\d+[CW]$ 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 urn:miriam:ydpm http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$id YAL001C http://www-deletion.stanford.edu/YDPM/ Stanford University School of Medicine, Stanford, California USA WormBase RNAi wormbase.rnai ^WBRNAi\d{8}$ WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes. false urn:miriam:wormbase.rnai http://www.wormbase.org/species/c_elegans/rnai/$id WBRNAi00086878 http://www.wormbase.org/ Cold Spring Harbor Laboratory, Cold Spring, Harbor New York USA FunCat MIPS Functional Catalogue Database funcat ^\d{2}|\d{2}\.\d{2}|\d{2}\.\d{2}\.\d{2}|\d{2}\.\d{2}\.\d{2}\d{2}$ The Functional Catalogue (FunCat) is a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism. It has been applied for the manual annotation of prokaryotes, fungi, plants and animals. false urn:miriam:funcat http://mips.helmholtz-muenchen.de/funcatDB/cgi-bin/search_advanced.pl?action=2&wert=$id 32.01.01 http://mips.helmholtz-muenchen.de/funcatDB/ Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Neuherberg Germany PASS2 Protein Alignments organised as Structural Superfamilies pass2 ^\d+$ The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. false urn:miriam:pass2 http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$id 46977 http://caps.ncbs.res.in/pass2/ National centre for Biological Sciences, TIFR, GKVK campus, Bangalore, Karnataka India ICEberg element iceberg.element ^\d+$ 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. false urn:miriam:iceberg.element http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$id 100 http://db-mml.sjtu.edu.cn/ICEberg/ State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai China ICEberg family iceberg.family ^\d+$ 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. false urn:miriam:iceberg.family http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$id 1 http://db-mml.sjtu.edu.cn/ICEberg/ State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai China VFDB Genus Virulence Factor Database genus vfdb.genus ^\w+$ VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus. false urn:miriam:vfdb.genus http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$id Chlamydia http://www.mgc.ac.cn/VFs/ State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing China VFDB Gene vfdb.gene ^\w+$ VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes. false urn:miriam:vfdb.gene http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$id VFG2154 http://www.mgc.ac.cn/VFs/ State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing China MeSH 2013 mesh.2013 ^[A-Za-z0-9]+$ MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. false urn:miriam:mesh.2013 http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$id&view=expanded 17165 http://www.nlm.nih.gov/mesh/ U.S. National Library of Medicine, National Institute of Health, Maryland USA KEGG Module KEGG kegg.module ^([a-z]{3,5}_)?M\d{5}$ KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. false urn:miriam:kegg.module clustering http://www.kegg.jp/entry/$id M00002 http://www.kegg.jp/kegg/module.html Department of Computational Biology, University of Tokyo, Tokyo Japan KEGG Disease KEGG kegg.disease ^H\d+$ The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. false urn:miriam:kegg.disease disease http://www.kegg.jp/entry/$id H00076 http://www.genome.jp/kegg/disease/ Kyoto University Bioinformatics Center, Kyoto Japan MedlinePlus medlineplus ^\d+$ MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. false urn:miriam:medlineplus human encyclopedia http://www.nlm.nih.gov/medlineplus/ency/article/$id.htm 002804 http://www.nlm.nih.gov/medlineplus/ NCBI, NIH, Bethesda, Maryland USA LigandBox ligandbox ^D\d{5} LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. false urn:miriam:ligandbox chemical structure http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=$id D00001 http://ligandbox.protein.osaka-u.ac.jp/ligandbox//cgi-bin/index.cgi?LANG=en nstitute for Protein Research, Osaka University and Fujitsu Kyushu R&amp;D Center, Life Science Systems Dept., Fujitsu Japan GlycoEpitope glycoepitope ^EP\d{4}$ 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. false urn:miriam:glycoepitope interaction immunogenetics http://www.glycoepitope.jp/epitopes/$id EP0311 http://www.glycoepitope.jp/epitopes/ Kawasaki laboratory, Research Center for Glycobiotechnology, Ritsumeikan University Japan JCGGDB Japan Consortium for Glycobiology and Glycotechnology DataBase jcggdb ^JCGG-STR\d{6}$ 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. false urn:miriam:jcggdb lipid polysaccharide structure protein http://jcggdb.jp/idb/jcggdb/$id JCGG-STR008690 http://jcggdb.jp/index_en.html Advanced Science Institute(ASI), Chemical Biology Department Systems Glycobiology research Group, Saitama Japan NONCODE v4 Gene noncodev4.gene ^NONHSAG\d{5}$ NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions. false urn:miriam:noncodev4.gene expression gene sequence http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$id NONHSAG00001 http://www.bioinfo.org/NONCODEv4/ Bioinformatics Research Group, Chinese Academy of Sciences, Beijing China NONCODE v4 Transcript noncodev4.rna ^NONHSAT\d{6}$ 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. false urn:miriam:noncodev4.rna nucleotide expression http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$id NONHSAT000001 http://www.bioinfo.org/NONCODEv4/ Bioinformatics Research Group, Chinese Academy of Sciences, Beijing China Oryzabase Gene oryzabase.gene ^\d+$ Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information. false urn:miriam:oryzabase.gene gene plant http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$id 117 http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka Japan Oryzabase Mutant oryzabase.mutant ^\d+$ Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information. false urn:miriam:oryzabase.mutant plant phenotype http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$id 21393 http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka Japan Oryzabase Strain oryzabase.strain ^\d+$ 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. false urn:miriam:oryzabase.strain plant strain http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$id 1 http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka Japan Oryzabase Stage oryzabase.stage ^\d+$ 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. false urn:miriam:oryzabase.stage phenotype plant http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$id 34 http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka Japan Oryza Tag Line OTL otl ^A[A-Z]+\d+$ 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. false urn:miriam:otl plant phenotype http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$id AADB12 http://oryzatagline.cirad.fr/ CIRAD-INRA-SUPAGRO-UMII, Biological Systems Department, Montpellier France Gene Wiki genewiki ^\d+$ 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. false urn:miriam:genewiki encyclopedia gene human http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 http://en.wikipedia.org/wiki/Gene_Wiki Wikimedia Foundation, San Francisco, California USA PaxDb Organism paxdb.organism ^\d+$ 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. false urn:miriam:paxdb.organism genome expression protein http://pax-db.org/#!species/$id 9606 http://pax-db.org/ Institute of Molecular Life Sciences, University of Zurich, Zurich Switzerland PaxDb Protein paxdb.protein ^\d+$ 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. false urn:miriam:paxdb.protein protein expression http://pax-db.org/#!protein/$id 977869 http://pax-db.org/ Institute of Molecular Life Sciences, University of Zurich, Zurich Switzerland Protein Data Bank Ligand pdb.ligand ^[A-Za-z0-9]+$ The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands. false urn:miriam:pdb.ligand structure protein http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id TRQ http://www.pdbe.org/ European Bioinformatics Institute, Hinxton, Cambridge UK rcsb http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$id TRQ http://www.pdb.org/ Rutgers, The State University of New Jersey USA MEROPS Inhibitor merops.inhibitor ^I\d{2}\.\d{3}$ 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. false urn:miriam:merops.inhibitor protein interaction enzyme http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$id I31.952 http://merops.sanger.ac.uk/index.htm Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK Animal Diversity Web adw ^[A-Z_a-z]+$ Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. false urn:miriam:adw classification http://animaldiversity.ummz.umich.edu/accounts/$id/ Lycalopex_vetulus http://animaldiversity.ummz.umich.edu/ University of Michigan Museum of Zoology, Ann Arbor, Michigan USA GLIDA GPCR GPCR-LIgand DAtabase GPCR glida.gpcr ^[A-Z-_0-9]+$ 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. false urn:miriam:glida.gpcr interaction chemical http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$id ACM1_HUMAN http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto Japan GLIDA Ligand GPCR-LIgand DAtabase Ligand glida.ligand ^L\d+$ 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. false urn:miriam:glida.ligand interaction chemical http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$id L000001 http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto Japan GRSDB G-Rich Sequences DataBase grsdb ^\d+$ 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. false urn:miriam:grsdb nucleotide eukaryotic http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$id 10142 http://bioinformatics.ramapo.edu/GRSDB2/ Bioinformatics Group, School of Theoretical and Applied Science, Ramapo College of New Jersey, Mahwah USA F-SNP Functional Single Nucleotide Polymorphism fsnp ^rs\d+$ 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. false urn:miriam:fsnp nucleotide http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&amp;id_type=snp_id&amp;id_val=$id rs17852708 http://compbio.cs.queensu.ca/F-SNP/ Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, Ontario Canada Homeodomain Research hdr ^\d+$ 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 urn:miriam:hdr domain protein interaction http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&amp;view=proteins&amp;id=$id 63 http://research.nhgri.nih.gov/apps/homeodomain/web/ Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland USA NORINE norine ^NOR\d+$ Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings. false urn:miriam:norine microbial fungal protein http://bioinfo.lifl.fr/norine/result.jsp?ID=$id NOR00681 http://bioinfo.lifl.fr/norine/ Computer Science Laboratory of Lille, INRIA and ProBioGEM, University of Sciences and Technologies of Lille, Lille France Olfactory Receptor Database OrDB ordb ^\d+$ The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs). false urn:miriam:ordb sequence nucleotide http://senselab.med.yale.edu/ORDB/Data/$id 8497 http://senselab.med.yale.edu/OrDB/ Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut USA Odor Molecules DataBase OdorDB odor ^\d+$ OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors false urn:miriam:odor chemical http://senselab.med.yale.edu/OdorDB/Data/$id/?db=5 74 http://senselab.med.yale.edu/OdorDB Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut USA P3DB Protein p3db.protein ^\d+$ Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites. false urn:miriam:p3db.protein plant protein http://www.p3db.org/protein.php?id=$id&amp;ref=0 70 http://www.p3db.org/ Department of Computer Science, University of Missouri, Columbia, Missouri USA P3DB Site p3db.site ^\d+$ Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins. false urn:miriam:p3db.site protein plant http://www.p3db.org/phosphosite.php?id=$id&ref=0 65 http://www.p3db.org/ Department of Computer Science, University of Missouri, Columbia, Missouri USA TOPDB topdb ^[A-Z0-9]+$ 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. false urn:miriam:topdb protein http://topdb.enzim.hu/?m=show&id=$id AP00378 http://topdb.enzim.hu/ Institute of Enzymology, Hungarian Academy of Sciences, Budapest Hungary Animal Genome Cattle QTL cattleqtldb ^\d+$ 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 references cattle QTLs. false urn:miriam:cattleqtldb phenotype gene http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$id 4685 http://www.animalgenome.org/cgi-bin/QTLdb/BT/index Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa USA Animal Genome Chicken QTL chickenqtldb ^\d+$ 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 references chicken QTLs. false urn:miriam:chickenqtldb phenotype gene http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$id 14362 http://www.animalgenome.org/cgi-bin/QTLdb/GG/index Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa USA Animal Genome Pig QTL pigqtldb ^\d+$ 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 references pig QTLs. false urn:miriam:pigqtldb gene phenotype http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$id 14 http://www.animalgenome.org/cgi-bin/QTLdb/SS/index Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa USA Animal Genome Sheep QTL sheepqtldb ^\d+$ 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 references sheep QTLs. false urn:miriam:sheepqtldb gene phenotype http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$id 19803 http://www.animalgenome.org/cgi-bin/QTLdb/OA/index Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa USA Gramene Growth Stage Ontology gramene.growthstage ^GRO\:\d+$ 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 collection refers to growth stage ontology information in Gramene. true urn:miriam:gramene.growthstage ontology http://www.gramene.org/db/ontology/search?id=$id GRO:0007133 http://www.gramene.org/ Cold Spring Harbor Laboratory, New York USA NCBI GI ncbigi ^(GI|gi)\:\d+$ The NCBI GI (or "gi") identifier is the original form of identifier for sequence records processed by the NCBI. This 'GenInfo' identifier system was used to access GenBank and related databases, and was assigned to both protein and nucleotide sequences. false urn:miriam:ncbigi ncbi http://www.ncbi.nlm.nih.gov/protein/$id GI:9082283 http://www.ncbi.nlm.nih.gov/protein/ National Center for Biotechnology Information (NCBI) USA EBI Metagenomics Sample ebimetagenomics.samp ^[A-Z]+[0-9]+$ The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. false urn:miriam:ebimetagenomics.samp http://identifiers.org/ebimetagenomics/ urn:miriam:ebimetagenomics http://identifiers.org/ebimetagenomics.samp/ genome ebi http://www.ebi.ac.uk/metagenomics/samples/$id SRS086444 http://www.ebi.ac.uk/metagenomics European Bioinformatics Institute, Hinxton, Cambridge UK European Genome-phenome Archive Study EGA Study ega.study ^EGAS\d{11}$ The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. false urn:miriam:ega.study phenotype human gene ebi https://www.ebi.ac.uk/ega/studies/$id EGAS00000000001 https://www.ebi.ac.uk/ega/studies European Bioinformatics Institute, Hinxton, Cambridge UK European Genome-phenome Archive Dataset EGA Dataset ega.dataset ^EGAD\d{11}$ 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'. false urn:miriam:ega.dataset gene human phenotype ebi https://www.ebi.ac.uk/ega/datasets/$id EGAD00000000001 https://www.ebi.ac.uk/ega/dataset European Bioinformatics Institute, Hinxton, Cambridge UK ProteomeXchange px ^(R)?PXD\d+{6}$ The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. false urn:miriam:px urn:miriam:proteomexchange http://identifiers.org/px/ protein mass spectrometry http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$id PXD000500 http://www.proteomexchange.org/ Institute for Systems Biology, Seattle, WA, USA USA SBML RDF Vocabulary biomodels.vocabulary ^[A-Za-z]+$ Vocabulary used in the RDF representation of SBML models. false urn:miriam:biomodels.vocabulary http://biomodels.net/rdf/vocabulary.rdf#$id rateRule http://biomodels.net/rdf/vocabulary.rdf BioModels.net UK PRIDE Project pride.project ^P(X|R)D\d+{6}$ The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects. false urn:miriam:pride.project protein ebi http://www.ebi.ac.uk/pride/archive/projects/$id PXD000440 http://www.ebi.ac.uk/pride/ European Bioinformatics Institute, Hinxton, Cambridge UK Antibody Registry antibodyregistry ^\d+{6}$ 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. false urn:miriam:antibodyregistry registry immunogenetics http://antibodyregistry.org/AB_$id 493771 http://antibodyregistry.org/ Neuroscience Information Framework, University of California, San Diego, California USA Mathematical Modelling Ontology MAMO mamo ^MAMO_\d{7}$ The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. false urn:miriam:mamo bptl http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$id MAMO_0000026 http://bioportal.bioontology.org/ontologies/MAMO National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/mamo/terms?short_form=$id MAMO_0000026 http://www.ebi.ac.uk/ols/ontologies/mamo European Bioinformatics Institute, Hinxton, Cambridge UK Plant Environment Ontology Plant Environment Conditions eo ^(P)?EO\:\d{7}$ The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. true urn:miriam:peo http://identifiers.org/eo/ urn:miriam:eo controlled vocabulary plant bptl http://purl.bioontology.org/ontology/PECO/$id EO:0007404 http://bioportal.bioontology.org/ontologies/PECO National Center for Biomedical Ontology, Stanford USA http://archive.gramene.org/db/ontology/search?query=$id EO:0007404 http://archive.gramene.org/db/ontology/search_term?id=EO:0007359 Cold Spring Harbor Laboratory, New York USA ols http://www.ebi.ac.uk/ols/ontologies/eo/terms?obo_id=$id EO:0007404 http://www.ebi.ac.uk/ols/ontologies/eo European Bioinformatics Institute, Hinxton, Cambridge UK Identifiers.org Terms IdoT idot ^[A-Za-z]+$ Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. false urn:miriam:idot http://biomodels.net/vocab/idot.rdf#$id identifierPattern http://identifiers.org/ European Bioinformatics Institute, Hinxton, Cambridge UK HGNC Family hgnc.family ^[A-Z0-9-]+(#[A-Z0-9-]+)?$ 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 symbols for both structural and functional gene families. This collection refers to records using the HGNC family symbol. false urn:miriam:hgnc.family gene classification human http://www.genenames.org/genefamilies/$id PADI http://www.genenames.org/ European Bioinformatics Institute, Hinxton, Cambridge UK Yeast Intron Database v4.3 yeastintron ^[A-Z0-9]+$ The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]. false urn:miriam:yeastintron DNA sequence eukaryotic http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&amp;orfName=$id SNR17A http://intron.ucsc.edu/yeast4.3/ Baskin School of Engineering, Center for Molecular Biology of RNA, University of California, Santa Cruz, California USA Antibiotic Resistance Genes Database ARDB ardb ^[A-Z_]{3}[0-9]{4,}$ 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. false urn:miriam:ardb gene drug http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&amp;field=ni&amp;term=$id CAE46076 http://ardb.cbcb.umd.edu/ Center for Bioinformatics and Computational Biology, University of Maryland, Maryland USA Pathema pathema ^.+$ The over-arching goal of Pathema is to provide a core resource that will accelerated scientific progress towards understanding, detection, diagnosis and treatment of diseases caused by six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica — involved in new and re-emerging infectious diseases. Pathema provides comprehensive curated datasets for the targeted pathogen clades, along with advanced bioinformatics capabilities geared specifically towards biodefense requirements, and the identification of potential targets for vaccine development, therapeutics and diagnostics. false urn:miriam:pathema http://pathema.jcvi.org/$id http://pathema.jcvi.org/ ProteomicsDB Protein proteomicsdb.protein ^\d+$ ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins. false urn:miriam:proteomicsdb.protein human protein https://www.proteomicsdb.org/#human/proteinDetails/$id/summary 53504 https://www.proteomicsdb.org/#human Center for Integrated Protein Science, Munich, Germany ProteomicsDB Peptide proteomicsdb.peptide ^\d+$ 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. false urn:miriam:proteomicsdb.peptide human protein https://www.proteomicsdb.org/#human/proteinDetails/$id/peptides/ 53504 https://www.proteomicsdb.org/#peptideSearch Center for Integrated Protein Science, Munich Germany Human Proteome Map Protein HPM hpm.protein ^\d+$ The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. false urn:miriam:hpm.protein protein human http://www.humanproteomemap.org/protein.php?hpm_id=$id 1968 http://www.humanproteomemap.org/index.php Institute of Bioinformatics, International Tech Park, Bangalore India Human Proteome Map Peptide hpm.peptide ^\d+$ The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. false urn:miriam:hpm.peptide protein human http://www.humanproteomemap.org/spectrum.php?pep_id=$id 9606117 http://www.humanproteomemap.org/index.php Institute of Bioinformatics, International Tech Park, Bangalore India DrugBank Target v4 drugbankv4.target ^BE\d{7}$ 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 urn:miriam:drugbankv4.target protein chemical interaction http://www.drugbank.ca/biodb/bio_entities/$id BE0000048 http://www.drugbank.ca/targets Departments of Computing Science, Biological Sciences, University of Alberta Canada ZINC zinc ^(ZINC)?\d+$ ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. false urn:miriam:zinc structure chemical http://zinc15.docking.org/substances/$id ZINC1084 http://zinc15.docking.org/ Shoichet Laboratory, Department of Pharmaceutical Chemistry, University of California, San Francisco USA FooDB Compound foodb.compound ^FDB\d+$ FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. false urn:miriam:foodb.compound chemical structure http://foodb.ca/compounds/$id FDB002100 http://foodb.ca/foods University of Alberta, Edmonton, AB Canada UNII Substance Registration System Unique ingredient identifier unii ^[A-Z0-9]+$ 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. false urn:miriam:unii drug chemical http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$id 3G6A5W338E http://fdasis.nlm.nih.gov/srs/ U.S. Food and Drug Administration, Maryland USA Orphanet Rare Disease Ontology ORDO orphanet.ordo ^Orphanet(_|:)C?\d+$ The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10). false http://identifiers.org/orphanet.ordo/ http://www.orpha.net/ORDO/ urn:miriam:orphanet.ordo disease ontology ols http://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form=$id Orphanet_C023 http://www.ebi.ac.uk/ols/ontologies/ordo European Bioinformatics Institute, Hinxton, Cambridge UK Protein Affinity Reagents PSI-PAR psipar ^PAR:\d+$ 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. false urn:miriam:psipar ols http://www.ebi.ac.uk/ontology-lookup/?termId=$id PAR:0116 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR European Bioinformatics Institute, Hinxton, Cambridge UK ClinVar Record clinvar.record ^RCV\d+(\.\d+)?$ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. false urn:miriam:clinvar.record human phenotype gene ncbi http://www.ncbi.nlm.nih.gov/clinvar/$id/ RCV000033555.3 http://www.ncbi.nlm.nih.gov/clinvar/ National Center for Biotechnology Information (NCBI), NIH, Maryland USA EBI Metagenomics Project ebimetagenomics.proj ^[A-Z]+[0-9]+$ The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references projects. false urn:miriam:ebimetagenomics.proj genome ebi https://www.ebi.ac.uk/metagenomics/projects/$id ERP004492 https://www.ebi.ac.uk/metagenomics European Bioinformatics Institute, Hinxton, Cambridge UK EU Clinical Trials EU Clinical Trials Register euclinicaltrials ^\d{4}\-\d{6}\-\d{2}$ The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population. false urn:miriam:euclinicaltrials human pharmacogenomics disorder disease https://www.clinicaltrialsregister.eu/ctr-search/search?query=$id 2008-005144-16 https://www.clinicaltrialsregister.eu/ European Medicines Agency, London UK Google Patents google.patent ^[A-Z]{2}\d+([A-Z])?$ 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. false urn:miriam:google.patent registry https://www.google.com/patents/$id US4145692 https://www.google.com/patents/ Google Incorporated USPTO United States Patent and Trademark Office uspto ^(D|PP|R|T|H|X|AI)?\d+$ 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. false urn:miriam:uspto registry 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/$id 4145692 http://patft.uspto.gov/netahtml/PTO/index.html United States Patent and Trademark Office USA Cooperative Patent Classification CPC cpc ^([A-H,Y]|[A-H, Y]\d+{2}|[A-H, Y]\d+{2}[A-Z]|[A-H, Y]\d+{2}[A-Z]\d+{1,3}|[A-H, Y]\d+{2}[A-Z]\d+{1,3}(\/)?\d+{2,})$ The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. false urn:miriam:cpc classification http://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$id A01M1/026 http://worldwide.espacenet.com/classification Espace, European Patent Office GWAS Central Study gwascentral.study ^HGVST\d+$ GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. false urn:miriam:gwascentral.study phenotype human genome http://www.gwascentral.org/study/$id HGVST1828 http://www.gwascentral.org/studies Department of Genetics, University of Leicester, Leicester UK ExAC Variant exac.variant ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. false urn:miriam:exac.variant human genome phenotype http://exac.broadinstitute.org/variant/$id 22-46615880-T-C http://exac.broadinstitute.org/ Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts USA GWAS Central Marker gwascentral.marker ^HGVM\d+$ GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. false urn:miriam:gwascentral.marker human phenotype genome http://www.gwascentral.org/marker/$id HGVM15354 http://www.gwascentral.org/markers/ Department of Genetics, University of Leicester, Leicester UK GWAS Central Phenotype gwascentral.phenotype ^HGVP\d+$ GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. false urn:miriam:gwascentral.phenotype human genome phenotype http://www.gwascentral.org/phenotype/$id HGVPM623 http://www.gwascentral.org/phenotypes Department of Genetics, University of Leicester, Leicester UK LINCS Cell lincs.cell (^LCL-\d+{4}$)|(^LDC-\d+{4}$)|(^ES-\d+{4}$)|(^LSC-\d+{4}$)|(^LPC-\d+{4}$) The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease. false urn:miriam:lincs.cell human http://lincsportal.ccs.miami.edu/cells/#/view/$id LCL-2085 http://lincsportal.ccs.miami.edu/cells/ University of Miami, BD2K-LINCS DCIC USA LINCS Protein lincs.protein ^\d+$ The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. false urn:miriam:lincs.protein human http://lincs.hms.harvard.edu/db/proteins/$id/ 200282 http://lincs.hms.harvard.edu/db/proteins/ Harvard Medical School, Boston, Massachusetts USA LINCS Small Molecule lincs.smallmolecule ^LSM-\d+{4}$ 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). false urn:miriam:lincs.smallmolecule http://identifiers.org/lincs.smallmolecule/ urn:miriam:lincs.molecule human http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$id LSM-6306 http://lincsportal.ccs.miami.edu/SmallMolecules/ University of Miami, BD2K-LINCS DCIC, USA USA ExAC Transcript exac.transcript ^ENST\d{11}$ The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. false urn:miriam:exac.transcript genome phenotype human http://exac.broadinstitute.org/transcript/$id ENST00000407236 http://exac.broadinstitute.org/ Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts USA ExAC Gene exac.gene ^ENSG\d{11}$ 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. false urn:miriam:exac.gene phenotype human genome http://exac.broadinstitute.org/gene/$id ENSG00000169174 http://exac.broadinstitute.org/ Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts USA Wikidata wikidata ^Q\d+$ Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic. false urn:miriam:wikidata encyclopedia https://www.wikidata.org/wiki/$id Q2207226 https://www.wikidata.org/ Wikimedia Foundation, San Francisco, California USA SwissLipids swisslipid ^SLM:\d+$ SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions. true urn:miriam:swisslipid metabolite lipid http://www.swisslipids.org/#/entity/$id/ SLM:000048885 http://www.swisslipids.org/#/ Swiss Institute of Bioinformatics, Basel Switzerland UniPathway Compound unipathway.compound ^UPC\d{5}$ 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. false urn:miriam:unipathway.compound chemical structure metabolite http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$id UPC04349 http://www.grenoble.prabi.fr/obiwarehouse/unipathway Swiss Institute of Bioinformatics (SIB) and French National Institute for Research in Computer Science and Control Switzerland SEED Subsystem seed ^\w+$ 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. false urn:miriam:seed pathway http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$id Biotin_biosynthesis http://seed-viewer.theseed.org/seedviewer.cgi Argonne National Laboratory, University of Chicago, Argonne, Illinois USA SEED Compound seed.compound ^cpd\d+$ This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. false urn:miriam:seed.compound metabolite chemical structure http://modelseed.org/biochem/compounds/$id cpd15380 http://modelseed.org/ Argonne National Laboratory, University of Chicago, Argonne, Illinois USA BiGG Model bigg.model ^[a-z_A-Z0-9]+$ 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. false urn:miriam:bigg.model model http://bigg.ucsd.edu/models/$id iECABU_c1320 http://bigg.ucsd.edu/models Systems Biology Research Group at the University of California, San Diego USA BiGG Compartment bigg.compartment ^[a-z_A-Z]+$ BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. false urn:miriam:bigg.compartment model http://bigg.ucsd.edu/compartments/$id c http://bigg.ucsd.edu/compartments/ Systems Biology Research Group at the University of California, San Diego USA BiGG Metabolite bigg.metabolite ^[a-z_A-Z0-9]+$ 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 metabolotes. false urn:miriam:bigg.metabolite model http://bigg.ucsd.edu/models/universal/metabolites/$id 12dgr161 http://bigg.ucsd.edu/universal/metabolites Systems Biology Research Group at the University of California, San Diego USA BiGG Reaction bigg.reaction ^[a-z_A-Z0-9]+$ 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. false urn:miriam:bigg.reaction model http://bigg.ucsd.edu/models/universal/reactions/$id 13GS http://bigg.ucsd.edu/universal/reactions Systems Biology Research Group at the University of California, San Diego USA RRID Research Resource IDentifier rrid ^RRID:[A-Z_a-z-0-9]+$ 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. The 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. true urn:miriam:rrid registry https://scicrunch.org/resolver/$id RRID:AB_262044 https://scicrunch.org/resolver University of California, San Diego USA UMLS Unified Medical Language System umls ^C\d+$ 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. false urn:miriam:umls controlled vocabulary http://linkedlifedata.com/resource/umls/id/$id C0021390 http://linkedlifedata.com/ Linkedlifedata, Ontotext, Sofia Bulgaria MeSH Medical Subject Headings mesh ^(C|D)\d{6}$ 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. false urn:miriam:mesh http://id.nlm.nih.gov/mesh/$id C000100 http://id.nlm.nih.gov/mesh/ U.S. National Library of Medicine, National Institute of Health, Maryland USA Electron Microscopy Data Bank EMDB emdb ^EMD-\d{4}$ 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 urn:miriam:emdb mass spectrometry ebi http://www.ebi.ac.uk/pdbe/entry/emdb/$id EMD-1001 http://www.ebi.ac.uk/pdbe/emdb/ European Bioinformatics Institute, Hinxton, Cambridge UK miRTarBase mirtarbase ^MIRT\d{6}$ 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. false urn:miriam:mirtarbase nucleotide interaction http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$id MIRT000002 http://mirtarbase.mbc.nctu.edu.tw/ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu Taiwan MedDRA Medical Dictionary for Regulatory Activities meddra ^\d+$ 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). false urn:miriam:meddra ontology controlled vocabulary http://purl.bioontology.org/ontology/MEDDRA/$id 10015919 http://bioportal.bioontology.org/ontologies/MEDDRA National Center for Biomedical Ontology, Stanford USA DASHR Database of small human noncoding RNAs dashr ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ 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. false urn:miriam:dashr human nucleotide sequence http://lisanwanglab.org/DASHR/entry/$id hsa-mir-200a http://lisanwanglab.org/DASHR/ Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia USA DASHR expression dashr.expression ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ 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. false urn:miriam:dashr.expression sequence expression nucleotide human http://lisanwanglab.org/DASHR/entry/$id#exprPerTissueTable hsa-mir-200a http://lisanwanglab.org/DASHR/show-expression-table.php?start=0 Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia USA SPLASH splash ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$ The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance. false urn:miriam:splash metabolite mass spectrometry chemical http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$id splash10-0zq2000000-77302b0326a418630a84 http://mona.fiehnlab.ucdavis.edu/ University of Californai, Davis, California USA MetaNetX chemical metanetx.chemical ^MNXM\d+$ MetaNetx 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. false urn:miriam:metanetx.chemical model chemical http://metanetx.org/cgi-bin/mnxweb/chem_info?chem=$id MNXM55180 http://metanetx.org/ Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne Switzerland MetaNetX reaction metanetx.reaction ^MNXR\d+$ MetaNetx 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. false urn:miriam:metanetx.reaction reaction model http://metanetx.org/cgi-bin/mnxweb/equa_info?equa=$id MNXR3546 http://metanetx.org/ Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne Switzerland MetaNetX compartment metanetx.compartment ^MNXC\d+$ MetaNetx 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. false urn:miriam:metanetx.compartment model http://metanetx.org/cgi-bin/mnxweb/comp_info?comp=$id MNXC15 http://metanetx.org/ Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne Switzerland UniPathway Reaction unipathway.reaction ^UCR\d{5}$ 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. false urn:miriam:unipathway.reaction reaction http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$id UCR00226 http://www.grenoble.prabi.fr/obiwarehouse/unipathway Swiss Institute of Bioinformatics (SIB) and French National Institute for Research in Computer Science and Control Switzerland Human Phenotype Ontology HPO hp ^HP:\d{7}$ 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. true urn:miriam:hp http://purl.obolibrary.org/obo/HP urn:miriam:hpo http://identifiers.org/hp/ phenotype human ontology http://compbio.charite.de/hpoweb/showterm?id=$id HP:0000118 http://human-phenotype-ontology.github.io/ Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin, Berlin Germany ols http://www.ebi.ac.uk/ols/ontologies/hp/terms?obo_id=$id HP:0000118 http://www.ebi.ac.uk/ols/ontologies/hp European Bioinformatics Institute, Hinxton, Cambridge UK SASBDB Small Angle Scattering Biological Data Bank sasbdb ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$ Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. false urn:miriam:sasbdb structure domain http://www.sasbdb.org/data/$id SASDAX8 http://www.sasbdb.org/ Biological Small Angle Scattering Group, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg Germany HGNC gene family hgnc.genefamily ^\d+$ The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. false urn:miriam:hgnc.genefamily human http://www.genenames.org/cgi-bin/genefamilies/set/$id 141 http://www.genenames.org/ European Bioinformatics Institute, Hinxton, Cambridge UK MDM Medical Data Models mdm ^\d+$ The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. false urn:miriam:mdm human registry https://medical-data-models.org/forms/$id 4776 https://medical-data-models.org/ Institute of Medical Informatics, University of Muenster Germany ProbOnto Probability Distribution Ontology probonto ^PROB_c\d+$ 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. false urn:miriam:probonto ols http://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$id PROB_c0000005 http://www.ebi.ac.uk/ols/ontologies/probonto European Bioinformatics Institute, Hinxton, Cambridge UK APID Interactomes Agile Protein Interactomes DataServer apid.interactions ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. false urn:miriam:apid.interactions interaction protein http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$id P01116 http://cicblade.dep.usal.es:8080/APID/ Cancer Research Center (CiC-IBMCC), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Salamanca Spain STOREDB storedb ^STOREDB:(STUDY|FILE|DATASET)\d+$ STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. false urn:miriam:storedb https://www.storedb.org/?$id STOREDB:STUDY1040 https://www.storedb.org/ University of Cambridge, Department of Physiology, Downing Street, Cambridge UK Kyoto Encyclopedia of Genes and Genomes KEGG kegg ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$ Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. false urn:miriam:kegg chemical pathway genome http://www.kegg.jp/entry/$id hsa00190 http://www.kegg.jp/ Kyoto University Bioinformatics Center Japan Plant Transcription Factor Database PlantTFDB planttfdb ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$ 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. false urn:miriam:planttfdb DNA protein interaction http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$id Ath_AT1G01030.1 http://planttfdb.cbi.pku.edu.cn Center for Bioinformatics, Peking University, Beijing Peoples Republic of China Mammalian Phenotype Ontology mp ^MP:\d{7}$ The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. true urn:miriam:mp phenotype mammalian ontology ols http://www.ebi.ac.uk/ols/ontologies/mp/terms?obo_id=$id MP:0005452 http://www.ebi.ac.uk/ols/ontologies/mp/ European Bioinformatics Institute, Hinxton, Cambridge UK bptl https://bioportal.bioontology.org/ontologies/MP/$id MP:0005452 https://bioportal.bioontology.org/ontologies/MP National Center for Biomedical Ontology, Stanford USA http://www.informatics.jax.org/searches/Phat.cgi?id=$id MP:0005452 http://www.informatics.jax.org/ The Jackson Laboratory, Bar Harbor, Maine USA World Register of Marine Species WoRMS worms ^\d+$ 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. false urn:lsid:marinespecies.org:taxname:146421 urn:miriam:worms taxonomy classification http://www.marinespecies.org/aphia.php?p=taxdetails&id=$id 146421 http://www.marinespecies.org/ Flanders Marine Institute, Ostend Belgium MultiCellDS collection multicellds.collection ^MCDS_C_[a-zA-Z0-9]{1,10}$ MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). false urn:miriam:multicellds.collection model http://multicellds.org/MultiCellDB/$id MCDS_C_0000000001 http://multicellds.org/MultiCellDB.php Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California USA MultiCellDS Digital snapshot multicellds.snapshot ^MCDS_S_[a-zA-Z0-9]{1,10}$ MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. false urn:miriam:multicellds.snapshot model http://multicellds.org/MultiCellDB/$id MCDS_S_0000000001 http://multicellds.org/MultiCellDB.php Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California USA MultiCellDS Digital Cell Line multicellds.cell_line ^MCDS_L_[a-zA-Z0-9]{1,10}$ MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. false urn:miriam:multicellds.cell_line model http://multicellds.org/MultiCellDB/$id MCDS_L_0000000001 http://multicellds.org/MultiCellDB.php Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California USA E-cyanobacterium entity ecyano.entity ^\d+$ 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. false urn:miriam:ecyano.entity model metabolite http://e-cyanobacterium.org/bcs/entity/$id/ 23 http://www.e-cyanobacterium.org/bcs/entity/ Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno Czech Republic E-cyanobacterium model ecyano.model ^\d+$ 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 models. false urn:miriam:ecyano.model microbial model http://e-cyanobacterium.org/models/model/$id/ 26 http://e-cyanobacterium.org/models/ Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno Czech Republic E-cyanobacterium rule ecyano.rule ^\d+$ 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 rules. false urn:miriam:ecyano.rule reaction model http://e-cyanobacterium.org/bcs/rule/$id/ 56 http://www.e-cyanobacterium.org/bcs/rule/ Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno Czech Republic LINCS Data lincs.data ^LD[SG]-\d+$ 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). false urn:miriam:lincs.data human http://lincsportal.ccs.miami.edu/datasets/#/view/$id LDS-1110 http://lincsportal.ccs.miami.edu/datasets/ University of Miami, BD2K-LINCS DCIC USA AGRICOLA Agricultural Online Access argicola ^\d+$ AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. false urn:miriam:argicola http://ddr.nal.usda.gov/dspace/handle/10113/$id 50018 http://agricola.nal.usda.gov/ National Agricultural Library, United States Department of Agriculture USA Mass Spectrometry Controlled Vocabulary ms ^MS:\d{7}$ The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. true urn:miriam:ms controlled vocabulary mass spectrometry bptl http://purl.bioontology.org/ontology/MS/$id MS:1000001 https://bioportal.bioontology.org/ontologies/MS National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=$id MS:1000001 http://www.ebi.ac.uk/ols/ontologies/ms European Bioinformatics Institute, Hinxton, Cambridge UK Environment Ontology ENVO envo ^ENVO:\d{8}$ 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. true urn:miriam:envo ontology bptl http://purl.bioontology.org/ontology/ENVO/$id ENVO:09200010 http://purl.bioontology.org/ontology/ENVO/ National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=$id ENVO:09200010 http://www.ebi.ac.uk/ols/ontologies/envo European Bioinformatics Institute, Hinxton, Cambridge UK ARK Archival Resource Key ark ^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type. true urn:miriam:ark http://n2t.net/$id ark:/12345/fk1234 http://n2t.net/ California Digital Library, University of California Office of the President USA GRID Global Research Identifier Database grid ^grid\.[0-9]+\.[a-f0-9]{1,2}$ International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. false urn:miriam:grid https://www.grid.ac/institutes/$id grid.225360.0 https://www.grid.ac/ Digital Science &amp;amp; Research Ltd, London UK MedGen medgen ^[CN]*\d{4,7}$ 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. false urn:miriam:medgen human gene phenotype ncbi https://www.ncbi.nlm.nih.gov/medgen/$id 760050 https://www.ncbi.nlm.nih.gov/medgen/ National Center for Biotechnology Information (NCBI), NIH, Maryland USA ClinVar Submission clinvar.submission ^SCV\d+(\.\d+)?$ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. false urn:miriam:clinvar.sub urn:miriam:clinvar.submission http://identifiers.org/clinvar.submission/ ncbi http://www.ncbi.nlm.nih.gov/clinvar?term=$id SCV000151292 http://www.ncbi.nlm.nih.gov/clinvar/ National Center for Biotechnology Information (NCBI), NIH, Maryland USA ClinVar Variant clinvar ^\d+$ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. false urn:miriam:clinvar ncbi https://www.ncbi.nlm.nih.gov/clinvar/variation/$id 12345 http://www.ncbi.nlm.nih.gov/clinvar/ National Center for Biotechnology Information (NCBI), NIH, Maryland USA BioAssay Ontology bao ^\d{7}$ 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 urn:miriam:bao bptl http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$id 0002989 http://bioportal.bioontology.org/ontologies/BAO/ National Center for Biomedical Ontology, Stanford USA ols http://www.ebi.ac.uk/ols/ontologies/bao/terms?obo_id=BAO:$id 0002989 http://bioportal.bioontology.org/ontologies/BAO/ European Bioinformatics Institute, Hinxton, Cambridge UK Cellosaurus cellosaurus CVCL_[A-Z0-9]{4} The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines. false urn:miriam:cellosaurus sib http://web.expasy.org/cellosaurus/$id CVCL_0030 http://web.expasy.org/cellosaurus/ Swiss Institute of Bioinformatics Swizerland Identifiers.org Registry mir ^MIR:\d{8}$ 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. true urn:miriam:mir ebi http://identifiers.org/registry?query="$id" MIR:00100037 http://identifiers.org/registry European Bioinformatics Institute, Hinxton, Cambridge UK Progenetix Cancer Genome Knowledge Resource pgx ^[\w\-:,]{3,64}$ The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 32317 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1026 articles and represents 364 different cancer types, according to the International classification of Diseases in Oncology (ICD-O). false urn:miriam:pgx http://progenetix.org/pgx:$id icdom:8500_3 http://progenetix.org/ University of Zurich Switzerland COSMIC Gene Catalogue of Somatic Mutations in Cancer Gene cosmic ^[A-Z0-9]+$ 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. false urn:miriam:cosmic http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$id BRAF http://cancer.sanger.ac.uk/cosmic/ Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK dbGaP Database of Genotypes and Phenotypes dbgap ^phs[0-9]{6}.v\d+.p\d+$ The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. false urn:miriam:dbgap ncbi https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$id phs000768.v2.p1 https://www.ncbi.nlm.nih.gov/projects/gap National Center for Biotechnology Information (NCBI) USA