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ID_MAPPING.csv

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URIRecommended nameRegistry identifierAlternative name(s)DescriptionIdentifier patternType
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http://identifiers.org/clinicaltrials/clinicaltrialMIR:00000137NCTClinicalTrials.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^NCT\d{8}$Entity
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http://identifiers.org/hgnc/hgncMIR:00000080HUGO Gene Nomenclature CommitteeThe HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.^((HGNC|hgnc):)?\d{1,5}$Entity
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http://identifiers.org/kegg.drug/kegg.drugMIR:00000025KEGGKEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.^D\d+$Entity
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http://identifiers.org/ensembl.protein/ensembl.proteinEntity
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http://identifiers.org/refseq/refseqMIR:00000039The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?$Entity
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http://identifiers.org/drugbank/drugbankMIR:00000102The 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.^DB\d{5}$Entity
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http://identifiers.org/inchi/inchiMIR:00000383IUPAC International Chemical IdentifierThe 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.^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$Entity
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http://identifiers.org/kegg.pathway/kegg.pathwayMIR:00000012KEGGKEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.^\w{2,4}\d{5}$Entity
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http://identifiers.org/hp/hpMIR:00000571hpThe 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.^HP:\d{7}$Entity
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http://identifiers.org/dbsnp/dbsnpMIR:00000161The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.^rs\d+$Entity
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http://identifiers.org/reactome/ReactomeMIR:00000018Reactome Stable IDThe Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.(^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$)Entity
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http://identifiers.org/pubmed/pubmedMIR:00000015PubMed 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.^\d+$Entity
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http://identifiers.org/ensembl/ensemblMIR:00000003Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.^((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$Entity
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http://identifiers.org/uniprot/uniprotMIR:00000005UniProtKB UniProt Protein Knowledgebase UniProt-TrEMBL UniProt/TrEMBL UniProtKB/Swiss-ProtThe 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.^([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+)?$Entity
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http://identifiers.org/unigene/unigeneMIR:00000346A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.^\d+$Entity
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http://identifiers.org/ensembl.transcript/ensembl.transcriptEntity
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http://identifiers.org/hgnc.symbol/hgnc.symbolMIR:00000362HUGO Gene Nomenclature Committee SymbolThe HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.^[A-Za-z-0-9_]+(\@)?$Entity
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http://identifiers.org/ensembl.gene/ensembl.geneEntity
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http://identifiers.org/clinicalsignificance/clinicalsignificanceEntity
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http://identifiers.org/ensembl.translation/ensembl.translationEntity
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http://identifiers.org/mgi/mgiMIR:00000037MGD MGI Mouse Genome InformaticsThe Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.^MGI:\d+$Entity
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http://identifiers.org/pdb/pdbMIR:00000020PDBThe Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.^[0-9][A-Za-z0-9]{3}$Entity
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http://identifiers.org/hgvs/hgvsEntity
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http://identifiers.org/ccds/ccdsMIR:00000375CCDSThe Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.^CCDS\d+\.\d+$Entity
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http://identifiers.org/kegg.compound/kegg.compoundMIR:00000013KEGGKEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.^C\d+$Entity
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http://identifiers.org/biocarta.pathway/biocarta.pathwayMIR:00000421BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps.^([hm]\_)?\w+Pathway$Entity
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http://identifiers.org/clinvar/clinvarMIR:00000596ClinVar 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.^\d+$Entity
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http://identifiers.org/wikipathways/wikipathwaysMIR:00000076WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style. All content is under the Creative Commons Attribution 3.0 Unported license.WP\d{1,5}(\_r\d+)?$Entity
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http://identifiers.org/rxcui/rxnormEntity
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http://identifiers.org/efo/efoMIR:00000391EFOThe Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.^\d{7}$Entity
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http://identifiers.org/pubchem.compound/pubchem.compoundMIR:00000034PubChem Compound PubChem CIDPubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.^\d+$Entity
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http://identifiers.org/unii/uniiMIR:00000531Substance Registration System Unique ingredient identifierThe 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‰Ûªs molecular structure and/or descriptive information.^[A-Z0-9]+$Entity
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http://identifiers.org/chembl/chemblEntity
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http://identifiers.org/iuphar.ligand/iuphar.ligandMIR:00000457The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.^\d+$Entity
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http://identifiers.org/ncbigene/ncbigeneMIR:00000069Entrez GeneEntrez 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.^\d+$Entity
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http://identifiers.org/chebi/chebiEntity
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http://identifiers.org/zfin/zfinEntity
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http://identifiers.org/omim/omimOnline Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.^[*#+%^]?\d{6}$Entity
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http://identifiers.org/inchikey/inchikeyMIR:00000387hashed InChIThe 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.^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?Entity
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http://identifiers.org/doid/doMIR:00000233DOThe 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.^DOID\:\d+$Entity
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http://identifiers.org/taxonomy/taxonomyMIR:00000006NEWT NCBI taxonomyThe taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.^\d+$Entity
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http://identifiers.org/orphanet/orphanetMIR:00000220OrphaOrphanet is a reference portal for information on rare diseases and orphan drugs. It‰Ûªs aim is to help improve the diagnosis, care and treatment of patients with rare diseases.^\d+$Entity
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http://identifiers.org/pharmgkb.pathways/pharmgkb.pathwayMIR:00000089The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.^PA\d+$Entity
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http://biothings.io/terms/drugname/drugnameEntity
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http://identifiers.org/mesh/meshMIR:00000560Medical Subject HeadingsMeSH (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.^(C|D)\d{6}$Entity
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http://identifiers.org/ncit/nciMIR:00000139NCI thesaurusNCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code.^C\d+$Entity
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http://identifiers.org/snomedct/snomedMIR:00000269SNOMED 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. ^(\w+)?\d+$Entity
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http://identifiers.org/umls/umlsMIR:00000559Unified Medical Language SystemThe Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.^C\d+$Entity
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http://biothings.io/concepts/genotypes/Genotype ObjectObject
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http://biothings.io/concepts/phenotypes/Phenotype ObjectObject
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http://biothings.io/concepts/ptm/PTM ObjectObject
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http://biothings.io/concepts/molecular_processing/Molecular Processing ObjectObject
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http://biothings.io/concepts/topology/TOPLOGY ObjectObject
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http://biothings.io/concepts/clinical_evidence/Clinical Evidence ObjectObject
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http://biothings.io/concepts/disease_name/Disease NameEntity
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http://biothings.io/concepts/drug_interaction/Drug Interaction ObjectObject