DrugBank MITAB2.6 File Format

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Revision as of 14:10, 8 February 2011 by PaulBoddie (talk | contribs) (→‎Format Summary: Added columns.)

Last edited: 2011-02-08


This document describes usage of the PSI-MITAB2.6 format in order to represent the drug-protein and drug-drug interactions provided by DrugBank in a form suitable for consumption by MITAB-aware tools and services such as MITAB parsers and PSICQUIC Web services.

Although MITAB2.6 is used by iRefIndex (as described in the format documentation), certain elements of that extended format are not directly applicable to DrugBank data, whereas other elements (such as a general checksum for an interactor) are applicable but not directly equivalent to the kind of data provided by iRefIndex: although a drug may have an InChIKey - a form of checksum or hash of the chemical structure of the drug - it is not equivalent or directly comparable to the ROG (redundant object group) employed by iRefIndex.

Format Summary

Field Description Example Source
uidA A DrugBank identifier DrugBank:DB00123 drug/drugbank-id
uidB For proteins: the given UniProt identifiers
For drugs: see uidA
UniProtKB:P18440 <partner>/external-identifiers/external-identifier/identifier (for proteins)
altA DrugBank secondary accessions having the form drugbank:accession (compatible with MI:2002)
InChIKey values of the form InChIKey:key
External identifiers for the drug
altB For proteins: external identifiers (other than UniProt identifiers) of the form database:identifier
For drugs: see altA
GNC:7645 <partner>/external-identifiers/external-identifier/identifier (for proteins)
aliasA DrugBank synonyms and brand names using DrugBank_synonym and DrugBank_brand as qualifiers DrugBank_synonym:Hirudin variant-1
aliasB For proteins: synonyms having the form DrugBank_synonym:protein name
For drugs: see aliasA
DrugBank_synonym:Arylamine N-acetyltransferase 1 <partner>/name (for proteins)
Method Not used
author Not used
pmids PubMed identifiers describing an interaction pubmed:10505536 drug/<partners>/<partner>/references (filtered)
taxA Not used
taxB Taxonomy identifier for protein 9606 UniProt
interactionType Not used
sourcedb Source database reference having the form ontology-term-code(ontology-term-name) (see MI:2002) MI:2002(drugbank) implicit
interactionIdentifier The DrugBank identifier used by uidA DrugBank:DB00123 drug/drugbank-id
confidence Not used
expansion Not used
biological_role_A Not used
biological_role_B Not used
experimental_role_A Not used
experimental_role_B Not used
interactor_type_A An ontology reference having the form ontology-term-code(ontology-term-name) where appropriate MI:0326(protein) derived from drug/protein-sequences
interactor_type_B An ontology reference having the form ontology-term-code(ontology-term-name) where appropriate MI:0326(protein) derived from <partner>/protein-sequence or drug/protein-sequences