Difference between revisions of "DrugBank MITAB2.6 File Format"
From irefindex
PaulBoddie (talk | contribs) (→Format Summary: Fixed protein alias source, added an example column.) |
PaulBoddie (talk | contribs) (→Format Summary: Added columns.) |
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| <tt>pubmed:10505536</tt> | | <tt>pubmed:10505536</tt> | ||
| <tt>drug/<partners>/<partner>/references</tt> (filtered) | | <tt>drug/<partners>/<partner>/references</tt> (filtered) | ||
| + | |- | ||
| + | | taxA | ||
| + | | colspan="3" | ''Not used'' | ||
| + | |- | ||
| + | | taxB | ||
| + | | Taxonomy identifier for protein | ||
| + | | <tt>9606</tt> | ||
| + | | ''UniProt'' | ||
| + | |- | ||
| + | | interactionType | ||
| + | | colspan="3" | ''Not used'' | ||
| + | |- | ||
| + | | sourcedb | ||
| + | | Source database reference having the form <tt>ontology-term-code(ontology-term-name)</tt> (see [http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A2002&termName=drugbank MI:2002]) | ||
| + | | <tt>MI:2002(drugbank)</tt> | ||
| + | | ''implicit'' | ||
| + | |- | ||
| + | | interactionIdentifier | ||
| + | | The DrugBank identifier used by uidA | ||
| + | | <tt>DrugBank:DB00123</tt> | ||
| + | | <tt>drug/drugbank-id</tt> | ||
| + | |- | ||
| + | | confidence | ||
| + | | colspan="3" | ''Not used'' | ||
| + | |- | ||
| + | | expansion | ||
| + | | colspan="3" | ''Not used'' | ||
| + | |- | ||
| + | | biological_role_A | ||
| + | | colspan="3" | ''Not used'' | ||
| + | |- | ||
| + | | biological_role_B | ||
| + | | colspan="3" | ''Not used'' | ||
| + | |- | ||
| + | | experimental_role_A | ||
| + | | colspan="3" | ''Not used'' | ||
| + | |- | ||
| + | | experimental_role_B | ||
| + | | colspan="3" | ''Not used'' | ||
| + | |- | ||
| + | | interactor_type_A | ||
| + | | An ontology reference having the form <tt>ontology-term-code(ontology-term-name)</tt> where appropriate | ||
| + | | <tt>MI:0326(protein)</tt> | ||
| + | | derived from <tt>drug/protein-sequences</tt> | ||
| + | |- | ||
| + | | interactor_type_B | ||
| + | | An ontology reference having the form <tt>ontology-term-code(ontology-term-name)</tt> where appropriate | ||
| + | | <tt>MI:0326(protein)</tt> | ||
| + | | derived from <tt><partner>/protein-sequence</tt> or <tt>drug/protein-sequences</tt> | ||
|} | |} | ||
Revision as of 14:10, 8 February 2011
Last edited: 2011-02-08
Description
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 |
drugbank:APRD00123 InChIKey:MSTNYGQPCMXVAQ-KIYNQFGBSA-N |
drug/secondary-accession-numbers/secondary-accession-number drug/calculated-properties/calculated-property drug/external-identifiers/external-identifier/identifier |
| 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 DrugBank_brand:Refludan |
drug/synonyms/synonym drug/brands/brand |
| 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 |
