Difference between revisions of "DrugBank MITAB2.6 File Format"

From irefindex
(→‎Format Summary: Added sources, more fields.)
(→‎Format Summary: Fixed protein alias source, added an example column.)
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! Field
 
! Field
 
! Description
 
! Description
 +
! Example
 
! Source
 
! Source
 
|-
 
|-
 
| uidA
 
| uidA
| A DrugBank identifier having the form <tt>DrugBank:DB00123</tt>
+
| A DrugBank identifier
 +
| <tt>DrugBank:DB00123</tt>
 
| <tt>drug/drugbank-id</tt>
 
| <tt>drug/drugbank-id</tt>
 
|-
 
|-
 
| uidB
 
| uidB
 
| For proteins: the given UniProt identifiers<br>For drugs: see uidA
 
| For proteins: the given UniProt identifiers<br>For drugs: see uidA
 +
| <tt>UniProtKB:P18440</tt>
 
| <tt>&lt;partner&gt;/external-identifiers/external-identifier/identifier</tt> (for proteins)
 
| <tt>&lt;partner&gt;/external-identifiers/external-identifier/identifier</tt> (for proteins)
 
|-
 
|-
 
| altA
 
| altA
| DrugBank secondary accessions having the form <tt>drugbank:APRD00123</tt> (compatible with [http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A2002&termName=drugbank MI:2002])<br>InChIKey values of the form <tt>MSTNYGQPCMXVAQ-KIYNQFGBSA-N</tt><br>External identifiers for the drug
+
| DrugBank secondary accessions having the form <tt>drugbank:accession</tt> (compatible with [http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A2002&termName=drugbank MI:2002])<br>InChIKey values of the form <tt>InChIKey:key</tt><br>External identifiers for the drug
 +
| <tt>drugbank:APRD00123</tt><br><tt>InChIKey:MSTNYGQPCMXVAQ-KIYNQFGBSA-N</tt>
 
| <tt>drug/secondary-accession-numbers/secondary-accession-number</tt><br><tt>drug/calculated-properties/calculated-property</tt><br><tt>drug/external-identifiers/external-identifier/identifier</tt>
 
| <tt>drug/secondary-accession-numbers/secondary-accession-number</tt><br><tt>drug/calculated-properties/calculated-property</tt><br><tt>drug/external-identifiers/external-identifier/identifier</tt>
 
|-
 
|-
 
| altB
 
| altB
| For proteins: external identifiers other than UniProt identifiers<br>For drugs: see altA
+
| For proteins: external identifiers (other than UniProt identifiers) of the form <tt>database:identifier</tt><br>For drugs: see altA
 +
| <tt>GNC:7645</tt>
 
| <tt>&lt;partner&gt;/external-identifiers/external-identifier/identifier</tt> (for proteins)
 
| <tt>&lt;partner&gt;/external-identifiers/external-identifier/identifier</tt> (for proteins)
 
|-
 
|-
 
| aliasA
 
| aliasA
| DrugBank synonyms and brand names having the form <tt>DrugBank_synonym:drug name</tt> and <tt>DrugBank_brand:drug name</tt> respectively
+
| DrugBank synonyms and brand names using <tt>DrugBank_synonym</tt> and <tt>DrugBank_brand</tt> as qualifiers
 +
| <tt>DrugBank_synonym:Hirudin variant-1</tt><br><tt>DrugBank_brand:Refludan</tt>
 
| <tt>drug/synonyms/synonym</tt><br><tt>drug/brands/brand</tt>
 
| <tt>drug/synonyms/synonym</tt><br><tt>drug/brands/brand</tt>
 
|-
 
|-
 
| aliasB
 
| aliasB
 
| For proteins: synonyms having the form <tt>DrugBank_synonym:protein name</tt><br>For drugs: see aliasA
 
| For proteins: synonyms having the form <tt>DrugBank_synonym:protein name</tt><br>For drugs: see aliasA
| <tt>&lt;partner&gt;/external-identifiers/external-identifier/identifier</tt> (for proteins)
+
| <tt>DrugBank_synonym:Arylamine N-acetyltransferase 1</tt>
 +
| <tt>&lt;partner&gt;/name</tt> (for proteins)
 
|-
 
|-
 
| Method
 
| Method
| colspan="2" | ''Not used''
+
| colspan="3" | ''Not used''
 
|-
 
|-
 
| author
 
| author
| colspan="2" | ''Not used''
+
| colspan="3" | ''Not used''
 
|-
 
|-
 
| pmids
 
| pmids
| PubMed identifiers describing an interaction having the form <tt>pubmed:10505536</tt>
+
| PubMed identifiers describing an interaction
 +
| <tt>pubmed:10505536</tt>
 
| <tt>drug/&lt;partners&gt;/&lt;partner&gt;/references</tt> (filtered)
 
| <tt>drug/&lt;partners&gt;/&lt;partner&gt;/references</tt> (filtered)
 
|}
 
|}

Revision as of 18:25, 31 January 2011

Last edited: 2011-01-31

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)