View source for DrugBank MITAB2.6 File Format

Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}

== Description ==

This document describes usage of the PSI-MITAB2.6 format in order to represent the drug-protein and drug-drug interactions provided by [http://drugbank.ca/ DrugBank] in a form suitable for consumption by MITAB-aware tools and services such as [[iRefIndex_MITAB2.6_Parser|MITAB parsers]] and [[README_PSICQUIC_web_services_for_iRefIndex|PSICQUIC Web services]].

Although MITAB2.6 is used by iRefIndex (as described in the [[README_MITAB2.6_for_iRefIndex_8.0|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 ==

{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
! Field
! Description
! Example
! Source
|-
| uidA
| A DrugBank identifier
| <tt>drugbank:DB00123</tt>
| <tt>drug/drugbank-id</tt>
|-
| uidB
| 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)
|-
| altA
| 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>
|-
| altB
| 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)
|-
| aliasA
| 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>
|-
| aliasB
| For proteins: synonyms having the form <tt>drugbank_synonym:protein name</tt><br>For drugs: see aliasA
| <tt>drugbank_synonym:Arylamine N-acetyltransferase 1</tt>
| <tt>&lt;partner&gt;/name</tt> (for proteins)
|-
| Method
| colspan="3" | ''Not used''
|-
| author
| colspan="3" | ''Not used''
|-
| pmids
| PubMed identifiers describing an interaction
| <tt>pubmed:10505536</tt>
| <tt>drug/&lt;partners&gt;/&lt;partner&gt;/references</tt> (filtered)
|-
| taxA
| colspan="3" | ''Not used''
|-
| taxB
| Taxonomy identifier for protein
| <tt>9606</tt>
| taken from 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
| The action of the drug in the context of its partners
| <tt>antagonist</tt>
| <tt>drug/&lt;partners&gt;/&lt;partner&gt;/actions/action</tt>
|-
| 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
| colspan="2" | See interactor_type_B
| derived from <tt>&lt;partner&gt;/protein-sequence</tt> or <tt>drug/protein-sequences</tt>
|-
| xrefs_A
| colspan="3" | ''Not used''
|-
| xrefs_B
| colspan="3" | ''Not used''
|-
| xrefs_Interaction
| colspan="3" | ''Not used''
|-
| Annotations_A
| colspan="3" | ''Not used''
|-
| Annotations_B
| colspan="3" | ''Not used''
|-
| Annotations_Interaction
| colspan="3" | ''Not used''
|-
| Host_organism_taxid
| colspan="3" | ''Not used''
|-
| parameters_Interaction
| colspan="3" | ''Not used''
|-
| Creation_date
| The DrugBank creation date
| <tt>2005-06-13 07:24:05 -0600</tt>
| <tt>drug/@created</tt>
|-
| Update_date
| The DrugBank update date
| <tt>2011-01-04 14:50:20 -0700</tt>
| <tt>drug/@updated</tt>
|-
| Checksum_A
| For drugs: the InChIKey prefixed with <tt>inchikey:</tt> if available<br>For proteins: the ROG identifier (rogid) prefixed with <tt>rogid:</tt>
| <tt>inchikey:PAJMKGZZBBTTOY-YRIDSSQKSA-N</tt><br><tt>rogid:XgNg624m2wB07gcr/v+a02LvhNM6421</tt>
| InChIKey references occur in <tt>drug/calculated-properties/property</tt><br>ROG identifiers are derived from <tt>drug/protein-sequences</tt>
|-
| Checksum_B
| colspan="2" | See Checksum_A
| InChIKey references occur in <tt>drug/calculated-properties/property</tt><br>ROG identifiers are derived from <tt>&lt;partner&gt;/protein-sequence</tt> or <tt>drug/protein-sequences</tt>
|-
| Checksum_Interaction
| For combinations of identifiers from Checksum_A and Checksum_B: the RIG identifier (rigid) prefixed with <tt>rigid:</tt>
| <tt>rigid:mIwyIi4hME210rHllHmsQ5t3n9k</tt>
| derived from Checksum_A and Checksum_B
|}