Difference between revisions of "DrugBank MITAB2.6 File Format"
From irefindex
PaulBoddie (talk | contribs) (Changed DrugBank to drugbank and InChIKey to inchikey for general consistency. Added the remaining columns.) |
PaulBoddie (talk | contribs) (→Format Summary: Updated the taxonomy description and adjusted the formatting.) |
||
| Line 26: | Line 26: | ||
|- | |- | ||
| altA | | 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 | + | | DrugBank secondary accessions having the form <tt>drugbank:<em>accession</em></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:<em>key</em></tt><br>External identifiers for the drug |
| <tt>drugbank:APRD00123</tt><br><tt>inchikey:MSTNYGQPCMXVAQ-KIYNQFGBSA-N</tt> | | <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) of the form <tt>database:identifier</tt><br>For drugs: see altA | + | | For proteins: external identifiers (other than UniProt identifiers) of the form <tt><em>database</em>:<em>identifier</em></tt><br>For drugs: see altA |
| <tt>GNC:7645</tt> | | <tt>GNC:7645</tt> | ||
| <tt><partner>/external-identifiers/external-identifier/identifier</tt> (for proteins) | | <tt><partner>/external-identifiers/external-identifier/identifier</tt> (for proteins) | ||
| Line 41: | Line 41: | ||
|- | |- | ||
| 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:<em>protein name</em></tt><br>For drugs: see aliasA |
| <tt>drugbank_synonym:Arylamine N-acetyltransferase 1</tt> | | <tt>drugbank_synonym:Arylamine N-acetyltransferase 1</tt> | ||
| <tt><partner>/name</tt> (for proteins) | | <tt><partner>/name</tt> (for proteins) | ||
| Line 60: | Line 60: | ||
|- | |- | ||
| taxB | | taxB | ||
| − | | Taxonomy identifier for protein | + | | Taxonomy identifier for protein of the form <tt>taxid:<em>identifier</em></tt> |
| − | | <tt>9606</tt> | + | | <tt>taxid:9606</tt> |
| taken from UniProt | | taken from UniProt | ||
|- | |- | ||
| Line 68: | Line 68: | ||
|- | |- | ||
| sourcedb | | 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]) | + | | Source database reference having the form <tt><em>ontology-term-code</em>(<em>ontology-term-name</em>)</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> | | <tt>MI:2002(drugbank)</tt> | ||
| implicit | | implicit | ||
| Line 98: | Line 98: | ||
|- | |- | ||
| interactor_type_A | | interactor_type_A | ||
| − | | An ontology reference having the form <tt>ontology-term-code(ontology-term-name)</tt> where appropriate | + | | An ontology reference having the form <tt><em>ontology-term-code</em>(<em>ontology-term-name</em>)</tt> where appropriate |
| <tt>MI:0326(protein)</tt> | | <tt>MI:0326(protein)</tt> | ||
| derived from <tt>drug/protein-sequences</tt> | | derived from <tt>drug/protein-sequences</tt> | ||
Revision as of 17:08, 21 March 2011
Last edited: 2011-03-21
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 of the form taxid:identifier | taxid:9606 | taken from 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 | The action of the drug in the context of its partners | antagonist | drug/<partners>/<partner>/actions/action |
| 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 | See interactor_type_B | derived from <partner>/protein-sequence or drug/protein-sequences | |
| xrefs_A | Not used | ||
| xrefs_B | Not used | ||
| xrefs_Interaction | Not used | ||
| Annotations_A | Not used | ||
| Annotations_B | Not used | ||
| Annotations_Interaction | Not used | ||
| Host_organism_taxid | Not used | ||
| parameters_Interaction | Not used | ||
| Creation_date | The DrugBank creation date | 2005-06-13 07:24:05 -0600 | drug/@created |
| Update_date | The DrugBank update date | 2011-01-04 14:50:20 -0700 | drug/@updated |
| Checksum_A | For drugs: the InChIKey prefixed with inchikey: if available For proteins: the ROG identifier (rogid) prefixed with rogid: |
inchikey:PAJMKGZZBBTTOY-YRIDSSQKSA-N rogid:XgNg624m2wB07gcr/v+a02LvhNM6421 |
InChIKey references occur in drug/calculated-properties/property ROG identifiers are derived from drug/protein-sequences |
| Checksum_B | See Checksum_A | InChIKey references occur in drug/calculated-properties/property ROG identifiers are derived from <partner>/protein-sequence or drug/protein-sequences | |
| Checksum_Interaction | For combinations of identifiers from Checksum_A and Checksum_B: the RIG identifier (rigid) prefixed with rigid: | rigid:mIwyIi4hME210rHllHmsQ5t3n9k | derived from Checksum_A and Checksum_B |
