iRefIndex MITAB Mapping

From irefindex
Revision as of 16:09, 10 June 2011 by Sabry (talk | contribs)

Unlike the parsing of PSI MI XML files, whose attributes correspond to certain tables and columns in the iRefIndex schema, the parsing and interpretation of MITAB files involves a separate mapping of MITAB format columns to such tables and columns in the schema.

MITAB columns Data components Entity iRefIndex table and column assignments iRefIndex category UID to use
uidA database:identifier Interactor int_xref.dbid = id(database)
int_xref.acc = identifier
object_primaryref
uidB
altA object_secondaryref
altB
aliasA int_name.name = identifier
int_name.MI = 'MI:0000'
object_alias
aliasB
method code(description) Experiment int_xref.dbid = id('psi-mi')
int_xref.acc = code
int_ditection_primaryref
int_name.MI = code
int_name.name = description
int_ditection_shortlbl
authors (free text) Experiment
pmids pubmed:identifier int_experiment.ex_bib_pri = identifier (not applicable)
taxA taxid:identifier Interactor int_xref.taxid = identifier (part of interactor entries labelled with object_primaryref and object_secondaryref only)
taxB
interactionType code(description) Interaction int_xref.dbid = id('psi-mi')
int_xref.acc = code
int_type_primaryref
int_name.MI = code
int_name.name = description
int_type_sh
sourcedb Interactor/interaction int_source.source = id(description)
int_object.source = id(description)
int_source2object.source = id(description)
(not applicable)
interactionIdentifiers database:identifier Interaction int_xref.dbid = database
int_xref.acc = identifier
interaction_primaryref
confidence