iRefIndex MITAB Mapping

From irefindex
Revision as of 16:32, 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
uidA database:identifier Interactor int_xref.dbid = id(database)
int_xref.acc = identifier
altA object_secondaryref
aliasA = identifier
int_name.MI = 'MI:0000'
method code(description) Experiment int_xref.dbid = id('psi-mi')
int_xref.acc = code
int_name.MI = code = description
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)
interactionType code(description) Interaction int_xref.dbid = id('psi-mi')
int_xref.acc = code
int_name.MI = code = description
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

Summary mapping

Column_Number Column_Name UID_to _use Table_to_use Category_to_use Category_ID
1 uidA Interactor_A int_xref object_primaryref 2
2 uidB Interactor_B int_xref object_primaryref 2
3 altA Interactor_A int_xref object_secondaryref 3
4 altB Interactor_B int_xref object_secondaryref 4
5 aliasA (First ) Interactor_A int_name First entry object_shortlbl 10,11
6 aliasB(First) Interactor_B int_name First entry object_shortlbl 10,11
5 aliasA(From second) Interactor_A int_name object_alias
6 aliasB(From second) Interactor_B int_name object_alias
7 Method (MI identfier) Experiment int_xref int_detection_primaryref 6
7 Method (name) Experiment int_name int_detection_shortlbl 24
8 author Experiment int_name experim_shortlbl 18
9 Pmids (frist one) Experiment int_xref bib_primaryref 4
9 Pmids (Second one onwards) Experiment int_xref bib_secondaryref 5
10 taxa (used with uidA)
11 taxb (used with uidB)
12 interactionType Interaction int_name int_type_sh 27
13 sourcedb (used with interactionIdentifier)
14 interactionIdentifier Interaction int_xref interaction_primaryref 0