iRefIndex MITAB Mapping

From irefindex
Revision as of 18:18, 10 June 2011 by PaulBoddie (talk | contribs) (Attempt to incorporate summary table details into the mapping table. Not sure about the interactionType, however.)

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'
object_shortlbl (first entry)
object_alias (second and subsequent entries)
method code(description) Experiment int_xref.dbid = id('psi-mi')
int_xref.acc = code
int_name.MI = code = description
authors (free text) Experiment int_name.MI = 'MI:0000' = authors
pmids pubmed:identifier int_xref.dbid = id('pubmed')
int_xref.acc = identifier
bib_primaryref (first entry)
bib_secondaryref (second and subsequent entries)
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 14
6 aliasB(From second) Interactor_B int_name object_alias 14
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