iRefIndex MITAB Mapping

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	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

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