Difference between revisions of "iRefIndex MITAB Mapping"

From irefindex
(Attempt to incorporate summary table details into the mapping table. Not sure about the interactionType, however.)
(Removed lower table, added category tag.)
Line 82: Line 82:
 
|}
 
|}
  
−
=== Summary mapping ===
+
[[Category:iRefIndex]]
−
{|border="1" cellspacing="0" cellpadding="5" style="margin: 2em" {{table}}
 
−
| align="center" style="background:#f0f0f0;"|'''Column_Number'''
 
−
| align="center" style="background:#f0f0f0;"|'''Column_Name'''
 
−
| align="center" style="background:#f0f0f0;"|'''UID_to _use'''
 
−
| align="center" style="background:#f0f0f0;"|'''Table_to_use'''
 
−
| align="center" style="background:#f0f0f0;"|'''Category_to_use'''
 
−
| align="center" style="background:#f0f0f0;"|'''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
 
−
|
 
−
|}
 

Revision as of 09:25, 15 June 2011

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_shortlbl (first entry)
object_alias (second and subsequent entries)
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 int_name.MI = 'MI:0000'
int.name.name = authors 		experim_shortlbl
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)
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
Retrieved from "http://irefindex.vib.be/wiki/index.php?title=iRefIndex_MITAB_Mapping&oldid=3496"