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Difference between revisions of "iRefIndex MITAB Mapping"

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(Attempt to document the MITAB format in terms of the iRefIndex schema.)
 
(Added int_xref.dbid for interactionType, interactionIdentifiers.)
Line 58: Line 58:
 
| rowspan="3" | <tt>''code''(''description'')</tt>
 
| rowspan="3" | <tt>''code''(''description'')</tt>
 
| rowspan="2" | Interaction
 
| rowspan="2" | Interaction
| <tt>int_xref.acc = ''code''</tt>
+
| <tt>int_xref.dbid = id('psi-mi')</tt><br><tt>int_xref.acc = ''code''</tt>
 
| int_type_primaryref
 
| int_type_primaryref
 
|-
 
|-
Line 72: Line 72:
 
| <tt>''database'':''identifier''</tt>
 
| <tt>''database'':''identifier''</tt>
 
| Interaction
 
| Interaction
| <tt>int_xref.acc = ''identifier''</tt>
+
| <tt>int_xref.dbid = ''database''</tt><br><tt>int_xref.acc = ''identifier''</tt>
 
| interaction_primaryref
 
| interaction_primaryref
 
|-
 
|-

Revision as of 08:06, 10 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_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