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.)
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| aliasA
 
| aliasA
 
| rowspan="2" | <tt>int_name.name = ''identifier''</tt><br><tt>int_name.MI = 'MI:0000'</tt>
 
| rowspan="2" | <tt>int_name.name = ''identifier''</tt><br><tt>int_name.MI = 'MI:0000'</tt>
| rowspan="2" | object_alias
+
| rowspan="2" | object_shortlbl (first entry)<br>object_alias (second and subsequent entries)
 
|-
 
|-
 
| aliasB
 
| aliasB
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| (free text)
 
| (free text)
 
| rowspan="2" | Experiment
 
| rowspan="2" | Experiment
|
+
| <tt>int_name.MI = 'MI:0000'</tt><br><tt>int.name.name = ''authors''</tt>
|
+
| experim_shortlbl
 
|-
 
|-
 
| pmids
 
| pmids
 
| <tt>pubmed:''identifier''</tt>
 
| <tt>pubmed:''identifier''</tt>
| <tt>int_experiment.ex_bib_pri = ''identifier''</tt>
+
| <tt>int_xref.dbid = id('pubmed')</tt><br><tt>int_xref.acc = ''identifier''</tt>
| (not applicable)
+
| bib_primaryref (first entry)<br>bib_secondaryref (second and subsequent entries)
 
|-
 
|-
 
| taxA
 
| taxA

Revision as of 18:18, 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_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

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