Difference between revisions of "iRefIndex MITAB Mapping"

From irefindex
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=== Summary mapping ===
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{|border="1" cellspacing="0" cellpadding="5" style="margin: 2em" {{table}}
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| align="center" style="background:#f0f0f0;"|'''Column_Number'''
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| align="center" style="background:#f0f0f0;"|'''Column_Name'''
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| align="center" style="background:#f0f0f0;"|'''UID_to _use'''
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| align="center" style="background:#f0f0f0;"|'''Table_to_use'''
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| align="center" style="background:#f0f0f0;"|'''Category_to_use'''
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| align="center" style="background:#f0f0f0;"|'''Category_ID'''
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|-
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| 1||uidA||Interactor_A||int_xref||object_primaryref||2
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|-
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| 2||uidB||Interactor_B||int_xref||object_primaryref||2
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| 3||altA||Interactor_A||int_xref||object_secondaryref||3
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|-
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| 4||altB||Interactor_B||int_xref||object_secondaryref||4
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|-
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| 5||aliasA (First )||Interactor_A||int_name||First entry object_shortlbl||10,11
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| 6||aliasB(First)||Interactor_B||int_name||First entry object_shortlbl||10,11
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|-
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| 5||aliasA(From second)||Interactor_A||int_name||object_alias||
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| 6||aliasB(From second)||Interactor_B||int_name||object_alias||
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|-
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| 7||Method (MI identfier)||Experiment||int_xref||int_detection_primaryref||6
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| 7||Method (name)||Experiment||int_name||int_detection_shortlbl||24
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| 8||author||Experiment||int_name||experim_shortlbl||18
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| 9||Pmids (frist one)||Experiment||int_xref||bib_primaryref ||4
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| 9||Pmids (Second one onwards)||Experiment||int_xref||bib_secondaryref ||5
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| 10||taxa||(used with uidA)||||||
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| 11||taxb||(used with uidB)||||||
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| 12||interactionType||Interaction||int_name||int_type_sh||27
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| 13||sourcedb||(used with interactionIdentifier)||||||
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| 14||interactionIdentifier||Interaction||int_xref||interaction_primaryref||0
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Revision as of 16:32, 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

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
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