Difference between revisions of "iRefIndex MITAB Mapping"

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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.
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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 [http://code.google.com/p/psicquic/wiki/PsimiTabFormat PSI-MI TAB] (MITAB) files involves a separate mapping of MITAB format columns to such tables and columns in the schema.
  
 
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
 
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
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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>
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| rowspan="2" | object_alias
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| 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
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|
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| <tt>int_name.MI = 'MI:0000'</tt><br><tt>int.name.name = ''authors''</tt>
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|
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| experim_shortlbl
 
|-
 
|-
 
| pmids
 
| pmids
 
| <tt>pubmed:''identifier''</tt>
 
| <tt>pubmed:''identifier''</tt>
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| <tt>int_experiment.ex_bib_pri = ''identifier''</tt>
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| <tt>int_xref.dbid = id('pubmed')</tt><br><tt>int_xref.acc = ''identifier''</tt>
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| (not applicable)
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| bib_primaryref (first entry)<br>bib_secondaryref (second and subsequent entries)
 
|-
 
|-
 
| taxA
 
| taxA
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|}
 
|}
  
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=== Summary mapping ===
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[[Category:iRefIndex]]
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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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|-
 
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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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|-
 
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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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|-
 
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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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|-
 
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| 7||Method (name)||Experiment||int_name||int_detection_shortlbl||24
 
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|-
 
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| 8||author||Experiment||int_name||experim_shortlbl||18
 
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|-
 
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| 9||Pmids (frist one)||Experiment||int_xref||bib_primaryref ||4
 
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|-
 
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| 9||Pmids (Second one onwards)||Experiment||int_xref||bib_secondaryref ||5
 
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|-
 
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| 10||taxa||(used with uidA)||||||
 
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|-
 
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| 11||taxb||(used with uidB)||||||
 
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|-
 
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| 12||interactionType||Interaction||int_name||int_type_sh||27
 
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|-
 
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| 13||sourcedb||(used with interactionIdentifier)||||||
 
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|-
 
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| 14||interactionIdentifier||Interaction||int_xref||interaction_primaryref||0
 
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|
 
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|}
 

Latest revision as of 15:37, 29 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 PSI-MI TAB (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
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