Difference between revisions of "iRefIndex MITAB Mapping"
From irefindex
PaulBoddie (talk | contribs) (Attempt to incorporate summary table details into the mapping table. Not sure about the interactionType, however.) |
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| Line 23: | Line 23: | ||
| 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 | ||
| Line 39: | Line 39: | ||
| (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> | + | | <tt>int_xref.dbid = id('pubmed')</tt><br><tt>int_xref.acc = ''identifier''</tt> |
| − | | ( | + | | 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 |
