Difference between revisions of "iRefIndex MITAB Mapping"
From irefindex
PaulBoddie (talk | contribs) (Attempt to document the MITAB format in terms of the iRefIndex schema.) |
PaulBoddie (talk | contribs) (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 15:06, 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 |
