iRefIndex MITAB Mapping
From irefindex
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 |
