iRefIndex MITAB Mapping
From irefindex
Revision as of 18:18, 10 June 2011 by PaulBoddie (talk | contribs) (Attempt to incorporate summary table details into the mapping table. Not sure about the interactionType, however.)
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 |
