PSI-MI TAB Formatted Downloads

The MITAB format is part of the PSI-MI 2.5 standard. It is derived from the TAB 1.0 format provided by the BioGRID. MITAB only described binary interactions with one pair of interactions per row. Columns are separated by tabulations.

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How to Detect a PSI-MI TAB file

PSI-MI Tab files are denoted by the extension .mitab.txt or .mitab.zip

Column Definitions

The column contents of PSI-MI Tab files should be as follows:

  1. Unique identifier for interactor A, represented as databaseName:ac, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the unique primary identifier of the molecule in the database. Identifiers from multiple databases can be separated by “|”. It is recommended that proteins be identified by stable identifiers such as their UniProtKB or RefSeq accession number.
  2. Unique identifier for interactor B. Same structure as Point 1.
  3. Alternative identifier for interactor A, for example the official gene symbol as defined by a recognised nomenclature committee. Representation as databaseName:identifier. Multiple identifiers separated by “|”.
  4. Alternative identifier for interactor B. Same stucture as Point 3.
  5. Aliases for A, separated by “|”. Representation as databaseName:identifier. Multiple identifiers separated by “|”.
  6. Aliases for B. Same stucture as point 5.
  7. Interaction detection methods, taken from the corresponding PSI-MI controlled vocabulary, and represented as darabaseName:identifier(methodName), separated by “|”.
  8. First author surname(s) of the publication(s) in which this interaction has been shown, optionally followed by additional indicators, e.g. “Stephenson A (2005)”
  9. Identifier of the publication in which this interaction has been shown. Database name taken from the PSI-MI controlled vocabulary, represented as databaseName:identifier. Multiple identifiers separated by “|”.
  10. NCBI Taxonomy identifier for interactor A. Database name for NCBI taxid taken from the PSI-MI controlled vocabulary, represented as databaseName:identifier. Multiple identifiers separated by “|”. Note: In this column, the databaseName:identifier(speciesName) notation is only there for consistency. Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -1 to indicate “in vitro” and -2 to indicate “chemical synthesis”.
  11. NCBI Taxonomy identifier for interactor B. Same Stucture as Point 10.
  12. Interaction types, taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(interactionType), separated by “|”.
  13. Source databases and identifiers, taken from the corresponding PSI-MI controlled vocabulary, and represented as databaseName:identifier(sourceName). Multiple source databases can be separated by “|”.
  14. Interaction identifier(s) in the corresponding source database, represented by databaseName:identifier
  15. Confidence score. Denoted as scoreType:value. There are many different types of confidence score, but so far no controlled vocabulary. Thus the only current recommendation is to use score types consistently within one source. Multiple scores separated by “|”.

All columns are mandatory so columns with no values are filled with “-“

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psi_mitab_file.txt · Last modified: 2016/10/13 22:59 (external edit)