InteroPorc: Description of output files


Predicted interactions:

Predicted interactions are described in InteroPorc.predictedInteractions.mitab in mitab format. All interactions present in the source interaction file can't be predicted as new. Thus they do not appear in the prediction file. Neverthelss, another file is available with both predicted and known interactions.

Known interactions:

This file contains interactions present in the source interaction file for this species.

Known & Predicted interactions:

This file contains predicted interactions as well as interactions present in the source interaction file for this species.

PSI25-XML Format:

PSI25-XML is the standard molecular interaction data exchange format defined by the Proteomics Standards Initiative (PSI). All information are on the PSI website: ttp://www.psidev.info/

MITAB25 Format:

MITAB25 describes binary interactions, one pair of interactors per row. Columns are separated by tabulators. Fore more information, see:

The MITAB25 format has been derived from the tabular format provided by BioGrid. MITAB25 only describes binary interactions, one pair of interactors per row. Columns are separated by tabulators.

The colum contents 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.
  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.
  5. Aliases for A, separated by "|". Representation as databaseName:identifier. Multiple identifiers separated by "|".
  6. Aliases for B.
  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. "Doe-2005-a". Separated by "|".
  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.
  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 "|".
  16. All further columns are currently undefined.

All columns are mandatory. Where values are missing, an empty cell is marked by "-".

Source interactions transferred:

All source interactions used during the process are described in the srcInteractionsUsed.txt file. It is a tabulated text file containing the following columns:

For more infomation on the detection methods, see the Molecular Interaction ontology: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI