Release 1.0: November 23, 2006
We required BIND data in PSIMI 1.0 in order to use it in cpath, an open source software tool for
collecting, storing, browsing and querying biological pathways. Aproximately 1600 BIND data files were
downloaded on July 22, 2006 from the BIND ftp site - ftp://ftp.bind.ca/pub/BIND/data/datasets/taxon/xml in BIND XML and converted to PSI MI 1.0 using an xslt, programmed by Ahmet Rasit,
a student from Bilkent University who joined us for the summer in the Emililab at the University of Toronto.
The BIND data was converted in collaboration with the
Emiliab and the Bader Lab.
- Total number of BIND interactions converted - 87,878
- Drosophila melanogaster - 23,585
- Homo sapiens - 18,271
- Saccharomyces cerevisiae - 11,902
- Mus musculus - 5,699
- Caenorhabditis elegans - 5,426
- Human immunodeficiency virus 1 - 3,115
- Escherichia coli - 2,734
- Rattus norvegicus - 2,008
- synthetic construct - 1,623
- Helicobacter pylori - 1,472
- Bos taurus - 1,466
- Arabidopsis thaliana - 1,201
- Rest of the species(1212 more species) - 9,376
While we have made every effort to accurately convert BIND files, we can't guarantee the accuracy of the conversion.
Updates to the scripts are welcome and we will post them on the page.
The code and data is provided as is. We will try to reply to messages concerning the code, but can't guarantee our ability to reply to all messages.
Notes about the conversion:
- The BIND data has not been changed over the past 6 months but if new records are added we will redo the conversion.
- In some cases there was a loss of data but we tried to maximize the data extracted.
- In a single record, both of the interactors must be proteins.
- Only entries stored under /BIND-Submit/BIND-Submit_interactions/BIND-Interaction-set/BIND-Interaction-set_interactions/BIND-Interaction tag are converted.
- Experiment description ids are generated randomly.
- Protein interactor ids are generated randomly and they are unique.
- Protein Complex records are not converted
- Binding sites are not converted
BIND XML fields used for the conversion include:
Scripts used for processing and converting the files: