I need to programmatically access human protein-protein interactions to retrieve interactions between specific classes of molecules, but there are many protein-protein interactions databases around, especially for Homo sapiens (e.g. BIOGrid, HPRD, Reactome, MINT, DIP, STRING... just to name a few).
What's the most comprehensive resource altogether? Is there a database that somehow integrates all of the other ones? I'd just need a flat text file with all the interactions and the classes of the interacting molecules (e.g. 'transcription factor', 'GTPase', 'lipid phosphatase'...).
Thanks!
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enricoferrero
This is a good suggestion - It looks to me like HIPPIE provides more human interactions thatn Bisogenet, and the database can easily be downloaded.
http://cbdm.mdc-berlin.de/tools/hippie/download.php
I will probably use this resource in the future!
For open-source resources try PSIQUIC View (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml). Set the organism field to 'human'.
If your institution has a license, IPA should contain information from most of all of these databases. This is what I would use.
MetaGO is another commercial program that I know of with similar functionality that could probably also accomplish this.
For an open-source solution, I would check out the files provided by NCBI. For example, if you search any gene (like BRCA1) in NCBI Gene, you can find all of this information. Therefore, I assume the information can be obtained somehow from the NCBI flat files:
Example: http://www.ncbi.nlm.nih.gov/gene/672
NCBI FTP: http://www.ncbi.nlm.nih.gov/Ftp/
I found Bisogenet cytoscape plugin very helpful. It uses sysbiomics database that includes most of the above.
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David has suggested a R code for my question earlier. It might be useful. Check this link: http://brainchronicle.blogspot.co.uk/2012/05/obtain-protein-protein-interaction-from.html