Hello,
I am trying to parse the MIPS database , I read this code but it does not work for me. can someone help me to solve the problem?
Hi Learner,
The MIPS data available at http://mips.helmholtz-muenchen.de/proj/ppi/ is quite old now, and still released in an obsolete PSI format. Nevertheless you should still be able to use an application I write on this purpose when the PSI-MI standard was first released and is still working for both PSI-MI 1.0 format: https://github.com/arnaudceol/psimi-maker-flattener/releases
You can use the xmlflattener-gui script (to "flatten" xml to tab delimited file) to launch the graphical interface, load the flattener default mapping file, load the xml file downloaded from MIPS and create the txt file! From the graphical interface you can select additional fields if you wish.
Arnaud
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@Arnaud Ceol thanks, does your code make the PPI matrix too, what does it parse from the xml file ? also I found that your code is working under Windows, right ?
This is a Java app, working under windows/linux/macos. The example provided here extract binary interactions: pubmed and a pair of uniprot Acs. It is possible to browse the "tree" representation of the XML schema to select additional fields. What information are you looking for exactly?
@Arnaud Ceol I am searching to make the data like what is reported here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060787/
From the reference [37], I understand the authors refers to the CYGD database (the yeast PPI database from MIPS). Unfortunately it looks like the website is not available anymore. Indeed the network available from the MIPS website contains less than 2000 interactions (human proteins, at least for the first ones I've seen), whereas the authors refer to 6880 interactions.
Maybe you could try to reproduce the work of this paper with the network from another database. For instance you could download the yeast network from intact