Generating PPI Networks from BioGRID

Question

[stackf01]

Hello. I am building a web application which can display protein interaction networks. I am downloading psi file from BioGRID. Which columns should I take to extract this data from the psi (xml) file and insert this in a table of MySQL? I want to make a search field on the web page, so that a user can enter a UniProt ID and get the protein interaction networks of this UniProt id. How do I achieve this in the simplest way possible?​

Answer 1

[Pierre Lindenbaum]

I wrote a XSLT stylesheet to convert biogrid to SQL: https://github.com/lindenb/xslt-sandbox/#psibiogrid-to-sql

(tested with sqlite3)

xsltproc -o tmp.sql psi2sql.xslt BIOGRID-ALL-3.4.129.psi.xml
sqlite3 db.sqlite3 < tmp.sql

Find the interactions for B4DG32 (http://www.uniprot.org/uniprot/B4DG32)

$ sqlite3 -header db.sqlite3  'select distinct I1.shortLabel,I2.shortLabel from interaction as L,interaction2interactor as I2I1, interaction2interactor as I2I2, interactor as I1 ,interactor as I2, xref as X1 where X1.pk="B4DG32" and X1.interactor_pk=I1.pk and I2I1.interaction_pk = L.pk and I2I1.interactor_pk = I1.pk and I2I2.interaction_pk = L.pk and I2I2.interactor_pk = I2.pk'

shortLabel|shortLabel
SH2D3C|BCAR1
SH2D3C|EFS
SH2D3C|EGFR
SH2D3C|LYN
SH2D3C|NEDD9
SH2D3C|SH2D3C
SH2D3C|SNCAIP

[stackf01]

What is shortlabel ?

[Pierre Lindenbaum]

$ curl -s "http://string.embl.de/api/psi-mi/interactions?identifier=YOL086C"  | xmllint --format - | grep -A 5 -B 5 shortLabel

      <interactor id="18">
        <names>
          <shortLabel>ADH1</shortLabel>
          <fullName>Alcohol dehydro(...)</fullName>
        </names>(...)

[stackf01]

I have downloaded the psi xml file from BioGRID. How do I integrate this data into a MySQL table?