How to obtain a proof for presence of PP interaction through String API

Question

[tierprot]

Hello, fellas! Does any one know how to pull references to proofs through String API (some paper ref., or cross-links to other db's) for a list of interactors (if its possible at all)?

Answer 1

[Pierre Lindenbaum]

it's is described in the PSI-MI.xml output e.g: for the pair 4932.YML115C 4932.YJR075W

http://string-db.org/api/psi-mi/interactionsList?identifiers=4932.YML115C%0D4932.YJR075W%0D4932.YEL036C&required_score=900

(...)

            <primaryRef db="pubmed" id="10077608"/>
            <primaryRef db="pubmed" id="10200254"/>
            <primaryRef db="pubmed" id="10427000"/>
            <primaryRef db="pubmed" id="14681412"/>
            <primaryRef db="pubmed" id="15608229"/>
            <primaryRef db="pubmed" id="15608232"/>
            <primaryRef db="pubmed" id="15808823"/>
            <primaryRef db="pubmed" id="9843981"/>
            <secondaryRef db="pubmed" id="10573422"/>
            <secondaryRef db="pubmed" id="12519996"/>
            <secondaryRef db="pubmed" id="12934013"/>
            <secondaryRef db="pubmed" id="15193308"/>
            <secondaryRef db="pubmed" id="15608231"/>
            <secondaryRef db="pubmed" id="16046493"/>
            <secondaryRef db="pubmed" id="9787636"/>

(...)

[tierprot]

I pasted your request but can't find those links in xml output, could you pls describe where to dig for them?

[Pierre Lindenbaum]

$ curl -s "http://string-db.org/api/psi-mi/interactionsList?identifiers=4932.YML115C%0D4932.YJR075W%0D4932.YEL036C&required_score=900" | xmllint --format  - | grep pubmed |sort| uniq
            <primaryRef db="pubmed" id="10077608"/>
            <primaryRef db="pubmed" id="10200254"/>
            <primaryRef db="pubmed" id="10427000"/>
            <primaryRef db="pubmed" id="14681412"/>
            <primaryRef db="pubmed" id="15608229"/>
            <primaryRef db="pubmed" id="15608232"/>
            <primaryRef db="pubmed" id="15808823"/>
            <primaryRef db="pubmed" id="9843981"/>
            <secondaryRef db="pubmed" id="10573422"/>
            <secondaryRef db="pubmed" id="12519996"/>
            <secondaryRef db="pubmed" id="12934013"/>
            <secondaryRef db="pubmed" id="15193308"/>
            <secondaryRef db="pubmed" id="15608231"/>
            <secondaryRef db="pubmed" id="16046493"/>
            <secondaryRef db="pubmed" id="9787636"/>

[tierprot]

Aha, so simple paste of such request in browser(for example) wont result in correct db crossreferences placement, one need to use some advanced xml processor... Ok, will try it, thx for advice!

[tierprot]

Ok, seems that its not the thing I was asking for - those pubmed links, they link to articles which are not about sources on the basis of which proof was made but kind of proof, so, saying xml gives you A interacts with B and it was proved by text-mining but not A interacts with B and it was proved by text-mining on the basis of following pubmed id's. So question is still open.