An idea: Twitter as a tool to build a protein-protein interactions database

In this post I describe the idea about how http://twitter.com could be used as a tool to build a collaborative database of protein-protein interactions. This idea was inspired by the recent creation of http://twitter.com/omnee: Omnee is said to be the "first organic directory for Twitter which you can control directly via your tweets": Using a tag-based structure in your tweets this gives you the freedom to add yourself to multiple "groups" quickly and easily.

e.g.:

Chris Upton's tags

+informatics, +ipod touch, +genomics, +proteomics, +dnasequencing, + mac, +semanticweb, -ipodtoch, +bioinformatics, +virology, #omnee

.

How about building a collaborative biological database with this kind of tool ?. One could create a database of protein-protein interactions using twitter. For example, say the @biotecher account will be used as the core account to harvest the tweets, anybody could send a new component of the interactome by sending a tweet to @biotecher with the gi of the two proteins, a pubmed-id as reference and a special hashtag say #interactome.

E.g: Rotavirus protein NSP3 interacts with human EIF4G1 (view tweet )

Tweet

@biotecher gi:41019505 gi:255458 pmid:9755181 #interactome

With such system the metadata ( who gave this information ? when ?) is also recorded by tweeter.com so we can imagine to filter the information according to our network ("I don't trust the information supplied by this user, discard it")

I've also created a short piece of code as a proof of concept: the program fetches search for the tweets about #interactome and bound to @biotecher. It then download a few information from the NCBI (get the organism and name of the protein, get the title of the paper, etc...) and output the network as a RDF graph. The code (java) of this program is available at: http://code.google.com/p/lindenb/source/browse/trunk/proj/tinytools/src/org/lindenb/tinytools/TwitterOmics.java.

Here is the output with 3 interactions. As you will see, each interaction is stored in the rdf:Class <Interaction>. The interaction is identified by the URL of the tweet. Each interaction contains a reference of the author, the proteins , the date and the article in pubmed.

<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns="http://twitteromics.lindenb.org"
>

<foaf:Person rdf:about="http://twitter.com/yokofakun">
<foaf:name>yokofakun (Pierre Lindenbaum)</foaf:name>
</foaf:Person>

<Organism rdf:about="lsid:ncbi.nlm.nih.gov:taxonomy:4932">
<taxId>4932</taxId>
<dc:title>Saccharomyces cerevisiae</dc:title>
</Organism>

<Protein rdf:about="lsid:ncbi.nlm.nih.gov:protein:417441">
<gi>417441</gi>
<dc:title>RecName: Full=Polyadenylate-binding protein, cytoplasmic and nuclear; Short=Poly(A)-binding protein; Short=PABP; AltName: Full=ARS consensus-binding protein ACBP-67; AltName: Full=Polyadenylate tail-binding protein</dc:title>
<organism rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:4932"/>
</Protein>

<Organism rdf:about="lsid:ncbi.nlm.nih.gov:taxonomy:9606">
<taxId>9606</taxId>
<dc:title>Homo sapiens</dc:title>
</Organism>

<Protein rdf:about="lsid:ncbi.nlm.nih.gov:protein:41019505">
<gi>41019505</gi>
<dc:title>RecName: Full=Eukaryotic translation initiation factor 4 gamma 1; Short=eIF-4-gamma 1; Short=eIF-4G 1; Short=eIF-4G1; AltName: Full=p220</dc:title>
<organism rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:9606"/>
</Protein>

<bibo:Article rdf:about="http://www.ncbi.nlm.nih.gov/pubmed/9418852">
<bibo:pmid>9418852</bibo:pmid>
<dc:title>RNA recognition motif 2 of yeast Pab1p is required for its functional interaction with eukaryotic translation initiation factor 4G.</dc:title>
</bibo:Article>

<Interaction rdf:about="http://twitter.com/yokofakun/statuses/1058586293">
<interactor rdf:resource="lsid:ncbi.nlm.nih.gov:protein:417441"/>
<interactor rdf:resource="lsid:ncbi.nlm.nih.gov:protein:41019505"/>
<reference rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/9418852"/>
<dc:creator rdf:resource="http://twitter.com/yokofakun"/>
<dc:date>2008-12-15T14:51:42Z</dc:date>
</Interaction>

<Organism rdf:about="lsid:ncbi.nlm.nih.gov:taxonomy:10922">
<taxId>10922</taxId>
<dc:title>Simian rotavirus</dc:title>
</Organism>

<Protein rdf:about="lsid:ncbi.nlm.nih.gov:protein:255458">
<gi>255458</gi>
<dc:title>NS34=gene 7 nonstructural protein [simian rotavirus, SA114F, serotype G3, Peptide, 315 aa]</dc:title>
<organism rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:10922"/>
</Protein>

<Protein rdf:about="lsid:ncbi.nlm.nih.gov:protein:6176338">
<gi>6176338</gi>
<dc:title>ubiquitous tetratricopeptide containing protein RoXaN [Homo sapiens]</dc:title>
<organism rdf:resource="lsid:ncbi.nlm.nih.gov:taxonomy:9606"/>
</Protein>

<bibo:Article rdf:about="http://www.ncbi.nlm.nih.gov/pubmed/15047801">
<bibo:pmid>15047801</bibo:pmid>
<dc:title>RoXaN, a novel cellular protein containing TPR, LD, and zinc finger motifs, forms a ternary complex with eukaryotic initiation factor 4G and rotavirus NSP3.</dc:title>
</bibo:Article>

<Interaction rdf:about="http://twitter.com/yokofakun/statuses/1058292539">
<interactor rdf:resource="lsid:ncbi.nlm.nih.gov:protein:255458"/>
<interactor rdf:resource="lsid:ncbi.nlm.nih.gov:protein:6176338"/>
<reference rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/15047801"/>
<dc:creator rdf:resource="http://twitter.com/yokofakun"/>
<dc:date>2008-12-15T11:01:10Z</dc:date>
</Interaction>

<bibo:Article rdf:about="http://www.ncbi.nlm.nih.gov/pubmed/9755181">
<bibo:pmid>9755181</bibo:pmid>
<dc:title>Rotavirus RNA-binding protein NSP3 interacts with eIF4GI and evicts the poly(A) binding protein from eIF4F.</dc:title>
</bibo:Article>

<Interaction rdf:about="http://twitter.com/yokofakun/statuses/1058290564">
<interactor rdf:resource="lsid:ncbi.nlm.nih.gov:protein:41019505"/>
<interactor rdf:resource="lsid:ncbi.nlm.nih.gov:protein:255458"/>
<reference rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/9755181"/>
<dc:creator rdf:resource="http://twitter.com/yokofakun"/>
<dc:date>2008-12-15T10:59:19Z</dc:date>
</Interaction>

</rdf:RDF>

What do you think ?

Pierre