I felt in love with geography since I discovered google earth. Can I mix GIS (geographical information system) with biology ? Yes ! Connotea handles gotagging and it is used to find location of papers dealing with epidemiology. I also just created a group called laboratories used to locate all the labs in the world.
I also discovered tagzania, a GIS version of del.ico.us, which I used to locate a few labs I know near Paris.
I just discovered www.43people "what are the 43 persons I'm looking for ?". Like www.43things and www.43places it seems to be a useless, egocentric, but so fun tool for social netwoking.
There was a short paragraph about me in the Bioinform newsletter where I said a few words about what we are doing with the semantic web at Integragen. Mum ! Im' famous ! :-)
This week, there where numerous mails from people introducing themselves on the 'semantic web in life science' mailing list. A wiki page of those people was created, but I also suggested to use connotea or O'Reilly Connections. This could be used for any kind of scientific/IT social network. Here is a copy
This is a copy of the mail I sent to the mailing list of the phd students of INRA.
Many papers about text mining trying to extract the semantic value of pubmed the abstracts can now be found in the litterature.
I wish publishers could join a semantic abstract (RDF based ?) to their classic abstract, that would be an incredible (and safe) source of knowledge for "systems biology". I imagine the following paper:
<rdf:RDF (...)>
<bio:Protein
rdf:about='http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=77120248'
ncbi:taxon='http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&id=10923'
>
<rdfs:label>NSP3</rdfs:label>
<rdfs:description>Rotavirus Non Structural Protein 3</rdfs:description>
</bio:Protein>
<bio:Protein
rdf:about='http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=38201627'
ncbi:taxon='http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&id=9606'
>
<rdfs:label>EIF4G</rdfs:label>
<rdfs:description>eukaryotic translation initiation factor 4 gamma</rdfs:description>
</bio:Protein>
<bio:interaction rdf:ID='NSP3-EIF4G'>
<bio:entity rdf:resource='http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=77120248'/>
<bio:entity rdf:resource='http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=38201627'/>
<bio:method rdf:resource='#2YH'/>
<bio:reference rdf:resource='#paper'>
</bio:interaction>
<bio:Paper rdf:ID='paper'>
<dc:title>Rotavirus RNA-binding protein NSP3 interacts with eIF4GI and evicts the poly(A) binding protein from eIF4F</dc:title>
<rdf:seeAlso rdf:resource='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9755181'/>
</bio:Paper>
<bio:Method rdf:ID='2YH'>
<rdfs:label>2YH</rdfs:label>
<rdfs:description>Yeast two hybrid system</rdfs:description>
</bio:Method>
(...)
</rdf:RDF>
I discovered today the social web site from O'Reilly. This is a social network designed for people working for IT. There are some nice features such as generating a FOAF file, printing a resume,etc...
There are more and more such social web site dedicated to networking. I like to use:
I just created a search engine for firefox to search in connotea.
The engine is available at http://www.urbigene.com/connoteasearch/.
It was not as difficult as I expected: as you may see in your firefox directory:more ${HOME}/.mozilla/firefox/XXXXX.default/searchplugins/*.src
this is really a short piece of code.
I wrote a greasemonkey script called pubmed2connotea. This script alters the web page when you're surfing on NCBI with firefox 1.5 and it adds a hyperlink to insert a new reference in your connotea library.
