21 December 2005

EMBO Journal Cover Contest.

Like in the previous years, the EMBO journal organizes a contest to select the best cover image for 2006.
In 1998, the was no contest but I sent a drawing to be joined with the following paper written by Maria Piron:

Maria Piron by Pierre Lindenbaum

They didn't take my drawing.
I hate EMBO :-)

18 December 2005

Biology & GIS

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.

I'm famous

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 ! :-)

08 December 2005

People from semantic web in life science

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

Connotea is a free online reference management service. It allows you to save links to all your favourite articles, references, websites and other online resources with one click. Connotea is also a social bookmarking tool, so you can view other people's collections to discover new, interesting content. A group about semantic web in life science was created by Eric Jain. Papers and references about semantic web can be found using http://www.connotea.org/group/semweb-lifesci/tag/semantic%20web.
If you want to introduce yourseld use connotea the following way:

  1. register on connotea

  2. register to the group semweb-lifesci

  3. add a new bookmarklets which links to your home page. Do use semantic web and me as tags. You can use the comment field to write a short bio. And you can also add a geotagged tag in order to answer the following question: "where is your laboratory ?", "who is playing with the semantic web near me ?". geotagged tag can also be used to generate an input for google-earth

An example:

Suggestion 2

O'Reilly publishing has released a new web site called O'Reilly Connections used for IT networking. This site can be used to generate FOAF. Register that site, add semantic web and/or semweb-lifesci in your skills and you can also send invitations to your colleagues to grow your network.

07 December 2005

PhD Student at INRA/Jouy-en-Josas

This is a copy of the mail I sent to the mailing list of the phd students of INRA.

< xml:lang='fr'>


Ancien thesard de la VIM (2000) je tiens à rendre
compte de l'expérience très bénéfique qu'a été la
formation "Projet Professionnel et Personnel" (PPP).
Nous avons débarqué en petit groupe pour cette
formation sans trop savoir où nous débarquions et avec
des tas d'idées préconçues sur la personne (épatante)
qui nous recevais (Anne Caillieres-Divoux du cabinet
du meme nom): certains culpabilisaient déja d'avoir
abandonné pendant 1/2 journée la paillasse, d'autres
redoutaient le jugement négatif de leur directeur de
thèse, etc... Les profils étaient différents, certains
n'avaient aucun papier en 4eme année, d'autres
achevaient d'écrire leur 2eme "Nature" à peine sortit
du DEA (ah les fourbes!).
Cette formation a été l'opportunité de (re)découvrir
que la thèse n'était pas une finalité, que nous (les
thésards) avions des tas de choses en commun (surtout
des problèmes à vrai dire :-) mais malgré cela nous
avions développé une "expertise" (recherche de
l'information, élaboration de projets, présentation
orale, travaille d'écriture, synthèse.. etc... etc...
). Ces quelques jours nous ont tous vraiment "boosté"
et certains de mes compagnons en ont profité pour
monter la premiere asso de thèsards de jouy (ASIJ). En
résumé: foncez à cette formation !


Troisieme point: je fais ma pub pour
http://www.connota.org . Connotea est un site de
'social bookmarking',auquel je collabore de temps en
temps, et créé par 'Nature'. Plutot que d'accumuler
des 'bookmarks' sur votre ordinateur, des references
de pubmed, etc... ajoutez les ( avec quelques mots
clefs) sur ce site: cela vous permettra de les
archiver et surtout de découvrir des
articles/personnes ayant les meme centres d'interet
que vos recherche.

AYE, j'ai finis !

Semantic Abstracts.

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:

Piron M, Vende P, Cohen J, Poncet D.
Rotavirus RNA-binding protein NSP3 interacts with eIF4GI and evicts the poly(A) binding protein from eIF4F.

would be turned into something like that...

<rdf:RDF (...)>
<rdfs:description>Rotavirus Non Structural Protein 3</rdfs:description>

<rdfs:description>eukaryotic translation initiation factor 4 gamma</rdfs:description>

<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: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:Method rdf:ID='2YH'>
<rdfs:description>Yeast two hybrid system</rdfs:description>


Please Mr Nature, Springer, Elsevier :-) ....

06 December 2005

Science & social networks

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:

  • LinkedIn (easy to find people, many features are free)

  • OpenBC (prints a nice path with pictures of the contacts of your contacts)

  • academici (Same as OpenBC, but designed for the academic world)

  • In France, there are Viaduc (many features requires a subscription) and 6nergies (a little bit messy...)

  • Young scientifics may also be interested in YEBN which is also as a linkedin group

  • ...

I always have problems to ask my contacts to accept those invitations. Most non-IT people I known (where are historians, biologists, artists... ?) don't see what can be the benefits of joining such network ("I know my friends, why should I list them on this big-brother-web site" ?). Moreover, people don' wan't to build as much social networks than there are social web sites. But such site sare great to build work communities, to find skills, to keep contact, to retrieve old friends, to find a postdoc, to find references, etc...

Connotea search engine

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.


05 December 2005


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.