My own little scifoo camp 2006.
Back from holidays at Montresor where, as the leader of Nature Network BrieComte Robert, I organized my own little private rainy scifoo camp.
29 August 2006
11 August 2006
The Life Sciences Semantic Web is Full of Creeps!
An article published in " Briefings in Bioinformatics Advance Access".
The Life Sciences Semantic Web is Full of Creeps!
Benjamin M. Good and Mark D. Wilkinson
Abstract:The Semantic Web for the Life Sciences (SWLS), when realized, will dramatically improve our ability to conduct bioinformatics analyses using the vast and growing stores of web-accessible resources. This ability will be achieved through the widespread acceptance and application of standards for naming, representing, describing and accessing biological information. The W3C-led Semantic Web initiative has established most, if not all, of the standards and technologies needed to achieve a unified, global SWLS. Unfortunately, the bioinformatics community has, thus far, appeared reluctant to fully adopt them. Rather, we are seeing what could be described as ‘semantic creep’--timid, piecemeal and ad hoc adoption of parts of standards by groups that should be stridently taking a leadership role for the community. We suggest that, at this point, the primary hindrances to the creation of the SWLS may be social rather than technological in nature, and that, like the original Web, the establishment of the SWLS will depend primarily on the will and participation of its consumers.
Mark Wilkinson is one of the creators of BioMoby. Bio Moby is a system for interoperability between biological data hosts and analytical services. Benjamin Good is a PhD student in the British Columbia Strategic Training Program in Bioinformatics. Both of them have a profile on connotea (users bgood, mwilkinson), group:Wilkinson Laboratory).
Although I'm convinced that the semantic web/RDF/XML model is the format of choice for any application (please ! use it for your output format !), I admit I never had the time and the technical knowledge about web services to really understand how BioMoby works , why I should use it and why I should use a LSID instead of an good old URI... :-)
hey, I'm going to ask them an offprint :-)
09 August 2006
A Bookmarklet for Offprint Requests
Hi, I'm pleased to share the javascript Bookmarklet I wrote today. A bookmarklet is a small JavaScript program that can be stored as a URL within a bookmark in most popular web browsers, or within hyperlinks on a web page. This bookmarklet invokes a new mail, from thunderbird, filled with a message requesting an offprint request fo an article. The first <a href="mailto:xxx@xxx.xxx"> tag found in the current page is used as the recipient of the mail and the subject is the title of the current page.
Here is the bookmarklet (you have to modify it by editing its properties in order to include your own message...):
Drag this Link: Offprint Request up to your Bookmarks Toolbar.
The bookmarklet was successfully tested on firefox/thunderbird with Bioinformatics: Building chromosome-wide LD maps Bioinformatics 2006 22(16):1933-1934 and NAR SYBR Green real-time telomeric repeat amplification protocol for the rapid quantification of telomerase activity Nucleic Acids Research, 2002, Vol. 31, No. 2 e3.
Example of mail generated from the previous paper from NAR:
From: me
To: xxxx@ucdavis.xxx
Subject: [offprint request] SYBR Green real-time telomeric repeat amplification protocol for the rapid quantification of telomerase activity -- Wege et al. 31 (2): e3 -- Nucleic Acids Research
Hi,
my name is Bruce Banner, I'm a nuclear physicist working on gamma radiations at Los-Alamos. Your recent paper titled
"SYBR Green real-time telomeric repeat amplification protocol for the rapid quantification of telomerase activity -- Wege et al. 31 (2): e3 -- Nucleic Acids Research"
caught my attention.
Would it be possible for you to forward me a PDF copy ? I thank you in advance.
Best Regards.
B. Banner
--
Bruce Banner PhD.
Gamma Radiation Laboratory
Los Alamos
http://www.marvel.com/universe/Hulk
07 August 2006
Drawing Networks, Interaction Networks, Social Networks
There is a cool presentation on google-tech-talks where Tamara Munzner introduce 15 algorithms describing how to draw a graph. That might be of interest for people working with "systems biology".
About those talks, the information is not displayed on google-video web site but it is now possible to get a RSS to keep track of the new talks at the following URL: http://video.google.com/videosearch?q=engEDU&so=1&output=rss (just add
&output=rss at the end).About networks, I've (re-)discovered a interesting source of data for protein-protein interactions. The database is called BioGrid(http://www.thebiogrid.org/index.php) and it was described in the database issue of NAR (BioGRID: a general repository for interaction datasets). I like this kind of resource because all interactions described in that database are manually curated from pubmed abstracts. This is much more rigourous than the large interaction maps screenings because, in the case of experiments using the yeast two hybrid system, for each distinct interaction, there should have some test to confirm the interaction. At the time I was using this assay, I used the method described by Bartel &. al (inverting the bait and the pray, co-immunoprecipitation, etc...) to confirm any interaction. But let's be fair, I have not read much bibliography about this subject since 1999...
The graphics from BioGrid can be exported in SVG...
....and the whole database can be downloaded in the PSI format.
PSI is a simple XML format describing
....interactors...
(...)
<proteinInteractor id="BIOGRID-109561">
<names>
<shortLabel>HGNC:5261</shortLabel>
</names>
<xref>
<primaryRef db="MIM" id="118190" secondary="" version=""/>
</xref>
<organism ncbiTaxId="9606">
<names>
<shortLabel>Human</shortLabel>
<fullName>Homo sapiens</fullName>
</names>
</organism>
</proteinInteractor>
(...)
... and interactions....
(...)
<interaction>
<names>
<shortLabel>1</shortLabel>
</names>
(...)
<participantList>
<proteinParticipant>
<proteinInteractorRef ref="BIOGRID-106718"/>
<role>bait</role>
</proteinParticipant>
<proteinParticipant>
<proteinInteractorRef ref="BIOGRID-106718"/>
<role>prey</role>
</proteinParticipant>
</participantList>
<interactionType>
<names>
<shortLabel>Invivo</shortLabel>
</names>
<xref>
<primaryRef db="" id="" secondary="" version=""/>
</xref>
</interactionType>
<xref>
<primaryRef db="pubmed" id="12081471" secondary="" version=""/>
</xref>
</interaction>
(...)
as far as I know,PSI is much more simplier than SBML or BIOPAX for describing simple protein-protein interactions (no biochemistry, no pKa, etc... however the format could be modernized by supporting a RDF/XML syntax). I also sent them a mail, asking how to sublit a new interaction but I still got no answer.
About social networks: David Wolber has introduced his social network in a google tech talk. There are a few good ideas about social networks: document and people are linked by a semantic property like in a FOAF document.
via google: Peoplicious is a collaborative research tool. Unlike systems such as del.icio.us, people are first-class data objects, along with documents. Users can create people, provide structured information about people (image, homepage, blog feed, delicious name, etc.), and create lists of people (people-tagging). Users can also bookmark documents and associate documents with people (personmarks). Any user can enter information about any person. Peoplicious is where del.icio.us meets RSS reader all within a modern day address book. There is a working prototype that can be accessed at: http://peoplicious.com/Technorati/lists. It is designed so that new sites can easily be created for particular domains (e.g., see http://peoplicious.com/USF/lists).
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