nodalpoint.org - mashup - Comments

Semantic Biomedical Mashups finally published

Duncan — Thu, 02 Oct 2008 06:43:20 -0400

Journal of BioInformatics Special Issue on Semantic Biomedical Mashup officially published, see http://lists.w3.org/Archives/Public/public-semweb-lifesci/2008Oct/0002.h...

What, exactly, is the point of Elsevier?

Duncan — Wed, 02 Apr 2008 07:26:07 -0400

I've been waiting for this special issue on semantic biomedical mashups for a while now. The latest scheduled production date is September 2008, which makes it exactly one whole year from Call for papers to publication. Damn thats quick, faster than a speeding glacier! Those hot hot research results must be popping of the printing press at an alarming rate!

Which makes me wonder, what, exactly is the point of Elsevier? Why does it take them so long to publish? Some, in the Open-Access publishing community have suggested this kind of publishing is a slow and expensive way to assign copyright to information that should be in the public domain, while lining shareholders pockets. As a young scientist, I'm completey baffled as to why it should take this long to shuffle a few emails and Word documents around the internet in order to publish.

Anyway, enough of the griping. Every now and then, a pre-print pops up in the Journal of Biomedical informatics feed from PubMed. So while you're waiting for Elsevier, you can read one of the first papers in the special issue below.

Carole Goble and Robert Stevens (year unknown) State of the nation in data integration for bioinformatics, Journal of Biomedical Informatics, officially published sometime before the heat-death of the Universe (but don't hold your breath). DOI:10.1016/j.jbi.2008.01.008, pubmed.gov/18358788

-10 Ooops

Duncan — Fri, 10 Aug 2007 05:05:19 -0400

Ooops, my semantic web agent did the sums wrong (bad ontology) and made Jim aged 89 not 79....corrected it now!

+10 ?

radmap — Thu, 09 Aug 2007 23:30:12 -0400

Man, that sequence must have been pretty scary ... seeing his own genome sequence instantly aged Lucky Jim an extra 10 years! ;-)

A snip at $250,000

Duncan — Tue, 07 Aug 2007 09:12:03 -0400

Nice camera, but a little expensive for my pocket at $250,000. The sales guy told me he'd cut me a deal of 10 cameras for $1m if I wanted.

Don't forget the hotel bar

mndoci — Mon, 06 Aug 2007 17:22:09 -0400

Where else can you get a presentation on the coolest 3D camera in the world

REST and recuperation

Duncan — Tue, 06 Jun 2006 06:00:59 -0400

Thanks Greg, I'm glad someone is enjoying my rambling posts to nodalpoint!

I don't know why there aren't more REST style services out there, why has everyone plumped for the "over-engineering" of SOAP+WSDL? Maybe its because many of these services are provided by large government-funded bodies like the NCBI and EBI who employ professional software engineers (not bioinformatics hackers) to deploy these services. Many software engineers like big complicatd over-engineered solutions that only they truly understand :)

I think the NCBI method of supplying both REST as well as SOAP+WSDL is a sensible one, you choose the interface that you like best, rather than the "one true interface"...

Firstly, thank you for all

Greg — Sun, 04 Jun 2006 23:10:44 -0400

Firstly, thank you for all these great posts, you're putting us regulars all to shame.

many publicly available biomedical services, are not the simpler RESTian type, but the more complex SOAP-and-WSDL type of web service.

For as long as I have been doing this I've always felt that most in-the-trenches bioinformatics hackers would be vehemently opposed to the over engineering that is SOAP+WSDL and prefer the intuitive and straight forward REST style. NCBI's EUtils looks like the only game in town if you want REST based webservices, everything else as you point out is based on SOAP. Why is that ?