chem-bla-ics: October 2007

BioSpider: another molecule search engine

I just ran into BioSpider. Unlike ChemSpider, BioSpider crawls the internet (well, this list of sources really) to find information, and depending on what it finds it continues the search. Below is a screenshot of an intermediate point after starting with the InChI of methane:

After the search it generates a long HTML page with all the information it found on the molecule you queried for. This approach is much more scalable than storing all in one database.

This crawling of information is something I was working on myself a bit too, and I think this is a good approach. However, I think the use of a central website is not the right approach. Instead, the search should be distributed too: the crawling should be done on the client machine; it should be done in Taverna or Bioclipse instead.

Oct

My FOAF network #1: the FOAFExplorer

In this series I will introduce the technologies behind my FOAF network. FOAF means Friend-of-a-Friend and[t]he Friend of a Friend (FOAF) project is creating a Web of machine-readable pages describing people, the links between them and the things they create and do.

My FOAF file (draft) will give you details on who I am, who I collaborate with (and other types of friends), which conferences I am attending, what I published etc. That is, I'll try to keep it updated. BTW, FOAF is a RDF language.

Oct

One Billion Biochemical RDF Triples!

That must be a record! Eric Jain wrote on public-semweb-lifesci:

The latest release of the UniProt protein database contains just over a

billion triples*! PRESS RELEASE :-)

The data is all available via the (Semantic or otherwise) Web:

http://beta.uniprot.org/

...or can be bulk-downloaded from:

ftp://ftp.uniprot.org/

* Counting some reification statements, and assuming no overlap between

"named graphs".

P.S.

Oct

My blog turned 2

A bit over two years I posted my first blog item, Chem-bla-ics, introducing the topic of my blog. In January this year I explained why I like blogging.

Oct

Bob improved the POV-Ray export of Jmol

Bob has set up a new interface between the data model and the Jmol renderer, which allows him to define other types of export too. One of this is a POV-Ray export, which allows creating of high quality images for paper. Jmol has had POV-Ray export for a long time now, but never included the secondary structures or other more recent visual featues. PyMOL is well-known for its POV-Ray feature, and often used to create publication quality protein prints.

Oct

More QSAR in Bioclipse: the JOELib extension

I added a Bioclipse plugin for JOELib (GPL, by Joerg) which comes with many QSAR descriptors, several of which are now available in the QSAR feature of Bioclipse:

Meanwhile, the Bioclipse team in Uppsala has set up the obligatory scatter plot functionality, but leave that screenshot for them to show. Therefore, time for integration with R.

Oct

Open Data Misconception #1: you do not get cited for your contributions

The Open Data/ChemSpider debate is continuing, and Noel wondered in the ChemSpider Blog item on the Open Data spectra in ChemSpider. The spectra in ChemSpider come from four persons, two of which released their data as Open Data (Robert and Jean-Claude) and two as proprietary data.

Oct

Lunch at Nature HQ (with Euan, Joanna, Ian and Ålf)

On my way back from the Taverna workshop I visited Nature HQ, as Ian reported about on Nascent. It was a (too) short meeting, but very nice to meet Euan (finally; he wrote the postgenomic.com software which I use for Chemical blogspace), Joanna (whom I met in Chicago already, where she had two presentations, and is responsible for Second Nature), Ian (who works on Connotea, and commented on my tagging molecule blog) and Ålf (who works on Scintilla) and briefly Timo (who rules them all).

Oct

ChemSpider: the SuSE GNU/Linux of chemical databases?

A molecular structure without any properties in meaningless. Structure generators can easily build up a database of molecules of unlimited size. 30 million in CAS, 20 million in ChemSpider or 15 million in PubChem is nothing yet. The value comes in when linking those structures with experimental properties.

Oct

CompLife2007, Utrecht/NL. Day 1 and 2

CompLife 2007 was held 1.5 weeks ago in Utrecht, The Netherlands. The number of participants was much lower than last year in Cambridge. Ola and I gave a tutorial on Bioclipse, and Thorsten one on KNIME. Since a visit to Konstance to meet the KNIME developers, I had not been able to develop a KNIME plugin, but this was a nice opportunity to finally do so.