SWAT4LS2009 – James Eales: Mining Semantic Networks of Bioinformatics eResources from Literature

November 20, 2009 Leave a comment

eResource Annotations could help with

  • making better choices: which resource is best?
  • which is available?
  • reduce curation
  • help with service discovery

Approach: link bioinformatics resources using semantic descriptors generated from text mining….head terms for services can be used to assign services to types..e.g. applications, data sources etc.

Reblog this post [with Zemanta]

Filed under informatics, semantic web, Text Mining Tagged with , , ,

The Microsoft Biology Foundation

November 6, 2009 Leave a comment

As most of you may know, Microsoft – and in particular the folks at Microsoft (External) Research – have started to make major inroads into developing tools for scientists, be that in the area of scholarly communication with a repository offering as well as an ontology plugin for Word or in chemistry with Chem4Word, which is currently being developed by Joe Townsend, Jim Downing and Peter Murray-Rust here at Cambridge and the team at Microsoft External Research.

Now they have also announced a first version of the Microsoft Biology Foundation. From the announcement:

“The Microsoft Biology Foundation (MBF) is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework. Currently it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological Web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, and documentation are freely downloadable […]”

Now every time Microsoft gets involved in something like this, it is bound to generate discussion and debate, such as happened around Chem4Word (see here and links contained in this). I, for one, am happy about every constructive and open contribution to the canon of scientific tools available to the community and welcome the news.

Reblog this post [with Zemanta]

Filed under code, informatics Tagged with , , , , ,

Just a quick note from the International Conference on Biomedical Ontology

July 23, 2009 Leave a comment

I am normally pretty noisy these days when it comes to blogging or tweeting conferences….but haven’t produced anything for ICBO so far. This has mainly to do with the fact that I am far too busy learning, thinking and absorbing people’s ideas and yet again realising just how far ahead biology/biomedicine is in thinking how to deal with data properly. In any case, all I wanted to say was that ICBO has its own friendfeed group where Robert Hoehndorf and others are doing a sterling job documenting the conference and discussing what is said during the tutorial sessions that are currently going on. The friendfeed page is here:

http://friendfeed.com/icbo

So do read along if you want to follow what is going on from afar!

Filed under blogging, ontology Tagged with , , ,