“I am not a scientist, I am a number”

On Monday I was at the BioLINK Special Interest Group at the Intelligent Systems for Molecule Biology meeting in Stockholm. Amongst the many thought-provoking talks was one by Phil Bourne, he of the Protein Data Bank, SciVee and other goodies. Phil made a cogent plea for a system of unique identifiers for scientists.  Read more

Pre-prints and DOIs

We and our partners at the U.S National Cancer Institute recently had an article describing our Pathway Interaction Database accepted by Nucleic Acids Research. I’m not posting to puff that up: during the submission process, the NAR editors raised a couple of perfectly reasonable questions about preprints and unique identifiers.  Read more

WikiProteins – are a million minds listening?

A couple of days ago Barend Mons and colleagues published an article in Genome Biology about WikiProteins – a new way of asking a “million minds to annotate a million [biomedical] concepts”. On the face of it, it seems like an fine idea: combine text mining and other database trawling (Medline, GO, UniProt and others), distill some concept maps from that (Knowlets, they call them) and invite scientists to chip in via a wiki.  Read more

How to spend millions? The iPlant way.

At NPG, as at all forward thinking places, we have more ideas than we can follow through. For Governments funding heavy duty science informatics infrastructure, deciding which projects to support is an especially difficult task. There are various strategies funders use to help them. I recently talked to Richard Jorgensen, director of the new iPlant Collaborative about an interesting approach the NSF is taking to formulate next-generation plant biology informatics infrastructure.  Read more

Where next for UK PubMed Central?

What do UK researchers want from UKPMC, their free archive of full-text journal articles? That was the subject of a meeting today at the Wellcome Trust in London. Launched a year ago, UKPMC has become established as a part of the national research infrastructure but as with all online projects the scope for enhancement is ever present.  Read more

BASE powers of indexing metadata

The industrious folks at BASE (see their home page or my previous post) have added Nature Precedings and the Signaling Gateway to their search engine, despite the fact that neither provides OAI-PMH metadata. I like BASE — do a search for “inhibitor” for example and see how many hits you get by data source, document type, free vs not, etc etc.  Read more