Zzzoot

Rod Page 's demo for his Elsevier Grand Challenge submission (" Towards realising Darwin’s dream: setting the trees free ") shows the type of enrichment of biological - if not all research - articles that is quickly becoming possible. Taking a published article (" Mitochondrial paraphyly in a polymorphic poison frog species (Dendrobatidae; D. pumilio "), various additional biological, geographical and other metadata are extracted and added to a web page for the article. These include: Map showing all localities mentioned in the paper, with their enclosing polygon List of other studies which have samples in area enclosed by the study polygon Each of the following are linked through to their underlying databases (such as NIH accession number and NCBI nucleotide viewer or linked to ubio taxonomic name viewer record: List of sequence features (such as genes) in the article List of taxa sequenced in the article List of gene sequences cited by the article An image c...

This paper takes a more semantic web and forward looking view than recent cyberinfrastructure articles: Stein, L. D. (2008).Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges Nat Rev Genet, 9(9) , 678-688. DOI: 10.1038/nrg2414 Things like Semantic Web Pipes - missing from the article - can be found on the wiki page for the article (Thanks Matthias Samwald). Related recent articles: Goble, C., Stevens, R. (2008). State of the nation in data integration for bioinformatics. Journal of Biomedical Informatics DOI: 10.1016/j.jbi.2008.01.008 Stockinger, H., Attwood, T., Chohan, S.N., Cote, R., Cudre-Mauroux, P., Falquet, L., Fernandes, P., Finn, R.D., Hupponen, T., Korpelainen, E., Labarga, A., Laugraud, A., Lima, T., Pafilis, E., Pagni, M., Pettifer, S., Phan, I., Rahman, N. (2008). Experience using web services for biological sequence analysis. Briefings in Bioinformatics DOI: 10.1093/bib/bbn029 Garciasanchez, F., Fernandezbreis, J., Valenciagarcia...

The NSF announced today announced it would be awarding $50M to the iPlant Collective , a " dynamic web portal for the Plant Science Cyberinfrastructure Collaborative Community " to address the ' grand challenges' in plant science. The effort will create a global centre bringing together (virtually and actually) computer scientists, information scientists and plant scientists to work on projects untenable until this project due to such issues as complexity, scale, discipline boundaries, lack of collaboration structures, etc. The centre "... will bring together and leverage the resources and information generated through the National Plant Genome Initiative , enabling more breadth and depth of research in every aspect of plant science " and will serve as a model for other disciplines on how collaborative cyberinfrastructure can be applied.

OA Librarian points out a press release from Dec 5 2007 a news release from Nature Publishing Group announcing that genome sequences: "Nature Publishing Group (NPG) announced today that is introducing a Creative Commons licence for original research articles publishing the primary sequence of an organism’s genome for the first time in any of the Nature journals." Of particular interest: "Wherever possible, NPG will apply the Creative Commons Attribution-Non-Commercial-Share Alike licence retrospectively [emphasis added] to original research articles reporting novel primary genome-wide sequences that have previously been published in Nature journals." Nature Editorial: Shared Genomes (Nature 450, 762 6 December 2007) It is good to see Nature trying to fill some of the leadership void in this area. Taxonomy, with a longer history in publishing, needs a similar effort, as pointed-out by Donat Agosti on the Taxacom mailing list (in reference to the NPG announcem...

Wiki for Professionals : VERY ambitious & exciting While the name does not really inspire me ;-) this is an amazing initiative and the various quotes by researchers describing Barend Mons ' project as visionary are completely justified. He (they) are trying to pull together the Semantic Web with a variety of biological databases and PubMed in a suped-up semantically-enhanced Wiki environment that is meant to be used by -- and be useful to -- biological researchers.