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 Science Commons project looks at the restrictions on life science databases: Dulong de Rosnay, M. (2008). Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness . Nature Precedings DOI: 10.1038/npre.2008.2083.1 Abstract: Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds upon research led by Science Commons demonstrating why open data and the freedom to integrate facilitate innovation and how this openness can be achieved. The taxonomy describes technical and legal restrictions applicable to life science databases, and its metadata have been used to assess terms of use of databases hosted by Life Science Resource Name (LSRN) Schema. While a few public domain policies are standardized, most terms of use are not harmonized, difficult to understand and impose controls that pre...

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...