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Eureka Alert! - 3 hours 46 min ago
(Harvard University) A groundbreaking study by Harvard University's Harvard Forest and the Smithsonian Institution reveals that, if left unchecked, recent trends in the loss of forests to development will undermine significant land conservation gains in Massachusetts, jeopardize water quality, and limit the natural landscape's ability to protect against climate change.
Nature Newsblog - Tue, 2013-12-10 19:01
The internet’s wealth of free chemistry data just got significantly larger. Today, the European Bioinformatics Institute (EBI) has launched a website – www.surechembl.org – that allows anyone to search through 15 million chemical structures, extracted automatically by data-mining software from world patents.
The initiative makes public a 4-Terabyte database that until now had been sold on a commercial basis by a software firm, SureChem, which is folding. SureChem has agreed to transfer its information over to the EBI – and to allow the institute to use its software to continue extracting data from patents.
“It is the first time a world patent chemistry collection has been made publicly available, marking a significant advance in open data for use in drug discovery,” says a statement from Digital Science – the company which owned SureChem, and which itself is owned by Macmillan Publishers, the parent company of Nature Publishing Group.
Under the agreement, Digital Science retains use of the SureChem software; the company is being wound up because Macmillan wants to focus on serving researchers, not commercial clients such as drug firms, says SureChem’s co-founder, Nicko Goncharoff.
“We are delighted to take on the stewardship of this resource,” says John Overington, head of computational chemical biology at the EBI, which is part of the European Molecular Biology Laboratory in Hinxton, UK. “Scientists are accustomed to doing literature searches, but the patent literature is often where the real gems lie – especially in translational science,” he adds. Published papers lag the patents literature by about two years, he points out.
Overington says that the EBI plans to interlock information on chemical compounds from different public resources. For example, a search on a compound such as Pfizer’s Viagra (sildenafil) will reveal its presence in patents (from SureChemBL), as well as its interactions with potential protein drug targets (from databases such as the EBI’s ChemBL which catalogues experiments done on compounds).
Later, Overington hopes to apply SureChem software to extract structures mentioned in research papers, starting with open-access papers held in repositories such as Europe PubMedCentral. But, he adds, reconstruction of chemical data from papers is harder, because structures are often not named or pictured explicitly, but only alluded to as variants on a common molecular skeleton.
Historically, chemists have not had a wealth of free online data, and have been used to paying to get information from private databases. SureChem released data on 10 million molecules into the public database PubChem last year, but the information was restricted (as the information on links to patents could only downloaded one molecule at a time). But the web’s resources of searchable public chemical data are fast-expanding. “I think it’s a really exciting time for chemistry,” Overington says.
Biology News - Tue, 2013-12-10 17:21
Eurofins Scientific (EUFI.PA), a European leader in Genomics Services, Forensics and Paternity Testing, announces a milestone in genetic and forensic research. A multidisciplinary Eurofins team in the Eurofins flagship Genomics laboratory in Ebersberg, Germany, has successfully completed a research project to genetically discriminate "identical" monozygotic twins.
Biology News - Tue, 2013-12-10 17:21
This is a view eastward along the spine of the Azorean island of São Jorge, showing the area where the new orchid has been discovered. Image: Rob Poot. Researchers studying speciation of butterfly orchids on the Azores have been startled to discover that the answer to a long-debated question "Do the islands support one species or two species?" is actually "three species". Hochstetter's Butterfly-orchid, newly recognized following application of a battery of scientific techniques and reveling in a complex taxonomic history worthy of Sherlock Holmes, is arguably Europe's rarest orchid species. Under threat in its mountain-top retreat, the orchid urgently requires conservation recognition.
Ernst Mayr Library Blog - Sat, 2013-12-07 10:16
I was privileged to attend and present as part of a symposium at the Biodiversity Information Standards (TDWG) meeting October 28-November 1, 2013. The theme for 2013 was “Virtual Communities for Biodiversity Science”, an apt theme for the global virtual Biodiversity Heritage Library. The venue was beautiful Florence, Italy and the weather was warm.
Six members of the Global BHL community participated in the symposium, “Crafting the Future of a Global Biodiversity Heritage Library for Diverse Communities’ Needs“. My contribution to the symposium was a review of feedback the BHL has received through surveys, interviews and messages, looking for common threads and what has been resolved.The most common thread throughout the years and echoed by the 50 or so audience members is: “Scan more!!”.
TDWG is a long and information-packed meeting that incorporates many topics of interest to the Biodiversity Heritage Library and librarians. Metadata, vocabularies for taxonomy, interoperability and linked open data are common themes at TDWG to which librarians, particularly those engaged in biological information, can relate. I particularly enjoyed the poster sessions. There were 31 posters and I will highlight a few in this post.
BHL partners such as ViBRANT http://vbrant.eu/), OpenUp http://open-up.eu/), BioStor http://biostor.org/), and Zookeys http://www.pensoft.net/journals/zookeys/) and others were represented at TDWG ensuring lively discussions. The poster “Bibliography of Life: Comprehensive services for biodiversity bibliographic references” (https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/339) addressed de-duplicating and parsing the components of references from a variety of sources to improve and expand literature searching. Other posters highlighted object digitization and the TDWG Audubon Core (http://www.tdwg.org/standards/638/)metadata standard. The Naturalis Biodiversity Center reviewed their work digitizing collection objects, including videos, (https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/395) using the Audubon Core standard for metadata. Another poster from Belgian institutions, Agora 3D Evaluating the Digitisation of Scientific Collections, reviewed scanning technology and techniques for biological specimens to develop a set of standards and protocols for museums (https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/398). Other posters highlighted taxonomic information such as “From Dendroeca blackburniae to Dendrceca blackburniae: what’s in a name” https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/344 citing the need for clean, correct scientific names to support names-based architecture and ” ComTax: Community-driven Curation for Taxonomic Databases”, a project designed to support manual correction and verification of name data (http://taxoncuration.myspecies.info/). The TDWG meeting has much to offer archivists and librarians looking for the biological perspective on metadata and curation. For the curious, you can find the uploaded presentations at the TDWG site.
- Harvard study shows sprawl threatens water quality, climate protection, and land conservation gains
- Patent database of 15 million chemical structures goes public
- Eurofins' scientists discover genetic differences between 'identical' twins
- Europe's rarest orchid rediscovered on 'lost world' volcano in the Azores
- Librarian travels: Biodiversity Information Standards (TDWG)