Bio Saga Blog - A Chronicle of Life Sciences & Informatics

While this is very encouraging what's going to be it's impact on the industry on proprietary database vendors? More & more of open database consortia and open curation models are on the offing, with high level of participation from both the academia and the Industry. The European Molecular Biology Laboratory's European Bioinformatics Institute has launched a "vast online database" of genomic-based drug and small molecule information available in an open access format for researchers seeking new therapeutics, according to EMBL-EBI. The ChEMBLdb holds translational information on more than 520,000 small molecules, including data on target binding, the affect these compounds have on cells and organisms, and information about the molecules' absorption, distribution, metabolism, excretion, and toxicity. "The data lie at the heart of translating information from the human genome into successful new drugs in the clinic," EMBL-EBI said this week. EMB...

XTractor now has a ready reckoner on Drugs , Diseases , Proteins & Processes along with sample manually annotated sentences form PubMed available on each of those Drugs , Diseases , Proteins & Processes listed there. This is really going to be handy for any bench scientist. Be part of XTractor community. XTractor the first of its kind - Literature alert service , provides manually curated & annotated sentences for the Keywords of your choice XTractor maps, extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies Enables customized report generation. With XTractor the sentences are categorized into biologically significant relationships The categorized sentences could then be tagged and shared across multiple users Provides users with the ability to create his own database for a set of Key terms Users could change the Keywords of preference from time to time, with changing research needs XTractor thus proves to be a platform for gett...

XTractor - Discovering Newer Scientific Relations Across Abstracts http://www.xtractor.in/ Literature alert service, that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with the ability to create his own database for a set of Key terms. Also the user could change the Keywords of preference from time to time, with changing research needs. The categorized sentences could then be tagged and shared across multiple users. Thus XTractor proves to be a platform for getting real-time highly accurate data along with the ability to Share and collaborate. This has been added to Biological Informatics Subject Tracer Information Blog. This has been added to the tools section of Research Resources Subjec...

The European Commission has awarded €4.5 million ($7 million) to a consortium of 32 research organizations, universities, and companies from 13 countries to determine how to transform Europe’s biomedical data resources into a transnational “sustainable integrative bioinformatics network” for the life sciences. The consortium is led by the European Bioinformatics Institute. The first year and a half of this project, called ELIXIR, for European Life-science Infrastructure for Biological Information, is aimed at gathering input, performing technical-feasibility studies, and doing user surveys among researchers who generate and use data, and develop tools. Much like the Oxford English Dictionary, which will remain useful as long as people speak English, so, too, will “the infrastructure for biological information … continue as long as people are interested in biology, health, and medicine,” she said. But provisions must be made to allow that to happen, including upgrading the infrast...

Hoping to bring together “a million minds” to annotate proteins, a team of researchers has launched a large-scale, community-based project called WikiProteins that combines automated text, data, and concept mining, manual annotation, and a newly developed software component called the Knowlet. The project, which aims to annotate proteins and protein-related biomedical concepts such as diseases or organisms, will be powered by a platform technology designed by a group of scientists and a Rockville, Md.-based startup and will be made available free of charge in perpetuity for the scientific community and the public. Called WikiProfessional , the platform “in a technical sense powers the community-version that we have now put out there, but you could take exactly the same technology platform and install it locally at a pharmaceutical company for them to do drug-lead discovery,” said Albert Mons, a computational linguist and co-founder of the startup, Knewco. “Philosophically we wante...

The International Conference in Trends for Scientific Information Professionals Habitual attendees say that "it is the meeting to which they go to spot the trends, as well as the meeting that provides unparalleled opportunities for networking" Trends and networking will be high on the Nice agenda in October 2008. The ICIC meeting covers trends in the field of scientific and professional information with an impressive line-up of significant figures in the information world. Among the topics that will be covered and discussed by the 22+ speakers are: Tools for Competitive Intelligence ( e.g., mining tools, visualisation tools, analysis tools, etc ) Challenges for the information community over the next five years Changes in the information environment for patents, innovation and intellectual property Trends in Search Engines and Information Retrieval ( also see ) Case Studies in Data and Content Integration