Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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Canada has started a national online archive that will house papers and data coming from government-funded research, and will be funded by the Canadian Institutes of Health Research. Modeled on the National Institutes of Health's PubMed Central, the PubMed Central Canada resource was launched to provide Canadians with a free and open national digital repository of peer-reviewed health and life sciences literature, including research funded by CIHR. PMC Canada was developed through a partnership between the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), which will build the infrastructure and manage the repository, the US National Library of Medicine, and CIHR. The resource supports the Policy on Access to Research Outputs, which requires that CIHR grant recipients make their peer-reviewed publications freely accessible online within six months after they are published. "The global movement to provide barrie...

Indian Life Sciences Informatics Company, Molecular Connections announced today, that their XTractor Premium platform now has more that 503,985 " Expert " annotated biomedical facts from literature and is the fastest growing knowledgebase currently. XTractor Premium platform is Fast Becoming the definitive Semantic Knowledge discovery & Expert curated Knowledgebase for Life Science Researchers. The XTractor Premium Knowledgebase in addition to more than 503,985 relationships on proteins, drugs, biological process and diseases has advanced semantic search, concept linking analytics for effective knowledge discovery and modeling. XTractor Premium provides Precision based mining of the most relevant facts. Compared to natural language processing engines, manual annotation approach reduces false positives rate by 12-35%. XTractor premium serves as a platform to stay current with weekly updates from PubMed. Provides “Topic Tracking” with email alerts on spe...

“ … LigerCat is a search tool for NCBI’s PubMed that uses tag clouds to provide an overview of important concepts and trends. LigerCat aggregates multiple articles in PubMed , summing their MeSH descriptors and presenting them in a cloud, weighted by frequency “. LigerCat is an abbreviation for Literature and Genomics Resource Catalog , which is a free PubMed search tool developed in 2009 as part of the Biology of Aging project at the MBLWHOI Library at the Woods Hole Marine Biological Laboratory . LigerCat is great news for geneticists or anyone involved in translational research, a fairly effortless means of data mining for dynamic links to a very complex literature. LigerCat can be used to search in several ways: 1) to locate and select a list of individual journal titles indexed in PubMed , 2) search using terms from the National Library of Medicine’s Medical Subject Heading (MeSH) list , 3) search using keywords, 4) search on Genes found in the NCBI database...

"There does appear to be a distinction between the way curation is used in the bio-sciences, and elsewhere. In particular, the term "curated database" tends to mean a manually constructed database that links literature to data, curated by experts who provide authority (eg see the Wikipedia definition of Biocurator ). The earliest mention of the term "curated database" I can find is in the abstract (and only in the abstract) of Larsen et al (1993)." Chris Rusbridge Digital Curation Blog Since these database are hand curated by experts (manually curated), they always promise a accuracy & quality better than uncurated or NLP based databases. While NLP based databases follow a automated curation provide quick updates and tend to be large in terms of the quantum of data. While they may trade off in accuracy due to their automated curation process. While platforms like XTractor Premium follow a unique approach by trying to adopt the best of both worlds. A ...

One of my recent post discussed the dawn of the new era and new breed of search engines Search Wars . YEBOL a youngling from the the Stanford stable, a new search in the block. Yebol's mission is to build human-like world's knowledge base and provide knowledge based search (semantics) and services. Yebol utilizes a combination of patented algorithms paired with human knowledge to build a Web directory for each query and each user. Instead of the common “listing” of Web search queries, Yebol automatically clusters and categorizes search terms, Web sites, pages and contents. Yebol allows for a multi-dimensional search result instead of the normal one-dimensional search seen by most web search engines today. This provides a more accurate summary of top sites and categories; a wider array of related search terms; a longer and richer expansion for query results; and a deeper base of links and keywords in search result pages. Unlike ...

Indian Life Sciences Informatics Company, Molecular Connections announced today, that their XTractor Premium platform surpasses 200,000 "Expert" annotated facts from PubMed. XTractor Premium – is a platform for discovery, analysis and modeling of published biomedical facts. The application also comes with - XTractor Premium Knowledgebase - the only knowledgebase, which provides " Expert " annotated facts from PubMed on a daily basis. The XTractor Premium Knowledgebase now has more than 202,847 relationships on proteins, drugs, biological process and diseases and is ever growing with more than 600 relationships being added every single day. XTractor provides manually categorized updates on the latest published facts from PubMed for more than 20 categories which include : Biomarkers, clinical trials, dosage, pathways, toxicology, RNAi studies, mutations, knockouts, diseases mechanisms, protein- drug relationships and much more. Expert Annotated Facts make XTractor Pr...

The US House of Representatives on Friday passed a 2010 budget for the Departments of Labor, Health and Human Services, and Education that would increase funding for the National Institutes of Health by nearly $1 billion over its appropriation for 2009. The bill, which passed the house by a vote of 264 to 153, seeks an NIH appropriation for 2010 of $30.97 billion, which is an increase of $940 million over the 2009 level, excluding funding from the American Recovery and Reinvestment Act. That increase also would boost NIH funding by $500 million over the $30.5 million asked for by President Barack Obama in his budget request. The bill also seeks $6.8 billion for the Centers for Disease Control and Prevention, an increase of $67 million over the 2009 appropriation and $38.4 million over the White House's 2010 request. The Federation of American Societies for Experimental Biology, which supports increased funding for biomedical research , said passage of the bill makes it more like...

There's a great deal of wisdom in a crowd, but how do you listen to a thousand people talking at once? Identifying the wants, needs, and knowledge of internet users can be like listening to a mob. In the Web 2.0 era, leveraging the collective power of user contributions, interactions, and feedback is the key to market dominance. A new category of powerful programs and web based technology lets you discover the patterns, inter-relationships, and individual profiles-the collective intelligence, locked in the data people leave behind as they surf websites, post blogs, and interact with other users. XTractor Premium is one such initiative, epitome of Collective Intelligence in Action for bio medical data. Implemens collective intelligence concepts of vital data gathering and mining techniques like analyzing trends, discovering relationships, and making predictions. It provides a pragmatic approach to personalization by combining content-based analysis with collaborative approaches ...

A not very long time ago, in a galaxy near, very near by.... SEARCH WARS Search, Search engines, While the Search engine big wigs fight for a niche in the search engines landscape .... The Google , Yahoo & now Micorsoft too (with their Bing ) There are the Wolfram | Alpha likes that are forming a separatist and slowly gaining power over the Google order. In fact google has managed to bring balance to both with its Google Squared . While platforms like XTractor , NextBio , Novoseek , GoPubMed , BioMedSearch have specialized in searching biomedical and biological knowledge are even more strengthening the separatists. Now to see and know who is more powerful, the galactic empire or the separatist? I leave it to the 'Republic' i.e. You users! to judge, in the form of your comments and experiences with such tools and searches! you could even voice your opinions here

Biomedical Data mining happens to be a long-standing problem in scientific research. Scientists are constantly in search of newer and innovative means to mine biomedical data. Be a part of the XTractor community. XTractor is the first of its kind - 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 ...

18 Ways to Improve your PubMed searches Be a part of the XTractor community. XTractor is the first of its kind - 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. Sign up it's free, and takes less than a minute. Just click here: www.xtractor.in .

It is a chilly Tuesday night and outside the Dana Cafe in London a queue of young people spills on to the pavement. A glamorous woman with a walkie-talkie and clipboard guards the bar's door and turns away anyone who is not on the guest list. The attraction is not the latest band, exclusive club or film screening, but a science lecture। Inside, Aubrey de Grey, a scientist from the Methuselah Foundation, a research group, is swigging from a bottle of Guinness as he tries to persuade a sceptical audience - which includes designers, artists and television producers - how society would benefit if we all lived forever. Clutching a glass of red wine, Alex Wilkie, a 32-year-old design lecturer, believes that science is undergoing a revolution and should not be dismissed as nerdy. 'It's an increasingly scientific society that we live in,' he said. 'Understanding what's going on in science helps put everything in context.' De Grey gives more than 30 such talks a year...

Have you been wondering about possibility of automating every scientific workflow? : The Taverna Interaction Service: enabling manual interaction in workflows by Anders Lanzén and Tom Oinn Taverna is an application that eases the integration of tools and databases for life science research by the construction of workflows. The Taverna Interaction Service extends the functionality of Taverna by defining human interaction within a workflow and acting as a mediation layer between the automated workflow engine and one or more users. Try Taverna plugin is very likely an answer to automation of bioinformatics workflows... (Bioinformatics Advance Access abstract)

Leading scientists discuss DNA database at April 7-8 Meeting For a quarter century, GenBank has helped advance scientific discovery worldwide. Established by the National Institutes of Health (NIH) in 1982, the database of nucleic acid sequences is one of the key tools that scientists use to conduct biomedical and biologic research. Since its creation, GenBank has grown at an exponential rate, doubling in size every 18 months. In celebration of this vital resource and its contribution to science over the last 25 years, the National Center for Biotechnology Information, National Library of Medicine (NLM), NIH, is holding a two-day conference on GenBank. The conference will take place April 7-8, 2008 at the Natcher Conference Center on the main NIH campus in Bethesda, Maryland. For details on the meeting, see the conference Web site, at http://www.tech-res.com/GenBank25 . The conference is open to the public and also will be available via live and archived webcast; the April 7 proceedin...