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PubMed Canada to Store Government-Funded Studies

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 barrier-free access to research is gaining strength and with good reason, said Ian Graham, CIHR's VP of Knowledge Translation, in a statement.

"Having desktop access to a searchable, permanent and freely accessible archive of Canadian health research will serve as a valuable resource for researchers, enabling them to translate that knowledge into solutions to important health issues," NRC-CISTI Director General Pam Bjornson added.

The first phase of PMC Canada includes development of a bilingual interface and help desk and a manuscript submission system. The planned second phase of the repository will incorporate a customized web front-end and enhanced reporting and alerting features for system funders and users.

PMC Canada's future development will be guided by an advisory committee that will include health researchers and other stakeholders.

World's fastest growing Semantic discovery & Expert Curated Knowledgebase platform crosses 500,000 biomedical facts now

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 specific biological entities of interest via the “Watch List” feature.

The Highlights

Semantic Search: The first of its kind highly advanced search feature, where in one could query the XTractor Premium Knowledgebase using multiple ontologies. This would enable you to narrow down on your targets at ease.

Concept Linking: Our advanced query feature would enable you to make assumptions from multiple abstracts, and discover facts, which are hitherto not published.

Bibliographic search: Search based on author, organization, affiliation or country.

Save Export and Visualize: Save and export the data in user-friendly formats, also XTractor Premium is made compatible with CytoScape - so one can visualize the networks rendered using a in-house CytoScape plug-in.

Web based and onsite installation available

To know more about the advantages of the XTractor Premium and to register for a free trial account and a webex demo please visit XTractor Premium portal www.xtractor.in/premium.

About XTractor Premium Knowledgebase
XTractor knowledgebase currently contains 503,985 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions, toxicity, pharmacokinetics, disease mechanisms. It is the Only Knowledgebase that gets updated everyday with manually annotated relationships from the latest PubMed publications and contains more than more than 1,269 Unique Drugs, 3,602 Unique Diseases, 11,407 Unique Proteins, and 3,266 Unique Biological Processes. Hence in no time one gets to access one of the largest and the most current manually annotated datasets across the world.

About Molecular Connections
Molecular Connections is a pioneering In silico Discovery Services Company. It provides high quality, cost effective curation, literature informatics solutions and annotation services as well as products. Dr. Limsoon Wong is the Chairman of Molecular Connections. Customers of Molecular Connections include leading pharmaceutical and biotechnology, drug discovery, genomics, proteomics, medical technology, equipment companies and academic institutions spanning across the globe. In addition, Molecular Connections has powerful tool development, database integration, effective data visualization capabilities, specific expertise in building knowledge bases for rapidly growing needs in, ADME Tox, clinical, drugs, chemistry and patent industries. For more information write to us at xtractorpremium@molecularconnections.com

Recent Awards
Deloitte Technology Fast 50 India Winners |Deloitte Technology Fast 500 APAC Winners |CNBC - ICICI Emerging India Awards ‘Small Enterprise of the Year’

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at an Special Introductory Offer. Subscribe now and save!
  
• Request for a Trial
  

Search Engines, Genomics, Medical Literature: Tag Clouds come to PubMed via LigerCat

“… 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 databases.

Do you want to know more?

for more reading:

• Do you hate Pubmed? Here is the solution!
• Getcloudlet Brings Tag Clouds Plus Better Search Terms On Google Search Engine
• GoPubMed – “Searching is now Sorted”

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at an Special Introductory Offer. Subscribe now and save!
  
• Request for a Trial
  

Curated databases and data curation

"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 hybrid approach of a first level of NLP which promises a quick turnaround and large quantum of data followed by expert curation to preserve and maintain the high quality promised by expert curated database. XTractor Premium is a specialized biomedical text mining platform with semantically enriched search (Semantic search) and analytics to that enable discovery, knowledge sharing, analysis and modelling of published biomedical facts.

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at an Special Introductory Offer. Subscribe now and save!
  
• Request for a Trial
  

Search Wars Episode II. Yebol a new search!

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 current search platforms, Yebol provides hundreds of easily identified and accessibly categorized results in one easily navigable page. The results not only provide users with a rich search experience, but also help them quickly scan the results to find targeted information. In essence, generate a unique “homepage look” for each search query.

Yebol provides a productive experience for both main types of search – general investigation of a topic and specific target search. For users who want to research and explore a topic, Yebol provides rich information from several dimensions. For users who want a specific type of targeted results, they can quickly focus on their category and navigate to the target.

A search for APOE, top most hit (first) gave a expanded definition Apolipoprotein E - on Wikipedia. Followed by link to GHR, wikigenes, gene cards, AD genetics fact sheet form NIA.

It also gives live context sensitive Twitter streaming too.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at an Special Introductory Offer. Subscribe now and save!
  
• Request for a Trial
  

XTractor Premium surpasses 200,000 mark of Expert Annotated PubMed Facts

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 Premium a High Quality Knowledgebase and the vast coverage of all biological entities wrapped with in intuitive and analytical software allows researchers more time for science and eliminates the need to consult BioIT experts.

The entities are out linked to over 30 different public databases such as patent databases, wikipedia, clinical trials, and other protein/drug databases.

With XTractor Premium one can,

· Quickly access relevant, high quality expert annotated biomedical facts

· Understand multiple target preferences for a specific drug

· Track common gene polymorphisms across multiple diseases

· Understand Pharmacologic actions, protein interactions and toxicity studies of drugs

And for more, please visit the case study section.

About XTractor Premium

The Knowledgebase: XTractor knowledgebase currently contains 202,847 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions, toxicity, pharmacokinetics, disease mechanisms. It is the Only Knowledgebase that gets updated everyday with manually annotated relationships from the latest PubMed publications and contains more than 856 Unique Drugs, 2569 Unique Diseases, 9286 Unique Proteins, and 2102 Unique Biological Processes. Hence in no time one gets to access one of the largest and the most current manually annotated datasets across the world.

To know more about the advantages of the XTractor Premium and to register for a free trial account and a webex demo please visit XTractor Premium portal www.xtractor.in/premium.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at an Special Introductory Offer. Subscribe now and save!
  
• Request for a Trial
  

House Passes Proposed 3 Percent NIH Funding Increase

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 likely that the House will pass all of the fiscal appropriations for fiscal year 2010 before Congress breaks for its late summer recess, which runs from Aug. 4, through the Labor Day weekend.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at an Special Introductory Offer. Subscribe now and save!
  
• Request for a Trial
  

Collective Intelligence in Action - XTractor Premium

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 for effective literature mining in todays eonomy...

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.

• The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis
  
• Innovative Features like Semantic Search, Concept Linking, Bibliographic search, Save, Export and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at an Special Introductory Offer. Subscribe now and save!
  
• Request for a Trial
  

Search Wars

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

Freely mining PUBMED for your drug discovery needs everyday

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 collaborate.

Sign up it's free, and takes less than a minute. Just click here:www.xtractor.in.

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.

Café Scientifique

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 and believes that people are excited by the humanitarian potential of science, rather than the theory. 'By and large, young people are more open-minded about my message, but I wouldn't say that implies they're more interested in science,' he said. 'I think for most the interest is in the "why" first and the "how" second.'

Most science cafes are loosely affiliated through an international umbrella organisation called Café Scientifique, which was founded in Leeds in 1998 and inspired by the French Café Philosophique movement. There are now more than 30 across the country.

In a rare reversal of cultural exchange, it is one trend that Britain has exported to America, which is now home to 60 cafes. There are a further 120 worldwide. Founder Duncan Dallas said that by taking science out of the classroom it changed the expectation of both audience and speaker. 'Science is the most important force in our culture and is increasingly impinging on our public and personal lives, through subjects like genetics and climate change. So public engagement with science is bound to increase,' said Dallas. 'But, for me, the whole point of science cafes isn't to promote science or make more kids become scientists, but is about everyone being able to discuss topics which are revolutionary.'

The subjects discussed are diverse। One night at the Dana Cafe, in South Kensington, a hot debate raged about robotics, specifically a man-made fly-eating machine going by the name of 'EcoBot', which was invented by the Bristol Robotics Laboratory. Other topics include the smell of romance, the science of sleep and marine pollution.

for more details

Semi-automated workflows - Taverna Interaction Service

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)

GenBank celebrates 25 years of service

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 proceedings can be viewed at http://www.videocast.nih.gov/summary.asp?live=6670 and the April 8 proceedings at http://www.videocast.nih.gov/summary.asp?live=6671.

The conference will bring together a slate of world-renowned scientists in molecular biology, genetics, bioinformatics and other areas to discuss GenBank's applications, the discoveries it has enabled, its history, and future directions. Speakers include Rich Roberts, Ph.D., a Nobel Prize winner for his discoveries of split genes, and currently Chief Scientific Officer at New England BioLabs; Sydney Brenner, Ph.D., a Nobel Prize winner for his work on genetic regulation of organ development and programmed cell death, and currently a professor at the Salk Institute; Francis Collins, M.D., Ph.D., who led the Human Genome Project and is Director of NIH's National Human Genome Research Institute; and Craig Venter, Ph.D., who led the private-sector effort to sequence the human genome and is President of the J. Craig Venter Institute. More than a dozen other eminent scientists will be speaking; the full list of presenters can be viewed at the GenBank conference Web site.

"Each day, researchers across the world submit tens of thousands of sequences to GenBank and collaborating databases in Europe and Japan," said Donald A. B. Lindberg, M.D., Director of the National Library of Medicine. "Because of these contributions, GenBank has become an essential tool for molecular biology. The National Library of Medicine is proud to partner with the research community in making this valuable resource available."

Rich Roberts, Ph।D., Chief Scientific Officer at New England BioLabs, commented, "GenBank has provided a foundation upon which much of contemporary biology is now based. It is becoming almost impossible to conceive of any serious biological study of a new organism that does not begin with the determination of its DNA sequence, which of course must be stored in GenBank." Roberts, one of the early proponents of the database, added, "the availability of this wealth of sequence information in a single repository is something we could only dream about in 1979 at the Rockefeller Conference that led to its creation and which we could not imagine being without today."

for more details