Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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...

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 ...

Blogging about curation in the past several issues have been discussed but here is something very critical. To thrive, the field that links biologists and their data urgently needs structure, recognition and support. Biocuration , the activity of organizing, representing and making biological information accessible to both humans and computers, has become an essential part of biological discovery and biomedical research. But curation increasingly lags behind data generation in funding, development and recognition. Three urgent actions to advance this key field. First, authors, journals and curators should immediately begin to work together to facilitate the exchange of data between journal publications and databases. Second, in the next five years, curators, researchers and university administrations should develop an accepted recognition structure to facilitate community-based curation efforts . Third, curators, researchers, academic institutions and funding agencies should, in the ...

Previously blogging about Smart tools to track, analyze and visualize research discussed about the latest trends in literature abstraction, alert services and analysis tools. This time as a sequel check out one of the finest alert service using the web 2.0 technology. It is absolutely FREE! It is very simple, just visit the site www.xtractor.in and register. Almost immediately you are provided with a user-name and pw to access the alert service. Smart tools to track, analyze and visualize research II Talking about the development in the field of literature and scientific publication search. Looking beyond NLP some of the advancements and service models based on NLP and other advanced methods. Today to the user's delight there are quite a few companies and organization that provide services that absolutely make a scientist life easy! These services revolve around customized alert services for selected search terms, specific research area of interest even more so pertaining to a ...

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 .

Sigma-Aldrich announced that its highly acclaimed chemistry review journal, Aldrichimica Acta, has again been ranked #1 by Impact Factor, out of 56 similar journals in the field of Organic Chemistry. In 2007, the latest year for which such rankings are available, the Acta achieved an Impact Factor of 11.929. The Acta was also ranked #1 in 2006 and 2005. These rankings appear annually in the Science Edition of Journal Citation Reports(R) (JCR), which is published by Thomson ISI(R). JCR, Science Edition, tracks close to 5,900 international science journals annually and offers quantifiable statistical data, which allows the systematic and objective ranking of journals by relative importance within their subject categories. The Aldrichimica Acta publishes in-depth reviews on topics of current interest to chemists. It is published four times a year and distributed at no charge to about 130,000 subscribers worldwide who are members of the scientific community.

The first of its kind - SCIENTIFIC LITERATURE alert service which also provides manually annotated sentences for the keywords of YOUR preference Highly accurate , manually annotated sentences for given keywords. Daily scientific literature updates at your desktop along with extracted facts - manually curated. Provision to change keywords with your changing research preferences. Annotated sentences and abstracts get stored in your profile, as and when they get updated in PubMed. Classify and create your own datasets of annotated facts. Enhanced experiences of reading & analyzing literature. Access your profile / datasets from anytime, anywhere. Discover and Create newer relations from scientific facts classified by the XTractor™ Community. Tag your favorite abstracts and share them across other users. Much more faster and an Absolutely Free Service PRODUCT HIGHLIGHTS Abstract Summarization The XTractor™ system would provide extracted relations in addition to id...

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...

Anyone who has ever built a website knows that maintaining it is a lot of work. There’s just making sure it hasn’t gone offline because the httpd daemon died. Constant monitoring for script kiddies and their SQL injections. Not to mention continually feeding it with fresh content, lest your audience become bored and desert. I’ve always thought it would be cool to build a site that could more or less look after itself. There’s a myriad of content management systems to choose from, most of which are somewhat hackable in whatever language they happen to be coded in. One of the more mature in this respect is Drupal - which is the engine behind Eureka! Science News . It’s a fully-automated science news portal, using a bunch of customised Drupal modules to aggregate, cluster, categorise and rank articles. First impressions are excellent. Coders will enjoy this post at Drupal explaining how it all works.

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

Already blogging on similar lines and the subject of Bring in data from the published literature in my earlier blog Smart tools to track, analyze and visualize research , here is another interesting experiment on similar lines: The experiment centres on Structured Digital Abstracts (SDA). SDA are extensions of the normal journal article abstracts that describe the relationship between two biological entities , mentioning the method used to study the relationship. Each sentence is preceded by one or more identifiers pointing to the corresponding database entries that contain the full details of the interaction e.g. protein A interacts with protein B, by method X . The aim of SDA is to assist data entry, text mining and literature searching by extracting the salient data from the article into simple sentences using a defined structure and controlled vocabularies. Gianni Cesareni, Editor of FEBS Letters explains: Many articles in biological journals describe relationships between ent...

The Protein Data Bank Japan (PDBj) curates , edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes 25–30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies : (i) a Java-based molecular graphics viewer, j V; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, e F-site, as well as a search service for similar molecular surfaces, e F-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the...

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)

Yes i am talking about the development in the field of literature search and scientific publication search. Looking beyond NLP some of the advancements and service models based on NLP and other advanced methods. Today to the user's delight there are quite a few companies and organization that provide services that absolutely make an scientist life easy! These services revolve around customized alert services for selected search terms, specific research area of interest even more so pertaining to a list of custom key-word and search terms that the service providers allow the user to choose form. The scientist can simply subscribe to such service, sit back and wait for daily updates. The updates are provided on a day to day basis at his desktop. He gets abstract summarization , full text summarization so that he need not actually go through the ordeal of reading through pages of scientific literature. Some once else does the job for him and just pick up the right things that he woul...

What is this? is this a new industry? or a old wine in a new bottle? may be the later is true, bioinformatics is more popularly known by this name in the industry circle these days! Well Life Sciences and Informatics can be any thing form anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining , database creation, in the area of biology, chemistry , bio-chem space. Cheminformatics , insilico chemistry and insilico biology how best to describe the host of activities involved that companies do to serve their clients and earn revenues for their firms... There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies operation in this sphere. there are companies with the sole focus as informatics as business to name a few : Molecular Connections Pvt. Ltd. Jubilant Biosys Strand Life Sciences Ocimumbio (hyderbad) While IT companies which are also in to Life Sciences as one of thei...