Bio Saga Blog - A Chronicle of Life Sciences & Informatics

C SHALS is the premier annual event focused on the use of semantic technologies in the pharmaceutical industry, including hospitals/healthcare institutions and academic research labs. Rather than a Semantic Web conference, CSHALS focuses on specific applications of semantic technologies. Attendees will gain a better understanding of where the field is headed and be prepared to advance with the field. Themes of past CSHALS conferences: Clinical Information Management Discovery Information Integration Integrated Healthcare and Semantics in Electronic Health Records Translational Medicine / Safety Search and Document Management/Business Intelligence/Text Mining Text Mining/ Information Extraction For further details visit   Share |

e-LICO multi-omics prediction challenge with background knowledge on Obstructive Nephropathy We present a biological data-mining problem that poses a number of significant challenges: The available data are of high dimensionality but of extre... Time Left:  90 days Teams:  84 Prize:  2500 EUR Share |

Is Facebook a phenomenon — or a fad? In the two years since Facebook opened its platform to outside developers, more than 300,000 Facebook applications, or "apps," have been created — games, quizzes, digital gifts and more. The successful apps boost users' engagement with Facebook — sometimes called "stickiness" — but do not directly provide revenue. Piggybacking on Facebook has been profitable for several startups. Zynga, which according to some reports is raking in annual revenues of $100 million with the poker game Texas Hold'em and other games, has grown from 45 employees to more than 250 in the past year, Pincus said. About "70 percent, perhaps 80 percent" of Zynga's growth, he said, could be attributed to Facebook. Flixster's growth also illustrates Facebook's role as a driver of Web innovation. Founded in January 2006, Flixster.com was attracting about 4 million monthly unique visitors when Facebook opened its development ...

Last week the XTractor Premium Knowledgebase has clocked 150,000 manually categorized biomedical facts. The knowledgebase currently grows at a rate of more than 700 facts every single day from PubMed and covers information on Biomarkers , Disease mechanisms, Clinical Trials, polymorphisms , mutations , knockouts and pathways . The knowledgebase recently crossed landmark of more 10000 relationships on knockout and mutation studies alone in XTractor. Knockout/Knockdown related facts: 10132 Mutation related facts: 14331 So not only you get the most relavant scientific facts everyday but also individual uptodate knowledge on knockouts, mutations, biomarkers , SNP and so on… XTractor Premium - A Platform for discovery , 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 a...

Life sciences informatics company Molecular Connections , India, has announced the availability of XTractor Premium, a knowledge management platform, for the biomedical research community. The product is projected to provide scientists with new and refined ways to access the latest scientific facts from PubMed. Pharmaceutical companies, researchers and scientists can use the platform to identify, verify and develop predictive relationships from PubMed Literature. Leveraging the ability to transform data to knowledge and to assist experts is seen to be crucial to the success of research investigation today. XTractor Premium offers several enhancements over the beta version in managing large volume of published biomedical data to accelerate decision making. The XTractor knowledgebase currently contains 150,000 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions and disease mechanisms. The knowledgebase is updated everyday with manually a...

XTractor Premium - a platform for discovery, analysis and modelling of published biomedical facts. The application also comes with -XTractor Premium Knowledgebase - the only knowledgebase, which provides "manually" annotated facts from PubMed on a daily basis.The XTractor Premium Knowledgebase now has more than 150000 relationships. TAGS: text mining, manual annotation, data alerts, pubmed, genes, drugs, processes, diseases, free, data mining, tag, drug discovery, web 2.0, natural language processing, data analysis, visualization, concept linking, abstraction, precision, recall, data accuracy, proteins, interactions, index, query, MeSH, NLM, manual curation, protein interactions, abstraction, abstracts, accuracy, accurate, data, annotations, biological process, biomedical literature, categorization, colloborations, concept linking, curate, curation, data accuracy, data alerts, literature, categorization, colloborations, concept linking curate curation data accuracy data ale...

text mining, manual annotation, data alerts, pubmed, genes, drugs, processes, diseases, free, data mining, tag, drug discovery, web 2.0, natural language processing, data analysis, visualization, concept linking, abstraction, precision, recall, data accuracy, proteins, interactions, index, query, MeSH, NLM, manual curation, protein interactions, abstraction, abstracts, accuracy, accurate, data, annotations, biological process, biomedical literature, categorization, colloborations, concept linking, curate, curation, data accuracy, data alerts, literature, categorization, colloborations, concept linking curate curation data accuracy data alerts da, abstracts, annotations, biological process, categorization, colloborations, data accuracy, data analysis, data mining, drug discovery, MeSH, molecules, natural language processing, NLM, NLP, precision, processes, protein function, protein interactions, publishing, pubmed, query, rec...

The Alzheimer Research Forum ( http://www.alzforum.org ), a dynamic, biomedical Web community that is heavily used by Alzheimer researchers around the world, is preparing to migrate to a new platform that will enable it to more fully exploit social networking (" Web 2.0 ") and the Semantic Web ("Web 3.0"). Founded 13 years ago when the Web was still in its infancy, the "Alzforum" has more than 5,000 registered members and is familiar to most Alzheimer scientists in the world. Ever since launching in 1996, the Alzforum Web site has been interactive, posting researchers' comments on published papers and research news. The site has published thousands of peer commentaries and mini-reviews by leading scientists in the field, and has established itself as the "go to" Web site for anyone who wished to be up to date on Alzheimer research. Members can post commentaries on any journal article or news story, and can participate in live discussion for...

Bangalore, India — Indian Life Sciences Informatics Company, Molecular Connections announced today, the launch of XTractor Premium ( www.xtractor.in/premium ), a new Knowledge Management Platform designed to enable Pharmaceutical Companies, Researchers, Scientists identify, verify and develop predictive relationships from PubMed Literature. “ The release of XTractor Premium reflects the evolution of our client’s knowledge management needs and our continued commitment to provide knowledge solutions which add value & bring better efficiencies in Drug discovery,” said Jignesh Bhate CEO Molecular Connections. Leveraging the ability to transform DATA to KNOWLEDGE to assist experts is crucial to the success of drug development today. XTractor Premium offers several enhancements over the beta version in managing large volume of published biomedical data to accelerate decision making in drug discovery. Data Search: One would be able to perform searches over the entire XTra...

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 ...

Atrium Research has published the 2008 Electronic Laboratory Notebook Survey . This study contains the results and analysis of a survey of information technology, management, and scientific personnel in the life sciences, chemical, academic, government and food markets. Comprehensive data and analysis are reported on dozens of questions answered by 527 professionals from more than 20 countries. The report highlights user and prospective user opinions on data management challenges, technology interest, motivations, project goals, purchase timing, integration needs, and supplier product and brand perception. According to the report, the market for ELNs is exploding, with more than 30 suppliers offering commercial solutions. One of the fastest growing informatics markets with a growth rate of nearly 20 per cent per year, ELNs are radically improving the effectiveness of laboratory operations. ELNs enable new approaches to knowledge management, collaboration, and data integration. 'We ...

HCL founder and chairman and chief strategy officer of HCL Technologies Shiv Nadar was named for the Padma Bhushan honour . Here is yet an interesting and inspiring story of another Shiva, to those aspiring a career in informatics as well as all aspiring entrepreneurs. In the 26 years since he first arrived at MIT as a freshman, V.A. Shiva Ayyadurai has earned four MIT degrees and started two multimillion dollar companies. This fall, he will use his most recent degree, a Ph.D. in computational systems biology, and a Fulbright Scholarship to explore one of his lifelong interests: the intersection of Eastern and Western medicine. Ayyadurai started dreaming as a child in India, where his grandfather was a farmer and his grandmother a shaman, or traditional healer. He became interested in medicine watching his grandmother diagnose and treat patients based on a system of "elements"--earth, water, fire, metal and wood. That approach may seem strange to Westerners, but "you...

Among number of challenges faced by informatics one of the long standing and critical challenge has been the Biodiversity informatics: the challenge of linking data and the role of shared identifiers . A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases . Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity datab...