Conference on Semantics in Healthcare and Life Sciences (CSHALS)

CSHALS 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

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 |

Even as the globe has lurched into recession, the Facebook economy seems to be booming

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 platform. Fearing competition, Flixster built its own Facebook app. That app's traffic quickly surpassed visitors to Flixster.com.

More recently, Flixster built an app for Apple's iPhone — and it's activated via Facebook Connect. "It's the glue," Greenstein said.

The success of Facebook's development platform has inspired a trend: Google, MySpace, Twitter, Bebo, Yahoo and the Apple iPhone have all opened up to outside developers.

Do you want to know more?

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
  

The Perfect database to consult for SNP, Knockout/Knockdown related studies

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 and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at Introductory Offer of $450 for Academic Researchers. Subscribe now and save $300!
  
• Register for WebEx
  
• Request for a Trial
  
  

XTractor Premium for scientists to access data stored in PubMed says Knowledgespeak

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 annotated relationships from the latest PUBMED publications. Other premium features include semantic search functionality; concept linking; bibliographic search; and the option to save and export data in user-friendly formats.

The XTractor Premium Knowledgebase surpasses 150000 mark

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 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, recall, tag, text
gathering, visualization, web 2.0

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 and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at Introductory Offer of $450 for Academic Researchers. Subscribe now and save $300!
  
• Register for WebEx
  
• Request for a Trial
  
  

Tracking common gene polymorphisms across multiple Diseases with XTractor Premium

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, recall, tag, text gathering, visualization, web 2.0

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 and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at Introductory Offer of $450 for Academic Researchers. Subscribe now and save $300!
  
• Register for WebEx
  
• Request for a Trial
  
  

Pioneering Biomedical Web Community Poised For Leap To Web 3.0

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 forums. Researchers frequently reference Alzforum in scientific papers and conduct weekly "Alzforum" sessions in their labs to discuss current findings. The AlzGene database, designed and curated by researchers at Massachusetts General Hospital and developed and hosted by Alzforum, is a workhorse of the global genetic community, and has generated a primary research publication in Nature Genetics. Alzforum has built numerous other data resources for the research community.

This spring, Alzforum will re-develop its site using the Scientific Collaboration Framework (SCF), a project based on open-source Drupal technology that is designed for building scientific Web communities. SCF was piloted by the Harvard Stem Cell Institute to build a Web publication called StemBook (www.stembook.org). Alzforum will develop some new software modules in Drupal and contribute them back to the SCF, where they will be freely available for other research organizations that are building their own Web communities. (SCF software is available at http://www.sciencecollaboration.org).

SCF is well-suited for publishing articles, comments, forums and blogs, and for managing member communities with fine degrees of editorial control. "We want it to be very easy for anyone to participate, but it's also essential for our editors to vet all postings in order to maintain civil and productive discourse," says Alzforum's co-founder and Executive Editor June Kinoshita.

A feature of SCF that Alzforum's editors are excited about is a semantic tagging module that locates scientific terms within an article, such as names of genes, organisms, and biological processes, and proposes them as tags that describe key concepts in the article. The tags enable the user to search other content with matching or related tags, so that an article about a gene can be automatically linked to a description of the gene, to articles about the gene, and even to the profiles of scientists who study that gene.

"The possibilities this opens up for scientists to navigate a knowledge network of articles, databases, and people is amazing," says Kinoshita. "And all of the Web communities that share the SCF platform will be interconnected. Alzforum has always been about building a research community without walls. Using the SCF, we will take this idea to a whole other level."

• 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 and Visualize
  
• Only Knowledgebase with daily updations from PubMed
  
• XTractor Premium now at Introductory Offer of $450 for Academic Researchers. Subscribe now and save $300!
  
• Register for WebEx
  
• Request for a Trial
  
  

Molecular Connections Launches XTractor Premium for Effective Knowledge Management and real time access to Biomedical data

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 XTractor knowledgebase of 120600 relationships on proteins, drugs, biological process and diseases (which is ever growing). On an average more than 600 manually annotated facts get added to XTractor everyday, thus it is the ONLY Knowledgebase that gets updated everyday with manually annotated relationships from the latest PUBMED publications. 733 Unique Drugs, 2254 Unique Diseases, 7626 Unique Proteins, 1449 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.

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

Concept Linking: Construct hypothesis from multiple abstracts and discover new facts and relationships, which are hitherto not easily decipherable.

Bibliographic search: Would also enable one to search based on author, organization or country.

Save, Export and Visualize: Provides the utility to save and export data in user-friendly formats. Integration with CytoScape provides better knowledge representation and visualization.

All these Premium Features are available via four licensing options; Academic, Commercial, Governmental and Onsite Installation. XTractor Premium is now available with an Attractive Introductory Offer for Academic Researchers. Subscribe now and save! Visit www.xtractor.in/premium for more details.

Currently, XTractor’s user base includes Abbott, AstraZeneca, Bayerhealthcare, Celera, Cephalon, GSK, JNJ, Novartis, Pfizer, P&G, Wyeth, Vertex, USFDA, NIH, NCI, MD Anderson, Harvard Medical School, Max Planck, Scripps Inst. and many more.

About XTractor Premium

XTractor Premium, a platform for discovery, analysis and modeling of published biomedical facts. The application also comes with XTractor Premium Knowledgebase, the only knowledgebase, which provides "manually" annotated facts from PubMed on a weekly basis.

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 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.comThis e-mail address is being protected from spam bots, you need JavaScript enabled to view it

Recent Awards

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

The future of biocuration

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 next ten years, increase the visibility and support of scientific curation as a professional career.

Failure to address these three issues will cause the available curated data to lag farther behind current biological knowledge. Researchers will observe an increasing occurrence of obvious gaps in knowledge. As these gaps expand, resources will become less effective for generating and testing hypotheses, and the usefulness of curated data will be seriously compromised. When all the data produced or published are curated to a high standard and made accessible as soon as they become available, biological research will be conducted in a manner that is quite unlike the way it is done now.

Researchers will be able to process massive amounts of complex data much more quickly. They will garner insight about the areas of their interest rapidly with the help of inference programs. Digesting information and generating hypotheses at the computer screen will be so much faster that researchers will get back to the bench quickly for more experiments. Experiments will be designed with more insight; this increased specificity will cause an exponential growth in knowledge, much as we are experiencing exponential growth in data today.

Also read this

Do you want to know more?

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.

Market study reveals 20 per cent growth for ELNs

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 project sustained double-digit growth for ELNs for at least the next three years,' said Michael H Elliott, founder and CEO of Atrium Research. 'Our study shows the use of the technology expanding beyond early adopters in research synthetic chemistry into domains such as biology and analytical chemistry. Commercial life sciences continue to lead adoption; more than 30 per cent of biopharmaceutical companies have installed an ELN in at least one department.'

2008 Electronic Laboratory Notebook Survey

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.

East meets West, yet another story of an successful Indian entrepreneur

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'd see people actually getting healed," he says.

In 2004, Ayyadurai returned to MIT, this time to work on a Ph.D. in systems biology, a relatively new field that integrates biology, engineering and computer science. The goal of systems biology is to figure out how the layers of a biological system, from genes to cells to organs to the whole body, are linked.

Systems biologists start by figuring out how individual cellular pathways work, but deciphering just one pathway can take years. To speed up that process, Ayyadurai developed a computer model that can integrate the activities of all the different pathways in a cell--work that formed the basis of his doctoral thesis. Shiva not only provided the basic system called Cytosolve, but he used it to create a new composite model of the upregulation of interferon following viral infection.

Now, he wants to explore what Eastern and Western medical traditions can learn from each other. Ayyadurai sees the exchange as a two-way street: He plans to apply Western scientific rigor to testing the long-established traditions of the East, and to study how the Eastern "elements" can inform Western medicine.

He points out that the market for alternative therapies based on Eastern medicine is growing every year, even without scientific evidence to support their usefulness.

"Let's look at glucosamine and see if it really works. Let's look at ginkgo and see if it really works," he says.

Ayyadurai departs for India this month to begin his studies, and he also plans to start raising funds to launch an MIT-affiliated center to study Eastern medicine.

Yet another challenge to informatics, well does it have the answer this time?

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 databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers [such as Digital Object Identifiers (DOIs) and Life Science Identifiers (LSIDs)], and the implementation of services that link those identifiers.