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 

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Search PubMed with the advanced Semantically Annotated Biomedical Search XTractor Lite

XTractor Lite

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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
  

SAAS product startup from India XTractor

Was going through a recent blog on indiblogger about the NASSCOM Product Conclave. Where this time is themed and focused on SAAS & related services.

In the recent times SAAS or Software as a Service has even captured the attention of Life Science and biomedical community globally. Indian Life Sciences Informatics Company, Molecular Connections' year old SAAS product startup is www.XTractor.in. In July 2008 came of with a commercial version of the product XTractor Premium- expert curated biomedical discovery, analysis and knowledge modeling platform, based on semantic curation and annotation of biomedical facts from PubMed. Has very handy analytics to search and narrow down the most relevant facts, build and discover relationships between biomedical facts check out some of the user CaseStudies.

XTractor Premium knowledgebase currently contains 302,269 relationships categorized on 24 categories Gene-Gene , Gene-Drug , Gene-Disease , Gene-Process , Gene-Mutation/Polymorphism, Drug Disease , Gene Knock-out/RNAi, Gene Pathways , Drug Process , Disease Process , Biomarker/Marker Disease , Prognosis, Diagnosis, Therapeutic or Therapy, Clinical Trials, Drug Bioavailability , Drug clearance , Drug Dosage , Drug-Drug , Disease-Disease , Drug Pharmacokinetics , Drug toxicity , Drug route of administration , Drug pharmacodynamics.

The platform has a recently completed an seamless link-out integration with NCBI EntrezGene.

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
  

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
  

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’

Web 2.0 and Semantic Web for Bioinformatics

Here is a hand picked item, one of my favorites among the recent blogs that came across. This articles reflects and talks about many things which i have appreciated in the recent times and have blogged in the past web 2.0....

Why should a (bioinformatics) scientist learn web development ?

Up to now bioinformatics research with genomics datasets, has been happening like that: you download the data from a website of a big-iron institution (NCBI, TAIR), set them up locally, BLAST ‘em, MySQL’em, parse them with Perl script, and do all other sorts of un-imaginable things. Even though bioinformaticians might be un-aware of the term, part of the local processing that happens with the data is a mashup. This term translates to the combination of pieces of data from different sources, something akin to what has been happening on the web (see also Web 2.0 or programmable web). In no way this is close to the myriad of Web 2.0 mashups that exist out there, created using APIs offered openly by different servers. In this case different sets of data are brought together by the mashup developer, who also adds value to them through their re-combination (and reciprocally adds value to the providing server, through spreading out and offering a better view of their offered data).

While the big-iron bioinformatics institutions don’t quite live in a parallel universe from Web 2.0 (we have to credit the NCBI server for its GCI interface), there are light years away from the programmable web. That is both because of the technologies their are using (forget about Ruby on Rails and REST), but also because of the small number of institutions like NCBI offering APIs.

So why should a (bioinformatics) scientist learn web development ? Because this situation I am describing above will change. These bioinformatics institutions will adopt Web 2.0 at some point during the next years - I can bet you now that, OK maybe in 5 years, we will have an NCBI running a nice REST API backed by Rails or Django. But it might happen even earlier, when people take things at their own hands. And for that I refer you to Amazon Web Services, where bioinformaticians can build their own NCBI running on Rails and sell it to other Web 2.0-minded scientists, who understand the (added) value of an inter-operable web of data.

Be part of XTractor community.

• XTractor the first of its kind Web 2.0 - Literature alert service, provides manually curated & annotated sentences for the Keywords of your choice
  
• XTractor maps, extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies
  
• Enables customized report generation. With XTractor the sentences are categorized into biologically significant relationships
  
• The categorized sentences could then be tagged and shared across multiple users
  
• Provides users with the ability to create his own database for a set of Key terms
  
• Users could change the Keywords of preference from time to time, with changing research needs
  
• XTractor thus 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.

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.