Category Archives: Semantic Web

discovery, healthcare, integration, knowledge integration, Knowledge Management, medicine, ontology, search, Semantic Web, Semantically Annotated, semantics, text mining

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

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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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discovery, healthcare, integration, knowledge integration, Knowledge Management, medicine, ontology, search, Semantic Web, Semantically Annotated, semantics, text mining

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Leave a comment
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 |

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biomedical literature, data mining, database, Dieases, drugs, expert curation, genes, Knowledge Management, literature mining, manual annotation, NLP, pubmed, Semantic Web, text mining

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

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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.

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biomedical literature, data mining, database, Dieases, drugs, expert curation, genes, Knowledge Management, literature mining, manual annotation, NLP, pubmed, Semantic Web, text mining

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

1 Comment

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.

addthis_url=”; addthis_title=”; addthis_pub=’jkbioinfo’;

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bioinformatics, Entrez gene, India, Indian companies, indiblogger, informatics, informatics industry, nasscom, nasscompc, ncbi, NIH, SAAS, Semantic Web

SAAS product startup from India XTractor

4 Comments

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.

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bioinformatics, Entrez gene, India, Indian companies, indiblogger, informatics, informatics industry, nasscom, nasscompc, ncbi, NIH, SAAS, Semantic Web

SAAS product startup from India XTractor

3 Comments

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.

addthis_url=”; addthis_title=”; addthis_pub=’jkbioinfo’;

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document.write(unescape(“%3Cscript src='” + gaJsHost + “google-analytics.com/ga.js’ type=’text/javascript’%3E%3C/script%3E”));

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annotated, annotation, bioit, biomedical, biomedical literature, curate, curation, data accuracy, data mining, database, manual annotation, Manually annotated, NLP, Semantic Web, text mining, tools

Curated databases and data curation

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“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.

addthis_url=”; addthis_title=”; addthis_pub=’jkbioinfo’;

var gaJsHost = ((“https:” == document.location.protocol) ? “https://ssl.” : “http://www.”);
document.write(unescape(“%3Cscript src='” + gaJsHost + “google-analytics.com/ga.js’ type=’text/javascript’%3E%3C/script%3E”));

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annotated, annotation, bioit, biomedical, biomedical literature, curate, curation, data accuracy, data mining, database, manual annotation, Manually annotated, NLP, Semantic Web, text mining, tools

Curated databases and data curation

Leave a comment

“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.

addthis_url=”; addthis_title=”; addthis_pub=’jkbioinfo’;

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