Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Courtesy: Dr Raghava &  Bioclues PubDNA Finder is an online repository to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features, (1) searching for papers mentioning one or more specific sequences of nucleic acids and (2) retrieving the genetic sequences appearing in different articles. These additional query capabilities are provided by a searchable index that was created by using the full text of the 176672 papers available at PubMed Central at the time of writing and the sequences of nucleic acids appearing in them. To automatically  extract the genetic sequences occurring in each paper an original method has been developed. The database is updated monthly by automatically connecting to the PubMed Central FTP site to retrieve and index...

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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...

“ … LigerCat is a search tool for NCBI’s PubMed that uses tag clouds to provide an overview of important concepts and trends. LigerCat aggregates multiple articles in PubMed , summing their MeSH descriptors and presenting them in a cloud, weighted by frequency “. LigerCat is an abbreviation for Literature and Genomics Resource Catalog , which is a free PubMed search tool developed in 2009 as part of the Biology of Aging project at the MBLWHOI Library at the Woods Hole Marine Biological Laboratory . LigerCat is great news for geneticists or anyone involved in translational research, a fairly effortless means of data mining for dynamic links to a very complex literature. LigerCat can be used to search in several ways: 1) to locate and select a list of individual journal titles indexed in PubMed , 2) search using terms from the National Library of Medicine’s Medical Subject Heading (MeSH) list , 3) search using keywords, 4) search on Genes found in the NCBI database...

Indian Life Sciences Informatics Company, Molecular Connections announced today, that their XTractor Premium platform surpasses 200,000 "Expert" annotated facts from PubMed. XTractor Premium – is a platform for discovery, analysis and modeling of published biomedical facts. The application also comes with - XTractor Premium Knowledgebase - the only knowledgebase, which provides " Expert " annotated facts from PubMed on a daily basis. The XTractor Premium Knowledgebase now has more than 202,847 relationships on proteins, drugs, biological process and diseases and is ever growing with more than 600 relationships being added every single day. XTractor provides manually categorized updates on the latest published facts from PubMed for more than 20 categories which include : Biomarkers, clinical trials, dosage, pathways, toxicology, RNAi studies, mutations, knockouts, diseases mechanisms, protein- drug relationships and much more. Expert Annotated Facts make XTractor Pr...

Published Literature findings act as a key driver for decision making in drug discovery and biotechnology industry. Majority of the researchers prefer PubMed for published literature since it is a free resource for dissemination of scientific information. Data mining biomedical information from PubMed has been a long-standing problem for many researchers across the globe. On an average more than 50,000 scientific abstracts get published in PubMed every month and for a researcher it is a highly time consuming task to pick the most relevant abstracts everyday and annotate them accurately for research purposes. Though many text mining NLP (Natural Language Processing) engines are used to address this problem, manually annotated data has its own advantages in terms of accuracy and quality of the data that is captured. However, one of the major disadvantages with manual data mining still happens to be the processing time and its cost intensive nature. So the need arises for a system, which ...

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...

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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...

The Journal of Visualized Experiments (JoVE) is a new way to publish original methods in the areas of biological and biomedical science in a video format. The focus is on making demonstration of techniques and experimental approaches clear and easy to follow. Articles published in JoVE are listed in Pubmed and MEDLINE so you can still get your paper cited by other authors. All submissions go through peer review and editorial review and the editorial board consists of 22 distinguished professors from Harvard, Princeton, NIH and other leading institutions in the US, Europe and Japan. Do you want to know more? Be part of XTractor community. XTractor the first of its kind - 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 signi...

XTractor now has a ready reckoner on Drugs , Diseases , Proteins & Processes along with sample manually annotated sentences form PubMed available on each of those Drugs , Diseases , Proteins & Processes listed there. This is really going to be handy for any bench scientist. Be part of XTractor community. XTractor the first of its kind - 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 gett...

Biomedical Data mining happens to be a long-standing problem in scientific research. Scientists are constantly in search of newer and innovative means to mine biomedical data. 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 ...

Provision to change keywords with user’s changing research preferences in PUBMED data 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.xt...

XTractor now has over Over 150 registered users from FDA , NIH , NCI , Astra Zeneca , Wyeth , MD Anderson Cancer Institute , Washington university , Scripps institute , Max Planck , Harvard Medical school and many more in less than 3 weeks !!! More than 600 annotated facts added everyday. A total of 25,000 facts added till date!!! 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 the...

Bangalore, India — Indian Life Sciences Informatics Company, Molecular Connections announced today, the release of XTractor™, a first of its kind manually curated literature alert service. XTractor™ can be accessed free of charge by the scientific community world wide. XTractor™ acts as a literature alert service, which provides scientists with manually annotated scientific facts from literature. It enables researchers to be up-to-date with the latest scientific publications in the STM arena, as and when they are published. Once registered the scientists have the freedom to choose their keywords of choice and also set the frequency at which they wish to receive these alerts. Mining scientific literature to retrieve accurate hits or extract entity relationship has always been a long-standing problem in research. It is a daunting task to identify the right gene name or the right drug name and extract relations/association with diseases, processes; pathways etc accurately fo...

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 .

Bangalore, India — Indian Life Sciences Informatics Company, Molecular Connections announced today, the release of XTractor™, a first of its kind manually curated literature alert service. XTractor™ can be accessed free of charge by the scientific community world wide. XTractor™ acts as a literature alert service, which provides scientists with manually annotated scientific facts from literature. It enables researchers to be up-to-date with the latest scientific publications in the STM arena, as and when they are published. Once registered the scientists have the freedom to choose their keywords of choice and also set the frequency at which they wish to receive these alerts. Mining scientific literature to retrieve accurate hits or extract entity relationship has always been a long-standing problem in research. It is a daunting task to identify the right gene name or the right drug name and extract relations/association with diseases, processes; pathways etc accurately ...