PubDNA Finder

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 new manuscripts. Users can query the database via the web
interface provided. Availability: PubDNA Finder can be freely accessed
at http://servet.dia.fi.upm.es:8080/pubdnafinder

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Freely mining PUBMED for your drug discovery needs everyday

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 collaborate.

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XTractor crosses 150 user registration in 3 weeks!!!!

• 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 schooland 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 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.

Launch of XTractor™ -a powerful scientific literature alert & abstraction system, now with unlimited free access.

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 form unstructured text. Text mining engines are fast enough but not accurate. XTractor™ with its efficient workflows combines the speed of a text-mining engine, with the accuracy of manual, expert curation.

XTractor™ is highly accurate and more efficient than many of NLP engines, since it is a hybrid model using technology and manual validation. Since the annotation is highly accurate researchers would also be able to perform complex queries and retrieve the most complex relations available in literature, which is currently not possible with the conventional NLP systems. Other than this XTractor™ acts as a platform for data sharing and categorization. Scientists can share their data with others and even tag data into customized datasets. Above all the data stored in one’s profile is accessible anytime, anywhere.

J Kamesh, Business Development Manager at Molecular Connections mentioned, “XTractor™ is a technology, which can and should be used by all life science researchers who want to stay current and updated in their field of interest. XTractor™ provides scientists with the ability to customize his own data needs. The researchers have the flexibility to change their keywords in tune with their changing research needs. The alerts get updated automatically for the new set of Keywords.”

To know more about the advantages of the XTractor™ and to register for a free trial account please logon to the Molecular Connections’ XTractor portal www.XTractor.in.

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.

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.

Smart tools to track, analyze and visualize research II

Previously blogging about Smart tools to track, analyze and visualize research discussed about the latest trends in literature abstraction, alert services and analysis tools. This time as a sequel check out one of the finest alert service using the web 2.0 technology. It is absolutely FREE! It is very simple, just visit the site www.xtractor.in and register. Almost immediately you are provided with a user-name and pw to access the alert service.

Smart tools to track, analyze and visualize research II

Talking about the development in the field of literature and scientific publication search. Looking beyond NLP some of the advancements and service models based on NLP and other advanced methods. Today to the user's delight there are quite a few companies and organization that provide services that absolutely make a scientist life easy!

These services revolve around customized alert services for selected search terms, specific research area of interest even more so pertaining to a list of custom key-word and search terms that the service providers allow the scientist to choose form. The scientist can simply subscribe to such service, sit back and wait for daily updates. The updates are provided on a day to day basis at his desktop.

A scientist gets abstract summarization, full text summarization so that he need not actually go through the ordeal of reading through pages of scientific literature. Some once else does the job for him and just pick up the right things that he would look for in such papers. It is a very interactive service where on a daily basis the user can keep track of the quality of the service and set it right so that he can make sure that he just gets the right things he ever wants and nothing else other than that.

Over and above the service is provided using cutting edge technology, attractive web interface. Such interface come in all colour with floating dockable modules which is easy to use and some smart tools too. These smart tools enable the user to track, analyze, visualize and develop relationships among blocks of data that is being provided as "lego blocks".

Check out this product, XTRACTOR™ the first of its kind - SCIENTIFIC LITERATURE alert service which also provides manually annotated sentences for the keywords of YOUR preference

• Highly accurate, manually annotated sentences for given keywords.
• Daily scientific literature updates at your desktop along with the extracted facts – manually curated.
• Provision to change keywords with your changing research preferences
• Annotated sentences and abstracts get stored in your profile, as and when they get updated in LITERATURE.
• Classify and create your own datasets of annotated facts
• Enhanced experiences of reading & analyzing literature
• Access your profile/ datasets from anytime, anywhere
• Discover and Create newer relations from scientific facts classified by the XTractor™ Community.
• Tag your favorite abstracts/sentences and share them across other users
• Much more faster and an Absolutely Free Service

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.

Launch of XTractor™ -a powerful scientific literature alert & abstraction system, now with unlimited free access.

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 form unstructured text. Text mining engines are fast enough but not accurate. XTractor™ with its efficient workflows combines the speed of a text-mining engine, with the accuracy of manual, expert curation.

XTractor™ is highly accurate and more efficient than many of NLP engines, since it is a hybrid model using technology and manual validation. Since the annotation is highly accurate researchers would also be able to perform complex queries and retrieve the most complex relations available in literature, which is currently not possible with the conventional NLP systems. Other than this XTractor™ acts as a platform for data sharing and categorization. Scientists can share their data with others and even tag data into customized datasets. Above all the data stored in one’s profile is accessible anytime, anywhere.

J Kamesh, Business Development Manager at Molecular Connections mentioned, “XTractor™ is a technology, which can and should be used by all life science researchers who want to stay current and updated in their field of interest. XTractor™ provides scientists with the ability to customize his own data needs. The researchers have the flexibility to change their keywords in tune with their changing research needs. The alerts get updated automatically for the new set of Keywords.”

To know more about the advantages of the XTractor™ and to register for a free trial account please logon to the Molecular Connections’ XTractor portal www.XTractor.in.

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 and effective data visualization capabilities. Molecular Connections has specific expertise in building knowledge bases for rapidly growing needs in genomics, proteomics, ADME Tox, clinical, drugs, chemistry and patent industries.