Transfer of pharmaceutical data resources, private to public domain has greatest impact

While this is very encouraging what's going to be it's impact on the industry on proprietary database vendors? More & more of open database consortia and open curation models are on the offing, with high level of participation from both the academia and the Industry.

The European Molecular Biology Laboratory's European Bioinformatics Institute has launched a "vast online database" of genomic-based drug and small molecule information available in an open access format for researchers seeking new therapeutics, according to EMBL-EBI.

The ChEMBLdb holds translational information on more than 520,000 small molecules, including data on target binding, the affect these compounds have on cells and organisms, and information about the molecules' absorption, distribution, metabolism, excretion, and toxicity.

"The data lie at the heart of translating information from the human genome into successful new drugs in the clinic," EMBL-EBI said this week.

EMBL-EBI is hosting the database, which was transferred from the biotech company Galapagos through a £4.7 million ($7.7 million) Strategic Award from the Wellcome Trust.

"This unprecedented transfer of pharmaceutical data resources from the private sector to the public domain should have the greatest impact on researchers in academia and in small companies on limited budgets," Alan Schafer, director of science funding at the Wellcome Trust, said in a statement.

"ChEMBLdb will be a major resource of information for driving forward medicinal chemistry and drug development in the UK and internationally," Schafer said.

EMBL-EBI also said that, along with partner Wellcome Trust, it has released an integrated resource of sequence, compound, and screening data from a range of sources for protein kinases, called Kinase SARfari.

A cool ready reckoner on Drugs, Dieases, Proteins & Processes

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 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.

XTractor @ Biological Informatics.info - Discovering Newer Scientific Relations Across Abstracts

XTractor - Discovering Newer Scientific Relations Across Abstracts
http://www.xtractor.in/

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. This has been added to Biological Informatics Subject Tracer Information Blog. This has been added to the tools section of Research Resources Subject Tracer Information Blog.

http://theshortnames.com/2008/08/xtractor-discovering-newer-scientific-relations-across-abstracts

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.

EBI-Led Consortium to Study How to Turn EU Bio-Databases Into Bioinformatic Network

The European Commission has awarded €4.5 million ($7 million) to a consortium of 32 research organizations, universities, and companies from 13 countries to determine how to transform Europe’s biomedical data resources into a transnational “sustainable integrative bioinformatics network” for the life sciences.

The consortium is led by the European Bioinformatics Institute. The first year and a half of this project, called ELIXIR, for European Life-science Infrastructure for Biological Information, is aimed at gathering input, performing technical-feasibility studies, and doing user surveys among researchers who generate and use data, and develop tools.

Much like the Oxford English Dictionary, which will remain useful as long as people speak English, so, too, will “the infrastructure for biological information … continue as long as people are interested in biology, health, and medicine,” she said.

But provisions must be made to allow that to happen, including upgrading the infrastructure itself, promoting database interoperability, and using distributed annotation technologies.

ELIXIR will not unfold with “a big bang” but rather evolve in stages. And it does not solely concern the lions of the European database world such as EBI and the Swiss Institute of Bioinformatics, said Thornton. There are internationally collaboratively maintained databases such as InterPro and IntAct, and also many small ones.

According to Thornton, of the world’s approximately 900 biomedical databases, 40 percent are in Europe, many of which are specialist databases. “They are often in an individual’s laboratory; a research group may have developed a data resource that other people begin to use, and we really need to find a way to incorporate those data resources into the larger network in a way that people can access them easily and without necessarily knowing that they were there in the first place,” she said.

ELIXIR will help link the core and the specialist resources more closely while remaining as “seamless and transparent as possible to our users,” said Thornton. Clicking through databases from link to link is possible for researchers, she said, but clickthrough gymnastics becomes an impossible exercise when a microarray delivers a list of hundreds of genes that must be analyzed with a systems perspective, requiring data to be plowed and mined that is stored in different ways with differing vocabularies.

Interactive WikiProteins Project Invites Researchers to Annotate Biological Concepts

Hoping to bring together “a million minds” to annotate proteins, a team of researchers has launched a large-scale, community-based project called WikiProteins that combines automated text, data, and concept mining, manual annotation, and a newly developed software component called the Knowlet.

The project, which aims to annotate proteins and protein-related biomedical concepts such as diseases or organisms, will be powered by a platform technology designed by a group of scientists and a Rockville, Md.-based startup and will be made available free of charge in perpetuity for the scientific community and the public.

Called WikiProfessional, the platform “in a technical sense powers the community-version that we have now put out there, but you could take exactly the same technology platform and install it locally at a pharmaceutical company for them to do drug-lead discovery,” said Albert Mons, a computational linguist and co-founder of the startup, Knewco.

“Philosophically we wanted to hand off the responsibility for the quality of the content of the system to the community and then provide generic technology that can be used to grow the knowledgebase on a daily basis,”

Given high-throughput data and the increasing number of papers describing them, “comprehensive and timely annotation of the literature for facts by any central team of experts [is] an unachievable goal. Computer assistance in the annotation process is, therefore urgently needed,” the scientists wrote in a paper published in the current issue of Genome Biology.

WikiProteins was created over the last two years and announced on May 28, by a team of scientists from the Swiss Institute of Bioinformatics, the GO consortium and the IntAct database at the European Molecular Biology Laboratory-European Bioinformatics Institute, Erasmus Medical Centre, Leiden University Medical Centre, both in the Netherlands, the Brazilian Stela Institute, the WikiMedia Foundation, and Knewco.

The project is an interactive and semantically supported workspace based on Wiki pages and contains a knowledgebase, a navigation tool, and a section on the people in its annotating community. Beneath that layer is a relational Wiki based on WikiData software, an indexer, and software that creates components called Knowlets, which stores the relationships between all the mined concepts.

Knowlets are at the core of this platform, a proprietary concept mining software component and ontology format that Knewco has developed over the last two years.

Writing in the Genome Biology paper, the team said information is mined from scientific publications and the Knowlet links two given concepts, but records that information only once.

“This approach results in a minimal growth of the ‘concept space’ as compared to the text space,” the authors wrote. New and unique facts in the scientific literature expand the corpus to a much lesser degree than the totality of the text generated by new academic journal articles.

Concept pairs are placed in what the WikiProteins creators call a “related concept cloud.” By applying a meta-analysis algorithm, the software calculates a semantic association to reflect the strength and type of relationship the concepts have.

The relationship is dynamic and recalculated based on newly mined information. Its calculated value is based on three factors: factual statements found in the scientific literature or databases, increasing co-occurrence of two concepts in a sentence or a paragraph, and predictive associations based on the overlap of the two concepts.

The WikiProteins terminology has been mapped to concept identifiers in the Wiki-based terminology system called OmegaWiki. WikiProteins and OmegaWiki are driven by a relational database that is linked to the Knowlets by on-the-fly indexing of all Wiki pages. An indexer called Peregrine is designed to recognize concepts by the Wiki, and the indexer is coupled to a terminology system derived from OmegaWiki.

Each biomedical concept has its own page that includes up-to-date annotations. Registered users can become annotators and edit records. WikiProteins shows the new record alongside the original one that was mined from the authoritative databases. Professional annotators at their respective databases can choose to incorporate some of new community-entered information into their database.

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Molecular Connections Pvt. Ltd. to Sponsor ICIC for the second time

The International Conference in Trends for Scientific Information Professionals

Habitual attendees say that "it is the meeting to which they go to spot the trends, as well as the meeting that provides unparalleled opportunities for networking" Trends and networking will be high on the Nice agenda in October 2008.

The ICIC meeting covers trends in the field of scientific and professional information with an impressive line-up of significant figures in the information world. Among the topics that will be covered and discussed by the 22+ speakers are:

• Tools for Competitive Intelligence (e.g., mining tools, visualisation tools, analysis tools, etc)
• Challenges for the information community over the next five years
• Changes in the information environment for patents, innovation and intellectual property
• Trends in Search Engines and Information Retrieval (also see)
• Case Studies in Data and Content Integration