Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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 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 PubMed. 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 and share them across other users. Much more faster and an Absolutely Free Service PRODUCT HIGHLIGHTS Abstract Summarization The XTractor™ system would provide extracted relations in addition to id...

By studying the variety of chemical substances and their structures recorded in the CAS REGISTRY SM database, Chemical Abstracts Service (CAS) scientists have discovered that a limited number of molecular shapes are the frameworks for a disproportionately large percentage of reported substances. As shown in the CAS study , half of the known organic chemical substances can be described by just 143 shapes. The analysis, published in The Journal of Organic Chemistry , explains why certain molecular frameworks are more likely to be used in new compounds and may also help identify new regions of chemistry space ripe for exploration.

Anyone who has ever built a website knows that maintaining it is a lot of work. There’s just making sure it hasn’t gone offline because the httpd daemon died. Constant monitoring for script kiddies and their SQL injections. Not to mention continually feeding it with fresh content, lest your audience become bored and desert. I’ve always thought it would be cool to build a site that could more or less look after itself. There’s a myriad of content management systems to choose from, most of which are somewhat hackable in whatever language they happen to be coded in. One of the more mature in this respect is Drupal - which is the engine behind Eureka! Science News . It’s a fully-automated science news portal, using a bunch of customised Drupal modules to aggregate, cluster, categorise and rank articles. First impressions are excellent. Coders will enjoy this post at Drupal explaining how it all works.

“For example, the presence of a specific protein in the blood or in any body fluid might indicate a specific infection. Once an association between a biomarker and a disease is clearly established, the one can be used to signal the other, and to a high degree of certainty. As well, changes in the prevalence of a biomarker in the organism can immediately and reliably signpost a patient’s response to treatment” Some pharmaceutical companies are already advancing their research and harnessing the power of biomarkers, which can: Be used to detect the predisposition for disease in a population, screen for its presence, confirm its diagnosis, assess its severity, predict its response to available therapies and measure its clinical course Be used as targets to discover new drugs Be a decisive factor in determining whether or not to continue research on an entity Show early in the development phase whether an entity could lead to side effects that should terminate further research Help to mak...

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 datab...

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

Already blogging on similar lines and the subject of Bring in data from the published literature in my earlier blog Smart tools to track, analyze and visualize research , here is another interesting experiment on similar lines: The experiment centres on Structured Digital Abstracts (SDA). SDA are extensions of the normal journal article abstracts that describe the relationship between two biological entities , mentioning the method used to study the relationship. Each sentence is preceded by one or more identifiers pointing to the corresponding database entries that contain the full details of the interaction e.g. protein A interacts with protein B, by method X . The aim of SDA is to assist data entry, text mining and literature searching by extracting the salient data from the article into simple sentences using a defined structure and controlled vocabularies. Gianni Cesareni, Editor of FEBS Letters explains: Many articles in biological journals describe relationships between ent...

Darwin's private papers online - the largest publication of Darwin's papers in history. Read about it here . Browse the papers here . The complete works of Charles Darwin -- a god among scientists and the bane of every creationist’s existence – are finally available for anyone, anywhere to read. And it only took 126 years and another scientific revolution to make it happen. Cambridge University , where Darwin studied theology, has digitized and published on the internet its collection of some 30,000 items and 90,000 images by the man who changed the course of science by writing the evolutionary primer, The Origin of Species , in 1859. Cambridge was given the collection by the Darwin family and Pilgrim Trust after World War II. As described in 1960 : They were in parcels each containing small packets of manuscript wrapped in tissue paper on which the subjects had been noted in Darwin's hand. They were presumably just as Darwin left them, and accordingly this arrangem...

Yes i am talking about the development in the field of literature search 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 an 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 user 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. He 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 woul...