Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces complexity and has increased explanatory power. We discuss the evolution of knowledge base–driven pathway analysis over its first decade, distinctly divided into three generations. We also discuss the limitations that are specific to each generation, and how they are addressed by successive generations of methods. We identify a number of annotation challenges that must be addressed to enable development of the next generation of pathway analysis methods. Furthermore, we identify a number of methodological challenges that the next generation of methods must tackle to take advantage of the technological advances in genomics and proteomics in order to improve specificity, sensitivity, and relevance of pathway analysis. Do you wish to know more?

Sciclips has recently launched a unique database of bioinformatics tools and software for reserchers. This database contains links to more than 2000 web-based bioinformatics and software tools for DNA, RNA, proteins, genomics, proteomics, drug discovery research and many more. This database is the largest online collection for bioinformatics tools and software that is freely available to the researchers. This one-stop extensive bioinformatics database will help researchers in retrieving, analysing the most relevant biological data and extracting information from them efficiently for genomics, proteomics and drug discovery and other areas of research. Bioinformatics Tools and Database Protocols

One of my recent post discussed the dawn of the new era and new breed of search engines Search Wars . YEBOL a youngling from the the Stanford stable, a new search in the block. Yebol's mission is to build human-like world's knowledge base and provide knowledge based search (semantics) and services. Yebol utilizes a combination of patented algorithms paired with human knowledge to build a Web directory for each query and each user. Instead of the common “listing” of Web search queries, Yebol automatically clusters and categorizes search terms, Web sites, pages and contents. Yebol allows for a multi-dimensional search result instead of the normal one-dimensional search seen by most web search engines today. This provides a more accurate summary of top sites and categories; a wider array of related search terms; a longer and richer expansion for query results; and a deeper base of links and keywords in search result pages. Unlike ...

A not very long time ago, in a galaxy near, very near by.... SEARCH WARS Search, Search engines, While the Search engine big wigs fight for a niche in the search engines landscape .... The Google , Yahoo & now Micorsoft too (with their Bing ) There are the Wolfram | Alpha likes that are forming a separatist and slowly gaining power over the Google order. In fact google has managed to bring balance to both with its Google Squared . While platforms like XTractor , NextBio , Novoseek , GoPubMed , BioMedSearch have specialized in searching biomedical and biological knowledge are even more strengthening the separatists. Now to see and know who is more powerful, the galactic empire or the separatist? I leave it to the 'Republic' i.e. You users! to judge, in the form of your comments and experiences with such tools and searches! you could even voice your opinions here

XTractor Knowledgebase XTractor is the first of its kind web 2.0 application which enables researchers to analyze the most current complex biological and chemical relationships published in PUBMED everyday. XTractor Knowledgebase now contains more than 100000 relationships on interactions, regulations and modulations between proteins, drugs, processes and disease. It is the only knowledgebase that updates its data content on a daily basis. The Approach: The Data behind XTractor comes from manual annotation, which is carried out by qualified scientists at Molecular Connections, INDIA ( www.molecularconnections.com ). Our scientists regularly handpick and annotate the most relevant sentences to public ontologies. Each of the data points is quality checked to ensure the highest levels of data accuracy. The extracted facts are also referenced back to the PubMed abstract(s).The sentences in XTractor are also manually c...

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...

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...

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 .