Literature Analysis

PubGene

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Pubgene helps retrieval of information on genes and proteins. The underlying structure of PubGene can be viewed as a "gene-centric" database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a "literature network" organizing information in a form that is easy to navigate. No one researcher can be expected to stay informed on all that is happening in genetics. PubGene helps in the finding of  connections and speed the discovery process! (See Jenssen et al. 2001).

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Ariadne MedScan

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PubMed meets the needs for a central repository of biomedical literature. Researchers can go to PubMed and search for any topic and articles of interest, much like a web type of search. However, just like a web type of search, PubMed also provides a list of all the hits with a link to the articles. If a single article, or even just a few, are sought, this search approach is useful. Alternatively, MedScan will list all the articles of interest but additionally scans the text for "relationships", highlights these relationships in the articles and then lists these relationships and the biological molecules and processes involved in the relationships in separate tables. The tables of relationships can be viewed graphically in Pathway Studio and can be saved into the ResNet database for use in experimental data analysis.

PubMatrix

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PubMatrix is a simple way to rapidly and systematically compare any list of terms against any other list of terms in PubMed. It reports back the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table. Lists of terms can be anything; gene names, diseases, gene functions, authors... pretty much anything. The user can then quickly sort or browse the frequency matrix table to do individual searches independently.

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NextBio

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NextBio Basic is a free, publicly available web application which allows researchers to explore the power of NextBio. NextBio Basic provides access to a curated, correlated database of public data; integrated literature, clinical trials, and scientific news. In addition, NextBio Basic allows registered users to personalize their NextBio experience and communicate, collaborate, and share data with the entire NextBio community.

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Matrix Editor

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Matrix Editor is a windows application, that designated to simplify the processes of creation and editing TRANSFAC(r) nucleotide weight matrices (transcription factor weight matrices), and appropriate matrix sets profiles.

 

 

 

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