Agilent Literature Search is a meta-search tool for automatically querying multiple text-based search engines (both public and proprietary) in order to aid biologists faced with the daunting task of manually searching and extracting associations among genes/proteins of interest.
Agilent Literature Search can be used in conjunction with Cytoscape, which provides a means of generating an overview network view of gene/protein associations.
Agilent Literature Search Features
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Agilent Literature Search provides an easy-to-use interface to its powerful search capabilities. A set of queries can be defined interactively, then submitted to multiple user-selected search engines. The retrieved results (documents) are fetched from their respective sources and each document is then parsed into sentences and analyzed for protein-protein associations. Agilent Literature Search uses a set of lexicons for defining protein names (and aliases) and association terms (verbs) of interest. An association is extracted for every sentence containing at least two protein names and one verb. Associations are then converted into interactions, which are further grouped into a network. The sentences and source hyperlinks for each association are further stored as attributes of the corresponding interactions .
The networks can be viewed and manipulated in Cytoscape.
Development
Agilent Literature
Search is a research prototype tool developed by the Systems Biology
project of Agilent Laboratories, the central research organization of Agilent
Technologies.
Visit
http://www.agilent.com/labs/research/mtl/projects/sysbio.html for more information.
License
Agilent Literature Search
is protected under the terms of the Agilent Literature Search License
Agreement. The License is included as an appendix to this
manual, but can also be found online at http://www.labs.agilent.com/sysbio/LiteratureSearchLicenseAgreement.html
.
Agilent Literature Search also includes a number of other open source libraries, which are detailed in the Section on Acknowledgements.