Welcome to Agilent Literature Search

 

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
  • Meta-search engine combining Information Retrieval (IR) & Knowledge Extraction (KE)
  • Uses PubMed, OMIM, and USPTO search engines
  • Load/Save/Reanalyze search results
  • Paged search results view
  • User context-based symbol normalization
  • File-based context management
  • Symbol identification, alias resolution and highlighting, interaction extraction
  • Putative network generation from literature
  • Literature-based evidence gathering for Cytoscape Edges
  • Expand a Cytoscape network using evidence gathered from the literature

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.