AgilentLiteratureSearch

Mines scientific literature to find publications related to search terms and to create interaction networks based on the search result.
Categories: literature mining, network generation, online data import, search
Agilent Literature Search Software 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 Software can be used in conjunction with Cytoscape, which provides a means of generating an overview network view of gene/protein associations. Agilent Literature Search Software provides an easy-to-use interface to its powerful querying capabilities. When a query is entered, it is submitted to multiple user-selected search engines, and the retrieved results (documents) are fetched from their respective sources. Each document is then parsed into sentences and analyzed for protein-protein associations. Agilent Literature Search Software uses a set of "context" files (lexicons) for defining protein names (and aliases) and association terms (verbs) of interest. Associations extracted from these documents are collected into a Cytoscape network. The sentences and source hyperlinks for each association are further stored as attributes of the corresponding Cytoscape edges.
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3.1.1

Works with Cytoscape 3.1

Apps that depend on this release

Release Notes

For general info on installing, running, and configuring Agilent Literature Search (ALS), see the <A HREF="http://blueoaksoftware.com/Agilent/ALS/README-user.pdf">ALS User README</A>. <P>An ALS-generated network should now have full functionality when saved and restored from sessions--there is no longer a need to use the <em>File->Import->Agilent Literature Search Network...</em> or </em>File->Export->as Agilent Literature Search Network...</em> except for legacy purposes. However, you must accept the ALS license agreement before the added ALS functions are enabled (e.g., <em>Evidence form Literature->Show Sentences from the Literature</em>). <P>Additions include: 1. Added 'Source' and 'Target' attributes to ALS network edges where the Source attribute gives the name of the source node connected to that edge and the Target attribute gives the targe node name. 2. Changed ALS to determine its data directory using Cy3 CyApplicationConfiguration.getAppConfigurationDirectoryLocation(). 3. Fixed deadlock bug where Cy3 TaskMonitor would interfere with ALS messages issued. 4. Fixed attribute setting bug where the first attribute value set for any node or edge was being ignored. 5. Fixed USPTO searching to work again. Was broken by changes in search results returned by these websites. 6. Removed OMIM searching (due to licensing issues). 7. Changed threshold for laying out networks as a grid vs hierarchical layout from 250 edges to 500 edges. 8. Updated license agreement.

3.0.3.beta

Works with Cytoscape 3.0

Release Notes

This beta should be a fully functioning version of AgilentLiteratureSearch for Cytoscape 3.0. However, two known issues are: 1) The Help documentation has not been updated for running in Cytoscape 3.0. 2) When you first install AgilentLiteratureSearch, menu items are duplicated--but the duplication will disappear the next time you run Cy3.
CYTOSCAPE 3

Version 3.1.1

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Released 1 Aug 2014

Works with Cytoscape 3.1

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