The Agilent Literature Search tool automatically searches for and extracts information from multiple textual databases, such as those of the U.S. Patent Office and the National Center for Biotechnology Information (PubMed). The plug-in pulls information from these sources and represents it within Cytoscape as a map of the relationships between the biological entities, such as genes and proteins. A microarray or an LC/MS-proteomics experiment can typically result in hundreds of genes and proteins of interest. Biologists can use the new plug-in to avoid the daunting task of manually searching for each gene and protein in the scientific literature and patents.
"Mining past literature for information about proteins and protein interactions is a critical step for building models of cells," said Trey Ideker, assistant professor at the University of California, San Diego, and lead researcher/program manager for the Cytoscape project. "Agilent's Literature Search plug-in for Cytoscape makes automatic literature mining freely accessible to the public, with an algorithmic approach that is first-rate."
"Agilent is committed to accelerating the productivity of biologists," said Jim Hollenhorst, director of the Molecular Technologies Laboratory for Agilent Laboratories. "This literature search tool was developed within Labs to facilitate our own research collaborations and has proved very successful for us. We are excited to provide this to researchers everywhere so that they can analyze their own data more effectively and put it into a biological context. "
With the Agilent Literature Search tool, researchers enter the names of all genes of interest, along with keywords that describe the types of relationships being looked for. The plug-in searches accessible databases and generates a computational representation of gene/protein associations grouped into a network that biologists can see and manipulate within Cytoscape. This network view includes a node represented by a geometric shape for each gene and protein, and links to indicate relationships. Each node includes hyperlinks to descriptions and articles relevant to that gene or protein.
Agilent Laboratories is using the plug-in as part of its collaborations with two other organizations on systems biology projects: the Stanford University School of Medicine on auto-immune diabetes; and the Translational Genomics Research Institute (TGen) on melanoma, autism and pancreatic cancer. Labs researchers are focusing on proteomics and metabolomics for these diseases as a complement to Labs collaborators' work in genomics. Using Labs' systems biology informatics prototypes, Labs researchers have built qualitative biological models based on experimental data, scientific knowledge from published papers and curated biological network databases. This shared, multi-disciplinary knowledge provides a more comprehensive view of disease.
Cytoscape 2.1 is free open-source software. The Agilent Literature Search tool is currently available as a free but unsupported plug-in to Cytoscape. Both are downloadable at www.cytoscape.org. Agilent's plug-in and additional information are available at www.labs.agilent.com/research/mtl/projects/sysbio/sysinformatics/download.html.
Screen shots of Agilent Literature Search Software in action are available at www.labs.agilent.com/research/mtl/projects/sysbio/sysinformatics/litsearch_screens.html.
Cytoscape is a bioinformatics software platform for visualizing molec ular interaction networks and integrating these interactions with gene expression profiles and other data. The platform supports gene functional annotations from Gene Ontology (GO) and KEGG databases, biological models from Systems Biology Markup Language (SBML), protein-protein interactions from BIND and TRANSFAC databases. Additional features are available as plug-ins for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. More information about the Cytoscape platform and project is available on the Web at www.cytoscape.org.