Agilent Literature Search Recipe

Allan Kuchinsky

Agilent Technologies

Biological Use Case: Generate biological networks by extracting associations from scientific literature and other unstructured text. This demonstration is associated with a study into cardiovascular disease, in which the interpretation of microarray data is augmented by generating biological networks for a list of highly regulated genes.


Cytoscape version: Version number (2.6)

Plugins to Load: Plugins and urls

GUI steps:




generate a biological network for a set of genes or proteins

Bring up Agilent Literature Search plugin via Plugins menu.

Type a list of gene names into Terms pane of Agilent Literature Search GUI. For this example, use the terms gpx1, ros1, tfrc, tnfrsf6, abl1

these were high-scoring genes in microarray study

click on 'Use Aliases' in Search Controls

you should see a set of aliases inserted into query string in Query Editor pane.

click Use context off, then back on

you should see the Query Editor pane elimate the AND statement and its right hand side, then restore it when you click on Use Context. User context serves the limit the scope of the search, e.g. if you are interested in a particular disease.

click on the 'Play' button in the control panel

you should see the literature search tool begin to exercise queries. A term Search in progress message will appear in the Query Results pane. When the query completes, you will see a list of citations in the Query Results spane. You will then see a network laid out in a "New Network" window.

Examine literature references that support a given association (edge).

Right click on an edge, select evidence from literature => show sentences from the literature

you will see a list of sentences come up in a popup window. Each sentence should contain the two terms for the source and target of the selected edge

click on one of the sentences

you should see a web browser page come up containing pubMed abstract in which that sentence is contained. This is akin to having a visual table of contents for the literature around a set of biological terms of interest.

right-click on one of the sentences and select Delete. Repeat until there are no sentences left.

At the point when you delete the last remaining sentence in the Show Sentences window, the edge that you are examining will be eliminated, since there is no longer evidence backing it. Any nodes that become disconnected when edge is eliminated will also be themselves eliminated|

choose Select -> Evidence From Literature -> Highight Search Terms

you will see that the original search terms you typed in are now highlighted in the network view.

expand a network

select a node in the network. Then right click with mouse and pick Evidence from Literature -> Extend Network from the Literature

you should see new nodes appear, connected by edges to the node you selected.

gather evidence to support an existing interaction

Select File -> Import -> Network and load galfiltered.sif from the testData folder. Drag mouse to select an edge in the network. Chose Select -> Evidence From Literature -> Gather Evidence From the Literature. You will see a status window come up while the Gather Evidence process is executing. When the process is done and the status window goes away, right click again on your chosen edge and select evidence from literature -> show sentences from the literature

You should see a list of sentences

Data / Session Files: in testData folder of Cytoscape installation. Presentation: Attach your presentation

Webstart: Attach a webstart

Video: Attach a video link

AgilentLiteratureSearchRecipe (last edited 2009-02-12 01:03:27 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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