Tutorial:Agilent Literature Search

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Slideshow Agilent_Literature_Search (about ?? minutes)
Handout Agilent_Literature_Search.pdf (?? pages)

Tutorial Sources
Tutorial Curators Anna Kuchinsky

Agilent Literature Search

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.


  1. Using Cytoscape version number 2.6, upload the Agilent Literature Search plugin. Go to Plugins->Manage Plugins. The Agilent Literature Search plugin will be in the Available for install folder.

Generate a biological network for a set of genes or proteins

  1. Bring up the Agilent Literature Search plugin via the Plugins menu.
  2. Type a list of gene names into the 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.
  3. Click on Use Aliases in Search Controls. You should see a set of aliases inserted into query string in the Query Editor pane.
  4. Click Use context off, then back on. You should see the Query Editor pane eliminate the AND statement and its right hand side, then restore it when you click on Use Context. User context serves to limit the scope of the search, e.g. if you are interested in a particular disease.
  5. Click on the blue 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 pane. You will then see a network laid out in a New Network window.
Completed Agilent Literature Search

Examine literature references that support a given association (edge)

  1. Right click on an edge and select evidence from literature->show sentences from literature. You will see a list of sentences come up in a pop-up window. Each sentences should contain the two terms for the source and target of the selected edge.
Show Sentences from Literature
  1. Click on one of the sentences. You should see a web browser page come up containing a 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.
  2. 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 windown, 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.
  3. Choose Select->Evidence from Literature->Highlight Search Terms. You will see that the original search terms you typed in are now highlighted in the network view.

Expand your network

  1. Select a node in the network.
  2. Right-click with the mouse and pick Evidence from Literature->Extend Network from the Literature.
  3. You should see ner nodes appear, connected by edges to the node you selected.

Gather evidence to support an existing interaction

  1. Select File->Import->Network and load galfiltered.sif from the testData folder.
  2. Drag your mouse to select an edge in the network. Choose Select->Evidence from Literature->Gather Edivence from the Literature. You will see a status window come up wile the Gather Evidence process is executing.
  3. 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.