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| || || click on 'Use Aliases' in Search Controls|| || |
|| || 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 'Use Aliases' in Search Controls|| you should see a set of aliases inserted into query string in Query Editor pane. || || || click on 'Use Aliases' in Search Controls|| you should see a set of aliases inserted into query string in Query Editor pane. || || || click on 'Use Aliases' in Search Controls|| you should see a set of aliases inserted into query string in Query Editor pane. || |
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.
Recipe
Cytoscape version: Version number (2.6)
Plugins to Load: Plugins and urls
GUI steps:
Describe each step (story), the GUI action to take, and probable remarks
Story |
Action |
Remarks |
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 'Use Aliases' in Search Controls |
you should see a set of aliases inserted into query string in Query Editor pane. |
|
click on 'Use Aliases' in Search Controls |
you should see a set of aliases inserted into query string in Query Editor pane. |
|
click on 'Use Aliases' in Search Controls |
you should see a set of aliases inserted into query string in Query Editor pane. |
Data / Session Files: Attach (preferably) a session file or else the data files used in the workflow
Presentation: Attach your presentation
Webstart: Attach a webstart
Video: Attach a video link