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InviteWorkflow Entry: A template example workflow using U-Compare text mining system inside
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 Version 2 (latest)
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Version created on:
08/07/10 @ 21:14:45
by:
Yoshinobu Kano
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Last edited on: 02/09/10 @ 04:43:04 by: Yoshinobu Kano
Title: A template example workflow using U-Compare text mining system inside
Type: Taverna 2
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Description
An example workflow using the U-Compare text mining system inside embedded. Users can easily make their own workflow with U-Compare reusing this workflow. This workflow retrieves abstract texts from Pubmed with user specified query, inputs the texts to U-Compare, interprets the output of U-Compare. You have to download and store the UIMA CPE XML descriptor file (StdinPPIExtraction-CPE-EventMine.xml) to run the default setting, which runs a event extraction text mining workflow by U-Compare. See our publication, Kano, et al., 2010, "Text Mining Meets Workflow: Linking U-Compare with Taverna " http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq464 for details.
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http://www.myexperiment.org/workflows/1377/download?version=2
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Created: 08/02/11 @ 13:04:06 | Last updated: 10/02/11 @ 16:01:41
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.
Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 43 times | Downloaded: 23 times Tags (30): |
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Created: 10/02/11 @ 16:10:52 | Last updated: 18/02/11 @ 13:47:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMe...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 64 times | Downloaded: 19 times Tags (36): |
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Non-Information Resource URI: http://www.myexperiment.org/workflows/1377
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