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InviteWorkflow Entry: BioAID_ProteinDiscovery
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 Version 7 (latest)
(of 7)
|
Version created on:
12/01/12 @ 14:38:46
by:
Marco Roos
|
Revision comments 
Last edited on: 20/03/12 @ 17:16:09 by: Marco Roos
Title: BioAID_ProteinDiscovery
Type: Taverna 2
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Description
This protein discovery workflow extracts protein names from documents retrieved from MedLine based on a user Query (cf Apache Lucene syntax). The protein names are filtered by checking if there exists a valid UniProt ID for the given protein name.
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http://www.myexperiment.org/workflows/74/download?version=7
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Earliest Version:
[1] - BioAID_protein_discovery
Previous Versions:
[2] - BioAID_protein_discovery
[4] - BioAID_ProteinDiscovery
[5] - BioAID_ProteinDiscovery
[6] - BioAID_ProteinDiscovery
Latest Version:
[7] - BioAID_ProteinDiscovery
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Other workflows that use similar services
(6)
Only the first 2 workflows that use similar services are shown. View all workflows that use these services.
|
Original Uploader |
Created: 16/05/09 @ 01:06:26 | Last updated: 16/05/09 @ 01:13:18
Credits:
License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you.
Summary
This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps:
it retrieves documents relevant for the query string
i...
Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 1 | Citations: 0 Viewed: 150 times | Downloaded: 31 times Tags (10): |
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 Download (v7)
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|
Original Uploader |
Created: 28/05/09 @ 12:21:05
Credits:
Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow finds proteins relevant to the query string via the following steps:
A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste").
Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene)
Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach; the AIDA serv...
Rating: 0.0 / 5 (0 ratings) | Versions: 11 | Reviews: 0 | Comments: 1 | Citations: 0 Viewed: 454 times | Downloaded: 167 times Tags (9): |
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Download (v11)
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Linked Data
Non-Information Resource URI: http://www.myexperiment.org/workflows/74
Alternative Formats
Copyright © 2007 - 2011 The University of Manchester and University of Southampton
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This workflow was reported to occasionally have time out issues. Alan Williams (myGrid) e-mailed these pointers for addressing this problem:
"If it is only in the validation report, then you can either just ignore the report and still run the workflow. Or, you can change the timeout that the validator uses. To do that go to Preferences (under the top level menu Taverna or File) -> Validation report and change "Reporting timeout in seconds (per service)". By default it is 10 seconds. Note that the validation timeout can be short because it just does a quck "ping" to check that the remote machine is talking.
If you need to change the timeout for the running of the service, then see the e-mail thread at http://taverna-users.markmail.org/thread/xozdzqhkbxmuw4nc"
Many thanks to Alan for this information.
We are also in the process of updating and extending our BioSemantics Web Services, including the 'SynSets' service that is used in this workflow. More information about the BioSemantics group can be found on biosemantics.org.