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BioAID_ProteinDiscovery

Created: 2010-05-10 16:21:09      Last updated: 2013-08-16 11:37:33

The 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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Information Titles (1)
Information Descriptions (1)
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Inputs (2)
Processors (6)
Beanshells (4)
Outputs (2)
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Information Workflow Type

Taverna 2

Information Uploader

30?size=60x60 Nl Marco Roos

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Information Version 5 (of 8)

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Information Statistics

9609 viewings

5681 downloads

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Version History

In chronological order:

  1. BioAID_protein_discovery

    Created by Marco Roos on Wednesday 14 November 2007 12:46:33 (UTC)

    Last edited by Marco Roos on Thursday 15 November 2007 09:01:12 (UTC)

  2. BioAID_protein_discovery

    Created by Marco Roos on Monday 10 May 2010 14:14:35 (UTC)

  3. BioAID_ProteinDiscovery

    Created by Marco Roos on Monday 10 May 2010 16:21:09 (UTC)

    Last edited by Marco Roos on Thursday 28 October 2010 08:47:53 (UTC)

    Revision comment:

    Update to Taverna 2. The UniProtID operation of the Synsets service has a problem that was temporarily worked around by a quick hack (skipping the first value in the list of results).

  4. BioAID_ProteinDiscovery

    Created by Marco Roos on Friday 01 July 2011 08:40:26 (UTC)

    Last edited by Marco Roos on Friday 01 July 2011 08:41:18 (UTC)

    Revision comment:

    Bug fix: fixed a URL that pointed to 'bubbles.biosemantics.org'; it should be used without bubbles now. Also updated BioCatalogue.

  5. BioAID_ProteinDiscovery

    Created by Marco Roos on Friday 01 July 2011 08:50:34 (UTC)

    Last edited by Marco Roos on Friday 01 July 2011 08:51:22 (UTC)

    Revision comment:

    Something went wrong in uploading the fixed version 4. This version should have the bug fix claimed for version 4.

  6. BioAID_ProteinDiscovery

    Created by Marco Roos on Thursday 12 January 2012 14:26:01 (UTC)

    Last edited by Marco Roos on Thursday 12 January 2012 14:27:39 (UTC)

    Revision comment:

    Default number of input documents set to 5.

  7. BioAID_ProteinDiscovery

    Created by Marco Roos on Thursday 12 January 2012 14:38:46 (UTC)

    Last edited by Marco Roos on Tuesday 20 March 2012 17:16:09 (UTC)

    Revision comment:

    Added annotations.

  8. BioAID_ProteinDiscovery

    Created by Marco Roos on Tuesday 16 July 2013 07:59:15 (UTC)

    Revision comment:

    Replaced synonym service in ValidateByUniProtID with a BioMart service to perform this function. The service validates if a protein name has a registered UniProt ID.



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Comments Comments (1)

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  • 30?size=60x60 Nl Marco Roos
    		Wednesday 26 January 2011 08:53:13 (UTC)

    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.



Workflow 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.


Taverna 1
Uploader
30?size=60x60 Nl Marco Roos

Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

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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...

Created: 2009-05-28

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

Taverna 1
Uploader
30?size=60x60 Nl Marco Roos

Workflow BioAID_ProteinToDiseases (1)

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This workflow was based on BioAID_DiseaseDiscovery, changes: expects only one protein name, adds protein synonyms). This workflow finds diseases relevant to the query string via the following steps: A user query: a single protein name Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) Retrieve documents: finds relevant documents (abstract+title) based on query Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link proteins ...

Created: 2007-11-14 | Last updated: 2007-11-15

Credits: User Marco Roos User Martijn Schuemie Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

Funded by: BioVeL, EPSRC, JISC, Microsoft

Affiliates: myGrid, Taverna, BioCatalogue
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