Created: 2008-02-27 00:49:44      Last updated: 2008-03-03 22:08:39

Example workflow demonstrating how to use GeneIlluminator_GetPubMedQuery, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service uses GeneIlluminator to create clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. GeneIlluminator provides also aliases associated to the input gene symbol. Finally, using the cluster characteristics it creates a boolean PubMed query that could be used to unambiguously retrieve documents related to the gene from the cluster the input gene symbol was assigned to.

Please note that GeneIlluminator_GetPubMedQuery provides a query string that can be used to query PubMed, but it does not query PubMed itself. You'll have to do that by other means. When you do query PubMed at the NCBI using some automated procedure, make sure to throttle your queries! Otherwise you'll have your university/institute/company disconnected from the NCBI servers in no time. Visit for guidelines for automated/scripted acces to NCBI resources like PubMed.

Visit for more info about GeneIlluminator.

GeneIlluminator services use a secure connection over HTTPS. To make this work you *must* import our SSL certificates in your local Java keystores. More information can be found on

Information Preview

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
[ More InfoExpand ]

Information Workflow Components

Inputs (2)
Processors (4)
Beanshells (0)
Outputs (1)
Links (6)
Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

View version:

Information Credits (2)


Information Attributions (0)



Information Tags (5)

Log in to add Tags

Information Shared with Groups (0)


Information Featured In Packs (0)


Log in to add to one of your Packs

Information Attributed By (0)



Information Favourited By (0)

No one

Information Statistics


Citations (0)


Version History

In chronological order:

Reviews Reviews (0)

No reviews yet

Be the first to review!

Comments Comments (0)

No comments yet

Log in to make a comment

Workflow Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.