Perfrom a text based search through PubMed

Created: 2010-07-05 13:03:35 Last updated: 2010-07-05 13:03:37

Download Workflow

This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/1374/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
PubMed_identifiers

Processors (2)

Name	Type	Description
run_eFetch	wsdl	Wsdl http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_pubmed.wsdl Wsdl Operation run_eFetch
run_eFetch_inpp	xmlsplitter

Beanshells (0)

Outputs (1)

Name	Description
xml_output

Datalinks (3)

Source	Sink
run_eFetch_inpp:output	run_eFetch:inpp
PubMed_identifiers	run_eFetch_inpp:id
run_eFetch:outp	xml_output

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

(Workflows/Files)

None

Information Tags (5)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

1763 viewings

1548 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Perfrom a text based search through PubMed

Created by Paul Fisher on Monday 05 July 2010 13:03:35 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

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 2

Uploader

Paul Fisher

Gene to Pubmed (3)

Download

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.

Created: 2010-07-05 | Last updated: 2011-01-26

Credits: Paul Fisher

Taverna 2

Uploader

Yoshinobu Kano

A template example workflow using U-Compar... (2)

Download

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. S...

Created: 2010-07-05 | Last updated: 2010-09-02

Credits: Yoshinobu Kano

Perfrom a text based search through PubMed

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Reviews (0)

Comments (0)

Other workflows that use similar services (6)