XPath Pubmed Ids

Created: 2011-03-23 16:19:10 Last updated: 2011-03-30 09:28:13

Download Workflow

This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml. The xml is then parsed to retrieve a list of PubMed ids

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://myexperiment.org/workflows/1976/download?version=2
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (3)

Descriptions (4)

Dependencies (0)

Inputs (1)

Name	Description
search_term

Processors (4)

Name	Type	Description
pubmed_database	stringconstant	Value pubmed
run_eSearch	wsdl	Wsdl http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl Wsdl Operation run_eSearch
parametersXML	xmlsplitter
XPath_Service	xpath	Xpath Expression /default:eSearchResult/default:IdList

Beanshells (0)

Outputs (2)

Name	Description
pubmed_result
XPath_Service_nodelist

Datalinks (6)

Source	Sink
parametersXML:output	run_eSearch:parameters
search_term	parametersXML:term
pubmed_database:value	parametersXML:db
run_eSearch:parameters	XPath_Service:xml_text
run_eSearch:parameters	pubmed_result
XPath_Service:nodelist	XPath_Service_nodelist

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (1)

(Workflows/Files)

XPath Pubmed Ids

Information Tags (3)

Uploader tags

pubmed
|
xml
|
xpath

Log in to add Tags

Information Shared with Groups (1)

Bonn eScience Workshop

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 (1)

Philip Y.

Information Statistics

2068 viewings

1457 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

PubMed Search XPath

Created by Paul Fisher on Wednesday 23 March 2011 16:19:10 (UTC)

Last edited by Paul Fisher on Wednesday 23 March 2011 16:27:59 (UTC)
XPath Pubmed Ids

Created by Paul Fisher on Wednesday 30 March 2011 09:27:23 (UTC)

Last edited by Paul Fisher on Wednesday 30 March 2011 09:28:13 (UTC)

Revision comment:

fixed problem with xpath service not loading

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 (30)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Paul Fisher

Perform a search through NCBI eUtils eSearch (3)

Download

This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term. Example input for this workflow are given below: database: pubmed terms: cancer AND diabetes

Created: 2009-11-27 | Last updated: 2009-12-03

Taverna 1

Uploader

Saeedeh

Escherichia coli : From cDNA Microarray Ra... (1)

Download

This workflow takes in a CDNA raw file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the R and bioconductor. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed changes in the microarray data. By identifying the candidate pathways, more detailed...