XPath Pubmed Ids

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

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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

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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

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Information Shared with Groups (1)

Bonn eScience Workshop

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Information Attributed By (0)

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None

Information Favourited By (1)

Philip Y.

Information Statistics

2109 viewings

1501 downloads

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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

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