Phenotype to pubmed

Created: 2015-09-01 09:34:51

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This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

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Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
Phenotype_search_term

Processors (9)

Name	Type	Description
xpath	stringconstant	Value /[local-name(.)='eSearchResult']/[local-name(.)='IdList']/*[local-name(.)='Id']
run_eSearch	wsdl	Wsdl http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl Wsdl Operation run_eSearch
min_date	stringconstant	Value 2000/01/01
extractPMID	localworker	Script import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; SAXReader reader = new SAXReader(false); reader.setIncludeInternalDTDDeclarations(false); reader.setIncludeExternalDTDDeclarations(false); Document document = reader.read(new StringReader(xmltext)); List nodelist = document.selectNodes(xpath); // Process the elements in the nodelist ArrayList outputList = new ArrayList(); ArrayList outputXmlList = new ArrayList(); String val = null; String xmlVal = null; for (Iterator iter = nodelist.iterator(); iter.hasNext();) { Node element = (Node) iter.next(); xmlVal = element.asXML(); val = element.getStringValue(); if (val != null && !val.equals("")) { outputList.add(val); outputXmlList.add(xmlVal); } } List nodelist=outputList; List nodelistAsXML=outputXmlList;
max_return	stringconstant	Value 5000
pubmed_database	stringconstant	Value pubmed
max_date	stringconstant	Value 2010/10/31
parametersXML_eSearch	xmlsplitter
Fetch_Abstracts	workflow

Beanshells (0)

Outputs (1)

Name	Description
phenotype_abstracts

Datalinks (10)

Source	Sink
parametersXML_eSearch:output	run_eSearch:parameters
xpath:value	extractPMID:xpath
run_eSearch:parameters	extractPMID:xml-text
max_return:value	parametersXML_eSearch:RetMax
Phenotype_search_term	parametersXML_eSearch:term
pubmed_database:value	parametersXML_eSearch:db
max_date:value	parametersXML_eSearch:maxdate
min_date:value	parametersXML_eSearch:mindate
extractPMID:nodelist	Fetch_Abstracts:pubmed_ids
Fetch_Abstracts:abstracts	phenotype_abstracts

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Heiko Schoof

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

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Phenotype to pubmed

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Information Shared with Groups (1)

insilicoexp2015

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Information Statistics

1509 viewings

910 downloads

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Citations (0)

None

Version History

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Phenotype to pubmed

Created by Heiko Schoof on Tuesday 01 September 2015 09:34:48 (UTC)

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Phenotype to pubmed

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