Phenotype to pubmed

Created: 2010-07-05 14:07:33 Last updated: 2011-01-11 12:07:22

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This workflow takes in a list of terms to search across the MEDLINE database (through PubMed). Terms are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user via the eFetch service.

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Workflow Components

Authors (1)

Titles (2)

Descriptions (2)

Dependencies (0)

Inputs (1)

Name	Description
search_term

Processors (8)

Name	Type	Description
max_return	stringconstant	Value 500
xpath	stringconstant	Value /[local-name(.)='eSearchResult']/[local-name(.)='IdList']/*[local-name(.)='Id']
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;
pubmed_database	stringconstant	Value pubmed
parametersXML_eFecth	xmlsplitter
run_eSearch	wsdl	Wsdl http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl Wsdl Operation run_eSearch
merge_abstract_ids	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
Retrive_abstracts	workflow

Beanshells (1)

Name	Description	Inputs	Outputs
concat_abstract_ids		id abstract_text date_text	output

Outputs (1)

Name	Description
concat_data

Datalinks (9)

Source	Sink
run_eSearch:parameters	extractPMID:xml-text
xpath:value	extractPMID:xpath
search_term	parametersXML_eFecth:term
max_return:value	parametersXML_eFecth:RetMax
pubmed_database:value	parametersXML_eFecth:db
parametersXML_eFecth:output	run_eSearch:parameters
Retrive_abstracts:PMID_Date_Abstract	merge_abstract_ids:stringlist
extractPMID:nodelist	Retrive_abstracts:pubmed_ids
merge_abstract_ids:concatenated	concat_data

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 3)

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

(Workflows/Files)

None

Information Tags (18)

Uploader tags

abstracts
|
african trypanosomiasis
|
disease
|
efetch
|
entrez
|
esearch
|
loci
|
ncbi
|
phenotype
|
pubmed
|
qtl
|
quanitative
|
sleeping sickness
|
term
|
text
|
text mining
|
text mining; term extraction; entity recognition
|
trait

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Information Shared with Groups (1)

PhD Supplementary Information

Information Featured In Packs (2)

Text Mining Workflows
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Information Attributed By (2)

(Workflows/Files)

Item doesn't exist anymore
Phenotype to pubmed

Information Favourited By (1)

Philip Y.

Information Statistics

2968 viewings

1941 downloads

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Citations (0)

None

Version History

In chronological order:

Phenotype to Pubmed

Created by Paul Fisher on Monday 05 July 2010 14:07:33 (UTC)

Last edited by Paul Fisher on Wednesday 08 December 2010 11:51:26 (UTC)
Phenotype to pubmed

Created by Paul Fisher on Wednesday 08 December 2010 11:52:00 (UTC)

Last edited by Paul Fisher on Wednesday 08 December 2010 11:52:27 (UTC)

Revision comment:

Updated workflow to make it more compact
Phenotype to pubmed

Created by Paul Fisher on Tuesday 11 January 2011 12:06:51 (UTC)

Last edited by Paul Fisher on Tuesday 11 January 2011 12:07:22 (UTC)

Revision comment:

added nestwed workflow to remove non-ascii characters from text

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Other workflows that use similar services (31)

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

Taverna 2

Uploader

Paul Fisher

Pathway to Pubmed (2)

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.