Phenotype to pubmed

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

Download Workflow

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

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/4709/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

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)

Information Credits (2)

(People/Groups)

Information Attributions (1)

(Workflows/Files)

Phenotype to pubmed

Information Tags (2)

Uploader tags

Log in to add Tags

Information Shared with Groups (1)

insilicoexp2015

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

1512 viewings

910 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Phenotype to pubmed

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

Created: 2008-05-08 | Last updated: 2008-05-12

Credits: Saeedeh Paul Fisher

Attributions: HUMAN Microarray CEL file to candidate pathways

Phenotype to pubmed

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Value

Wsdl

Wsdl Operation

Value

Script

Value

Value

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (30)