PhenotypetopubmedPhenotype_search_term00
2010-12-24 17:14:53.933 GMT
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2010-12-24 17:14:53.933 GMT
phenotype_abstracts
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2010-12-24 17:14:53.933 GMT
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net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eSearchparametersextractPMIDxpathextractPMIDxml-textremove_Nullsinputconcat_abstract_idsidconcat_abstract_idsabstract_textconcat_abstract_idsdate_textmerge_phenotype_abstractsabstractsmerge_phenotype_abstractsphenotypemerge_abstractsstringlistparametersXML_eSearchRetMaxparametersXML_eSearchtermparametersXML_eSearchdbparametersXML_eSearchmaxdateparametersXML_eSearchmindatemerge_abstract_idsstringlistmerge_datesstringlistFetch_Abstractspubmed_idsclean_textinputphenotype_abstracts
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
2010-12-24 17:14:54.641 GMT
e3a6a719-26c2-4ba4-9ffb-43212b4e8bcf
2010-12-27 17:25:13.184 GMT
Paul Fisher
2010-12-24 17:14:54.641 GMT
7cd1de4f-fb83-4639-8d5c-c55c4f64556d
2010-12-24 17:21:44.629 GMT
435b5570-dcce-40e3-91b8-8fdf6303d0f5
2011-01-11 11:18:30.601 GMT
f604d404-8052-40df-b167-89b5696a5cbb
2010-12-24 17:17:14.872 GMT
c3c440c5-217e-4937-8d65-289ee9135fa4
2010-12-24 17:36:43.671 GMT
Phenotype to pubmed
2010-12-24 17:14:54.641 GMT
XPathPubmedIdspubmed_ids00
text/plain
2010-12-24 17:14:54.310 GMT
2010-12-24 17:14:54.310 GMT
pubmed_dates
text/plain
2010-12-24 17:14:54.310 GMT
abstracts
text/plain
2010-12-24 17:14:54.310 GMT
xpath2value00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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/*[local-name(.)='eFetchResult']/*[local-name(.)='PubmedArticleSet']/*[local-name(.)='PubmedArticle']/*[local-name(.)='MedlineCitation']/*[local-name(.)='Article']/*[local-name(.)='Abstract']/*[local-name(.)='AbstractText']
net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="eFetchRequest" name="parameters" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}eFetchRequest"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="db" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>db" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>id" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>WebEnv" /><s:basetype optional="true" unbounded="false" typename="string" name="query_key" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>query_key" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>tool" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>email" /><s:basetype optional="true" unbounded="false" typename="string" name="retstart" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>retstart" /><s:basetype optional="true" unbounded="false" typename="string" name="retmax" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>retmax" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>rettype" /><s:basetype optional="true" unbounded="false" typename="string" name="strand" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>strand" /><s:basetype optional="true" unbounded="false" typename="string" name="seq_start" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>seq_start" /><s:basetype optional="true" unbounded="false" typename="string" name="seq_stop" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>seq_stop" /><s:basetype optional="true" unbounded="false" typename="string" name="complexity" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>complexity" /><s:basetype optional="true" unbounded="false" typename="string" name="report" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/efetch}>eFetchRequest>report" /></s:elements></s:complextype></s:extensions>
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pubmed
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net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractDatesxpath0xml-text0nodelist11nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity
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net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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http://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_pubmed.wsdl
run_eFetch
net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeextractAbstractxpathextractAbstractxml-textparametersXMLidparametersXMLdbextractDatesxpathextractDatesxml-textrun_eFetchinpppubmed_datesabstracts
Paul Fisher
2010-12-24 17:14:54.640 GMT
This workflow takes in a number of search terms (as used in the normal PubMed interface) and retrieves a list of PubMed ids in a list format.
2010-12-24 17:14:54.640 GMT
fa9e3c15-b654-4364-b0ce-dd4f1bab3f6f
2010-12-24 17:36:31.757 GMT
XPath Pubmed Ids
2010-12-24 17:14:54.640 GMT
0d5a76a5-82c8-4719-9b78-afa89256efca
2010-12-24 17:17:15.417 GMT
clean_textinput00
text/plain
2010-12-27 17:24:56.320 GMT
2010-12-27 17:24:56.320 GMT
cleaned_textEncode_byte___to_base64bytes0base6400net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity
bytes
0
'application/octet-stream'
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commons-codec
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1
net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclean_textfile_direct_data0report00output00net.sf.taverna.t2.activitiessoaplab-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.soaplab.SoaplabActivity
http://phoebus.cs.man.ac.uk:1977/axis/services/text_mining.clean_text
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net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEncode_byte___to_base64bytesclean_textfile_direct_datastringToBytesstringcleaned_text
2010-12-27 17:24:56.632 GMT
clean_text
2010-12-27 17:24:56.632 GMT
52829fcd-29cd-4a65-a3a7-582f6b6376de
2010-12-27 17:24:56.804 GMT
2010-12-27 17:24:56.632 GMT