PhenotypetopubmedPhenotype_search_term00
2010-12-24 17:14:53.933 UTC
text/plain
2010-12-24 17:14:53.933 UTC
phenotype_abstracts1
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2010-12-24 17:14:53.933 UTC
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/*[local-name(.)='eSearchResult']/*[local-name(.)='IdList']/*[local-name(.)='Id']
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http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl
run_eSearch
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<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="eSearchRequest" name="parameters" qname="{http://www.ncbi.nlm.nih.gov/soap/eutils/esearch}eSearchRequest"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="db" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="term" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="WebEnv" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="QueryKey" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="usehistory" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="tool" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="field" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="reldate" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="mindate" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="maxdate" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="datetype" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="RetStart" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="RetMax" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="rettype" qname="{http://www.w3.org/2001/XMLSchema}string" /><s:basetype optional="true" unbounded="false" typename="string" name="sort" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elements></s:complextype></s:extensions>
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net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_eSearchparametersextractPMIDxpathextractPMIDxml-textparametersXML_eSearchRetMaxparametersXML_eSearchtermparametersXML_eSearchdbparametersXML_eSearchmaxdateparametersXML_eSearchmindateFetch_Abstractspubmed_idsphenotype_abstracts
435b5570-dcce-40e3-91b8-8fdf6303d0f5
2011-01-11 11:18:30.601 UTC
e3a6a719-26c2-4ba4-9ffb-43212b4e8bcf
2010-12-27 17:25:13.184 UTC
Paul Fisher
2010-12-24 17:14:54.641 UTC
06e536aa-b2a2-477f-b8a1-a528b5820c27
2015-09-01 08:46:36.95 UTC
Phenotype to pubmed
2010-12-24 17:14:54.641 UTC
c3c440c5-217e-4937-8d65-289ee9135fa4
2010-12-24 17:36:43.671 UTC
201fe3bf-3410-4010-9841-eabe3da12f39
2015-09-01 09:27:49.887 UTC
d7c61d76-8587-4685-a6c9-365e439a66c6
2015-09-01 09:18:23.65 UTC
7cd1de4f-fb83-4639-8d5c-c55c4f64556d
2010-12-24 17:21:44.629 UTC
41fd1f92-ace2-4fd4-ac9a-b8ff409f0d90
2015-09-01 09:32:25.324 UTC
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 UTC
f604d404-8052-40df-b167-89b5696a5cbb
2010-12-24 17:17:14.872 UTC
4cf52534-3d1a-47d5-aa29-883cb39f2023
2015-09-01 09:02:45.893 UTC
XPathPubmedIdspubmed_ids00
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2010-12-24 17:14:54.310 UTC
2010-12-24 17:14:54.310 UTC
abstracts0
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2010-12-24 17:14:54.310 UTC
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2015//EN" "http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_150101.dtd"><PubmedArticleSet><PubmedArticle><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">21030579</PMID><DateCreated><Year>2011</Year><Month>02</Month><Day>17</Day></DateCreated><DateCompleted><Year>2011</Year><Month>06</Month><Day>07</Day></DateCompleted><DateRevised><Year>2014</Year><Month>08</Month><Day>21</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1555-905X</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><Issue>2</Issue><PubDate><Year>2011</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Clinical journal of the American Society of Nephrology : CJASN</Title><ISOAbbreviation>Clin J Am Soc Nephrol</ISOAbbreviation></Journal><ArticleTitle>Role of residual renal function in phosphate control and anemia management in chronic hemodialysis patients.</ArticleTitle><Pagination><MedlinePgn>281-9</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.2215/CJN.04480510</ELocationID><Abstract><AbstractText Label="BACKGROUND AND OBJECTIVES" NlmCategory="OBJECTIVE">There is increasing awareness that residual renal function (RRF) has beneficial effects in hemodialysis (HD) patients. The aim of this study was to investigate the role of RRF, expressed as GFR, in phosphate and anemia management in chronic HD patients.</AbstractText><AbstractText Label="DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS" NlmCategory="METHODS">Baseline data of 552 consecutive patients from the Convective Transport Study (CONTRAST) were analyzed. Patients with a urinary output≥100 ml/24 h (n=295) were categorized in tertiles on the basis of degree of GFR and compared with anuric patients (i.e., urinary output<100 ml/24 h, n=274). Relations between GFR and serum phosphate and erythropoiesis-stimulating agent (ESA) index (weekly ESA dose per kg body weight divided by hematocrit) were analyzed with multivariable regression models.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Phosphate levels were between 3.5 and 5.5 mg/dl in 68% of patients in the upper tertile (GFR>4.13 ml/min per 1.73 m2), as compared with 46% in anuric patients despite lower prescription of phosphate-binding agents. Mean hemoglobin levels were 11.9±1.2 g/dl with no differences between the GFR categories. The ESA index was 31% lower in patients in the upper tertile as compared with anuric patients. After adjustments for patient characteristics, patients in the upper tertile had significantly lower serum phosphate levels and ESA index as compared with anuric patients.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This study suggests a strong relation between RRF and improved phosphate and anemia control in HD patients. Efforts to preserve RRF in HD patients could improve outcomes and should be encouraged.</AbstractText></Abstract><AuthorList CompleteYN="Y" Type="authors"><Author ValidYN="Y"><LastName>Penne</LastName><ForeName>E Lars</ForeName><Initials>EL</Initials><AffiliationInfo><Affiliation>Department of Nephrology, Room F03.223, University Medical Center-Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van der Weerd</LastName><ForeName>Neelke C</ForeName><Initials>NC</Initials></Author><Author ValidYN="Y"><LastName>Grooteman</LastName><ForeName>Muriel P C</ForeName><Initials>MP</Initials></Author><Author ValidYN="Y"><LastName>Mazairac</LastName><ForeName>Albert H A</ForeName><Initials>AH</Initials></Author><Author ValidYN="Y"><LastName>van den Dorpel</LastName><ForeName>Marinus A</ForeName><Initials>MA</Initials></Author><Author ValidYN="Y"><LastName>Nubé</LastName><ForeName>Menso J</ForeName><Initials>MJ</Initials></Author><Author ValidYN="Y"><LastName>Bots</LastName><ForeName>Michiel L</ForeName><Initials>ML</Initials></Author><Author ValidYN="Y"><LastName>Lévesque</LastName><ForeName>Renée</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>ter Wee</LastName><ForeName>Piet M</ForeName><Initials>PM</Initials></Author><Author ValidYN="Y"><LastName>Blankestijn</LastName><ForeName>Peter J</ForeName><Initials>PJ</Initials></Author><Author ValidYN="Y"><CollectiveName>CONTRAST investigators</CollectiveName></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>ClinicalTrials.gov</DataBankName><AccessionNumberList><AccessionNumber>NCT00205556</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016430">Clinical Trial</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D016448">Multicenter Study</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>10</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Clin J Am Soc Nephrol</MedlineTA><NlmUniqueID>101271570</NlmUniqueID><ISSNLinking>1555-9041</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015415">Biological Markers</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D006397">Hematinics</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D006454">Hemoglobins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010710">Phosphates</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Nephrol Dial Transplant. 2002;17 Suppl 5:28-31</RefSource><PMID Version="1">12091604</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Kidney Int. 2003 Dec;64(6):2238-43</RefSource><PMID Version="1">14633148</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nephrol Dial Transplant. 2002 Oct;17(10):1814-8</RefSource><PMID Version="1">12270990</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 2003 Jun;41(6):1212-8</RefSource><PMID Version="1">12776273</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 2003 Oct;42(4 Suppl 3):S1-201</RefSource><PMID Version="1">14520607</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Nephrol. 2003 Jul-Aug;16(4):546-51</RefSource><PMID Version="1">14696757</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nephron. 1999;83(3):219-25</RefSource><PMID Version="1">10529628</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 1999 Dec;34(6):1056-64</RefSource><PMID Version="1">10585315</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 2000 Jun;35(6):1076-82</RefSource><PMID Version="1">10845820</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Kidney Int Suppl. 2001 Feb;78:S67-72</RefSource><PMID Version="1">11168986</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nephrol Dial Transplant. 2001 Sep;16(9):1925-9</RefSource><PMID Version="1">11522881</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Am Soc Nephrol. 2001 Oct;12(10):2158-62</RefSource><PMID Version="1">11562415</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Kidney Int. 2002 Jan;61(1):256-65</RefSource><PMID Version="1">11786108</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Am Coll Cardiol. 2002 Feb 20;39(4):695-701</RefSource><PMID Version="1">11849871</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Am Soc Nephrol. 2004 Apr;15(4):1061-70</RefSource><PMID Version="1">15034110</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 2004 Apr;43(4):712-20</RefSource><PMID Version="1">15042549</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Am Soc Nephrol. 2004 Aug;15(8):2186-94</RefSource><PMID Version="1">15284304</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Am Soc Nephrol. 2004 Aug;15(8):2208-18</RefSource><PMID Version="1">15284307</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 2004 Nov;44(5 Suppl 2):34-8</RefSource><PMID Version="1">15486872</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 2004 Nov;44(5):866-76</RefSource><PMID Version="1">15492953</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Scand J Clin Lab Invest. 1990 Oct;50(6):611-8</RefSource><PMID Version="1">2247767</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Am Soc Nephrol. 1993 Nov;4(5):1205-13</RefSource><PMID Version="1">8305648</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Lab Clin Med. 1994 Apr;123(4):495-505</RefSource><PMID Version="1">8144998</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Int Urol Nephrol. 1994;26(1):125-31</RefSource><PMID Version="1">8026917</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Kidney Int. 1994 Jun;45(6):1689-96</RefSource><PMID Version="1">7933817</PMID></CommentsCorrections><CommentsCorrections 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Version="1">18094675</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 2008 Sep;52(3):519-30</RefSource><PMID Version="1">18514987</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Kidney Int Suppl. 2008 Dec;(111):S75-81</RefSource><PMID Version="1">19034333</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nephrol Dial Transplant. 2009 May;24(5):1580-7</RefSource><PMID Version="1">19155531</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nephrol Dial Transplant. 2009 May;24(5):1685-9</RefSource><PMID Version="1">19276104</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 2009 May;53(5):823-34</RefSource><PMID Version="1">19339087</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nephrol Dial Transplant. 2009 Aug;24(8):2502-10</RefSource><PMID Version="1">19240122</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Kidney Int Suppl. 2009 Aug;(113):S1-130</RefSource><PMID Version="1">19644521</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Clin J Am Soc Nephrol. 2010 Jan;5(1):80-6</RefSource><PMID Version="1">19965537</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Clin J Am Soc Nephrol. 2010 Apr;5(4):576-81</RefSource><PMID Version="1">20110344</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Kidney Dis. 2010 Aug;56(2):348-58</RefSource><PMID Version="1">20605303</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Kidney Int. 2002 Aug;62(2):639-47</RefSource><PMID Version="1">12110029</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="N" UI="D000368">Aged</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" 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ValidYN="Y"><LastName>Rensma</LastName><ForeName>P L</ForeName><Initials>PL</Initials></Investigator><Investigator ValidYN="Y"><LastName>Schrama</LastName><ForeName>Y</ForeName><Initials>Y</Initials></Investigator><Investigator ValidYN="Y"><LastName>van Hamersvelt</LastName><ForeName>H W</ForeName><Initials>HW</Initials></Investigator><Investigator ValidYN="Y"><LastName>Boer</LastName><ForeName>W H</ForeName><Initials>WH</Initials></Investigator><Investigator ValidYN="Y"><LastName>van Kuijk</LastName><ForeName>W H</ForeName><Initials>WH</Initials></Investigator><Investigator ValidYN="Y"><LastName>Vervloet</LastName><ForeName>M G</ForeName><Initials>MG</Initials></Investigator><Investigator ValidYN="Y"><LastName>Wauters</LastName><ForeName>I M</ForeName><Initials>IM</Initials></Investigator><Investigator ValidYN="Y"><LastName>Sekse</LastName><ForeName>I</ForeName><Initials>I</Initials></Investigator></InvestigatorList></MedlineCitation><PubmedData><History><PubMedPubDate 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/PubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText
net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_String_List_to_a_Stringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity
stringlist
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workflow
org.embl.ebi.escience.scuflworkers.java.StringListMerge
net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_PubMed_XML_By_PMIDidXPath_Servicexml_textMerge_String_List_to_a_Stringstringlistabstracts
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 UTC
959eb9bc-db9e-46e7-a0c4-afc23ca6f7ad
2015-09-01 08:45:14.991 UTC
4b4d04fd-4e27-4649-9aa5-0b4427377377
2015-09-01 09:32:09.219 UTC
e23f3978-7f8c-4306-b690-84e02955b913
2015-09-01 09:02:32.594 UTC
a8a6d710-d3a2-449c-81f4-3d0d3b38676c
2015-09-01 08:46:09.791 UTC
96aaaf63-a049-42fb-8dba-60de67eb871e
2015-09-01 09:17:25.115 UTC
XPath Pubmed Ids
2010-12-24 17:14:54.640 UTC
Paul Fisher
2010-12-24 17:14:54.640 UTC
0d5a76a5-82c8-4719-9b78-afa89256efca
2010-12-24 17:17:15.417 UTC
fa9e3c15-b654-4364-b0ce-dd4f1bab3f6f
2010-12-24 17:36:31.757 UTC
f259b222-7a52-43b7-a252-750f254b22f6
2015-09-01 08:44:06.551 UTC