Author_to_Wordcloudauthor_name00 Robert Winkler 2015-12-02 17:55:08.81 UTC The name of an author 2015-06-17 15:49:41.450 UTC wordcloud_image0searchPublicationsparameters0parameters00 The searchPublications calls the Europe PMC Web service to retrieve the bibliographic information, including abstracts, for all published work indexed in PubMed by author_name. 2015-12-02 17:50:03.134 UTC net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/europepmc/webservices/soap?wsdl searchPublications 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokebuild_queryauthor_name0queryString00 The build_query BeanShell constructs the Europe PMC search query for a single author, sorting the results by year. 2015-09-14 16:25:25.725 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity author_name 0 text/plain java.lang.String true queryString 0 0 workflow 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchPublications_inputqueryString0pageSize0resultType0output00net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity queryString 0 'text/plain' false resultType 0 'text/plain' false offSet 0 'text/plain' false pageSize 0 'text/plain' false synonym 0 'text/plain' false email 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="searchPublications" name="parameters" qname="{http://webservice.cdb.ebi.ac.uk/}searchPublications"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryString" qname="searchPublications&gt;queryString" /><s:basetype optional="true" unbounded="false" typename="string" name="resultType" qname="searchPublications&gt;resultType" /><s:basetype optional="true" unbounded="false" typename="int" name="offSet" qname="searchPublications&gt;offSet" /><s:basetype optional="true" unbounded="false" typename="string" name="pageSize" qname="searchPublications&gt;pageSize" /><s:basetype optional="true" unbounded="false" typename="boolean" name="synonym" qname="searchPublications&gt;synonym" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="searchPublications&gt;email" /></s:elements></s:complextype></s:extensions> 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokearticles_to_retrievevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 1000 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchPublications_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="searchPublicationsResponse" name="parameters" qname="{http://webservice.cdb.ebi.ac.uk/}searchPublicationsResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="responseWrapper" name="return" qname="searchPublicationsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="version" qname="responseWrapper&gt;version" /><s:basetype optional="true" unbounded="false" typename="int" name="hitCount" qname="responseWrapper&gt;hitCount" /><s:complextype optional="true" unbounded="false" typename="request" name="request" qname="responseWrapper&gt;request"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryString" qname="request&gt;queryString" /><s:basetype optional="true" unbounded="false" typename="string" name="internalQuery" qname="request&gt;internalQuery" /><s:basetype optional="true" unbounded="false" typename="string" name="resultType" qname="request&gt;resultType" /><s:basetype optional="true" unbounded="false" typename="string" name="profileType" qname="request&gt;profileType" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="request&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="request&gt;source" /><s:basetype optional="true" unbounded="false" typename="int" name="offSet" qname="request&gt;offSet" /><s:basetype optional="true" unbounded="false" typename="int" name="pageSize" qname="request&gt;pageSize" /><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="request&gt;database" /><s:basetype optional="true" unbounded="false" typename="string" name="semanticType" qname="request&gt;semanticType" /><s:basetype optional="true" unbounded="false" typename="boolean" name="synonym" qname="request&gt;synonym" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="request&gt;email" /><s:basetype optional="true" unbounded="false" typename="string" name="providerId" qname="request&gt;providerId" /></s:elements></s:complextype><s:complextype optional="true" unbounded="false" typename="profileListBean" name="profileList" qname="responseWrapper&gt;profileList"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="profile" name="source" qname="profileListBean&gt;source"><s:elementtype><s:complextype optional="false" unbounded="false" typename="profile" name="" qname="{http://webservice.cdb.ebi.ac.uk/}profile"><s:elements /><s:attributes><s:attribute optional="false" unbounded="false" typename="profile&gt;name" name="name" qname="profile&gt;name" /><s:attribute optional="false" unbounded="false" typename="profile&gt;count" name="count" qname="profile&gt;count" /></s:attributes></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="profile" name="pubType" qname="profileListBean&gt;pubType"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}profile" optional="false" unbounded="false" typename="profile" name="" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="profile" name="subset" qname="profileListBean&gt;subset"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}profile" optional="false" unbounded="false" typename="profile" name="" /></s:elementtype></s:arraytype></s:elements></s:complextype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="resultList" name="resultList" qname="responseWrapper&gt;resultList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="result" name="" qname="{http://webservice.cdb.ebi.ac.uk/}result"><s:elements><s:complextype optional="true" unbounded="false" typename="request" name="request" qname="result&gt;request"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryString" qname="request&gt;queryString" /><s:basetype optional="true" unbounded="false" typename="string" name="internalQuery" qname="request&gt;internalQuery" /><s:basetype optional="true" unbounded="false" typename="string" name="resultType" qname="request&gt;resultType" /><s:basetype optional="true" unbounded="false" typename="string" name="profileType" qname="request&gt;profileType" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="request&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="request&gt;source" /><s:basetype optional="true" unbounded="false" typename="int" name="offSet" qname="request&gt;offSet" /><s:basetype optional="true" unbounded="false" typename="int" name="pageSize" qname="request&gt;pageSize" /><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="request&gt;database" /><s:basetype optional="true" unbounded="false" typename="string" name="semanticType" qname="request&gt;semanticType" /><s:basetype optional="true" unbounded="false" typename="boolean" name="synonym" qname="request&gt;synonym" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="request&gt;email" /><s:basetype optional="true" unbounded="false" typename="string" name="providerId" qname="request&gt;providerId" /></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="result&gt;citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="result&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="result&gt;source" /><s:basetype optional="true" unbounded="false" typename="string" name="pmid" qname="result&gt;pmid" /><s:basetype optional="true" unbounded="false" typename="string" name="pmcid" qname="result&gt;pmcid" /><s:basetype optional="true" unbounded="false" typename="string" name="DOI" qname="result&gt;DOI" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="result&gt;title" /><s:basetype optional="true" unbounded="false" typename="string" name="authorString" qname="result&gt;authorString" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="authorsList" name="authorList" qname="result&gt;authorList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="authors" name="" qname="{http://webservice.cdb.ebi.ac.uk/}authors"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="collectiveName" qname="authors&gt;collectiveName" /><s:basetype optional="true" unbounded="false" typename="string" name="fullName" qname="authors&gt;fullName" /><s:basetype optional="true" unbounded="false" typename="string" name="firstName" qname="authors&gt;firstName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="authors&gt;lastName" /><s:basetype optional="true" unbounded="false" typename="string" name="initials" qname="authors&gt;initials" /><s:basetype optional="true" unbounded="false" typename="string" name="authorId" qname="authors&gt;authorId" /><s:basetype optional="true" unbounded="false" typename="string" name="affiliation" qname="authors&gt;affiliation" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="investigatorList" name="investigatorList" qname="result&gt;investigatorList"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}authors" optional="false" unbounded="false" typename="authors" name="" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="authorIdsList" name="authorIdList" qname="result&gt;authorIdList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="authorId" qname="{http://webservice.cdb.ebi.ac.uk/}authorId" /></s:elementtype></s:arraytype><s:complextype optional="true" unbounded="false" typename="journalInfo" name="journalInfo" qname="result&gt;journalInfo"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="issue" qname="journalInfo&gt;issue" /><s:basetype optional="true" unbounded="false" typename="string" name="volume" qname="journalInfo&gt;volume" /><s:basetype optional="true" unbounded="false" typename="int" name="journalIssueId" qname="journalInfo&gt;journalIssueId" /><s:basetype optional="true" unbounded="false" typename="string" name="dateOfPublication" qname="journalInfo&gt;dateOfPublication" /><s:basetype optional="true" unbounded="false" typename="byte" name="monthOfPublication" qname="journalInfo&gt;monthOfPublication" /><s:basetype optional="true" unbounded="false" typename="short" name="yearOfPublication" qname="journalInfo&gt;yearOfPublication" /><s:basetype optional="true" unbounded="false" typename="string" name="printPublicationDate" qname="journalInfo&gt;printPublicationDate" /><s:complextype optional="true" unbounded="false" typename="journal" name="journal" qname="journalInfo&gt;journal"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="journal&gt;title" /><s:basetype optional="true" unbounded="false" typename="string" name="ISOAbbreviation" qname="journal&gt;ISOAbbreviation" /><s:basetype optional="true" unbounded="false" typename="string" name="medlineAbbreviation" qname="journal&gt;medlineAbbreviation" /><s:basetype optional="true" unbounded="false" typename="string" name="NLMid" qname="journal&gt;NLMid" /><s:basetype optional="true" unbounded="false" typename="string" name="ISSN" qname="journal&gt;ISSN" /><s:basetype optional="true" unbounded="false" typename="string" name="ESSN" qname="journal&gt;ESSN" /></s:elements></s:complextype></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="string" name="journalTitle" qname="result&gt;journalTitle" /><s:basetype optional="true" unbounded="false" typename="string" name="issue" qname="result&gt;issue" /><s:basetype optional="true" unbounded="false" typename="string" name="journalVolume" qname="result&gt;journalVolume" /><s:basetype optional="true" unbounded="false" typename="string" name="pubYear" qname="result&gt;pubYear" /><s:basetype optional="true" unbounded="false" typename="string" name="journalIssn" qname="result&gt;journalIssn" /><s:basetype optional="true" unbounded="false" typename="string" name="pageInfo" qname="result&gt;pageInfo" /><s:basetype optional="true" unbounded="false" typename="string" name="abstractText" qname="result&gt;abstractText" /><s:basetype optional="true" unbounded="false" typename="string" name="affiliation" qname="result&gt;affiliation" /><s:basetype optional="true" unbounded="false" typename="string" name="language" qname="result&gt;language" /><s:basetype optional="true" unbounded="false" typename="string" name="pubModel" qname="result&gt;pubModel" /><s:basetype optional="true" unbounded="false" typename="string" name="pubType" qname="result&gt;pubType" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="pubTypeList" name="pubTypeList" qname="result&gt;pubTypeList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="brSummary" qname="result&gt;brSummary" /><s:complextype optional="true" unbounded="false" typename="bookOrReportDetails" name="bookOrReportDetails" qname="result&gt;bookOrReportDetails"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="publisher" qname="bookOrReportDetails&gt;publisher" /><s:basetype optional="true" unbounded="false" typename="byte" name="dayOfPublication" qname="bookOrReportDetails&gt;dayOfPublication" /><s:basetype optional="true" unbounded="false" typename="byte" name="monthOfPublication" qname="bookOrReportDetails&gt;monthOfPublication" /><s:basetype optional="true" unbounded="false" typename="short" name="yearOfPublication" qname="bookOrReportDetails&gt;yearOfPublication" /><s:basetype optional="true" unbounded="false" typename="string" name="numberOfPages" qname="bookOrReportDetails&gt;numberOfPages" /><s:basetype optional="true" unbounded="false" typename="string" name="edition" qname="bookOrReportDetails&gt;edition" /><s:basetype optional="true" unbounded="false" typename="string" name="isbn10" qname="bookOrReportDetails&gt;isbn10" /><s:basetype optional="true" unbounded="false" typename="string" name="isbn13" qname="bookOrReportDetails&gt;isbn13" /><s:basetype optional="true" unbounded="false" typename="string" name="seriesName" qname="bookOrReportDetails&gt;seriesName" /><s:basetype optional="true" unbounded="false" typename="string" name="seriesIssn" qname="bookOrReportDetails&gt;seriesIssn" /><s:basetype optional="true" unbounded="false" typename="string" name="comprisingTitle" qname="bookOrReportDetails&gt;comprisingTitle" /><s:basetype optional="true" unbounded="false" typename="string" name="comprisingTitleNonAscii" qname="bookOrReportDetails&gt;comprisingTitleNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="extraInformation" qname="bookOrReportDetails&gt;extraInformation" /></s:elements></s:complextype><s:complextype optional="true" unbounded="false" typename="patentDetailsInfo" name="patentDetails" qname="result&gt;patentDetails"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="countryCode" qname="patentDetailsInfo&gt;countryCode" /><s:basetype optional="true" unbounded="false" typename="string" name="country" qname="patentDetailsInfo&gt;country" /><s:basetype optional="true" unbounded="false" typename="string" name="typeCode" qname="patentDetailsInfo&gt;typeCode" /><s:basetype optional="true" unbounded="false" typename="string" name="typeDescription" qname="patentDetailsInfo&gt;typeDescription" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="patentClassifierList" name="classifierList" qname="patentDetailsInfo&gt;classifierList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="patentClassifierInfo" name="" qname="{http://webservice.cdb.ebi.ac.uk/}patentClassifierInfo"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="classification" qname="patentClassifierInfo&gt;classification" /><s:basetype optional="true" unbounded="false" typename="string" name="classificationType" qname="patentClassifierInfo&gt;classificationType" /><s:basetype optional="true" unbounded="false" typename="string" name="hyperlink" qname="patentClassifierInfo&gt;hyperlink" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:complextype optional="true" unbounded="false" typename="patentApplication" name="application" qname="patentDetailsInfo&gt;application"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="applicationNumber" qname="patentApplication&gt;applicationNumber" /><s:basetype optional="true" unbounded="false" typename="string" name="applicationDate" qname="patentApplication&gt;applicationDate" /><s:basetype optional="true" unbounded="false" typename="short" name="orderIn" qname="patentApplication&gt;orderIn" /></s:elements></s:complextype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="patentPriorityList" name="priorityList" qname="patentDetailsInfo&gt;priorityList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="patentPriorityData" name="" qname="{http://webservice.cdb.ebi.ac.uk/}patentPriorityData"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="priorityNumber" qname="patentPriorityData&gt;priorityNumber" /><s:basetype optional="true" unbounded="false" typename="string" name="priorityDate" qname="patentPriorityData&gt;priorityDate" /><s:basetype optional="true" unbounded="false" typename="short" name="orderIn" qname="patentPriorityData&gt;orderIn" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="patentFamilyList" name="familyList" qname="patentDetailsInfo&gt;familyList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="patentFamilyData" name="" qname="{http://webservice.cdb.ebi.ac.uk/}patentFamilyData"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="familyNumber" qname="patentFamilyData&gt;familyNumber" /><s:basetype optional="true" unbounded="false" typename="short" name="orderIn" qname="patentFamilyData&gt;orderIn" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="grantsList" name="grantsList" qname="result&gt;grantsList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="grantInfo" name="" qname="{http://webservice.cdb.ebi.ac.uk/}grantInfo"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="grantId" qname="grantInfo&gt;grantId" /><s:basetype optional="true" unbounded="false" typename="string" name="agency" qname="grantInfo&gt;agency" /><s:basetype optional="true" unbounded="false" typename="string" name="acronym" qname="grantInfo&gt;acronym" /><s:basetype optional="false" unbounded="false" typename="short" name="orderIn" qname="grantInfo&gt;orderIn" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="meshHeadingsList" name="meshHeadingList" qname="result&gt;meshHeadingList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="meshHeadingInfo" name="" qname="{http://webservice.cdb.ebi.ac.uk/}meshHeadingInfo"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="majorTopic_YN" qname="meshHeadingInfo&gt;majorTopic_YN" /><s:basetype optional="true" unbounded="false" typename="string" name="descriptorName" qname="meshHeadingInfo&gt;descriptorName" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="meshQualifierList" name="meshQualifierList" qname="meshHeadingInfo&gt;meshQualifierList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="meshQualifierInfo" name="" qname="{http://webservice.cdb.ebi.ac.uk/}meshQualifierInfo"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="abbreviation" qname="meshQualifierInfo&gt;abbreviation" /><s:basetype optional="true" unbounded="false" typename="string" name="qualifierName" qname="meshQualifierInfo&gt;qualifierName" /><s:basetype optional="true" unbounded="false" typename="string" name="majorTopic_YN" qname="meshQualifierInfo&gt;majorTopic_YN" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="keywordList" name="keywordList" qname="result&gt;keywordList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="chemicalList" name="chemicalList" qname="result&gt;chemicalList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="chemicalInfo" name="" qname="{http://webservice.cdb.ebi.ac.uk/}chemicalInfo"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="chemicalInfo&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="registryNumber" qname="chemicalInfo&gt;registryNumber" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="subSetList" name="subsetList" qname="result&gt;subsetList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="subSet" name="" qname="{http://webservice.cdb.ebi.ac.uk/}subSet"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="code" qname="subSet&gt;code" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="subSet&gt;name" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="fullTextUrlList" name="fullTextUrlList" qname="result&gt;fullTextUrlList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="fullTextURLInfo" name="" qname="{http://webservice.cdb.ebi.ac.uk/}fullTextURLInfo"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="availability" qname="fullTextURLInfo&gt;availability" /><s:basetype optional="true" unbounded="false" typename="string" name="availabilityCode" qname="fullTextURLInfo&gt;availabilityCode" /><s:basetype optional="true" unbounded="false" typename="string" name="documentStyle" qname="fullTextURLInfo&gt;documentStyle" /><s:basetype optional="true" unbounded="false" typename="string" name="site" qname="fullTextURLInfo&gt;site" /><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="fullTextURLInfo&gt;url" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="commentCorrectionList" 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qname="dbCrossReferenceInfo&gt;info2" /><s:basetype optional="true" unbounded="false" typename="string" name="info3" qname="dbCrossReferenceInfo&gt;info3" /><s:basetype optional="true" unbounded="false" typename="string" name="info4" qname="dbCrossReferenceInfo&gt;info4" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="citationList" name="citationList" qname="responseWrapper&gt;citationList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="CitationData" name="" qname="{http://webservice.cdb.ebi.ac.uk/}CitationData"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="CitationData&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="CitationData&gt;source" /><s:basetype optional="true" unbounded="false" typename="string" name="citationType" 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qname="referenceInfo&gt;unstructuredInformation" /><s:basetype optional="true" unbounded="false" typename="string" name="externalLink" qname="referenceInfo&gt;externalLink" /><s:basetype optional="true" unbounded="false" typename="string" name="comments" qname="referenceInfo&gt;comments" /><s:basetype optional="false" unbounded="false" typename="int" name="citedOrder" qname="referenceInfo&gt;citedOrder" /><s:basetype optional="true" unbounded="false" typename="string" name="match" qname="referenceInfo&gt;match" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="semanticTypeCounts" name="semanticTypeCountList" qname="responseWrapper&gt;semanticTypeCountList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="semanticCounts" name="" qname="{http://webservice.cdb.ebi.ac.uk/}semanticCounts"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="name" 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typename="labsProviderCountList" name="linksCountList" qname="responseWrapper&gt;linksCountList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="labsProviderCounts" name="" qname="{http://webservice.cdb.ebi.ac.uk/}labsProviderCounts"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="providerName" qname="labsProviderCounts&gt;providerName" /><s:basetype optional="true" unbounded="false" typename="int" name="linksCount" qname="labsProviderCounts&gt;linksCount" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="labsProviders" name="providers" qname="responseWrapper&gt;providers"><s:elementtype><s:complextype optional="false" unbounded="false" typename="labsProvider" name="" qname="{http://webservice.cdb.ebi.ac.uk/}labsProvider"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="id" qname="labsProvider&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="labsProvider&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="description" qname="labsProvider&gt;description" /><s:basetype optional="true" unbounded="false" typename="string" name="frontTab" qname="labsProvider&gt;frontTab" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="labsLinks" name="link" qname="labsProvider&gt;link"><s:elementtype><s:complextype optional="false" unbounded="false" typename="labsLinks" name="" qname="{http://webservice.cdb.ebi.ac.uk/}labsLinks"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="labsLinks&gt;title" /><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="labsLinks&gt;url" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchPublications_returninput0resultList00net.sf.taverna.t2.activitieswsdl-activity1.5net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false version 0 'text/plain' 0 hitCount 0 'text/plain' 0 request 0 'text/xml' 0 profileList 0 'text/xml' 0 resultList 0 'text/xml' 0 dbCountList 0 'text/xml' 0 dbCrossReferenceList 0 'text/xml' 0 citationList 0 'text/xml' 0 referenceList 0 'text/xml' 0 semanticTypeCountList 0 'text/xml' 0 semanticTypeList 0 'text/xml' 0 searchTermList 0 'text/xml' 0 linksCountList 0 'text/xml' 0 providers 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="responseWrapper" name="return" qname="searchPublicationsResponse&gt;return"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="version" qname="responseWrapper&gt;version" /><s:basetype optional="true" unbounded="false" typename="int" name="hitCount" qname="responseWrapper&gt;hitCount" /><s:complextype optional="true" unbounded="false" typename="request" name="request" qname="responseWrapper&gt;request"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="queryString" qname="request&gt;queryString" /><s:basetype optional="true" unbounded="false" typename="string" name="internalQuery" qname="request&gt;internalQuery" /><s:basetype optional="true" unbounded="false" typename="string" name="resultType" qname="request&gt;resultType" /><s:basetype optional="true" unbounded="false" typename="string" name="profileType" qname="request&gt;profileType" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="request&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="request&gt;source" /><s:basetype optional="true" unbounded="false" typename="int" name="offSet" qname="request&gt;offSet" /><s:basetype optional="true" unbounded="false" typename="int" name="pageSize" qname="request&gt;pageSize" /><s:basetype optional="true" unbounded="false" typename="string" name="database" qname="request&gt;database" /><s:basetype optional="true" unbounded="false" typename="string" name="semanticType" qname="request&gt;semanticType" /><s:basetype optional="true" unbounded="false" typename="boolean" name="synonym" qname="request&gt;synonym" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="request&gt;email" /><s:basetype optional="true" unbounded="false" typename="string" name="providerId" qname="request&gt;providerId" /></s:elements></s:complextype><s:complextype optional="true" unbounded="false" typename="profileListBean" name="profileList" qname="responseWrapper&gt;profileList"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="profile" name="source" qname="profileListBean&gt;source"><s:elementtype><s:complextype optional="false" unbounded="false" typename="profile" name="" qname="{http://webservice.cdb.ebi.ac.uk/}profile"><s:elements /><s:attributes><s:attribute optional="false" unbounded="false" typename="profile&gt;name" name="name" qname="profile&gt;name" /><s:attribute 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unbounded="false" typename="int" name="citedByCount" qname="CitationData&gt;citedByCount" /><s:basetype optional="true" unbounded="false" typename="string" name="text" qname="CitationData&gt;text" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="referencesList" name="referenceList" qname="responseWrapper&gt;referenceList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="referenceInfo" name="" qname="{http://webservice.cdb.ebi.ac.uk/}referenceInfo"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="referenceInfo&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="referenceInfo&gt;source" /><s:basetype optional="true" unbounded="false" typename="string" name="citationType" qname="referenceInfo&gt;citationType" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="referenceInfo&gt;title" /><s:basetype optional="true" unbounded="false" typename="string" name="authorString" qname="referenceInfo&gt;authorString" /><s:basetype optional="true" unbounded="false" typename="string" name="journalAbbreviation" qname="referenceInfo&gt;journalAbbreviation" /><s:basetype optional="true" unbounded="false" typename="string" name="issue" qname="referenceInfo&gt;issue" /><s:basetype optional="false" unbounded="false" typename="int" name="pubYear" qname="referenceInfo&gt;pubYear" /><s:basetype optional="true" unbounded="false" typename="string" name="volume" qname="referenceInfo&gt;volume" /><s:basetype optional="true" unbounded="false" typename="string" name="ISSN" qname="referenceInfo&gt;ISSN" /><s:basetype optional="true" unbounded="false" typename="string" name="ESSN" qname="referenceInfo&gt;ESSN" /><s:basetype optional="true" unbounded="false" typename="string" name="ISBN" qname="referenceInfo&gt;ISBN" /><s:basetype optional="true" unbounded="false" typename="string" name="pageInfo" qname="referenceInfo&gt;pageInfo" /><s:basetype optional="true" unbounded="false" typename="string" name="publicationTitle" qname="referenceInfo&gt;publicationTitle" /><s:basetype optional="true" unbounded="false" typename="string" name="publisherLoc" qname="referenceInfo&gt;publisherLoc" /><s:basetype optional="true" unbounded="false" typename="string" name="publisherName" qname="referenceInfo&gt;publisherName" /><s:basetype optional="true" unbounded="false" typename="string" name="seriesName" qname="referenceInfo&gt;seriesName" /><s:basetype optional="true" unbounded="false" typename="string" name="edition" qname="referenceInfo&gt;edition" /><s:basetype optional="true" unbounded="false" typename="string" name="editors" qname="referenceInfo&gt;editors" /><s:basetype optional="true" unbounded="false" typename="string" name="doi" qname="referenceInfo&gt;doi" /><s:basetype optional="true" unbounded="false" typename="string" name="unstructuredInformation" qname="referenceInfo&gt;unstructuredInformation" /><s:basetype optional="true" unbounded="false" typename="string" name="externalLink" qname="referenceInfo&gt;externalLink" /><s:basetype optional="true" unbounded="false" typename="string" name="comments" qname="referenceInfo&gt;comments" /><s:basetype optional="false" unbounded="false" typename="int" name="citedOrder" qname="referenceInfo&gt;citedOrder" /><s:basetype optional="true" unbounded="false" typename="string" name="match" qname="referenceInfo&gt;match" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="semanticTypeCounts" name="semanticTypeCountList" qname="responseWrapper&gt;semanticTypeCountList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="semanticCounts" name="" qname="{http://webservice.cdb.ebi.ac.uk/}semanticCounts"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="semanticCounts&gt;name" /><s:basetype optional="true" unbounded="false" typename="int" name="count" qname="semanticCounts&gt;count" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="minedTermsList" name="semanticTypeList" qname="responseWrapper&gt;semanticTypeList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="minedTerms" name="" qname="{http://webservice.cdb.ebi.ac.uk/}minedTerms"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="minedTerms&gt;name" /><s:basetype optional="false" unbounded="false" typename="int" name="total" qname="minedTerms&gt;total" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="minedSummary" name="tmSummary" qname="minedTerms&gt;tmSummary"><s:elementtype><s:complextype optional="false" unbounded="false" typename="minedSummary" name="" qname="{http://webservice.cdb.ebi.ac.uk/}minedSummary"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="term" qname="minedSummary&gt;term" /><s:basetype optional="false" unbounded="false" typename="int" name="count" qname="minedSummary&gt;count" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="minedAltName" name="altNameList" qname="minedSummary&gt;altNameList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="dbName" qname="minedSummary&gt;dbName" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="minedDbIDs" name="dbIdList" qname="minedSummary&gt;dbIdList"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="searchTerms" name="searchTermList" qname="responseWrapper&gt;searchTermList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="SearchTerm" name="" qname="{http://webservice.cdb.ebi.ac.uk/}SearchTerm"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="term" qname="SearchTerm&gt;term" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="string" name="dataSets" qname="SearchTerm&gt;dataSets"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="labsProviderCountList" name="linksCountList" qname="responseWrapper&gt;linksCountList"><s:elementtype><s:complextype optional="false" unbounded="false" typename="labsProviderCounts" name="" qname="{http://webservice.cdb.ebi.ac.uk/}labsProviderCounts"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="providerName" qname="labsProviderCounts&gt;providerName" /><s:basetype optional="true" unbounded="false" typename="int" name="linksCount" qname="labsProviderCounts&gt;linksCount" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="false" wrapped="true" typename="labsProviders" name="providers" qname="responseWrapper&gt;providers"><s:elementtype><s:complextype optional="false" unbounded="false" typename="labsProvider" name="" qname="{http://webservice.cdb.ebi.ac.uk/}labsProvider"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="id" qname="labsProvider&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="labsProvider&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="description" qname="labsProvider&gt;description" /><s:basetype optional="true" unbounded="false" typename="string" name="frontTab" qname="labsProvider&gt;frontTab" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="labsLinks" name="link" qname="labsProvider&gt;link"><s:elementtype><s:complextype optional="false" unbounded="false" typename="labsLinks" name="" qname="{http://webservice.cdb.ebi.ac.uk/}labsLinks"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="labsLinks&gt;title" /><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="labsLinks&gt;url" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_abstractTextxml_text0nodelist11 This XPath components extracts the paper abstracts as text. This is where conditionals can be added to filter the results by year, journal, number of citations etc. 2015-12-02 17:49:47.357 UTC net.sf.taverna.t2.activitiesxpath-activity1.5net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="UTF-8"?> <resultList><result><id>25873627</id><source>MED</source><pmid>25873627</pmid><pmcid>PMC4482065</pmcid><DOI>10.1093/nar/gkv281</DOI><title>Assessing the translational landscape of myogenic differentiation by ribosome profiling.</title><authorString>de Klerk E, Fokkema IF, Thiadens KA, Goeman JJ, Palmblad M, den Dunnen JT, von Lindern M, 't Hoen PA.</authorString><authorList><author><fullName>de Klerk E</fullName><firstName>Eleonora</firstName><lastName>de Klerk</lastName><initials>E</initials><authorId type="ORCID">0000-0001-9901-7803</authorId><affiliation>Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands.</affiliation></author><author><fullName>Fokkema IF</fullName><firstName>Ivo F A C</firstName><lastName>Fokkema</lastName><initials>IF</initials><affiliation>Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands.</affiliation></author><author><fullName>Thiadens KA</fullName><firstName>Klaske A M H</firstName><lastName>Thiadens</lastName><initials>KA</initials><affiliation>Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AMC/UvA, 1066CX 125 Amsterdam, The Netherlands.</affiliation></author><author><fullName>Goeman JJ</fullName><firstName>Jelle J</firstName><lastName>Goeman</lastName><initials>JJ</initials><affiliation>Biostatistics, Department for Health Evidence, Radboud University Medical Center, Postzone 133, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.</affiliation></author><author><fullName>Palmblad M</fullName><firstName>Magnus</firstName><lastName>Palmblad</lastName><initials>M</initials><authorId type="ORCID">0000-0002-5865-8994</authorId><affiliation>Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.</affiliation></author><author><fullName>den Dunnen JT</fullName><firstName>Johan T</firstName><lastName>den Dunnen</lastName><initials>JT</initials><affiliation>Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands.</affiliation></author><author><fullName>von Lindern M</fullName><firstName>Marieke</firstName><lastName>von Lindern</lastName><initials>M</initials><affiliation>Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AMC/UvA, 1066CX 125 Amsterdam, The Netherlands.</affiliation></author><author><fullName>'t Hoen PA</fullName><firstName>Peter A C</firstName><lastName>'t Hoen</lastName><initials>PA</initials><affiliation>Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands P.A.C._t_Hoen@lumc.nl.</affiliation></author></authorList><authorIdList><authorId type="ORCID">0000-0001-9901-7803</authorId><authorId type="ORCID">0000-0002-5865-8994</authorId></authorIdList><journalInfo><issue>9</issue><volume>43</volume><journalIssueId>2286225</journalIssueId><dateOfPublication>2015 May</dateOfPublication><monthOfPublication>5</monthOfPublication><yearOfPublication>2015</yearOfPublication><printPublicationDate>2015-05-01</printPublicationDate><journal><title>Nucleic acids research</title><ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation><medlineAbbreviation>Nucleic Acids Res</medlineAbbreviation><NLMid>0411011</NLMid><ISSN>0305-1048</ISSN><ESSN>1362-4962</ESSN></journal></journalInfo><pageInfo>4408-4428</pageInfo><abstractText>The formation of skeletal muscles is associated with drastic changes in protein requirements known to be safeguarded by tight control of gene transcription and mRNA processing. The contribution of regulation of mRNA translation during myogenesis has not been studied so far. We monitored translation during myogenic differentiation of C2C12 myoblasts, using a simplified protocol for ribosome footprint profiling. Comparison of ribosome footprints to total RNA showed that gene expression is mostly regulated at the transcriptional level. However, a subset of transcripts, enriched for mRNAs encoding for ribosomal proteins, was regulated at the level of translation. Enrichment was also found for specific pathways known to regulate muscle biology. We developed a dedicated pipeline to identify translation initiation sites (TISs) and discovered 5333 unannotated TISs, providing a catalog of upstream and alternative open reading frames used during myogenesis. We identified 298 transcripts with a significant switch in TIS usage during myogenesis, which was not explained by alternative promoter usage, as profiled by DeepCAGE. Also these transcripts were enriched for ribosomal protein genes. This study demonstrates that differential mRNA translation controls protein expression of specific subsets of genes during myogenesis. Experimental protocols, analytical workflows, tools and data are available through public repositories (http://lumc.github.io/ribosome-profiling-analysis-framework/).</abstractText><affiliation>Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands.</affiliation><language>eng</language><pubModel>Print-Electronic</pubModel><pubTypeList><pubType>Journal Article</pubType><pubType>Research Support, Non-U.S. Gov't</pubType></pubTypeList><meshHeadingList><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Cell Line</descriptorName></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Ribosomes</descriptorName><meshQualifierList><meshQualifier><abbreviation>ME</abbreviation><qualifierName>metabolism</qualifierName><majorTopic_YN>N</majorTopic_YN></meshQualifier></meshQualifierList></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Myoblasts, Skeletal</descriptorName><meshQualifierList><meshQualifier><abbreviation>ME</abbreviation><qualifierName>metabolism</qualifierName><majorTopic_YN>Y</majorTopic_YN></meshQualifier></meshQualifierList></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Animals</descriptorName></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Mice</descriptorName></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Ribosomal Proteins</descriptorName><meshQualifierList><meshQualifier><abbreviation>BI</abbreviation><qualifierName>biosynthesis</qualifierName><majorTopic_YN>N</majorTopic_YN></meshQualifier><meshQualifier><abbreviation>GE</abbreviation><qualifierName>genetics</qualifierName><majorTopic_YN>N</majorTopic_YN></meshQualifier></meshQualifierList></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>RNA, Messenger</descriptorName><meshQualifierList><meshQualifier><abbreviation>ME</abbreviation><qualifierName>metabolism</qualifierName><majorTopic_YN>Y</majorTopic_YN></meshQualifier><meshQualifier><abbreviation>CH</abbreviation><qualifierName>chemistry</qualifierName><majorTopic_YN>N</majorTopic_YN></meshQualifier></meshQualifierList></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Sequence Analysis, RNA</descriptorName><meshQualifierList><meshQualifier><abbreviation>MT</abbreviation><qualifierName>methods</qualifierName><majorTopic_YN>N</majorTopic_YN></meshQualifier></meshQualifierList></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Transcription, Genetic</descriptorName></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Gene Expression Regulation</descriptorName></meshHeading><meshHeading><majorTopic_YN>Y</majorTopic_YN><descriptorName>Peptide Chain Initiation, Translational</descriptorName></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Muscle Development</descriptorName><meshQualifierList><meshQualifier><abbreviation>GE</abbreviation><qualifierName>genetics</qualifierName><majorTopic_YN>Y</majorTopic_YN></meshQualifier></meshQualifierList></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>Promoter Regions, Genetic</descriptorName></meshHeading><meshHeading><majorTopic_YN>N</majorTopic_YN><descriptorName>High-Throughput Nucleotide Sequencing</descriptorName><meshQualifierList><meshQualifier><abbreviation>MT</abbreviation><qualifierName>methods</qualifierName><majorTopic_YN>N</majorTopic_YN></meshQualifier></meshQualifierList></meshHeading></meshHeadingList><chemicalList><chemical><name>RNA, Messenger</name><registryNumber>0</registryNumber></chemical><chemical><name>Ribosomal Proteins</name><registryNumber>0</registryNumber></chemical></chemicalList><subsetList><subset><code>IM</code><name>Index Medicus</name></subset></subsetList><fullTextUrlList><fullTextUrl><availability>Open access</availability><availabilityCode>OA</availabilityCode><documentStyle>pdf</documentStyle><site>Europe_PMC</site><url>http://europepmc.org/articles/PMC4482065?pdf=render</url></fullTextUrl><fullTextUrl><availability>Open access</availability><availabilityCode>OA</availabilityCode><documentStyle>html</documentStyle><site>Europe_PMC</site><url>http://europepmc.org/articles/PMC4482065</url></fullTextUrl><fullTextUrl><availability>Subscription required</availability><availabilityCode>S</availabilityCode><documentStyle>doi</documentStyle><site>DOI</site><url>http://dx.doi.org/10.1093/nar/gkv281</url></fullTextUrl></fullTextUrlList><isOpenAccess>Y</isOpenAccess><inEPMC>Y</inEPMC><inPMC>N</inPMC><citedByCount>1</citedByCount><hasReferences>Y</hasReferences><hasTextMinedTerms>Y</hasTextMinedTerms><hasDbCrossReferences>N</hasDbCrossReferences><hasPDF>Y</hasPDF><hasBook>N</hasBook><hasLabsLinks>N</hasLabsLinks><hasTMAccessionNumbers>Y</hasTMAccessionNumbers><tmAccessionTypeList><accessionType>pxd; sprot</accessionType></tmAccessionTypeList><dateOfCompletion>2015-07-31</dateOfCompletion><dateOfCreation>2015-05-20</dateOfCreation><dateOfRevision>2015-07-01</dateOfRevision><electronicPublicationDate>2015-04-14</electronicPublicationDate><firstPublicationDate>2015-04-14</firstPublicationDate><luceneScore>NaN</luceneScore></result></resultList> /resultList/result/abstractText 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.5net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokedraw_wordcloudabstracts1n_words0wordcloud_image00 This Rshell component draws the wordcloud using its R package namesake. It also uses tm for a series of basic text mining operations, and RColorBrewer to get a nice color palette. These three R packages must be installed on the R server before this workflow will run. 2015-12-02 17:48:36.491 UTC net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity abstracts 1 false n_words 0 false wordcloud_image 0 0 false localhost 6311 false false abstracts STRING_LIST n_words INTEGER wordcloud_image PNG_FILE 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokewords_to_drawvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 100 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeresultType_corevalue00 We must here specify the 'core' result type to retrieve everything, specifically the abstracts required by this workflow. 2015-12-02 17:51:05.360 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity core 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 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchPublicationsparameterssearchPublications_inputoutputbuild_queryauthor_nameauthor_namesearchPublications_inputqueryStringbuild_queryqueryStringsearchPublications_inputpageSizearticles_to_retrievevaluesearchPublications_inputresultTyperesultType_corevaluesearchPublications_outputinputsearchPublicationsparameterssearchPublications_returninputsearchPublications_outputreturnextract_abstractTextxml_textsearchPublications_returnresultListFlatten_Listinputlistextract_abstractTextnodelistdraw_wordcloudabstractsFlatten_Listoutputlistdraw_wordcloudn_wordswords_to_drawvaluewordcloud_imagedraw_wordcloudwordcloud_image eab96b96-0c4a-424e-8cc4-8ea8894519fe 2015-09-14 13:39:30.148 UTC Magnus Palmblad 2015-09-14 16:31:04.905 UTC 2bb1c86c-5062-46dd-b56b-f5d52977bd01 2015-12-02 15:30:48.416 UTC 0936b403-d12c-48e7-81f2-c273e31afd66 2015-12-02 15:26:33.826 UTC 7b2d8003-77ce-4f1d-8f31-aa5245c24550 2015-09-14 14:19:54.322 UTC 8c32cc05-cb12-4112-9992-e81bb4026d5a 2015-09-07 11:17:46.315 UTC 33c81e10-61cd-42ac-8e83-058a935d1094 2015-06-17 15:17:42.126 UTC 86de0556-3983-4da3-81c2-770d23ea8477 2015-09-14 14:23:12.911 UTC bb984250-4ebb-4140-8dcf-a752557661a6 2015-09-14 16:28:34.813 UTC b75da20d-9e6c-475f-9e51-df8f16205fc8 2015-09-07 11:34:02.237 UTC 0d039122-0f12-4c1e-aa6f-1b556fa907b5 2015-06-17 15:42:02.258 UTC 0ce3b0e2-ccda-4ac0-bf22-d1ed85cca271 2015-09-14 14:31:08.921 UTC 384475f1-0572-41ac-a485-a3eedb18463d 2015-06-17 15:49:48.583 UTC 15b76c3e-980b-4498-bfad-4b563b0f9257 2015-06-17 15:06:27.191 UTC 8c229ff8-0ea4-4589-a79a-d74ae268e461 2015-09-07 11:09:30.966 UTC 3468955e-2773-41f9-bc73-5b3d26d7a4d6 2015-12-02 17:03:25.461 UTC 65ae77f0-5d4b-4147-a539-8489e03aea19 2015-06-17 14:33:05.146 UTC 5123be55-0e2e-46cd-a37e-3365ac2c7981 2015-09-14 13:35:53.911 UTC bdd23257-ee1c-43de-8eb3-00963b9d4731 2015-12-02 15:20:18.474 UTC 80b07576-4311-495d-9571-7de3dc6704c4 2015-09-11 11:49:06.680 UTC d6ed72c5-d9e0-4eba-9f0f-9a483d297e97 2015-12-02 16:51:07.508 UTC 7b7abfe9-77a8-4131-b9ec-d5d9ed0ca3f8 2015-09-14 13:29:40.911 UTC 70cf69c3-c2e2-4411-9a1f-20cad89c1aa0 2015-09-14 14:46:45.859 UTC e97b650a-3717-4a64-8b48-460f39d857f8 2015-09-14 14:45:50.962 UTC d431e6d4-6e27-4467-8a0f-64c651d6492d 2015-12-02 17:05:25.540 UTC 9c9d05bd-5d98-4679-8f72-c0802cecab95 2015-09-14 09:45:04.643 UTC bd67ef81-3d37-495e-afc0-72dce735dfa5 2015-09-11 11:35:22.345 UTC 9f4ff55c-32d9-4f31-a7b7-5b0e40ec6cf0 2015-12-02 16:04:57.234 UTC 9fe83e28-9efb-4595-abb9-6fefc544c916 2015-09-11 11:12:56.947 UTC 082dff52-a2b5-4f8f-b212-8807a903b4a8 2015-09-11 11:22:00.354 UTC 37c1d08e-22a8-438d-8c7b-a4a1a0a6e6d3 2015-06-17 15:30:33.882 UTC db00d1bf-ba0d-4a56-9c66-18b2cb5e3005 2015-09-07 11:14:43.596 UTC 6bbd4637-7863-4d4e-8b25-011a42d911eb 2015-09-14 16:16:13.625 UTC Author to Wordcloud 2015-12-02 17:20:56.906 UTC e4dd5576-74c2-458f-bb9c-4137c59e8442 2015-12-02 15:58:24.605 UTC 8852a376-0f8c-4e3d-88d4-8cf6d801cd22 2015-09-07 11:25:31.627 UTC 7bf5b663-68bc-4130-90c1-ca0a8a94cd02 2015-12-02 17:51:15.908 UTC 4ecd9bc6-77fc-4a09-8fbb-a8de52a73c1a 2015-09-11 11:23:32.9 UTC a3f7ec89-7485-42d2-a891-cd3842737cd3 2015-09-11 11:25:03.733 UTC 3236a7f2-7fd4-4f7d-9f14-902de831173b 2015-09-17 16:38:09.321 UTC 64f9c2da-748b-4f5f-9deb-ff20b897653c 2015-09-14 13:41:30.407 UTC d1203ae9-7c42-48c2-aec0-52744ac17d76 2015-12-02 15:30:11.394 UTC 3b11cf8a-57af-47b8-bf66-3abb9686f8a8 2015-09-14 13:34:12.577 UTC 83920730-d196-4d35-a4f0-b498df439edf 2015-09-14 14:04:37.792 UTC d3cd9ed3-a9a1-4f50-87b7-9fff1fd3b2be 2015-12-02 15:49:38.567 UTC 49b50497-1aa9-45ae-b22c-914dc312f707 2015-06-17 15:05:10.52 UTC 35f57c4d-991c-43aa-ab8e-9dd52f63f1d6 2015-09-14 13:55:09.597 UTC cf104017-de0c-4f35-bc7c-4ff5d2564841 2015-09-11 11:33:25.399 UTC 8748ac94-5f94-453d-9f66-48c611262d9a 2015-09-11 11:46:44.940 UTC f0d3e185-9f45-4a06-9eb5-00a648d2d7ff 2015-09-07 11:26:01.20 UTC 0bd0ecdb-8459-40e7-94a8-4e5726183b8d 2015-09-14 13:52:48.711 UTC 9e88f3bf-3754-46ad-b65f-a5ee02dff950 2015-12-02 17:06:28.588 UTC 4729d116-3482-4ae9-9029-ba932485d36f 2015-06-17 15:48:39.671 UTC be914dc7-eed6-4f6a-b110-88703fc321db 2015-09-07 11:13:15.906 UTC b241f330-bc9f-48f3-b6a6-7ca3f82409d3 2015-12-02 16:00:00.744 UTC 9e6acb2a-c872-4de3-8ec1-44e6092051ad 2015-09-14 09:35:15.119 UTC 3795cff4-d941-4512-bd7c-ed495c315846 2015-09-11 11:20:58.988 UTC cb1be238-dcf8-4043-a8a3-95383539eafc 2015-09-11 11:14:43.559 UTC 0b545058-68d2-4d7f-911e-0e7cb591d243 2015-12-02 15:34:46.537 UTC f2cb4c03-2930-478f-8ac7-ef89382740c4 2015-12-02 17:00:06.130 UTC 767b33cf-2a10-4717-8bc0-80ef91da61bd 2015-06-17 14:45:24.545 UTC 72630699-e507-4a86-9dff-8199093ee0e6 2015-09-07 11:38:29.463 UTC 26194012-eeea-4fab-9934-62d7a83199b0 2015-09-11 11:41:14.784 UTC 982665a2-6bd0-4e3f-adef-46940c3621ca 2015-12-02 15:40:43.579 UTC de17cf39-56b7-4259-a564-e1dc6e7f8abb 2015-09-11 11:13:36.996 UTC 675d1068-90be-4feb-89c4-12752b17db1b 2015-12-02 17:53:11.905 UTC 10d7966c-b99d-4c1e-a8a5-8ff138fa4471 2015-06-17 15:45:31.358 UTC 131f876b-bedc-4846-8845-53eb62102ed1 2015-09-14 13:40:41.615 UTC 09e33109-9656-4d0f-a67c-0e1ef016c180 2015-09-14 16:31:06.363 UTC This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService). The workflow searches the publication of an author, extracts the abstracts, counts the word frequencies and plot a wordcloud using the R package of the same name. The Rshell plot_wordcloud also applies text mining operations (transformation to lower case, removing punctuation, stripping whitespace and removing English stopwords using the tm R package. 2015-12-02 17:26:00.476 UTC a864264e-6133-4e52-96bb-812885249778 2015-12-02 15:37:12.145 UTC cfb1581b-f62f-477a-8cf1-a61047bd0a62 2015-09-14 09:51:03.480 UTC 38d67a9b-0698-4db8-b1f7-6dc11a5d63fb 2015-09-07 11:22:10.705 UTC 05835153-e64d-4157-ac2a-58a8ef5f82d7 2015-09-14 14:27:39.146 UTC d05e470c-ba0a-48a1-a2cf-b954f6ca5c43 2015-09-14 09:49:36.629 UTC b59d5659-e802-44a6-9dab-4a9591f62952 2015-12-02 15:51:54.926 UTC 3cadb9d8-6320-4b23-a91e-e5a817ef8b9a 2015-12-02 17:26:34.463 UTC d72d7b75-14e1-4aa5-a179-1b090ee2f22c 2015-06-17 14:47:41.206 UTC 0cce7356-c5b8-489b-945a-cd795dd088d2 2015-09-11 11:16:05.338 UTC c016aef9-1140-4565-be4c-26d6e6c51c63 2015-09-11 11:35:08.162 UTC fc3a1ad5-91c9-4e47-af12-0cd5823ba039 2015-09-11 11:11:40.593 UTC a20e45c0-4102-4a38-9d39-2b00c7c03c88 2015-09-14 14:44:58.15 UTC 5c2fe851-3ca8-41ac-b814-c28552a0a48c 2015-09-07 11:33:05.932 UTC 4aab7c99-38d3-41ac-a446-75091de7b8e1 2015-12-02 15:32:43.752 UTC 5b0877a7-671f-4dd6-b068-31b128375135 2015-12-02 16:02:00.492 UTC 1350a7ed-51f3-4b8f-a01d-a0bd31d17495 2015-12-02 17:37:30.358 UTC c43d4b2b-9219-49fa-b332-de2b3a34b545 2015-09-11 11:06:55.938 UTC 7eea34c6-0c41-4b95-bbbf-e7a9a31be910 2015-12-02 15:23:33.627 UTC 05ce0e03-c860-42c0-8bc8-97450fa35fcd 2015-12-02 17:57:02.697 UTC 2fa75b66-7aff-4719-afbe-0e171859b51e 2015-06-17 14:48:29.871 UTC 8627c922-ea66-45ae-8fbe-4a7b9614ead7 2015-09-14 16:23:47.475 UTC 7fa8074f-4efa-4933-ab2b-3b423c54bfbd 2015-12-02 16:49:13.348 UTC