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<RESOURCE_PROFILE>
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<HEADER>
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<RESOURCE_IDENTIFIER
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value="b703be53-e2e9-4de3-ba94-210ea4a96b82_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="/>
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<RESOURCE_TYPE value="TransformationRuleDSResourceType"/>
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<RESOURCE_KIND value="TransformationRuleDSResources"/>
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<RESOURCE_URI value=""/>
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<DATE_OF_CREATION value="2019-06-21T12:30:02+00:00"/>
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</HEADER>
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<BODY>
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<CONFIGURATION>
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<IMPORTED/>
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<SCRIPT>
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<TITLE>xslt_cleaning_ORP-biotools</TITLE>
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<CODE>
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
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xmlns:oaf="http://namespace.openaire.eu/oaf"
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xmlns:datacite="http://datacite.org/schema/kernel-4"
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xmlns:functx="http://www.functx.com" xmlns:xs="http://www.w3.org/2001/XMLSchema"
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xmlns:TransformationFunction="eu.dnetlib.data.collective.transformation.core.xsl.ext.TransformationFunctionProxy"
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xmlns:dr="http://www.driver-repository.eu/namespace/dr"
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exclude-result-prefixes="TransformationFunction"
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extension-element-prefixes="TransformationFunction" version="2.0">
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<xsl:function as="xs:anyAtomicType*" name="functx:value-intersect">
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<xsl:param as="xs:anyAtomicType*" name="arg1"/>
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<xsl:param as="xs:anyAtomicType*" name="arg2"/>
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<xsl:sequence select=" distinct-values($arg1[.=$arg2]) "/>
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</xsl:function>
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<xsl:param name="varOfficialName"/>
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<xsl:param name="varDsType"/>
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<xsl:param name="varDataSourceId"/>
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<xsl:param name="index" select="0"/>
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<xsl:param name="transDate" select="current-dateTime()"/>
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<xsl:variable name="tf" select="TransformationFunction:getInstance()"/>
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<xsl:template match="/">
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<xsl:variable name="datasourcePrefix" select="normalize-space(//oaf:datasourceprefix)"/>
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<xsl:call-template name="validRecord"/>
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</xsl:template>
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<xsl:template name="terminate">
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<xsl:message terminate="yes">record is not compliant, transformation is interrupted.
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</xsl:message>
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</xsl:template>
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<xsl:template name="validRecord">
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<record>
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<xsl:apply-templates select="//*[local-name() = 'header']"/>
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<metadata><!--
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<xsl:apply-templates select="//*[local-name() = 'metadata']//*[local-name() = 'list']"/>
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-->
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<datacite:resource>
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<datacite:resourceType>
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<xsl:attribute name="resourceTypeGeneral" select="'Software'"/>
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<xsl:value-of select="//*[local-name() = 'toolType']"/>
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</datacite:resourceType>
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<xsl:for-each select="//*[local-name() = 'language']">
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<datacite:format>
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<xsl:value-of select="."/>
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</datacite:format>
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</xsl:for-each><!-- DOE CODE does not state languages; projects/funding: funders not known to OpenAIRE
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-->
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<datacite:publisher>
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<xsl:value-of select="$varOfficialName"/>
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</datacite:publisher>
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<datacite:relatedIdentifiers>
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<xsl:for-each
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select="//*[local-name() = 'documentation'][not(./*[local-name() = 'type'] = ('Terms of use', 'Citation instructions', 'Contributions policy', 'Governance'))]">
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<datacite:relatedIdentifier>
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<xsl:attribute name="relatedIdentifierType" select="'URL'"/>
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<xsl:attribute name="relationType" select="'IsDocumentedBy'"/>
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<xsl:value-of select="./*[local-name() = 'url']"/>
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</datacite:relatedIdentifier>
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</xsl:for-each><!-- paper references -->
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<xsl:call-template name="relatedPaper"/>
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</datacite:relatedIdentifiers>
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<datacite:alternateIdentifiers><!-- landing page, documentation, distribution -->
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<datacite:alternateIdentifier>
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<xsl:attribute name="alternateIdentifierType" select="'LandingPage'"/>
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<xsl:value-of
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select="concat('https://bio.tools/', //*[local-name() = 'biotoolsID'][0])"/>
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</datacite:alternateIdentifier><!--
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<xsl:for-each select="distinct-values((//*[local-name() = 'link'][./*[local-name() = 'type' and . = 'Repository']]/*[local-name() = 'url'], //*[local-name() = 'link'][./*[local-name() = 'url' and starts-with(., 'https://github.com/')]]/*[local-name() = 'url']/replace(., '(https://github.com/[^/]*/[^/]*)(/.*)?', '$1')))">
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-->
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<xsl:for-each
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select="distinct-values((//*[local-name() = 'link'][./*[local-name() = 'type' and . = 'Repository']]/*[local-name() = 'url'], //*[starts-with(., 'https://github.com/') and contains(., concat('/', //*[local-name() = 'id']))]/replace(., '(https://github.com/[^/]*/[^/]*)(/.*)?', '$1')))">
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<datacite:alternateIdentifier>
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<xsl:attribute name="alternateIdentifierType"
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select="'DistributionLocation'"/>
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<xsl:value-of select="."/>
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</datacite:alternateIdentifier>
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</xsl:for-each>
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</datacite:alternateIdentifiers>
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<datacite:identifier>
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<xsl:attribute name="identifierType" select="'URL'"/>
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<xsl:value-of
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select="concat('https://bio.tools/', //*[local-name() = 'biotoolsID'][0])"/>
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</datacite:identifier><!-- title -->
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<datacite:titles>
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<datacite:title>
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<xsl:value-of
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select="//*[local-name() = 'list']/*[local-name() = 'name']"/>
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</datacite:title>
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</datacite:titles><!-- version -->
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<xsl:if test="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]">
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<datacite:version>
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<xsl:value-of
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select="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]"/>
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</datacite:version>
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</xsl:if><!-- bio.tools' credit/typeRole Developer/... is not identical with statements on GitHub ??? (Scoary) -->
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<xsl:call-template name="authors"/>
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<datacite:contributors>
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<xsl:for-each
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select="//*[local-name() = 'contact']/*[local-name() = 'name' and not(. = 'null')]">
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<xsl:variable name="varContributorName"
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select="TransformationFunction:convertString($tf, ., 'Person')"/>
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<datacite:contributor>
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<xsl:attribute name="contributorType" select="'ContactPerson'"/>
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<datacite:contributorName>
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<xsl:value-of select="$varContributorName"/>
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</datacite:contributorName>
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<datacite:givenName>
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<xsl:value-of
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select="substring-after($varContributorName, ', ')"/>
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</datacite:givenName>
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<datacite:familyName>
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<xsl:value-of
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select="substring-before($varContributorName, ', ')"/>
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</datacite:familyName>
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</datacite:contributor>
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</xsl:for-each>
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</datacite:contributors>
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<datacite:descriptions>
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<datacite:description>
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<xsl:attribute name="descriptionType">
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<xsl:value-of select="'Abstract'"/>
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</xsl:attribute>
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<xsl:value-of select="//*[local-name() = 'description']"/>
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</datacite:description><!--
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<xsl:for-each select="//*[local-name() = 'operatingSystem'], //*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]">
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-->
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<xsl:for-each
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select="//*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]">
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<datacite:description>
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<xsl:attribute name="descriptionType" select="'Abstract'"/>
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<xsl:value-of select="."/>
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</datacite:description>
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</xsl:for-each>
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<xsl:for-each select="//*[local-name() = 'operatingSystem']">
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<datacite:description>
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<xsl:attribute name="descriptionType" select="'TechnicalInfo'"/>
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<xsl:value-of select="."/>
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</datacite:description>
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</xsl:for-each>
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</datacite:descriptions><!-- subject --><!-- dropping duplicate topics - funny that this seemingly works -->
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<datacite:subjects>
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<xsl:for-each
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select="//*[local-name() = 'topic'][index-of(distinct-values(//*[local-name() = 'topic']/*[local-name() = 'uri']), ./*[local-name() = 'uri'])]">
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<xsl:if test=".">
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<datacite:subject>
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<xsl:attribute name="subjectScheme" select="'EDAM Ontology'"/>
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<xsl:attribute name="schemeURI"
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select="'http://edamontology.org'"/>
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<xsl:attribute name="valueURI"
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select="./*[local-name() = 'uri']"/>
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<xsl:value-of select="./*[local-name() = 'term']"/>
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</datacite:subject>
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</xsl:if>
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</xsl:for-each>
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</datacite:subjects>
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</datacite:resource><!--
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CobjCategory, SuperType
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-->
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<xsl:variable name="varCobjCategory" select="'0029'"/>
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<xsl:variable name="varSuperType"
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select="TransformationFunction:convertString($tf, $varCobjCategory, 'SuperTypes')"/>
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<dr:CobjCategory>
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<xsl:attribute name="type" select="$varSuperType"/>
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<xsl:value-of select="$varCobjCategory"/>
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</dr:CobjCategory><!--
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access rights, licenses
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-->
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<xsl:for-each
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select="//*[local-name() = ('license', 'accessibility') and not(. = 'null')]">
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<oaf:accessrights>
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<xsl:variable name="varAccessRights"
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select="TransformationFunction:convertString($tf, ., 'AccessRights')"/>
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<xsl:choose>
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<xsl:when
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test="$varAccessRights = ('OPEN', 'OPEN SOURCE') and $varSuperType = 'software'">
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<xsl:value-of select="'OPEN SOURCE'"/>
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</xsl:when>
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<xsl:otherwise>
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<xsl:value-of select="$varAccessRights"/>
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</xsl:otherwise>
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</xsl:choose>
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</oaf:accessrights>
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</xsl:for-each>
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<xsl:for-each select="//*[local-name() = 'license' and not(. = 'null')]">
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<oaf:license>
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<xsl:value-of select="."/>
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</oaf:license>
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</xsl:for-each>
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<oaf:hostedBy>
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<xsl:attribute name="name" select="$varOfficialName"/>
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<xsl:attribute name="id" select="$varDataSourceId"/>
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</oaf:hostedBy>
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<oaf:collectedFrom>
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<xsl:attribute name="name" select="$varOfficialName"/>
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<xsl:attribute name="id" select="$varDataSourceId"/>
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</oaf:collectedFrom><!-- Check for person emails, tool name and elixirNode if we can set the concept for ELIXIR-GR -->
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<xsl:variable name="elixirGRAuthorMails"
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select="('achatzi@eie.gr','artemis.hatzigeorgiou@gmail.com','balomenos@upatras.gr','bezer@upatras.gr','D.R.Westhead@leeds.ac.uk','diwis@imis.athena-innovation.gr','epilalis@eie.gr','fpsom@issel.ee.auth.gr','geo.papoutsoglou@gmail.com','gpatrinos@upatras.gr','ikavakiotis@gmail.com','iliopj@med.uoc.gr','imichalop@bioacademy.gr','keklikoglou@hcmr.gr','lygerou@upatras.gr','mklapa@iceht.forth.gr','moulos@fleming.gr','mtheodo@biol.uoa.gr','mtsagris@yahoo.gr','n_moschonas@med.upatras.gr','nikolaou@uoc.gr','npapand@biol.uoa.gr','pbagos@compgen.org','ppaschou@mbg.duth.gr','secretariat@goldenhelix.org','sonja.althammer@gmail.com','thkoutsandreas@eie.gr','tsamard.it@gmail.com','vbur@iceht.forth.gr')"/><!-- List of tools provided by Elixir-GR RCD manager -->
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<xsl:variable name="elixirGRTools"
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select="('3DMem-enzyme','ACT','Align Paths','AMYL-PRED 2','ANASTASIA','BioTextQuest(+)','BioTranslator','BiP finder','BPM','BUFET','CHRONOS','DEsubs','DIANA-LNCBase','DIANA-microT','DIANA-mirExTra','DIANA-mirExTra v2.0','DIANA-miRGen','DIANA-miRGen v3.0','DIANA-mirPath','DIANA-miRPath v3','DruGeVar','easyFRAP','ePGA','FINDbase','g-Class','G-Class','GprotPRED','GWAR','GWAS Training','haplotypeAnalysisPipeline','M-IOLITE','MESBL GC-MS metabolite peak database','METAGEN','metaseqR','Micro-CTvlab','microTSS','MiGA','mirPub','MR-microT','MR-microT','Mutations-Meta-Analyser','Mutations-Meta-Analyser ','MXM','Network Analyzer','OMPdb','PICKLE','PRED-LIPO','PRED-SIGNAL','PRED-TAT','PRED-TMBB2','Proteosign','recoup','RNEA','SCENERY','SymCurv','TRES','Variant Ranker')"/>
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<xsl:variable name="authorMails" select="//credit/email"/>
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<xsl:if test="//elixirNode/text() = 'Greece' or $elixirGRTools=/list/name/text() or count(functx:value-intersect($authorMails, $elixirGRAuthorMails)) > 0">
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<oaf:concept>
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<xsl:attribute name="id" select="'elixir-gr'"/>
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</oaf:concept>
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</xsl:if><!-- date -->
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<oaf:dateAccepted>
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<xsl:value-of
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select="//*[local-name() = 'additionDate']/substring-before(., 'T')"/>
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</oaf:dateAccepted>
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</metadata>
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<xsl:copy-of select="//*[local-name() = 'about']"/>
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</record>
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</xsl:template>
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<xsl:template match="node() | @*">
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<xsl:copy>
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<xsl:apply-templates select="node() | @*"/>
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</xsl:copy>
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</xsl:template>
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<xsl:template match="//*[local-name() = 'metadata']//*[local-name() = 'resource']">
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<xsl:copy>
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<xsl:apply-templates select="node() | @*"/>
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</xsl:copy>
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</xsl:template>
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<xsl:template match="//*[local-name() = 'header']">
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<xsl:copy>
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<xsl:apply-templates select="node() | @*"/>
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<xsl:element name="dr:dateOfTransformation">
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<xsl:value-of select="$transDate"/>
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</xsl:element>
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</xsl:copy>
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</xsl:template>
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<xsl:template name="authors"><!-- Allowed roles :
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Developer
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Maintainer
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Provider
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Documentor
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Contributor
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Support
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Primary contact
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We'll consider Developer and Primary Contact as authors.
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-->
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<xsl:choose>
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<xsl:when
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test="not(//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]][./*[local-name() = 'name' and not(. = 'null')]])">
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<xsl:call-template name="terminate"/>
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</xsl:when>
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<xsl:otherwise>
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<creators>
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<xsl:for-each
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select="//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]]/*[local-name() = 'name' and not(. = 'null')]">
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<xsl:for-each select="tokenize(., ', ')">
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<xsl:variable name="varDeveloperName"
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select="TransformationFunction:convertString($tf, normalize-space(.), 'Person')"/>
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<creator>
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<creatorName>
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<xsl:value-of select="$varDeveloperName"/>
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</creatorName>
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<givenName>
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<xsl:value-of
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select="substring-after($varDeveloperName, ', ')"/>
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</givenName>
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<familyName>
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<xsl:value-of
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select="substring-before($varDeveloperName, ', ')"/>
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</familyName>
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</creator>
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</xsl:for-each>
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</xsl:for-each>
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</creators>
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</xsl:template><!--
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<xsl:template match="//*[local-name() = 'DOI']">
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<xsl:template name="relatedPaper">
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<xsl:for-each
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select="//*[local-name() = 'publication']/*[local-name() = ('doi', 'pmid', 'pmcid') and not(. = 'null')]">
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<xsl:element name="datacite:relatedIdentifier">
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<xsl:attribute name="relatedIdentifierType" select="upper-case(local-name())"/>
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<xsl:attribute name="relationType">
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<xsl:choose>
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<xsl:when test="../*[local-name() = 'type'] = 'Primary'">
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<xsl:value-of select="'isSupplementTo'"/>
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test="../*[local-name() = 'type'] = ('Review', 'Benchmark', 'Comparison')">
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<xsl:value-of select="'isReviewedBy'"/>
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<xsl:when test="../*[local-name() = 'type'] = 'Usage'">
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<xsl:value-of select="'isReferencedBy'"/>
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</xsl:when>
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<xsl:when test="../*[local-name() = 'type'] = 'Method'">
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<xsl:value-of select="'references'"/>
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<xsl:value-of select="'isReferencedBy'"/>
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<xsl:value-of select="."/>
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</xsl:stylesheet>
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</CODE>
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</SCRIPT>
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</CONFIGURATION>
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<STATUS/>
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<SECURITY_PARAMETERS/>
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</BODY>
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</RESOURCE_PROFILE>
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