298 lines
14 KiB
XML
298 lines
14 KiB
XML
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<!-- complete literature v4: xslt_cleaning_REST_OmicsDI ; transformation script production , 2021-03-17 -->
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
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version="2.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns:oaf="http://namespace.openaire.eu/oaf"
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xmlns:dr="http://www.driver-repository.eu/namespace/dr"
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xmlns:datacite="http://datacite.org/schema/kernel-4"
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xmlns:dc="http://purl.org/dc/elements/1.1/"
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xmlns:dri="http://www.driver-repository.eu/namespace/dri"
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xmlns:oaire="http://namespace.openaire.eu/schema/oaire/"
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xmlns:xs="http://www.w3.org/2001/XMLSchema"
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xmlns:vocabulary="http://eu/dnetlib/transform/clean"
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xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO"
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xmlns:personCleaner="http://eu/dnetlib/transform/person"
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exclude-result-prefixes="xsl vocabulary dateCleaner personCleaner">
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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="vCodes">
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<codes>
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<code source="arrayexpress-repository" id="re3data_____::r3d100010222" name="ArrayExpress Archive of Functional Genomics Data" sourceUrl="https://www.ebi.ac.uk/arrayexpress/" urlTemplate="https://www.ebi.ac.uk/arrayexpress/experiments/" />
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<code source="atlas-experiments" id="re3data_____::r3d100010223" name="Expression Atlas Database" sourceUrl="http://www.ebi.ac.uk/gxa/home" urlTemplate="" />
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<code source="biomodels" id="re3data_____::r3d100010789" name="BioModels Database" sourceUrl="https://www.ebi.ac.uk/biomodels-main/" urlTemplate="" />
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<code source="dbgap" id="re3data_____::r3d100010788" name="dbGaP (database of Genotypes and Phenotypes)" sourceUrl="https://www.ncbi.nlm.nih.gov/gap" urlTemplate="" />
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<code source="ega" id="re3data_____::r3d100011242" name="EGA Database (European Genome-phenome Archive)" sourceUrl="https://ega-archive.org" urlTemplate="" />
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<code source="eva" id="re3data_____::r3d100011553" name="EVA database (European Variation Archive)" sourceUrl="https://www.ebi.ac.uk/eva/" urlTemplate="" />
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<code source="geo" id="re3data_____::r3d100010283" name="GEO (Gene Expression Omnibus)" sourceUrl="https://www.ncbi.nlm.nih.gov/geo/" urlTemplate="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" />
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<code source="gnps" id="omicsdi_____::gnps" name="GNPS Database (Global Natural Products Social Molecular Networking)" sourceUrl="https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash2.jsp" urlTemplate="" />
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<code source="gpmdb" id="re3data_____::r3d100010883" name="GPMDB (Global Proteome Machine)" sourceUrl="http://gpmdb.thegpm.org/" urlTemplate="http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=" />
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<code source="jpost" id="re3data_____::r3d100012349" name="JPOST Repository (Japan ProteOme STandard Repository/Database)" sourceUrl="https://jpostdb.org/" urlTemplate="https://repository.jpostdb.org/entry/JPST000228" />
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<code source="lincs" id="re3data_____::r3d100011833" name="LINCS (Big Data to Knowledge / Library of Integrated Network-based Cellular Signatures)" sourceUrl="http://lincsportal.ccs.miami.edu/dcic-portal/" urlTemplate="http://lincsportal.ccs.miami.edu/datasets/#/view/" />
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<code source="massive" id="omicsdi_____::massive" name="MassIVE Database (Mass Spectrometry Interactive Virtual Environment)" sourceUrl="https://massive.ucsd.edu/ProteoSAFe/datasets.jsp" urlTemplate="" />
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<code source="metabolights_dataset" id="opendoar____::2970" name="MetaboLights Database" sourceUrl="http://www.ebi.ac.uk/metabolights/" urlTemplate="" />
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<code source="metabolome_express" id="omicsdi_____::metabolome" name="MetabolomeExpress" sourceUrl="https://www.metabolome-express.org/" urlTemplate="https://www.metabolome-express.org/datasetview.php?datasetid=" />
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<code source="metabolomics_workbench" id="re3data_____::r3d100012314" name="Metabolomics Workbench Database" sourceUrl="http://www.metabolomicsworkbench.org/" urlTemplate="http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?StudyID=" />
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<code source="NCBI" id="omicsdi_____::ncbi" name="NCBI" sourceUrl="https://www.ncbi.nlm.nih.gov/bioproject/" urlTemplate="https://www.ncbi.nlm.nih.gov/bioproject/" />
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<code source="omics_ena_project" id="re3data_____::r3d100010527" name="ENA (European Nucleotide Archive)" sourceUrl="https://www.ebi.ac.uk/ena" urlTemplate="https://www.ebi.ac.uk/ena/data/view/" />
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<code source="paxdb" id="omicsdi_____::paxdb" name="PAXDB (protein abundance database)" sourceUrl="http://pax-db.org/" urlTemplate="" />
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<code source="peptide_atlas" id="re3data_____::r3d100010889" name="PeptideAtlas Database" sourceUrl="http://www.peptideatlas.org/" urlTemplate="" />
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<code source="pride" id="re3data_____::r3d100010137" name="PRIDE Database (PRoteomics IDEntifications)" sourceUrl="http://www.ebi.ac.uk/pride/archive/" urlTemplate="http://www.ebi.ac.uk/pride/archive/projects/PXD008134" />
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</codes>
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</xsl:variable>
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<!--
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gnps, jpost, massive, metabolome_express, paxdb: no id/OpenAIRE-entry found
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ncbi: several OpenAIRE-entries found - is one the right?
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-->
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<xsl:key name="kCodeByName" match="code" use="string(@source)"/>
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<xsl:template match="/">
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<xsl:variable name="datasourcePrefix"
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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">
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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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<!--
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<xsl:apply-templates select="//*[local-name() = 'metadata']//*[local-name() = 'datasets']"/>
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-->
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<datacite:resource>
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<!-- OmicsDI does not state: languages, projects,
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-->
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<!-- landing page -->
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<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
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<datacite:alternateIdentifiers>
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<datacite:alternateIdentifier>
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<xsl:attribute name="alternateIdentifierType">
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<xsl:value-of select="'LandingPage'"/>
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</xsl:attribute>
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<xsl:choose>
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<xsl:when test="//*[local-name() = 'source'][. = ('gnps','massive','paxdb','peptide_atlas')]">
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<xsl:value-of select="concat('https://www.omicsdi.org/#/dataset/', //*[local-name() = 'source'], '/', //*[local-name() = 'id'])"/>
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</xsl:when>
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<xsl:when test="//*[local-name() = 'source'][. = 'metabolome_express']">
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<xsl:value-of select="concat(key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@urlTemplate, substring-after(//*[local-name()='id'], 'MEX'))"/>
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</xsl:when>
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<xsl:otherwise>
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<xsl:value-of select="concat(key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@urlTemplate, //*[local-name()='id'])"/>
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</xsl:otherwise>
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</xsl:choose>
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</datacite:alternateIdentifier>
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<datacite:alternateIdentifier>
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<xsl:attribute name="alternateIdentifierType">
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<xsl:value-of select="'local'"/>
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</xsl:attribute>
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<xsl:value-of select="//*[local-name()='id']"/>
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</datacite:alternateIdentifier>
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</datacite:alternateIdentifiers>
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</xsl:if>
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<!-- identifier; ... -->
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<!-- URL hindered by _et_: https://www.omicsdi.org/ws/dataset/get_acc=E-MTAB-6546_et_database=arrayexpress-repository -->
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<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
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<datacite:identifier>
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<xsl:attribute name="identifierType">
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<xsl:value-of select="'URL'"/>
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</xsl:attribute>
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<xsl:value-of select="concat('https://www.omicsdi.org/dataset/', //*[local-name() = 'source'], '/', //*[local-name() = 'id'])"/>
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</datacite:identifier>
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</xsl:if>
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<!-- title -->
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<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
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<datacite:titles>
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<datacite:title>
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<xsl:value-of select="//*[local-name() = 'title']"/>
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</datacite:title>
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</datacite:titles>
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</xsl:if>
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<!-- no authors in OmicsDI -->
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<!--
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<xsl:call-template name="authors" />
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-->
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<!--
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<xsl:call-template name="relatedPaper" />
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-->
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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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</datacite:descriptions>
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<!-- subject -->
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<datacite:subjects>
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<xsl:for-each select="distinct-values(//*[local-name()='omicsType'])">
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<datacite:subject>
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<xsl:value-of select="."/>
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</datacite:subject>
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</xsl:for-each>
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</datacite:subjects>
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</datacite:resource>
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<xsl:choose>
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<xsl:when test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
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<xsl:variable name='varCobjCategory'
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select="'0021'" />
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<dr:CobjCategory>
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<xsl:attribute name="type">
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<xsl:value-of select="vocabulary:clean($varCobjCategory, 'dnet:result_typologies')"/>
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</xsl:attribute>
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<xsl:value-of
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select="$varCobjCategory" />
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</dr:CobjCategory>
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</xsl:when>
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<xsl:otherwise>
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<!--
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<xsl:call-template name="terminate"/>
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-->
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</xsl:otherwise>
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</xsl:choose>
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<!--
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// review status: no review indications found so far
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-->
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<!--
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OMICSDI is ‘including both open and controlled data source’.
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-->
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<oaf:accessrights>
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<xsl:text>UNKNOWN</xsl:text>
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</oaf:accessrights>
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<xsl:if test="//*[local-name() = 'datasourceprefix'][.='NeuroVault__']">
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<oaf:concept>
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<xsl:attribute name="id">
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<xsl:value-of select="'ni'"/>
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</xsl:attribute>
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</oaf:concept>
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</xsl:if>
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<oaf:hostedBy>
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<xsl:attribute name="name">
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<xsl:value-of select="key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@name"/>
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</xsl:attribute>
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<xsl:attribute name="id">
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<xsl:value-of select="key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@id"/>
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</xsl:attribute>
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</oaf:hostedBy>
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<oaf:collectedFrom>
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<xsl:attribute name="name">
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<xsl:value-of select="$varOfficialName"/>
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</xsl:attribute>
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<xsl:attribute name="id">
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<xsl:value-of select="$varDataSourceId"/>
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</xsl:attribute>
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</oaf:collectedFrom>
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<!-- date -->
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<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
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<oaf:dateAccepted>
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<xsl:value-of select="replace(//*[local-name() = 'publicationDate'][not(.='null')],'(\d{4})(\d{2})(\d{2})','$1-$2-$3')"/>
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</oaf:dateAccepted>
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</xsl:if>
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</metadata>
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<xsl:copy-of select="//*[local-name() = 'about']" />
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</record>
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</xsl:template>
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<xsl:template match="node()|@*">
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<xsl:copy>
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<xsl:apply-templates select="node()|@*"/>
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</xsl:copy>
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</xsl:template>
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<xsl:template match="//*[local-name() = 'metadata']//*[local-name() = 'datasets']">
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<xsl:copy>
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<xsl:apply-templates select="node()|@*"/>
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</xsl:copy>
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</xsl:template>
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<xsl:template match="//*[local-name() = 'header']">
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<xsl:copy>
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<xsl:apply-templates select="node()|@*"/>
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<xsl:element name="dr:dateOfTransformation">
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<xsl:value-of select="$transDate"/>
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</xsl:element>
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</xsl:copy>
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</xsl:template>
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<!--
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no authors findable in OmicsDI">
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-->
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<!--
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<xsl:template match="//*[local-name() = 'authors']">
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-->
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<xsl:template name="authors">
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<xsl:choose>
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<xsl:when test="not(//*[local-name() = 'authors'][string-length(normalize-space(.)) > 0 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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<xsl:for-each select="tokenize(//*[local-name() = 'authors'], '(, and |,| and )')">
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<xsl:element name="datacite:creator">
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<xsl:element name="datacite:creatorName">
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<xsl:value-of select="personCleaner:normalize( .)"/>
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</xsl:element>
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<xsl:element name="datacite:givenName">
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<xsl:value-of select="normalize-space(substring-after(personCleaner:normalize(.), ','))"/>
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</xsl:element>
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<xsl:element name="datacite:familyName">
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<xsl:value-of select="substring-before(personCleaner:normalize(.), ',')"/>
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</xsl:element>
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</xsl:element>
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</xsl:for-each>
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</xsl:otherwise>
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</xsl:choose>
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</xsl:template>
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<!--
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<xsl:template match="//*[local-name() = 'DOI']">
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-->
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<xsl:template name="relatedPaper">
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<xsl:element name="datacite:relatedIdentifier">
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<xsl:attribute name="relatedIdentifierType">
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<xsl:value-of select="'DOI'"/>
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|
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</xsl:attribute>
|
|||
|
|
<xsl:attribute name="relationType">
|
|||
|
|
<xsl:value-of select="'isReferencedBy'"/>
|
|||
|
|
</xsl:attribute>
|
|||
|
|
<xsl:value-of select="//*[local-name() = 'DOI']"/>
|
|||
|
|
</xsl:element>
|
|||
|
|
</xsl:template>
|
|||
|
|
|
|||
|
|
</xsl:stylesheet>
|