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henrietteharmsehenrietteharmse
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Added data sources config.
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‎config/prod/zooma-annotation-dao.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<beans xmlns="http://www.springframework.org/schema/beans"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns:zooma="http://www.ebi.ac.uk/fgpt/zooma/zooma-owl-loader"
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xmlns:zoomacsv="http://www.ebi.ac.uk/fgpt/zooma/zooma-csv-loader"
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xsi:schemaLocation="
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http://www.springframework.org/schema/beans
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http://www.springframework.org/schema/beans/spring-beans.xsd
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http://www.ebi.ac.uk/fgpt/zooma/zooma-owl-loader
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http://www.ebi.ac.uk/fgpt/zooma/zooma-owl-loader.xsd
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http://www.ebi.ac.uk/fgpt/zooma/zooma-csv-loader
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http://www.ebi.ac.uk/fgpt/zooma/zooma-csv-loader.xsd">
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<!-- annotations derived from ontology labels -->
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<!-- <zooma:owlAnnotations name="efo"
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uri="http://www.ebi.ac.uk/efo"
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loadFrom="http://www.ebi.ac.uk/efo/efo.owl"
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exclusionClassURI="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"
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exclusionAnnotationURI="http://www.ebi.ac.uk/efo/organizational_class">
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<zooma:synonym uri="http://www.ebi.ac.uk/efo/alternative_term" />
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</zooma:owlAnnotations>
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<zooma:owlAnnotations name="po"
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loadFrom="http://www.berkeleybop.org/ontologies/po/po.owl" useReasoning="false"
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uri="http://purl.obolibrary.org/obo/po"
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exclusionAnnotationURI="http://www.w3.org/2002/07/owl#deprecated">
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym" />
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</zooma:owlAnnotations>
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<zooma:owlAnnotations name="to"
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loadFrom="http://www.berkeleybop.org/ontologies/to/to.owl" useReasoning="false"
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uri="http://purl.obolibrary.org/obo/to"
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exclusionAnnotationURI="http://www.w3.org/2002/07/owl#deprecated">
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym" />
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</zooma:owlAnnotations>
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<zooma:owlAnnotations name="eo" uri="http://purl.obolibrary.org/obo/eo.owl" useReasoning="false">
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym" />
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</zooma:owlAnnotations>
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<zooma:owlAnnotations name="cmpo"
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uri="http://www.ebi.ac.uk/cmpo/cmpo.owl"
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loadFrom="https://raw.github.com/EBISPOT/CMPO/master/release/cmpo-simple.owl"
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useReasoning="false">
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym" />
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<zooma:synonym uri="http://www.w3.org/2004/02/skos/core#prefLabel" />
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</zooma:owlAnnotations>
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<zooma:owlAnnotations name="orphanet"
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uri="http://www.orphadata.org/data/ORDO/ordo_orphanet.owl"
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exclusionClassURI="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass">
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<zooma:synonym uri="http://www.ebi.ac.uk/efo/alternative_term" />
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</zooma:owlAnnotations>
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-->
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<!--
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<zooma:owlAnnotations name="clo"
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uri="http://purl.obolibrary.org/obo/clo.owl"
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loadFrom="http://purl.obolibrary.org/obo/clo.owl"
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useReasoning="false">
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym" />
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<zooma:importMapping uri="http://purl.obolibrary.org/obo/clo/BFO_import.owl"
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loadFrom="http://clo-ontology.googlecode.com/svn/trunk/src/ontology/BFO_import.owl" />
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<zooma:importMapping uri="http://purl.obolibrary.org/obo/clo/CL_import.owl"
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loadFrom="http://clo-ontology.googlecode.com/svn/trunk/src/ontology/CL_import.owl" />
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<zooma:importMapping uri="http://purl.obolibrary.org/obo/clo/GO_import.owl"
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loadFrom="http://clo-ontology.googlecode.com/svn/trunk/src/ontology/GO_import.owl" />
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<zooma:importMapping uri="http://purl.obolibrary.org/obo/clo/IAO_import.owl"
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loadFrom="http://clo-ontology.googlecode.com/svn/trunk/src/ontology/IAO_import.owl" />
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<zooma:importMapping uri="http://purl.obolibrary.org/obo/clo/NCBITaxon_import.owl"
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loadFrom="http://clo-ontology.googlecode.com/svn/trunk/src/ontology/NCBITaxon_import.owl" />
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<zooma:importMapping uri="http://purl.obolibrary.org/obo/clo/OBI_import.owl"
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loadFrom="http://clo-ontology.googlecode.com/svn/trunk/src/ontology/OBI_import.owl" />
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<zooma:importMapping uri="http://purl.obolibrary.org/obo/clo/PATO_import.owl"
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loadFrom="http://clo-ontology.googlecode.com/svn/trunk/src/ontology/PATO_import.owl" />
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<zooma:importMapping uri="http://purl.obolibrary.org/obo/clo/UBERON_import.owl"
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loadFrom="http://clo-ontology.googlecode.com/svn/trunk/src/ontology/UBERON_import.owl" />
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<zooma:importMapping uri="http://purl.obolibrary.org/obo/clo/cellline_import.owl"
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loadFrom="http://clo-ontology.googlecode.com/svn/trunk/src/ontology/cellline_import.owl" />
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</zooma:owlAnnotations>
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-->
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<!-- HPO seems to be broken (looks like failed imports) as of 16/12/2015 -->
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<!--
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<zooma:owlAnnotations name="hpo"
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uri="http://purl.obolibrary.org/obo/hp.owl"
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loadFrom="http://compbio.charite.de/hudson/job/hpo/lastStableBuild/artifact/hp/hp.owl"
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exclusionAnnotationURI="http://www.w3.org/2002/07/owl#deprecated"
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useReasoning="false">
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym" />
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</zooma:owlAnnotations>
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-->
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<!-- <zooma:owlAnnotations name="mp"
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uri="http://purl.obolibrary.org/obo/mp.owl"
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loadFrom="ftp://ftp.informatics.jax.org/pub/reports/mp.owl"
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exclusionAnnotationURI="http://www.w3.org/2002/07/owl#deprecated"
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useReasoning="false">
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" />
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<zooma:synonym uri="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym" />
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</zooma:owlAnnotations>
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<zooma:owlAnnotations name="diab"-->
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<!--uri="http://purl.obolibrary.org/obo/Diabetes_Ontology_V13.owl"-->
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<!--loadFrom="http://data.bioontology.org/ontologies/DIAB/submissions/13/download?apikey=935d7da3-6571-4601-910d-5e421574a360" />
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-->
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<!-- annotations derived from curated CSV files -->
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<zoomacsv:csvAnnotations name="sysmicro"
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uri="https://www.ebi.ac.uk/fg/sym"
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loadFrom="https://www.ebi.ac.uk/cmpo/zooma-cmpo.csv"
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delimiter="," />
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<!-- <zoomacsv:csvAnnotations name="bmb-wp7"
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uri="http://www.biomedbridges.eu/workpackages/wp7-0"
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loadFrom="ftp://ftp.ebi.ac.uk/pub/databases/spot/zooma/data/annotations/bmb-wp7/latest/bmb-disease.tsv"
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delimiter="\t" />
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-->
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<zoomacsv:csvAnnotations name="atlas"
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uri="https://www.ebi.ac.uk/gxa"
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loadFrom="file:///nfs/production/parkinso/spot/zooma/prod/slurm_pipeline/data/ftp/zoomage_report.CURATED.tsv"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="ebisc"
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uri="https://cells.ebisc.org/"
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loadFrom="file:///nfs/production/parkinso/spot/zooma/prod/slurm_pipeline/data/ftp/ebisc.tsv"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="cttv"
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uri="https://www.targetvalidation.org"
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loadFrom="https://raw.githubusercontent.com/opentargets/platform_semantic/master/resources/zooma/cttv_indications.csv"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="uniprot"
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uri="https://www.ebi.ac.uk/uniprot"
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loadFrom="file:///nfs/production/parkinso/spot/zooma/prod/slurm_pipeline/data/ftp/uniprot_disease.csv"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="eva-clinvar"
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uri="https://www.ebi.ac.uk/eva"
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loadFrom="file:///nfs/production/parkinso/spot/zooma/prod/slurm_pipeline/data/ftp/eva_clinvar.txt"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="cbi"
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uri="https://www.ebi.ac.uk/biosamples"
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loadFrom="file:///nfs/production/parkinso/spot/zooma/prod/slurm_pipeline/data/ftp/biosample_plant.csv"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="clinvar-xrefs"
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uri="https://www.ncbi.nlm.nih.gov/clinvar"
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loadFrom="file:///nfs/production/parkinso/spot/zooma/prod/slurm_pipeline/data/ftp/clinvar_xrefs.txt"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="metabolights"
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uri="https://www.ebi.ac.uk/metabolights"
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loadFrom="file:///nfs/production/parkinso/spot/zooma/prod/slurm_pipeline/data/ftp/metabolights_zooma.tsv"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="ukbiobank"
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uri="https://github.com/EBISPOT/EFO-UKB-mappings"
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loadFrom="https://raw.githubusercontent.com/EBISPOT/EFO-UKB-mappings/master/ukbiobank_zooma.txt"
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delimiter="\t" />
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<!-- <zoomacsv:csvAnnotations name="EBI-BioSamples"
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uri="https://www.ebi.ac.uk/biosamples/"
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loadFrom="ftp://ftp.ebi.ac.uk/pub/databases/biosamples/zooma/biosamples_zooma_curations.csv"
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delimiter="\t" />-->
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<zoomacsv:csvAnnotations name="EBI-BioSamples"
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uri="https://www.ebi.ac.uk/biosamples/"
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loadFrom="file:///nfs/production/parkinso/spot/zooma/prod/slurm_pipeline/data/ftp/biosamples_zooma_curations.csv"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="FAANG"
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uri="https://www.ebi.ac.uk/vg/faang"
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loadFrom="https://api.faang.org/files/faang_zooma_mappings.tsv"
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delimiter="\t" />
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<zoomacsv:csvAnnotations name="HCA"
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uri="https://www.ebi.ac.uk/about/collaborations/human-cell-atlas"
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loadFrom="https://raw.githubusercontent.com/ebi-ait/hca-ebi-wrangler-central/master/src/outputs/current_zooma_import.txt"
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delimiter="\t" />
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<zoomacsv:csvAnnotations uri="http://www.ebi.ac.uk/gwas"
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name="GWAS"
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loadFrom="file:///nfs/production/parkinso/spot/zooma/prod/uploads/gwas/zooma.tsv"
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delimiter="\t" />
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</beans>

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