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project.xml
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project.xml
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<project type="bio">
<property name="target.model" value="genomic"/>
<property name="common.os.prefix" value="common"/>
<sources>
<source name="pombe-genes" type="pombe-genes" version="1.0.0">
<property name="src.data.dir" location="/micklem/data/pombemine/gene_data/current" />
<property name="dataSetTitle" value="Pombe-gene data set"/>
<property name="dataSourceName" value="PomBase"/>
</source>
<source name="pombe-fasta" type="fasta">
<property name="fasta.taxonId" value="4896"/>
<property name="fasta.dataSetTitle" value="Pombe-fasta data set"/>
<property name="fasta.dataSourceName" value="PomBase"/>
<property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
<property name="fasta.classAttribute" value="primaryIdentifier"/>
<property name="src.data.dir" location="/micklem/data/pombemine/fasta/current/"/>
<property name="fasta.includes" value="*.fa"/>
</source>
<source name="pombe-orthologue" type="pombe-orthologue" version="1.0.0">
<property name="src.data.dir" location="/micklem/data/pombemine/orthologues/current"/>
</source>
<source name="ncbi-gene" type="ncbi-gene" >
<property name="src.data.dir" location="/micklem/data/ncbi/current" />
<property name="organisms" value="9606" />
</source>
<!--
<source name="ncbi-gff" type="ncbi-gff">
<property name="gff3.taxonId" value="9606"/>
<property name="gff3.seqClsName" value="Chromosome"/>
<property name="gff3.dataSourceName" value="NCBI"/>
<property name="gff3.dataSetTitle" value="ncbi-gff"/>
<property name="src.data.dir" location="/micklem/data/human/gff/current"/>
</source>
-->
<source name="pombe-uniprot" type="pombe-uniprot" version="1.0.0">
<property name="uniprot.organisms" value="284812"/>
<property name="creatego" value="true"/>
<property name="src.data.dir" location="/micklem/data/uniprot/current"/>
</source>
<source name="interpro" type="interpro">
<property name="src.data.dir" location="/micklem/data/interpro/current" />
</source>
<!-- has to be after uniProtEntry because only loads protein domains for loaded uniProtEntries -->
<source name="pombe-protein2ipr" type="pombe-protein2ipr" version="1.0.0">
<property name="src.data.dir" location="/micklem/data/interpro/match_complete/current"/>
<property name="src.data.dir.includes" value="protein2ipr.dat"/>
<property name="protein2ipr.organisms" value="4896"/>
<property name="osAlias" value="os.production"/>
</source>
<source name="interpro-go" type="interpro-go">
<property name="src.data.dir" location="/micklem/data/interpro/ontology/current"/>
</source>
<source name="go" type="go">
<property name="src.data.file" location="/micklem/data/pombemine/go-annotation/current/go-basic.obo" />
</source>
<source name="pombe-go-annotation" type="pombe-go-annotation" version="1.0.0">
<property name="src.data.dir" location="/micklem/data/pombemine/pombe-go-annotation/current" />
<property name="src.data.includes" value="**/pombase-latest*" />
</source>
<source name="fypo" type="fypo" version="1.0.0">
<property name="src.data.file" location="/micklem/data/pombemine/phenotypes/ontologies/current/fypo-simple-pombase.obo" />
</source>
<source name="fypo-ext" type="fypo" version="1.0.0">
<property name="src.data.file" location="/micklem/data/pombemine/phenotypes/ontologies/current/fypo_extension.obo" />
</source>
<source name="fyeco" type="fyeco" version="1.0.0">
<property name="src.data.file" location="/micklem/data/pombemine/phenotypes/ontologies/current/fyeco.obo" />
</source>
<source name="eco" type="eco">
<property name="src.data.file" location="/micklem/data/eco/current/eco.obo"/>
</source>
<source name="mondo" type="mondo" version="1.0.0">
<property name="src.data.file" location="/micklem/data/mondo/mondo.obo"/>
</source>
<source name="pombe-alleles" type="pombe-alleles" version="1.0.0">
<property name="src.data.dir" location="/micklem/data/pombemine/phenotypes/current" />
<property name="src.data.dir.includes" value="**/phenotype_annotations*" />
<property name="dataSetTitle" value="PomBase phenotypes data set"/>
<property name="dataSourceName" value="PomBase"/>
</source>
<source name="pombe-diseases" type="pombe-diseases" version="1.0.0">
<property name="src.data.dir" location="/micklem/data/pombemine/disease/current" />
<property name="src.data.dir.includes" value="**/disease_association*" />
<property name="dataSetTitle" value="PomBase disease data set"/>
<property name="dataSourceName" value="PomBase"/>
</source>
<source name="biogrid" type="biogrid" dump="true">
<property name="src.data.dir" location="/micklem/data/biogrid/current" />
<property name="src.data.dir.includes" value="*psi25.xml" />
<property name="biogrid.organisms" value="4896" />
</source>
<source name="psi-mi-ontology" type="psi-mi-ontology">
<property name="src.data.file" location="/micklem/data/psi/ontology/current/psi-mi.obo"/>
</source>
<source name="panther" type="panther">
<property name="src.data.dir" location="/micklem/data/panther/current"/>
<property name="panther.organisms" value="284812"/>
<property name="panther.homologues" value="7227 10090 6239 10116 7955 4932 9606"/>
</source>
<source name="omim" type="omim" >
<property name="src.data.dir" location="/micklem/data/metabolic/omim/current" />
</source>
<source name="entrez-organism" type="entrez-organism" dump="true">
<property name="src.data.file" location="organisms.xml"/>
</source>
<source name="so" type="so">
<property name="src.data.file" location="so.obo" />
</source>
<source name="update-publications" type="update-publications">
<property name="src.data.file" location="publications.xml"/>
<property name="loadFullRecord" value="true"/>
</source>
</sources>
<post-processing>
<post-process name="create-references" />
<post-process name="create-chromosome-locations-and-lengths"/>
<post-process name="transfer-sequences"/>
<post-process name="create-gene-flanking-features" />
<post-process name="do-sources" />
<post-process name="create-location-overlap-index"/>
<post-process name="create-overlap-view" />
<post-process name="create-attribute-indexes"/>
<post-process name="summarise-objectstore"/>
<post-process name="create-autocomplete-index"/>
<post-process name="create-search-index"/>
</post-processing>
</project>