Script used to retrieve datasets for KB build.

get_sources.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+mkdir staging
+mkdir staging/sources
+cd staging/sources
+curl -L 'https://github.com/phenoscape/phenoscape-data/blob/master/MGI_static_data/mgi_anatomy.owl.gz?raw=true' >mgi_anatomy.owl.gz
+gunzip mgi_anatomy.owl.gz
+curl -L 'https://github.com/phenoscape/phenoscape-data/blob/master/MGI_static_data/mgi_expression_data.txt.gz?raw=true' >mgi_expression_data.txt.gz
+gunzip mgi_expression_data.txt.gz
+curl -L 'https://github.com/phenoscape/phenoscape-data/blob/master/MGI_static_data/mgi_phenotypes.txt.gz?raw=true' >mgi_phenotypes.txt.gz
+gunzip mgi_phenotypes.txt.gz
+curl -L 'ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.rpt' >mgi_genes.txt
+curl -L 'http://zfin.org/downloads/genetic_markers.txt' >zfin_genetic_markers.txt
+curl -L 'http://zfin.org/downloads/aliases.txt' >zfin_aliases.txt
+curl -L 'http://zfin.org/downloads/wildtype-expression.txt' >zfin_wildtype_expression.txt
+curl -L 'http://zfin.org/downloads/phenoGeneCleanData.txt' >zfin_phenotypes.txt
+curl -L 'ftp://ftp.xenbase.org/pub/GenePageReports/GenePageGeneralInfo_ManuallyCurated.txt' >xenbase_genes.txt
+curl -L 'ftp://ftp.xenbase.org/pub/GenePageReports/XenbaseGenepageToGeneIdMapping.txt' >xenbase_genepage_mappings.txt
+curl -L -O 'ftp://ftp.xenbase.org/pub/GenePageReports/GeneExpression_laevis.txt'
+curl -L -O 'ftp://ftp.xenbase.org/pub//GenePageReports/GeneExpression_tropicalis.txt'
+curl -L http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt >hp_phenotypes.txt
+
+svn checkout 'https://github.com/phenoscape/phenoscape-data/trunk/xenbase-phenotypes' xenbase-phenotypes
+
+cd ..
+svn checkout 'https://github.com/phenoscape/phenoscape-data/trunk/Curation Files' nexml