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Trying to restrict to human only 

monarch-initiative/owlsim-v3#58
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1 parent a8d608e commit 7ac3a50418007076d20f4aa61165fcd55bb40d72 @jnguyenx jnguyenx committed on GitHub Mar 8, 2017
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Showing with 18 additions and 17 deletions.
  1. +18 −17 server/Makefile
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35 server/Makefile
@@ -4,36 +4,37 @@ CATALOG = catalog-v001.xml
DATA = ../data
MIRROR= mirror
-MM = $(DATA)/Mus_musculus
+#MM = $(DATA)/Mus_musculus
##MM_G2P = $(MM)/Mm-gene-to-phenotype-BF.txt
-MM_G2P = $(MM)/Mm_gene_phenotype.txt
-MM_G2L = $(MM)/Mm_gene_labels.txt
+#MM_G2P = $(MM)/Mm_gene_phenotype.txt
+#MM_G2L = $(MM)/Mm_gene_labels.txt
-DR = $(DATA)/Danio_rerio
+#DR = $(DATA)/Danio_rerio
##DR_G2P = $(DR)/Dr-gene-to-phenotype-BF.txt
-DR_G2P = $(DR)/Dr_gene_phenotype.txt
-DR_G2L = $(DR)/Dr_gene_labels.txt
+#DR_G2P = $(DR)/Dr_gene_phenotype.txt
+#DR_G2L = $(DR)/Dr_gene_labels.txt
# TODO: genes
-DM = $(DATA)/Drosophila_melanogaster
-DM_G2P = $(DM)/Dm_gene_phenotype.txt
-DM_G2L = $(DM)/Dm_gene_labels.txt
+#DM = $(DATA)/Drosophila_melanogaster
+#DM_G2P = $(DM)/Dm_gene_phenotype.txt
+#DM_G2L = $(DM)/Dm_gene_labels.txt
-CE = $(DATA)/Caenorhabditis_elegans
-CE_G2P = $(CE)/Ce_gene_phenotype.txt
-CE_G2L = $(CE)/Ce_gene_labels.txt
+#CE = $(DATA)/Caenorhabditis_elegans
+#CE_G2P = $(CE)/Ce_gene_phenotype.txt
+#CE_G2L = $(CE)/Ce_gene_labels.txt
HS = $(DATA)/Homo_sapiens
HS_D2P = $(HS)/Hs_disease_phenotype.txt
HS_D2L = $(HS)/Hs_disease_labels.txt
-CASE = $(DATA)/Cases
-CASE_C2P = $(CASE)/UDP_case_phenotype.txt
-CASE_C2L = $(CASE)/UDP_case_labels.txt
+#CASE = $(DATA)/Cases
+#CASE_C2P = $(CASE)/UDP_case_phenotype.txt
+#CASE_C2L = $(CASE)/UDP_case_labels.txt
#ROOT = $(UPHENO)/metazoa.owl
#ROOT = $(UPHENO)/vertebrate.owl
-ROOT = $(UPHENO)/monarch.owl
+#ROOT = $(UPHENO)/monarch.owl
+ROOT = http://purl.obolibrary.org/obo/hp.owl
USECAT = --catalog-xml $(ONT)/catalog-v001.xml
@@ -52,7 +53,7 @@ $(CATALOG):
# TODO: trigger rebuild
all.owl: additional-associations.txt additional-labels.txt $(DR_G2P) $(MM_G2P) $(HS_D2P) $(DM_D2P) $(CE_G2P)
- $(OWLTOOLS) $(ROOT) --merge-imports-closure --load-instances additional-associations.txt --load-labels additional-labels.txt --load-instances $(MM_G2P) --load-labels $(MM_G2L) --load-instances $(DR_G2P) --load-instances $(CASE_C2P) --load-labels $(CASE_C2L) --load-labels $(DR_G2L) --load-instances $(HS_D2P) --load-labels $(HS_D2L) --load-instances $(DM_G2P) --load-labels $(DM_G2L) --load-instances $(CE_G2P) --load-labels $(CE_G2L) --merge-support-ontologies --remove-axioms -t ObjectPropertyDomain --remove-axioms -t ObjectPropertyRange --remove-axioms -t DisjointClasses -o $@
+ $(OWLTOOLS) $(ROOT) --merge-imports-closure --load-instances additional-associations.txt --load-labels additional-labels.txt --load-instances $(HS_D2P) --load-labels $(HS_D2L) --merge-support-ontologies --remove-axioms -t ObjectPropertyDomain --remove-axioms -t ObjectPropertyRange --remove-axioms -t DisjointClasses -o $@
owlsim.cache: all.owl

2 comments on commit 7ac3a50

@jnguyenx
Collaborator

jnguyenx replied Mar 8, 2017

@cmungall I'm getting an exception, probably because of the ROOT variable set to http://purl.obolibrary.org/obo/hp.owl. Any ideas how to fix that?

[Fatal Error] :1:50: White spaces are required between publicId and systemId.
2017-03-08 14:41:02,476 INFO  (ParserWrapper:82) Finished loading ontology: null from: http://purl.obolibrary.org/obo/hp.owl
2017-03-08 14:41:02,477 ERROR (CommandRunner:4317) could not parse:http://purl.obolibrary.org/obo/hp.owl
org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://purl.obolibrary.org/obo/hp.owl
Could not parse ontology.  Either a suitable parser could not be found, or parsing failed.  See parser logs below for explanation.
The following parsers were tried:
1) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@75b25825
2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@71984c3
3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@3f1c5af9
4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@5ab14cb9
6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
14) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@2c444798
15) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@e72dba7
17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@18e8473e
18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d


Detailed logs:
--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@75b25825
    Stack trace:
org.xml.sax.SAXParseException; systemId: http://purl.obolibrary.org/obo/hp.owl; lineNumber: 127412; columnNumber: 102; XML document structures must start and end within the same entity.        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1098)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1054)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:913)
        owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
        owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
        owltools.io.ParserWrapper.parse(ParserWrapper.java:132)
        owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4305)
XML document structures must start and end within the same entity.        org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
        org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
        org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
        org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
        org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
        org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
        org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.endEntity(Unknown Source)
        org.apache.xerces.impl.XMLDocumentScannerImpl.endEntity(Unknown Source)
        org.apache.xerces.impl.XMLEntityManager.endEntity(Unknown Source)
        org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
@cmungall
Owner

cmungall replied Mar 9, 2017

obophenotype/human-phenotype-ontology#742
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