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RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
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Error in Ontologies_Conversion #360

Open acevedol opened 5 months ago

acevedol commented 5 months ago

Traceback (most recent call last): File "/home/ubuntu/kg2-code/multi_ont_to_kg_jsonl.py", line 1277, in save_pickle) File "/home/ubuntu/kg2-code/multi_ont_to_kg_jsonl.py", line 147, in make_kg2

save_pickle) File "/home/ubuntu/kg2-code/multi_ont_to_kg_jsonl.py", line 71, in load_ont_fi le_return_ontology_and_metadata ontology = kg2_util.make_ontology_from_local_file(file_name, save_pickle=sav e_pickle) File "/home/ubuntu/RTX-KG2/kg2_util.py", line 871, in make_ontology_from_local _file check=True) File "/usr/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['owltools', 'umls-nci.ttl', '-o', '-f', 'json', '/tmp/kg2-1aer0nim.json']' returned non-zero exit status 1.

acevedol commented 5 months ago

./owltools umls-nci.ttl -o -f json /tmp/kg2-he1wqymp.json >> owltools-error.log

ubuntu@ip-172-31-29-113:~/kg2-build$ head -35 owltools-error.log 2024-01-17 23:35:37,062 ERROR (CommandRunner:4815) could not parse:umls-nci.ttl org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/home/ubuntu/kg2-build/umls-nci.ttl 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@1bb564e2 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@bcec031 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@423e4cbb 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@53499d85 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 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@5e63cad 15) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@109f5dd8 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@7c0da600 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d

acevedol commented 5 months ago

Reading ontology file: umls-nci.ttl; size: 39.51 KiB [Fatal Error] :25:43: The reference to entity "l" must end with the ';' delimiter.

saramsey commented 5 months ago

This is for UMLS version 2023AA

saramsey commented 5 months ago

This work is being done on kg290build.rtx.ai (54.190.190.167)

saramsey commented 5 months ago

This instance is running Ubuntu 22.04