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 10 months ago

acevedol commented 10 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 10 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 10 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 10 months ago

This is for UMLS version 2023AA

saramsey commented 10 months ago

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

saramsey commented 10 months ago

This instance is running Ubuntu 22.04