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IHTSDO / snomed-owl-toolkit

The official SNOMED CT OWL Toolkit. OWL conversion, classification and authoring support.
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Convert RF2 to Inferred relationships #89

Closed riannella closed 5 months ago

riannella commented 6 months ago

Hi, is there a way (or a plan) to support converting the RF2 snapshot to "inferred" relationships? (not the "stated" relns)

kaicode commented 6 months ago

Hi @riannella, I'm not sure if I understand the question. The inferred relationships are contained within each RF2 release, in the sct2_Relationship_Snapshot and sct2_RelationshipConcreteValues_Snapshot files.

riannella commented 6 months ago

I am using the UK SNOMED Mono distribution. I can see the Relationship file, and see all the inferred relationships in there... (But there is no ConcreteValues file)

When I used the conversion toolkit (with options -rf2-to-owl -rf2-snapshot-archives) all I get in the output OWL is the stated relationships.

riannella commented 6 months ago

Here is the log:

Creating Ontology using the following options:
  Snapshot archives: [/Users/renato/Documents/Temp/SnomedCT_MonolithRF2_PRODUCTION_20240313T120000Z.zip]
  Delta archive: -none-
  Ontology URI: http://snomed.info/sct/900000000000207008
  Ontology Version: 20240322
  Include Description Annotations: true

2024-03-22 15:20:00,792 [INFO  ] [main] org.snomed.otf.owltoolkit.conversion.RF2ToOWLService - Loading RF2 files
2024-03-22 15:20:02,860 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._Snapshot
2024-03-22 15:20:02,862 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._Refset
2024-03-22 15:20:02,862 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/.DS_Store
2024-03-22 15:20:02,863 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._.DS_Store
2024-03-22 15:20:02,863 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._Terminology
2024-03-22 15:20:02,864 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/.DS_Store
2024-03-22 15:20:02,864 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._.DS_Store
2024-03-22 15:20:02,864 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._Content
2024-03-22 15:20:02,865 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._Language
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2024-03-22 15:20:02,865 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._Metadata
2024-03-22 15:20:02,865 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_TextDefinition_MONOSnapshot-en_GB_20240313.txt
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2024-03-22 15:20:02,884 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_Concept_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:03,044 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526722024-03-22 15:20:03,044 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526722024-03-22 15:20:03,044 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526722024-03-22 15:20:03,044 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526722024-03-22 15:20:03,044 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526722024-03-22 15:20:03,044 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526722024-03-22 15:20:03,044 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._sct2_Concept_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:03,045 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_Description_MONOSnapshot-en_GB_20240313.txt
2024-03-22 15:20:04,355 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._sct2_Description_MONOSnapshot-en_GB_20240313.txt
2024-03-22 15:20:04,356 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_Identifier_MONOSnapshot_GB_20240313.txt
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2024-03-22 15:20:04,716 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._sct2_sRefset_OWLExpressionMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:04,716 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_Relationship_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:07,002 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._sct2_Relationship_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:07,003 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_StatedRelationship_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:07,003 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._sct2_StatedRelationship_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:07,003 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_Refset_SimpleMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:08,042 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._der2_Refset_SimpleMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:08,042 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cRefset_AssociationMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:08,274 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._der2_cRefset_AssociationMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:08,275 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cRefset_AttributeValueMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:08,987 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._der2_cRefset_AttributeValueMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:08,987 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cRefset_CareRecordElementMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:09,241 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._der2_cRefset_CareRecordElementMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:09,241 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cRefset_LanguageMONOSnapshot-en_GB_20240313.txt
2024-03-22 15:20:12,133 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._der2_cRefset_LanguageMONOSnapshot-en_GB_20240313.txt
2024-03-22 15:20:12,133 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_iissscRefset_ComplexMapMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:12,133 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._der2_iissscRefset_ComplexMapMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:12,134 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_iisssccRefset_ExtendedMapMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:12,134 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._der2_iisssccRefset_ExtendedMapMONOSnapshot_GB_20240313.txt
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2024-03-22 15:20:12,406 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._der2_sRefset_SimpleMapMONOSnapshot_GB_20240313.txt
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2024-03-22 15:20:13,523 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Unzipping file to /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/._der2_ssccRefset_MRCMAttributeRangeMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:13,546 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - RF2 release filename not recognised 'sct2_Identifier_MONOSnapshot_GB_20240313.txt'. This file will not be loaded.
2024-03-22 15:20:13,556 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Loading SNAPSHOT release files ReleaseFiles{conceptPaths=[/var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_Concept_MONOSnapshot_GB_20240313.txt], descriptionPaths=[/var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_Description_MONOSnapshot-en_GB_20240313.txt], textDefinitionPaths=[/var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_TextDefinition_MONOSnapshot-en_GB_20240313.txt], relationshipPaths=[/var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_Relationship_MONOSnapshot_GB_20240313.txt], concreteRelationshipPaths=[], statedRelationshipPaths=[/var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_StatedRelationship_MONOSnapshot_GB_20240313.txt], refsetPaths=[/var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cciRefset_RefsetDescriptorMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_Refset_SimpleMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cRefset_AssociationMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_ssRefset_ModuleDependencyMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cissccRefset_MRCMAttributeDomainMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_iissscRefset_ComplexMapMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_iisssccRefset_ExtendedMapMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cRefset_AttributeValueMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_ciRefset_DescriptionTypeMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_sssssssRefset_MRCMDomainMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cRefset_MRCMModuleScopeMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cRefset_LanguageMONOSnapshot-en_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_cRefset_CareRecordElementMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/sct2_sRefset_OWLExpressionMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_ssccRefset_MRCMAttributeRangeMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_sRefset_SimpleMapMONOSnapshot_GB_20240313.txt, /var/folders/tr/4vl7lb213gb_98lpy11mjsm00000gp/T/temp-rf2-unzip7526729157641068778/1/der2_iisssciRefset_ExtendedMapMONOSnapshot_GB_20240313.txt]}
2024-03-22 15:20:13,556 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Gathering effective dates for effective component filtering.
2024-03-22 15:20:13,562 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading concepts 
2024-03-22 15:20:14,771 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - 1092367 concepts read from sct2_Concept_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:14,784 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - includedReferenceSetPathPatterns: [der2_cRefset_Language.*, .*_sRefset_OWL.*, .*_cissccRefset_MRCMAttributeDomain.*]
2024-03-22 15:20:14,788 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - refset 'der2_cissccRefset_MRCMAttributeDomainMONOSnapshot_GB_20240313.txt' matches pattern '.*_cissccRefset_MRCMAttributeDomain.*'
2024-03-22 15:20:14,791 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - refset 'der2_cRefset_LanguageMONOSnapshot-en_GB_20240313.txt' matches pattern 'der2_cRefset_Language.*'
2024-03-22 15:20:14,791 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - refset 'sct2_sRefset_OWLExpressionMONOSnapshot_GB_20240313.txt' matches pattern '.*_sRefset_OWL.*'
2024-03-22 15:20:14,792 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading relationships 
2024-03-22 15:20:24,709 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - 8296808 relationships read from sct2_Relationship_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:24,711 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading concrete relationships 
2024-03-22 15:20:24,712 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading relationships 
2024-03-22 15:20:24,715 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - -1 relationships read from sct2_StatedRelationship_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:24,716 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading descriptions 
2024-03-22 15:20:29,018 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - 3124974 descriptions read from sct2_Description_MONOSnapshot-en_GB_20240313.txt
2024-03-22 15:20:29,019 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading descriptions 
2024-03-22 15:20:29,059 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - 10735 descriptions read from sct2_TextDefinition_MONOSnapshot-en_GB_20240313.txt
2024-03-22 15:20:29,059 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading reference set members 
2024-03-22 15:20:29,075 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - 167 reference set members read from der2_cissccRefset_MRCMAttributeDomainMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:29,075 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading reference set members 
2024-03-22 15:20:36,518 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - 6207433 reference set members read from der2_cRefset_LanguageMONOSnapshot-en_GB_20240313.txt
2024-03-22 15:20:36,518 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading reference set members 
2024-03-22 15:20:37,327 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - 423425 reference set members read from sct2_sRefset_OWLExpressionMONOSnapshot_GB_20240313.txt
2024-03-22 15:20:37,329 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading concepts 
2024-03-22 15:20:39,132 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - 1092367 concepts read from sct2_Concept_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:39,132 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - includedReferenceSetPathPatterns: [der2_cRefset_Language.*, .*_sRefset_OWL.*, .*_cissccRefset_MRCMAttributeDomain.*]
2024-03-22 15:20:39,136 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - refset 'der2_cissccRefset_MRCMAttributeDomainMONOSnapshot_GB_20240313.txt' matches pattern '.*_cissccRefset_MRCMAttributeDomain.*'
2024-03-22 15:20:39,137 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - refset 'der2_cRefset_LanguageMONOSnapshot-en_GB_20240313.txt' matches pattern 'der2_cRefset_Language.*'
2024-03-22 15:20:39,137 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - refset 'sct2_sRefset_OWLExpressionMONOSnapshot_GB_20240313.txt' matches pattern '.*_sRefset_OWL.*'
2024-03-22 15:20:39,141 [INFO  ] [pool-1-thread-3] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading relationships 
2024-03-22 15:20:39,142 [INFO  ] [pool-1-thread-2] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading concrete relationships 
2024-03-22 15:20:39,142 [INFO  ] [pool-1-thread-4] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading descriptions 
2024-03-22 15:20:39,142 [INFO  ] [pool-1-thread-5] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading descriptions 
2024-03-22 15:20:39,141 [INFO  ] [pool-1-thread-1] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading relationships 
2024-03-22 15:20:39,153 [INFO  ] [pool-1-thread-3] org.ihtsdo.otf.snomedboot.ReleaseImporter - -1 relationships read from sct2_StatedRelationship_MONOSnapshot_GB_20240313.txt
2024-03-22 15:20:39,307 [INFO  ] [pool-1-thread-5] org.ihtsdo.otf.snomedboot.ReleaseImporter - 10735 descriptions read from sct2_TextDefinition_MONOSnapshot-en_GB_20240313.txt
2024-03-22 15:20:50,407 [INFO  ] [pool-1-thread-4] org.ihtsdo.otf.snomedboot.ReleaseImporter - 3124974 descriptions read from sct2_Description_MONOSnapshot-en_GB_20240313.txt
2024-03-22 15:21:05,373 [INFO  ] [pool-1-thread-1] org.ihtsdo.otf.snomedboot.ReleaseImporter - 8296808 relationships read from sct2_Relationship_MONOSnapshot_GB_20240313.txt
2024-03-22 15:21:05,375 [INFO  ] [pool-1-thread-1] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading reference set members 
2024-03-22 15:21:05,375 [INFO  ] [pool-1-thread-4] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading reference set members 
2024-03-22 15:21:05,375 [INFO  ] [pool-1-thread-5] org.ihtsdo.otf.snomedboot.ReleaseImporter - Reading reference set members 
2024-03-22 15:21:05,415 [INFO  ] [pool-1-thread-1] org.ihtsdo.otf.snomedboot.ReleaseImporter - 167 reference set members read from der2_cissccRefset_MRCMAttributeDomainMONOSnapshot_GB_20240313.txt
2024-03-22 15:21:06,577 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised   10,000 axioms...
2024-03-22 15:21:06,899 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised   20,000 axioms...
2024-03-22 15:21:07,572 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised   30,000 axioms...
2024-03-22 15:21:07,780 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised   40,000 axioms...
2024-03-22 15:21:07,982 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised   50,000 axioms...
2024-03-22 15:21:08,193 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised   60,000 axioms...
2024-03-22 15:21:08,440 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised   70,000 axioms...
2024-03-22 15:21:08,675 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised   80,000 axioms...
2024-03-22 15:21:08,900 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised   90,000 axioms...
2024-03-22 15:21:09,110 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  100,000 axioms...
2024-03-22 15:21:09,308 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  110,000 axioms...
2024-03-22 15:21:09,504 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  120,000 axioms...
2024-03-22 15:21:09,738 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  130,000 axioms...
2024-03-22 15:21:09,936 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  140,000 axioms...
2024-03-22 15:21:14,346 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  150,000 axioms...
2024-03-22 15:21:14,568 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  160,000 axioms...
2024-03-22 15:21:14,761 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  170,000 axioms...
2024-03-22 15:21:14,951 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  180,000 axioms...
2024-03-22 15:21:15,139 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  190,000 axioms...
2024-03-22 15:21:15,350 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  200,000 axioms...
2024-03-22 15:21:15,546 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  210,000 axioms...
2024-03-22 15:21:15,740 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  220,000 axioms...
2024-03-22 15:21:15,936 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  230,000 axioms...
2024-03-22 15:21:16,125 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  240,000 axioms...
2024-03-22 15:21:16,320 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  250,000 axioms...
2024-03-22 15:21:16,511 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  260,000 axioms...
2024-03-22 15:21:16,911 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  270,000 axioms...
2024-03-22 15:21:17,107 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  280,000 axioms...
2024-03-22 15:21:17,302 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  290,000 axioms...
2024-03-22 15:21:17,496 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  300,000 axioms...
2024-03-22 15:21:17,684 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  310,000 axioms...
2024-03-22 15:21:17,888 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  320,000 axioms...
2024-03-22 15:21:18,115 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  330,000 axioms...
2024-03-22 15:21:18,311 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  340,000 axioms...
2024-03-22 15:21:18,502 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  350,000 axioms...
2024-03-22 15:21:18,725 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  360,000 axioms...
2024-03-22 15:21:18,917 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  370,000 axioms...
2024-03-22 15:21:19,114 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  380,000 axioms...
2024-03-22 15:21:19,309 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  390,000 axioms...
2024-03-22 15:21:19,824 [INFO  ] [pool-1-thread-5] org.snomed.otf.owltoolkit.taxonomy.AxiomDeserialiser - Deserialised  400,000 axioms...
2024-03-22 15:21:19,830 [INFO  ] [pool-1-thread-5] org.ihtsdo.otf.snomedboot.ReleaseImporter - 423425 reference set members read from sct2_sRefset_OWLExpressionMONOSnapshot_GB_20240313.txt
2024-03-22 15:21:23,074 [INFO  ] [pool-1-thread-4] org.ihtsdo.otf.snomedboot.ReleaseImporter - 6207433 reference set members read from der2_cRefset_LanguageMONOSnapshot-en_GB_20240313.txt
2024-03-22 15:21:23,076 [INFO  ] [main] org.ihtsdo.otf.snomedboot.ReleaseImporter - Release files read. JVM total memory is approx 12,071 MB.
2024-03-22 15:21:23,186 [INFO  ] [main] org.snomed.otf.owltoolkit.taxonomy.SnomedTaxonomyBuilder - Loaded release snapshot
2024-03-22 15:21:23,187 [INFO  ] [main] org.snomed.otf.owltoolkit.taxonomy.SnomedTaxonomyBuilder - Time taken deserialising axioms 11.881s
2024-03-22 15:21:23,187 [INFO  ] [main] org.snomed.otf.owltoolkit.taxonomy.SnomedTaxonomyBuilder - Loading complete.
2024-03-22 15:21:23,193 [INFO  ] [main] org.snomed.otf.owltoolkit.taxonomy.SnomedTaxonomyBuilder - SnomedTaxonomy loaded in 82.387 seconds
2024-03-22 15:21:23,193 [INFO  ] [main] org.snomed.otf.owltoolkit.taxonomy.SnomedTaxonomyBuilder - 789102 concepts loaded
2024-03-22 15:21:23,193 [INFO  ] [main] org.snomed.otf.owltoolkit.taxonomy.SnomedTaxonomyBuilder - 0 active stated relationships loaded
2024-03-22 15:21:23,233 [INFO  ] [main] org.snomed.otf.owltoolkit.taxonomy.SnomedTaxonomyBuilder - 400088 active axioms loaded
2024-03-22 15:21:23,251 [INFO  ] [main] org.snomed.otf.owltoolkit.taxonomy.SnomedTaxonomy - Using never grouped role list from MRCM reference set [1230370004, 733931002, 736476002, 736473005, 272741003, 774081006, 766939001, 774158006, 736518005, 1148793005, 1148969005, 733932009, 840560000, 1142141006, 736475003, 860781008, 411116001, 836358009, 1149367008, 1148967007, 827081001, 736472000, 1142139005, 733930001, 320091000221107, 736474004, 1142143009, 733933004, 1142140007, 1148965004, 1148968002, 763032000, 726542003, 733928003, 738774007, 774159003]
2024-03-22 15:21:23,251 [INFO  ] [main] org.snomed.otf.owltoolkit.conversion.RF2ToOWLService - Building Ontology
2024-03-22 15:21:23,598 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,612 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,615 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,615 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,615 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,615 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,616 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,616 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,617 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,618 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,618 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,619 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,619 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,619 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,619 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,619 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,619 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,619 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,619 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,620 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,620 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,621 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,621 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,622 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,622 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,622 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,622 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,622 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,622 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,623 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,623 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,624 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,624 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:23,626 [WARN  ] [main] org.snomed.otf.owltoolkit.ontology.OntologyService - Please add language reference set 999000691000001104 to language-refset-dialect-map.properties and recompile. The dialect ISO code could not be appended to the annotations because it was not found.
2024-03-22 15:21:50,330 [INFO  ] [main] org.snomed.otf.owltoolkit.conversion.RF2ToOWLService - RF2 to OWL Ontology conversion complete.
OWL Ontology file written to - ontology-2024-03-22_15-20-00.owl
kaicode commented 6 months ago

Now I understand the question. You would like an OWL ontology file containing the inferred relationships rather than the stated relationships. Could I ask what is the use case for this please?

The current use cases I know about for the OWL ontology file are reasoning and ontology maintenance. For those use cases the stated concept definitions are needed. I am interested to hear how the inferred form could be used.

Note that tools like Protege can create the inferred class hierarchy using the ELK reasoner. It does not however create the inferred attribute relationships.

riannella commented 6 months ago

There are two reasons (I can think of): 1) SNOMED is computationally complex (takes reasoners a long time to process) 2) If the inferences are already known (and part of the documented specification), then why not make them part of the asserted ontology

See the attached example. Because Diabetes Mellitus is a subclass of Disorder of endocrine system, then the Inferred History of Diabetes Mellitus then entails it is also a subclass of History endocrine disorder But this is not in the Stated view.

Screenshot 2024-04-05 at 14 39 45

kaicode commented 6 months ago

The ELK reasoner can process SNOMED CT in around 10 seconds to compute the inferred hierarchy. It's not an unreasonable amount of time. The OWL format is specifically for representing the complete stated definitions of concepts. We the RF2 format to distribute the inferred form. That is what can be loaded into non-OWL systems to support ECL and other types of query.

I understand the use case for having the inferred form, of course. But I don't understand the need to publish the inferred form in OWL format when OWL is there for expressing the stated definition of the concept classes and for computing the inferred form. The tools to do this are readily available. I am assuming tools that expect the OWL format have reasoning capability?

riannella commented 5 months ago

Thanks Kai