SNOMED CT subset generation

Use

1. Download and unzip a current version of the SNOMED CT RF2 distribution. For US citizens, the download can be found at the National Library of Medicine download site.
2. Install the SNOMED CT to OWL utility package

3. Run the gen_cancer_subset.sh script. ```bash (venv) > ./gen_cancer_subset.sh SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z Build transitive closure list Processing /SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z/Snapshot/Terminology/sct2_Relationship_Snapshot_INT_20170731.txt Filtering files Processing /SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z/Snapshot/Terminology/sct2_Relationship_Snapshot_INT_20170731.txt Processing /SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z/Snapshot/Terminology/sct2_StatedRelationship_Snapshot_INT_20170731.txt Iteration 1: 323 new concepts Processing /SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z/Snapshot/Terminology/sct2_Relationship_Snapshot_INT_20170731.txt

   …

Processing /SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z/Snapshot/Refset/Language/der2_cRefset_LanguageSnapshot-en_INT_20170731.txt Creating transitive relationships Processing RF2 files Processing der2_cRefset_LanguageSnapshot-en_INT_20170731.txt Processing sct2_Concept_Snapshot_INT_20170731.txt Processing sct2_Description_Snapshot-en_INT_20170731.txt Processing sct2_Relationship_Snapshot_INT_20170731.txt Processing sct2_TextDefinition_Snapshot-en_INT_20170731.txt Generating OWL concepts Generating OWL properties Adding localized descriptions Writing ../snomed_cancer_subset.ttl Summary: Concepts: 860 Definitions: 0 Equivalentclass: 346 Labels: 860 Prefnames: 88 Propchains: 1 Properties: 97 Rolegreoups: 32 Subclassof: 571 Synonyms: 4 Ungrouped: 0 (venv) > ```

1. Repeat step 3 for the gen_thyroid_subset.sh script. bash (venv) > ./gen_thyroid_subset.sh<path>/SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z Build transitive closure list Processing<path>/SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z/Snapshot/Terminology/sct2_Relationship_Snapshot_INT_20170731.txt Filtering files Processing<path>/SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z/Snapshot/Terminology/sct2_Relationship_Snapshot_INT_20170731.txt Processing<path>/SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z/Snapshot/Terminology/sct2_StatedRelationship_Snapshot_INT_20170731.txt Iteration 1: 5955 new concepts ... Processing <path>/SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T150000Z/Snapshot/Refset/Language/der2_cRefset_LanguageSnapshot-en_INT_20170731.txt Creating transitive relationships Processing RF2 files Processing der2_cRefset_LanguageSnapshot-en_INT_20170731.txt Processing sct2_Concept_Snapshot_INT_20170731.txt Processing sct2_Description_Snapshot-en_INT_20170731.txt Processing sct2_Relationship_Snapshot_INT_20170731.txt Processing sct2_TextDefinition_Snapshot-en_INT_20170731.txt Generating OWL concepts Generating OWL properties Adding localized descriptions Writing ../snomed_thyroid_subset.ttl Summary: Concepts: 11252 Definitions: 0 Equivalentclass: 5706 Labels: 11252 Prefnames: 90 Propchains: 1 Properties: 97 Rolegreoups: 2214 Subclassof: 8498 Synonyms: 9 Ungrouped: 212 (venv) >