Testing with BMDC files

schemaorg · Mar 19, 2024 · 2ac79be · 2ac79be
1 parent 041e674
commit 2ac79be
Show file tree

Hide file tree

Showing 3 changed files with 20 additions and 103 deletions.
diff --git a/software/scripts/bmdc2sdo/bmdc2sdo.sh b/software/scripts/bmdc2sdo/bmdc2sdo.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+export MCF=~/working/datcom/schema/biomedical_schema
+export DIR=../../../data/ext/pending
+
+# ok
+./mcf2turtle.py $MCF/biological_taxonomy.mcf > $DIR/bmdc_biological_taxonomy.ttl
+
+
+# not yet ok
+
+./mcf2turtle.py $MCF/disease.mcf  > $DIR/bmdc_disease.ttl
+
+# Files so far written:
+ls -l $DIR/bmdc*.ttl
diff --git a/software/scripts/bmdc2sdo/mcf2turtle.py b/software/scripts/bmdc2sdo/mcf2turtle.py
@@ -3,6 +3,10 @@
 # bmdc2sdo.py
 # find ../schema/biomedical_schema/ -name \*.mcf -exec ./bmdc2sdo.py {} \;
 
+# TODO:
+# - fix issue with multiple types in a rangeIncludes/subClassOf/domainIncludes.
+# - add enumerations exporter (and statvars?)
+
 # Usage: 
 # python mcf2turtle.py ~/working/datcom/schema/biomedical_schema/biological_taxonomy.mcf 
 # or several files
@@ -60,7 +64,7 @@
 sys.path.insert(1, '/home/danbri/working/datcom/data/')
 
 #DEBUG = os.getenv("DEBUG", "0") == "1"
-DEBUG = 1
+DEBUG = 0
 
 from util.mcf_dict_util import mcf_file_to_dict_list
 

diff --git a/software/scripts/bmdc2sdo/x b/software/scripts/bmdc2sdo/x
@@ -1,108 +1,6 @@
 Testing split_and_format_values function...
-DEBUG: Formatted value: dcs:Disease
-DEBUG: Formatted value: dcs:ICD10Code
-DEBUG: Formatted value: dcs:MeSHDescriptor
-DEBUG: Formatted value: schema:Text
-DEBUG: Formatted value: schema:Number
-DEBUG: Formatted value: dcs:Text
 All tests passed!
 All tests passed!
-DEBUG: Loaded MCF data: 39 entries
-DEBUG: Generating Turtle for class node: Disease
-DEBUG: Formatted value: :Thing
-DEBUG: Generating Turtle for class node: DiseaseDiseaseAssociation
-DEBUG: Formatted value: :Disease
-DEBUG: Generating Turtle for class node: DiseaseGeneAssociation
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: dcs:ICD10Code
-DEBUG: Generating Turtle for class node: DiseaseGeneticVariantAssociation
-DEBUG: Formatted value: :Disease
-DEBUG: Generating Turtle for class node: MeSHConcept
-DEBUG: Formatted value: :MeSHDescriptor
-DEBUG: Generating Turtle for class node: MeSHDescriptor
-DEBUG: Formatted value: :Intangible
-DEBUG: Generating Turtle for class node: MeSHQualifier
-DEBUG: Formatted value: :Intangible
-DEBUG: Generating Turtle for class node: MeSHSupplementaryRecord
-DEBUG: Formatted value: :MeSHDescriptor
-DEBUG: Generating Turtle for class node: MeSHTerm
-DEBUG: Formatted value: :MeSHConcept
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :DiseaseGeneAssociation
-DEBUG: Formatted value: :AssociationSourceEnum
-DEBUG: Formatted value: :DiseaseGeneAssociation
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :DiseaseGeneAssociation
-DEBUG: Formatted value: :Number
-DEBUG: Formatted value: :DiseaseGeneAssociation
-DEBUG: Formatted value: :Number
-DEBUG: Formatted value: :DiseaseGeneAssociation
-DEBUG: Formatted value: :DiseaseGeneAssociationStatusEnum
-DEBUG: Formatted value: :DiseaseGeneAssociation
-DEBUG: Formatted value: :Number
-DEBUG: Formatted value: :DiseaseGeneAssociation
-DEBUG: Formatted value: :Number
-DEBUG: Formatted value: :MeSHDescriptor
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :MeSHDescriptor
-DEBUG: Formatted value: dcs:MeSHSupplementaryRecord
-DEBUG: Formatted value: :Boolean
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: dcs:MeSHConcept
-DEBUG: Formatted value: :MeSHConcept
-DEBUG: Formatted value: schema:Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: dcs:GeneticVariant
-DEBUG: Formatted value: dcs:MeSHConcept
-DEBUG: Formatted value: dcs:MeSHDescriptor
-DEBUG: Formatted value: dcs:MeSHQualifier
-DEBUG: Formatted value: dcs:MeSHSupplementaryRecord
-DEBUG: Formatted value: :MeSHDescriptor
-DEBUG: Formatted value: schema:Text
-DEBUG: Formatted value: :MeSHQualifier
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :ChemicalCompound
-DEBUG: Formatted value: dcs:MeSHSupplementaryRecord
-DEBUG: Formatted value: :MeSHSupplementaryRecord
-DEBUG: Formatted value: schema:Text
-DEBUG: Formatted value: :MeSHConcept
-DEBUG: Formatted value: dcs:MeSHTerm
-DEBUG: Formatted value: :MeSHTerm
-DEBUG: Formatted value: schema:Text
-DEBUG: Formatted value: :MeSHDescriptor
-DEBUG: Formatted value: dcs:MeSHQualifier
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :MeSHConcept
-DEBUG: Formatted value: dcs:MeSHQualifier
-DEBUG: Formatted value: :MeSHQualifier
-DEBUG: Formatted value: schema:Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :ICD10Code
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :ICD10Code
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
-DEBUG: Formatted value: :Disease
-DEBUG: Formatted value: :Text
 
 @prefix : <https://schema.org/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .