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bmdc2sdo.sh
bmdc2sdo.sh
 
 
disease.sh
disease.sh
 
 
fixup-BMDC.ttl.dist
fixup-BMDC.ttl.dist
 
 
mcf2turtle.py
mcf2turtle.py
 
 
readme.md
readme.md
 
 
syntaxdebug.py
syntaxdebug.py
 
 

readme.md

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

find ~/working/datcom/schema/biomedical_schema/ -name *.mcf -exec ./mcf2turtle.py {} ;

to concatenate, or

find ~/working/datcom/schema/biomedical_schema/ -name *.mcf -exec ./mcf2turtle.py {} > ./{}.ttl ;

to echo filenames.

Schema.org Utility to import definitions from a Data Commons collection of MCF files.

Pass it a .mcf file, it should emit Schema.org configuration Turtle to STDOUT.

This allows us to spin up an instance of the Schema.org site codebase on AppSpot or elsewhere,

allowing draft proposals to be explored in their entirety.

Target TTL format is https://github.com/schemaorg/schemaorg/blob/main/data/ext/pending/issue-2862.ttl

OK:

via python mcf2turtle.py ~/working/datcom/schema/biomedical_schema/biological_taxonomy.mcf > tmp/biological_taxonomy.ttl

biological_taxonomy.mcf

TODO:

GeneticVariant_alt_id_database_properties.mcf

pharmGKB_id_properties.mcf

biomedical_stat_vars.mcf

GeneticVariant_GenVarSource_enums.mcf

chemical_compound_enum.mcf

genome_annotation_enum.mcf

virus_taxonomic_ranking_enum.mcf

chemical_compound.mcf

genome_annotation.mcf

virus_taxonomy_enum.mcf

disease_enum.mcf

human_cell_type_enum.mcf

virus_taxonomy.mcf

disease.mcf

human_tissue_enum.mcf

encode.mcf

interaction_type_enum.mcf

Sample MCF property definition:

Node: dcid:medicalSubjectHeadingSupplementaryRecordID

name: "medicalSubjectHeadingSupplementaryRecordID"

typeOf: schema:Property

rangeIncludes: dcs:MeSHSupplementaryRecord, schema:Text

domainIncludes: dcs:ChemicalCompound, dcs:MeSHSupplementaryRecord

description: "A unique ID for a Medical Subject Heading supplementary record."