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Biomedical Data Commons (BMDC) Schema MCF Files

This directory contains the MCF nodes for all defined domain specific schemas in Biomedical Data Commons. These files are kept in-sync with the Google repository via Copybara. Changes inside Google are immediately copied here. Approved GitHub pull requests are sent to the Google respository, where it is tested; if approved, the PR will merge into both the Google and GitHub repository.

Overview

  • GeneticVariant_GenVarSource_enums.mcf contains GenVarSourceEnum classes generated by script format_dbSNP_GenVarSource_enum_schema.py.
  • GeneticVariant_alt_id_database_properties.mcf contains GeneticVariant properties generated by script format_dbSNP_alt_ID_database_property_schema.py.
  • [biomedical_stat_vars.mcf] contains StatisticalVariable schema specific to Biomedical Data Commons.
  • [biological_taxonomy.mcf] contains schema for Species class.
  • chemical_compound.mcf contains schema for classes: ActiveIngredientAmount, BiomedicalElement, ChemicalCompound, ChemicalCompoundProteinInteraction, ChemicalCompoundDiseaseTreatment, ChemicalCompoundDiseaseContraindication, ChemicalCompoundGeneAssociation, Drug, DrugStrength, FDAApplication, HumanProteinOccurrence, PharmacologicClass Protein, and SideEffect.
  • chemical_compound_enum.mcf contains schema of enummerations, which populate properties in chemical_compound.mcf.
  • disease.mcf contains schema for classes: Disease, DiseaseGeneAssociation, DiseaseSymptomAssociation, MeSHConcept, MeSHDescriptor, and MeSHTerm.
  • disease_enum.mcf schema of enummerations, which populate properties in disease.mcf.
  • encode.mcf contains schema for ENCODE data.
  • genome_annotation.mcf contains schema for classes: Allele, BasePairs, BiologicalElement, Chromosome, Gene, GeneticAssociation, GeneticVariant, GeneticVariantGeneAssociation, GenomeAnnotation, GenomeAssembly, GenomeAssemblyUnit, Nucleotide, Position, and RNATranscript.
  • genome_annotation_enum.mcf contains schema of enummerations, which populate properties in genome_annotation.mcf.
  • human_cell_type_enum.mcf contains HumanCellTypeEnum classes generated by script parse_protein_atlas.py.
  • human_tissue_enum.mcf contains HumanTissueEnum classes generated by script parse_protein_atlas.py.
  • interaction_type_enum.mcf contains classes of InteractionTypeEnum that is automatically generated by parse_ebi.py and populates the interactionType property.
  • pharmGKB_id_properties.mcf contains Gene and ChemicalCompound alternative identifier properties automatically generated from pharmGKB data using script drug_gene_relations/config.py from pharmGKB data. This was then manually modified to remove existing properties and curate property domains.