biomedical_schema

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 the following classes: BiologicalEntity, Taxon, Species.
• [biological_taxonomy_enum] contains schema for enumerations which populate Taxon properties in biological_taxonomy.mcf.
• chemical_compound.mcf contains schema for classes: ActiveIngredientAmount, AnatomicalTherapeuticChemicalCode, Antibody, BiomedicalEntity, ChemicalCompound, ChemicalCompoundAssociation, ChemicalCompoundDiseaseTreatment, ChemicalCompoundDiseaseContraindication, ChemicalCompoundGeneAssociation, ChemicalCompoundGeneticVariantAssociation, ChemicalCompoundProteinInteraction, Drug, DrugStrength, FDAApplication, HumanProteinOccurrence, Protein, ProteinProteinInteraction, and USAdoptedNameStem.
• chemical_compound_enum.mcf contains schema of enummerations, which populate properties in chemical_compound.mcf.
• disease.mcf contains schema for classes: Disease, DiseaseAssociation, DiseaseDiseaseAssociation, DiseaseGeneAssociation, DiseaseSymptomAssociation, DiseaseGeneticVariantAssociation, MeSHConcept, MeSHDescriptor, MeSHQualifier, MeSHRecordType, MeSHSupplementaryConceptRecord, 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, Chromosome, Gene, GeneGeneAssociation, GeneGeneticVariantAssociation, GeneticAssociation, GeneticVariant, GeneticVariantGeneAssociation, GeneticVariantGeneticVariantAssociation, GenomeAnnotation, GenomeAssembly, GenomeAssemblyUnit, GenomicCoordinates, NonCodingRNA, Nucleotide, 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. -virus_taxonomic_ranking_enum.mcf contains enumerations generated by create_virus_taxonomic_ranking_enums.py as part of the ICTV Metadata Resource import.
  • virus_txonomy.mcf contains Virus, VirusIsolate, and VirusGenomeSegment classes and their associated properties.
  • virus_taxonomy_enum.mcf contains schema of enumerations, which populate properties in virus_taxonomy.mcf.