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bmeg / bmeg-etl

ETL configuration for BMEG
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Reverse edge direction between Program/Project/Case/Sample/Aliquot #318

Closed adamstruck closed 5 years ago

adamstruck commented 5 years ago

Or we may want to have bidirectional edges in this section of the graph for convenience.

kellrott commented 5 years ago

Draft for new edge schema:

Program hasProject  Project
Project hasCase Case
Case    hasSample   Sample
Sample  hasAliquot  Aliquot
Case    hasTreatment    Compound
Aliquot hasPhenotype    Phenotype
Aliquot hasCallset  Callset
Aliquot hasGeneExpression   GeneExpression
Aliquot hasCNA  CopyNumberAlteration
Aliquot hasTranscriptExpression TranscriptExpression
Callset hasSomaticMutation  Allele
Allele  alleleIn    Gene
PFAMClan    hasMember   PFAMFamily
PFAMFamily  hasAlignment    Protein
Gene    hasTranscript   Transcript
Transcript  hasExon Exon
Transcript  hasProtein  Protein
Protein hasStructure    ProteinStructure
MinimalAllele   alleleIn    Gene
G2PAssociation  hasMinimalAlleleFeature MinimalAllele
G2PAssociation  hasGeneFeature  Gene
G2PAssociation  hasSupportingReference  Publication
G2PAssociation  hasEnvironment  Compound
G2PAssociation  hasPhenotype    Phenotype
G2PAssociation  hasAlleleFeature    Allele
DrugResponse    responseTo  Compound
DrugResponse    responseIn  Aliquot
GeneOntologyTerm    isA GeneOntologyTerm
Gene    hasAnnotation   GeneOntologyTerm
PFAMFamily  hasAnnotation   GeneOntologyTerm
adamstruck commented 5 years ago

MinimalAllele was changed to GenomicFeature in ec36533

GenomicFeature  featureIn   Gene
G2PAssociation  hasGenomicFeature   GenomicFeature
kellrott commented 5 years ago

Addressed in #332