Map TCGA and CCLE samples to common ontology - Githubissues

bmeg / bmeg-etl

ETL configuration for BMEG

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Map TCGA and CCLE samples to common ontology #377

Open kellrott opened 1 year ago

kellrott commented 1 year ago

Need to make decision on phenotype mapping. Options include

NCI Thesaurus https://www.ebi.ac.uk/ols/ontologies/ncit
Mondo: https://www.ebi.ac.uk/ols/ontologies/mondo

For NCIT:

Cell lines found in https://www.cellosaurus.org/ are mapped
TCGA mapping can be found at https://bioconductor.org/packages/devel/bioc/vignettes/BiocOncoTK/inst/doc/maptcga.html

bwalsh commented 1 year ago

May be useful https://www.ebi.ac.uk/spot/oxo/terms/EFO:0000222