Schema Issues Found - Githubissues

PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.

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Schema Issues Found #240

Closed jjacobson95 closed 2 weeks ago

jjacobson95 commented 4 weeks ago

Some issues have arisen now that the schema checker correctly prints all errors.

beataml_mutations.csv has the additional values in its variant_classification.

missense_variant
frameshift_variant
splice_donor_variant
stop_gained
stop_lost
inframe_insertion
inframe_deletion

nci60_experiments.tsv and gdscv1_experiments.tsv

'inf' in dose_response_value as noted in #234.
A seperate error is noted in #236.

sgosline commented 4 weeks ago

is this a naming issue in the mapping file? for example, is there another word for frameshift_variant? or is this a new type of variant that must be added to the schema?