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RobokopU24 / ORION

Code that parses datasets from various sources and converts them to load graph databases.
MIT License
12 stars 13 forks source link

SIGNOR 3.0 parser. Updated to map SIGNOR phenotypes to GO terms when … #251

Open beasleyjonm opened 2 months ago

beasleyjonm commented 2 months ago

Updated to map SIGNOR phenotypes to GO terms when available from their mappings. A similar mapping process can be repeated for the complexes, protein families, and stimuli terms if SIGNOR ever updates their mappings.

matentzn commented 2 months ago

Sorry I don't know enough about your project to review, I am a colleague of @DnlRKorn from an entirely different KG land.. 😂 good luck with your work!

eKathleenCarter commented 2 months ago

@beasleyjonm

Currently, it cannot be run as written. 1) SIGNOR-ST.csv, SIGNOR-PH.csv files are not included. 2) self.data_path not set.

Please add files and define variable

EvanDietzMorris commented 2 months ago

self.data_path is actually set in the init of the SourceDataLoader interface, which all parsers inherit from, and should call with super().init so that is not an issue. Maybe not the easiest to read code design but that's how it works for all them.

https://github.com/RobokopU24/ORION/blob/b124dfb1921b1ffb60cfdf3ac964b647c4db1110/Common/loader_interface.py#L32-L37