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Update Mondo ontology - glygen/downloads/mondo/current (current file is a folder now but file remains the same) #51

Closed jeet-vora closed 1 year ago

jeet-vora commented 1 year ago
rykahsay commented 1 year ago

what is mondo ontology?

rykahsay commented 1 year ago

I don't know why you have assigned back to me without answering my question -- What exactly do you mean by "update mondo ontology"? What dataset file or any other file should be updated? What dataset was being created using file(s) under downloads/mondo/current/ ???

jeet-vora commented 1 year ago

This is the mondo file in downloads/mondo/current/mondo.owl The processing workflow remains the same. The files that use mondo.owl are protein_disease_idmap.csv and protein_disease_names.csv

rykahsay commented 1 year ago

No, protein_disease_idmap.csv and protein_disease_names.csv depend on downloads/ohsu/mondo.json. I have never used downloads/mondo/current/mondo.owl

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jeet-vora commented 1 year ago

@rykahsay ohsu folder was used for the dataset coming from them (glycophenotype). Mondo resource is multi-institutional.

Do you still want to use the ohsu folder for mondo.json or you want to start using mondo.json from the mondo folder. I have updated the files at both the locations. If ohsu is continued to be used there needs to be folder structure for dataset release like other download folders.

Let me know so the other files/folder can be removed/modified.

rykahsay commented 1 year ago

creare downloads/mondo/current/mondo.json and let me know

jeet-vora commented 1 year ago

The file is in /data/projects/glygen/downloads/mondo/current/mondo.json @rykahsay

rykahsay commented 1 year ago

done

JingyueWu commented 1 year ago

To me, it looks like Jeet has created mondo.json which I am able to open in my terminal. However, it is still a bit unclear to me what "mondo ontology" means or stands for based on this thread.

JingyueWu commented 1 year ago

@rykahsay Can you confirm that the file in /data/projects/glygen/downloads/mondo/current/mondo.json was used to generate protein_disease_idmap.csv and protein_disease_names.csv?

Is there anything else I can review?

rajamazumder commented 1 year ago

@rykahsay it looks like this task is done. If not can you please clarify what @JingyueWu needs to do?