Add new tasks based on UniProt keywords #37
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it's used in several places
not just domain anymore
Simplify, add docstrings and comments
Other tasks could be added but they are already covered so I chose not to add them.
yoavkt
approved these changes
Aug 20, 2024
| " ['Biological process', 'Cellular component', 'Coding sequence diversity', 'Disease', " | ||
| " 'Domain', 'Ligand', 'Molecular function', 'PTM', 'Technical term']" | ||
| "Can be multiply defined. Defaults to creating all of the possible keyword tasks.", | ||
| default=[ |
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The default should be the subset that we want. So without "Biological process," for example
| entities=pd.Series(gene_keyword_df_dict[task].index).rename("symbol"), | ||
| outcomes=gene_keyword_df_dict[task], | ||
| main_task_directory=main_task_directory, | ||
| task_name="UniProt keyword " + task, |
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we could do this using a f string
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UniProt keywords provide a nice array of new gene properties, specifically properties of the proteins coded by genes.
This PR would add the following
The ones that are really high value as they cover really new things are:
These are much more structural/chemical than our other properties and should provide a non-trivial differentiation between models.
We also have Cellular component, molecular function and disease but I think these are basically covered by HPA. Could be interesting to have another version of the same question but those are not so high value.
Also there are 'Technical term' and 'Coding sequence diversity' which do not appear to have much value at all.
What should I update in the Excel? Just the three really interesting ones?