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The Cbioportal is a great tool for explore clinical and omics data. We want to open widely the use the "summary" view of datasets to explore anonymised data across the institute. So we would want to s…
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Make relevant notes in the Requirements documentation.
Also use this as the basis for the #11 Clinical Process documentation
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We _could_ make separate packages (e.g. `substances.clinical`, `substances.chem`...) for specific domains, but those packages would only provide a dataframe of conversions, so I don't think it makes m…
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Ideally, we'd have access to the full text of all published paper of interest.
A few of issues with this:
- [ ] how to deal with paywalls?
- [ ] how to ensure selection of only clinical papers?…
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```
Suggest changing default schema name from 'fakedata2' to 'snofyre'
Some schema table names carry prefixes to indicate broad purpose e.g. epr_, but
this currently isn't carried through. It could …
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```
Suggest changing default schema name from 'fakedata2' to 'snofyre'
Some schema table names carry prefixes to indicate broad purpose e.g. epr_, but
this currently isn't carried through. It could …
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Adding some context to the visualization so they understand it better (on top of the paired clinical workflow).
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Can make it and/or "signs and symptoms" (GENEPIO_0001523)) about
"symptom" (SYMP_0000462) and perhaps "Clinical Findings Indicator" (NCIT_C181043)) for signs.
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Currently [special dates](https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=591) are removed by `tidy_gp_clinical()` and `tidy_gp_scripts()`.
This should be improved, as per [Darke et al](https://aca…