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License: MIT License
Collection of scripts / notebooks to reliably select datasets
License: MIT License
Do not hardcode priority of data sources, it'd be something like:
Kinases,KinHub,KLIFS,PKinFam
Kinase A,True,True,True
Kinase B,False,True,False
Kinase C,False,False,True
....
List of small things that could be added to the table
We need to check how well ChEMBL annotates mutations. Mutant information can be found in the columns Assay Variant Mutation
and Assay Variant Accession
.
Example data point:
Over the past few days kinase.com was not reachable. That site is used to cross-reference human kinases in human_kinases.ipynb.
Some kinases might be missing.
A new version of ChEMBL is out. Should the zip file be adapted to v.29?
Much of the necessary code is merged.
The release draft is here.
data/human_kinases_and_chembl_targets.chembl_33.csv
kinodata-0.5
The summary data in the last release (https://github.com/openkinome/kinodata/releases/tag/v0.2) differs from what reported by the notebooks and in the data files that are outputted by them:
Dataset | Non-curated | Curated |
---|---|---|
ChEMBL 27 | 182 223 | 148 836 |
ChEMBL 28 | 199 238 | 159 978 |
vs the number of unique records in the output .csv's and reported in the notebooks:
Dataset | Non-curated | Curated |
---|---|---|
ChEMBL 27 | 217 612 | 174 238 |
ChEMBL 28 | 237 336 | 186 972 |
The notebooks appear to run fine so I have added the data from the notebooks/output files themselves to the latest release (https://github.com/openkinome/kinodata/releases/tag/v0.3). But having looked at the data directly, I can't establish where the data in the first table comes from.
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