The Uniprot evidence parser outputs one single evidence file containing both uniprot_literature and uniprot_variants data sources. The generation of the uniprot variant data set is sorted out, however the literature based evidence set is not.
There are two option to prepare data:
As an interim solution, we can use the java parser to generate evidence, then extract the literature one.
As a stable solution implement the parser as part of the other OT maintained evidence parser.
If 2. could not be completed by the data submission for the December release, 1 can be applied to not block the release.
Requirements for the stable solution
[ ] Write SPARQL query to retrieve data from Uniprot.
[ ] Map the returned disease names to EFO.
[ ] Assign confidence to disease to target annotation.
The Uniprot evidence parser outputs one single evidence file containing both
uniprot_literatureanduniprot_variantsdata sources. The generation of the uniprot variant data set is sorted out, however the literature based evidence set is not.There are two option to prepare data:
If 2. could not be completed by the data submission for the December release, 1 can be applied to not block the release.
Requirements for the stable solution