Open hammer opened 5 years ago
Did eco_scores
, still need to do:
self.fix_target_id
: --> normalise_target_id
--> get_uniprot2ensembl
, get_reference_ensembl_id
. Hot mess I don't wanna handle right now.self.fix_disease_id
: --> get_ontology_code_from_url
get_ontology_code_from_url
Turns out get_ontology_code_from_url
is easy to import from https://github.com/opentargets/data_pipeline/blob/master/mrtarget/modules/EFO.py#L21, which makes fix_disease_id
easy to import too.
get_uniprot2ensembl
defined in https://github.com/opentargets/data_pipeline/blob/master/mrtarget/common/LookupTables.py, which ultimately queries the gene
index. This seems to come from the dbxref_extended
field in the data sourced from uniprot-uri
. It looks like https://www.uniprot.org/docs/dbxref.txt documents how that's populated. Maybe best way to do this mapping is with https://www.uniprot.org/help/download_mapping? Could use the XML or the flat file.get_reference_ensembl_id
calls out to EvidenceManager._map_to_reference_ensembl_gene
https://github.com/opentargets/data_pipeline/blob/master/mrtarget/common/EvidenceString.py#L153
Going to be harder because it relies on targets, diseases, and eco.