Laura Harris

decided not to to this at the moment as we are not loading data until new technology is implemented

Is this issue still outstanding @sajo-ebi

Putting this on ice for now as we are getting closer to generating reports in DepoCuration

@sajo-ebi In order to know whether this is an issue or not, I need to understand how the UPSTREAM_GENE_ID, DOWNSTREAM_GENE_ID and SNP_GENE_ID columns are generated. I suspect the mapping is...

@sprintell I need the process flow documentation to define this issue properly

Thanks @sajo-ebi. To clarify in step 2, "get overlapping genes", is this the gene name? And then the final step is to retrieve the ensembl id for the retrieved genes?

@ljwh2 to investigate further and provide Sajo with rsIDs to investigate

Some examples: rs5758209. This has genomic location chr22:41065861, upstream gene Y_RNA. Upstream gene ID is ENSG00000201314, but this ID maps to a genomic location on chr4. rs1705773 SNP maps to...

The problem is that there are several genes all called Y_RNA on different genomic locations, each having a different gene ID. But we give the same gene ID for all....

Note that these cannot be edited in the depocuration UI as the special characters are not visible there, only in the data download files from the UI