GlyGen Variation TSV Release 2020_03
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* dbSNP-homo-sapiens.tsv.gz
* dbSNP-mus-musculus.tsv.gz
* dbSNP-rattus-norvegicus.tsv.gz


Variation data is from UniProt using API calls:
curl -X GET --header 'Accept:application/json' 'https://www.ebi.ac.uk/proteins/api/variation?offset=0&size=-1&taxid=9606' > UP000005640_9606.dbSnp.json
curl -X GET --header 'Accept:application/json' 'https://www.ebi.ac.uk/proteins/api/variation?offset=0&size=-1&taxid=10090' > UP000000589_10090.dbSnp.json
curl -X GET --header 'Accept:application/json' 'https://www.ebi.ac.uk/proteins/api/variation?offset=0&size=-1&taxid=10116' > UP000002494_10116.dbSnp.json


Input JSON is parsed to get 30 columns:
> uniprotkb_accession	
> gene_name	
> protein_name	
> data_source  [list of comma separated data source names for given dbsnp_id]
> dbsnp_id	
> cosmic_id
> description  [variant description]
> evidence_ECO:0000269	[list of comma separated variant_evidence_database_name:variant_evidence_database_id for ECO:0000269]
> evidence_ECO:0000313  [list of comma separated variant_evidence_database_name:variant_evidence_database_id for ECO:0000313]
> cytogenic_band
> chromosome_id
> position
> ref_allele
> alt_allele
> ref_aa
> alt_aa
> begin_aa_pos
> end_aa_pos
> frequency
> mutation_type
> polyphen_score
> polyphen_prediction
> sift_score
> sift_prediction
> somatic_status [1 - somatic variant, 0 - germline]
> disease
> disease_description
> disease_xrefs [list of comma separated disease_xref_database:disease_xref_database_id (per disease)]
> disease_evidence_ECO:0000269 [list of comma separated disease_evidence_database_name:disease_evidence_database_id for ECO:0000269]
> disease_evidence_ECO:0000313 [list of comma separated disease_evidence_database_name:disease_evidence_database_id for ECO:0000313]


A variant info is included in dataset only if it has
> valid dbSNP id starting with rs OR valid cosmic id starting with COSM
> valid genomic location starting with NC

Each variant may have zero or more diseases. Each row in dataset corresponds to zero or one disease info with complete variant info.