ProtVar Xref Template from GlyGen-ProtVar

[jeet-vora]

Preethi to share Xref Template from GlyGen-ProtVar

[pkay47]

ProtVar can be linked by using

search terms using dbSNP id rs780386537 of P14210-1 https://www.ebi.ac.uk/ProtVar/query?search=rs780386537

genomic coordinates using Chr7:81762762C> of P14210-1 https://www.ebi.ac.uk/ProtVar/query?chromosome=7&genomic_position=81762762&reference_allele=C&alternative_allele=T

protein accession and position using position 67, reference & variant amino acid A->S of P14210 https://www.ebi.ac.uk/ProtVar/query?accession=P14210&protein_position=67&reference_AA=A&variant_AA=S

can also have comma separated combination of terms https://www.ebi.ac.uk/ProtVar/query?search=rs864622779,X%20149498202%20C%20G,P22309%2071%20Gly%20Arg

Source: 'Direct variant Link Help' in https://www.ebi.ac.uk/ProtVar/help

[jeet-vora]

Some GlyGen variatiats do not have entry in ProtVar eg P00533 229 | 229 | S → C

Is there a list of entries in ProtVar or can the xrefs be validated against entries?

[pkay47]

ProtVar API - Genomic Coordinate – Amino Acid Position Mappings can be used.

Input list of variants, uniprot accession, position & variant info. Sample input with one correct & one incorrect input [ "P00533 S229C", "P00533 S1229C" ]

If no mapping, error message is displayed

[pkay47]

@jeet-vora please let me know if more info is required.

[jeet-vora]

We need to discuss this for maybe 2.7

We can generate ProtVar xrefs but I am not sure all generated xrefs will be valid because some data won't exist in ProtVar