Retrieving Therapy information from CiViC VCF files

Question

[bt_cepo]

Hi all!

I downloaded CiViC's Accepted & Submitted Variants VCF from https://civicdb.org/releases/main. The INFO column format for the variants look like this:

##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from CIViC. Format: Allele|Consequence|SYMBOL|Entrez Gene ID|Feature_type|Feature|HGVSc|HGVSp
|CIViC Variant Name|CIViC Variant ID|CIViC Variant Aliases|CIViC Variant URL|CIViC Molecular Profile Name|CIViC Molecular Profile ID|CIViC Molecular Profile Aliases|C
IViC Molecular Profile URL|CIViC HGVS|Allele Registry ID|ClinVar IDs|CIViC Molecular Profile Score|CIViC Entity Type|CIViC Entity ID|CIViC Entity URL|CIViC Entity Sou
rce|CIViC Entity Variant Origin|CIViC Entity Status|CIViC Entity Significance|CIViC Entity Direction|CIViC Entity Disease|CIViC Entity Therapies|CIViC Entity Therapy 
Interaction Type|CIViC Evidence Phenotypes|CIViC Evidence Level|CIViC Evidence Rating|CIViC Assertion ACMG Codes|CIViC Assertion AMP Category|CIViC Assertion NCCN Gui
deline|CIVIC Assertion Regulatory Approval|CIVIC Assertion FDA Companion Test">

And the first variant's annotation as an example looks like this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       8073509 691     C       A       .       .       GN=ERRFI1;VT=E384*;CSQ=A|Stop_Gained&Loss_Of_Function_Variant|ERRFI1|54206|transcript|ENST00000377482.5|||E384
*|691|E384X&GLU384TER|https://civicdb.org/links/variants/691|ERRFI1_E384*|672||https://civicdb.org/links/molecular-profiles/672|NC\x5F000001\x2E10\x3Ag\x2E8073509C\x3
EA|CA338219584|NONE_FOUND|5.0|evidence|1724|https://civicdb.org/links/evidence/1724|24550739_(PUBMED)|SOMATIC|accepted|SENSITIVITYRESPONSE|SUPPORTS|Cholangiocarcinoma
_(DOID_4947)|<CIViC_Attribute_therapie_15>|||C|2|||||

I want to ask about the CIViC Entity Therapies section where in the example it is <CIViC_Attribute_therapie_15>.

I would like to know how I can retrieve the name of the drug used in the therapy as in the database I can only find them tagged by name or NClt ID. I do not find the way to relate this "Attribute_therapie" number to the drugs in the database.

Does anyone know?

Thank you so much"!!

Answer 1

[GenoMax]

Looks like you can use the API: https://civicdb.org/therapies/15/summary

So the therapie in your example is Erlotinib.

[bt_cepo]

Thanks, that can totally make the work.