pharmgkb OC and website differing annotations

[iranmdl]

Hi there! I have recently started using open-cravat (oc), and I have noticed some annotations missing when using pharmgkb. For example, for variant rs1803274, when using oc I get the following columns:

ID: PA166156332
chemicals: rivastigmine;donepezil;memantine rivastigmine
Phenotype Category: Efficacy

However, when using pharmgkb website: https://www.pharmgkb.org/variant/PA166156332/clinicalAnnotation I can see other chemicals as succinylcholine that are missing when using oc.

Am I missing something?

Thank you

[jasminebro]

Hi @iranmdl . Would you mind giving us more information about your issue? What did you use for your input(If so can you provide a sample file for reproduction)? Were you using the GUI on the web or a local installation? Once you ran OC did you select any filtering features?

[iranmdl]

Hi! Sure, it has been a while since I worked with oc, but this was the command:

oc run test_oc_issue201.vcf -l hg38 -a pharmgkb -t text -n oc_issue201_cli_out -i vcf -d

• Input file: test_oc_issue201.vcf.gz
• Output: oc_issue201_cli_out.tsv.gz
• oc version: 2.4.2

[jasminebro]

Apologies, we have since updated the pharmgkb package (feb 2024). Please let me know if the issue persists.

[iranmdl]

Hi again! I just tried this again, using oc version 2.5.0, the issue is the same, I get different results when using the command line vs using the interface. The variant I have used is rs1803274.

[iranmdl]

In the webpage it says that rs1803274 variant is related with toxicity for succinylcholine, I cannot see that when using oc cli.

[RachelKarchin]

Hi iranmdi

The run.opencravat.org website has this version of PharmGKB which is updated monthly,. The current version was updated on 3/1/24 and we will soon have the April update available. Module version: 2.4.0 Data source version: 2024-03-01

However, you must update your locally installed annotators when you run OC on your local machine, either with the gui or cli. Updating your oc does not automatically update your modules.

On the cli you can check which version of pharmgkb you have installed with:

oc module info pharmgkb

It looks ike you may not have pharmgkb version 2.4.0

To update to the latest pharmgkb version

oc module update pharmgkb

You could also update all your installed modules with

oc module update

Let us know if this solves your problem!

[iranmdl]

Hi @RachelKarchin this is what I get when I run oc module info pharmgkb

oc module info pharmgkb
code_size: 32093
data_size: 3650293
data_versions:
  1.0.0: 1.0.0
  1.1.0: 1.1.0
  1.1.1: 1.1.0
  2.0.0: 2.0.0
  2.1.0: 2.1.0
  2.2.0: 2.2.0
  2.3.0: 2.3.0
  2.3.1: 2.3.1
  2.3.2: 2.3.2
  2.3.3: 2.3.3
  2.3.4: 2.3.4
  2.3.5: 2.3.5
  2.3.6: 2.3.6
  2.3.7: 2.3.7
  2.3.8: 2.3.8
  2.3.9: 2.3.9
  2.4.0: 2.4.0
datasource: '2024-03-01'
description: Clinically actionable gene-drug associations and genotype-phenotype relationships
developer:
  name: Teri E. Klein
  email: feedback@pharmgkb.org
  organization: Shriram Center for Bioengineering and Chemical Engineering
  citation: 'M. Whirl-Carrillo, E.M. McDonagh, J. M. Hebert, L. Gong, K. Sangkuhl,
    C.F. Thorn, R.B. Altman and T.E. Klein. "Pharmacogenomics Knowledge for Personalized
    Medicine" Clinical Pharmacology & Therapeutics (2012) 92(4): 414-417'
  website: https://www.pharmgkb.org/
hidden: false
latest_version: 2.4.0
name: pharmgkb
publish_time: 2024-03-11T16:07:40.449974+0000
size: 3682386
tags:
- clinical relevance
- literature
- variants
title: PharmGKB
type: annotator
versions:
- 1.0.0 (data source None)
- 1.1.0 (data source None)
- 1.1.1 (data source None)
- 2.0.0 (data source 2021-01-14)
- 2.1.0 (data source 2021-03-03)
- 2.2.0 (data source 2021-03-03)
- 2.3.0 (data source 2021-04-01)
- 2.3.1 (data source 2021-05-01)
- 2.3.2 (data source 2021-06-01)
- 2.3.3 (data source 2021-08-01)
- 2.3.4 (data source 2021-09-01)
- 2.3.5 (data source 2021-10-01)
- 2.3.6 (data source 2022-11-01)
- 2.3.7 (data source 2023-01-01)
- 2.3.8 (data source 2023-02-01)
- 2.3.9 (data source 2024-02-01)
- 2.4.0 (data source 2024-03-01)
output columns:
  ID:
  Chemicals:
  Phenotype Category:
  All Annotations:
INSTALLED
UP TO DATE