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PanDrugsDB

Pandrugs is a bioinformatics platform to prioritize anticancer drug treatments according to individual genomic data. Its database version 2.0 integrates data from 23 primary sources.

The code to generate its content and the annotations for VCF files is available in this github repository.

This workflow summarizes PanDrugsDB composition and the steps implemented for its construction.

workflow

In this table are described the sources included in the database and in the annotation process along with versions and license.

Source Version/Access Date*/DOI License Retrieved Information
CIViC v2022-07-01 CC0 1.0 Drug-gene associations; Drug-gene annotations
DGIdb v4.2.0 MIT Drug-gene associations
DrugBank v5.1.9 CC BY-NC 4.0 Drug-gene associations
GDSC v8.2 CC BY-NC-ND 2.5 Drug-gene associations; Drug-gene annotations
MOAlmanac v2022-03-03 GPLv2 Drug-gene associations; Drug-gene annotations
OncoKB v3.14 Free for academic use Drug-gene associations; Drug-gene annotations; Gene annotations
Thera-SAbDab 2022-06-21 CC BY 4.0 Drug-gene associations
PubChem 2022-11-29 Free Drug standardisation
HGNC v2022-10-01 CC0 1.0 Gene standardisation
ClinicalTrials.gov 2022-03-15 Free Drug annotations
CLUE v1.2; build 1.44 CC BY 4.0 Drug annotations
Drugs@FDA 2022-03-14 Free Drug annotations
EMA 2022-05-31 Free Drug annotations
FDA Drug Labels 2022-06-01 CC0 1.0 Drug annotations
KEGG BRITE v101 Free for academic use Drug annotations
COSMIC's CGC v95 Free for non-commercial use Gene annotations
DepMap v22Q2 CC BY 4.0 Gene annotations; GScore calculation
KEGG PATHWAY v103 Free for academic use Gene annotations; Variant annotations
OncoVar v1.2 Free for non-commercial use Gene annotations; GScore calculation
Cancer Hallmarks 10.1038/s41598-018-25076-6 CC BY 4.0 GScore calculation
TDLs 10.1016/j.celrep.2022.110400 CC BY-NC-ND 4.0 GScore calculation
ClinVar v2022-05 Free Variant annotations
COSMIC v96 Free for non-commercial use Variant annotations
Domains 10.1371/journal.pcbi.1004147 CC BY 4.0 Variant annotations
InterPro v88.0 CC0 1.0 Variant annotations
Pfam v35.0 CC0 1.0 Variant annotations
UniProt v2022_01 CC BY 4.0 Variant annotations
VEP v109 Apache-2.0 Variant annotations
  • Dates are displayed in ISO 8601 standard format: YYYY-MM-DD.

Synthethic letal pairs

SL pairs are generated separately from the database and then merged back to the databse. The code responsible for generating and updating these pairs is stored here.