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PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project.

About this Publication
Title
PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project.
Pubmed ID
35900159 (View this publication on the PubMed website)
Digital Object Identifier
Publication
Bioinformatics. 2022 Jul 28
Authors
Ruan E , Nemeth E , Moffitt R , Sandoval L , Machiela MJ , Freedman ND , Huang WY , Wong W , Chen KL , Park B , Jiang K , Hicks B , Liu J , Russ D , Minasian L , Pinsky P , Chanock SJ , Garcia-Closas M , Almeida JS
Affiliations
  • Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA.
  • Division of Cancer Epidemiology and Genetics (DCEG).
  • Center for Biomedical Informatics and Information Technology (CBIIT).
  • Division of Cancer Prevention; National Cancer Institute, Rockville, MD, USA.
Abstract

MOTIVATION: The Division of Cancer Epidemiology and Genetics (DCEG) and the Division of Cancer Prevention (DCP) at the National Cancer Institute (NCI) have recently generated genome-wide association study (GWAS) data for multiple traits in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Genomic Atlas project. The GWAS included 110,000 participants. The dissemination of the genetic association data through a data portal called GWAS Explorer, in a manner that addresses the modern expectations of FAIR reusability by data scientists and engineers, is the main motivation for the development of the open-source JavaScript Software Development Kit (SDK) reported here.

RESULTS: The PLCO GWAS Explorer resource relies on a public stateless HTTP API deployed as the sole backend service for both the landing page's web application and third-party analytical workflows. The core PLCOjs SDK is mapped to each of the API methods, and also to each of the reference graphic visualizations in the GWAS Explorer. A few additional visualization methods extend it. As is the norm with Web SDKs, no download or installation is needed and modularization supports targeted code injection for web applications, reactive notebooks (Observable) and node-based Web services.

AVAILABILITY: code at https://github.com/episphere/plco; project page at https://episphere.github.io/plco.

SUPPLEMENTARY INFORMATION: Tutorial at https://youtu.be/87dXT9YtbfY (17 mins).

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