Evidence map›Paper›PMID 35900159›Full record

ArticleBioinformatics (Oxford, England)2022

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

Eric Ruan, Erika Nemeth, Richard Moffitt, Lorena Sandoval, Mitchell J Machiela, Neal D Freedman, Wen-Yi Huang, Wendy Wong, Kai-Ling Chen, Brian Park and 9 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors.

Eric RuanDepartment of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA.
Erika NemethDepartment of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA.
Richard MoffittDepartment of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA.ORCID 0000-0003-2723-5902
Lorena SandovalDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.
Mitchell J MachielaDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.
Neal D FreedmanDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.
Wen-Yi HuangDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.
Wendy WongDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.
Kai-Ling ChenCenter for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD 20850, USA.
Brian ParkCenter for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD 20850, USA.
Kevin JiangCenter for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD 20850, USA.
Belynda HicksDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.
Jia LiuDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.
Daniel RussDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.ORCID 0000-0003-4040-4416
Lori MinasianDivision of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA.
Paul PinskyDivision of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA.
Stephen J ChanockDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.
Montserrat Garcia-ClosasDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.
Jonas S AlmeidaDivision of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA.ORCID 0000-0002-7883-7922

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

motivationThe 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.

resultsThe PLCO GWAS Explorer resource relies on a public stateless HTTP application programming interface (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 AND IMPLEMENTATION: code at https://github.com/episphere/plco; project page at https://episphere.github.io/plco.

Indexed as

Colorectal NeoplasmsOvarian NeoplasmsFemaleGenome-Wide Association StudyHumansLungMaleNational Cancer Institute (U.S.)ProstateSoftwareUnited States

Identifiers

PMID35900159
PMCPMC9890300

What Socratic holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.