Evidence map›Paper›PMID 37894214›Full record

ArticleMicroorganisms2023

CPGminer: An Interactive Dashboard to Explore the Genomic Features and Taxonomy of Complete Prokaryotic Genomes.

Jaehyun Kim, Sunghyun Yoon, Sandeep Kondakala, Steven L Foley, Mark Hart, Dong-Heon Baek, Wenjun Wang, Sung-Kwan Kim, John B Sutherland, Seong-Jae Kim and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microorganisms, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

11 authors.

Jaehyun KimDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
Sunghyun YoonDivision of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.ORCID 0000-0003-2460-8080
Sandeep KondakalaDivision of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.ORCID 0000-0003-3958-7104
Steven L FoleyDivision of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
Mark HartDivision of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
Dong-Heon BaekDepartment of Oral Microbiology and Immunology, School of Dentistry, Dankook University, Cheonan 31116, Republic of Korea.
Wenjun WangDepartment of Management, Marketing, and Technology, University of Arkansas at Little Rock, Little Rock, AR 72204, USA.ORCID 0000-0002-1987-1119
Sung-Kwan KimDepartment of Management, Marketing, and Technology, University of Arkansas at Little Rock, Little Rock, AR 72204, USA.
John B SutherlandDivision of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
Seong-Jae KimDivision of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.ORCID 0000-0002-9793-3186
Ohgew KweonDivision of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Prokaryotes, the earliest forms of life on Earth, play crucial roles in global biogeochemical processes in virtually all ecosystems. The ever-increasing amount of prokaryotic genome sequencing data provides a wealth of information to examine fundamental and applied questions through systematic genome comparison. Genomic features, such as genome size and GC content, and taxonomy-centric genomic features of complete prokaryotic genomes (CPGs) are crucial for various fields of microbial research and education, yet they are often overlooked. Additionally, creating systematically curated datasets that align with research concerns is an essential yet challenging task for wet-lab researchers. In this study, we introduce CPGminer, a user-friendly tool that allows researchers to quickly and easily examine the genomic features and taxonomy of CPGs and curate genome datasets. We also provide several examples to demonstrate its practical utility in addressing descriptive questions.

Indexed as

complete genomedashboardgenome sequencinggenomic featuresmetadataprokaryotetaxonomy

Identifiers

PMID37894214
PMCPMC10609142

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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 OpenQuestion graph.