Evidence map›Paper›PMID 39235746›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

A Comprehensive Guide to Quality Assessment and Data Submission for Genomic Surveillance of Enteric Pathogens.

Ruth E Timme, Tina Pfefer, C Hope Bias, Marc W Allard, Xinyang Huang, Errol Strain, Maria Balkey

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. Genomic Surveillance of Foodborne Pathogens: Advances and Obstacles.Journal of public health management and practice : JPHMP
    Article
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

7 authors.

Ruth E TimmeCenter for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA. ruth.timme@fda.hhs.gov.
Tina PfeferCenter for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA.
C Hope BiasOak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, TN, USA.
Marc W AllardCenter for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA.
Xinyang HuangJoint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland - College Park, College Park, MD, USA.
Errol StrainCenter for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA.
Maria BalkeyCenter for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

This document outlines the steps necessary to assemble and submit the standard data package required for contributing to the global genomic surveillance of enteric pathogens. Although targeted to GenomeTrakr laboratories and collaborators, these protocols are broadly applicable for enteric pathogens collected for different purposes. There are five protocols included in this chapter: (1) quality control (QC) assessment for the genome sequence data, (2) validation for the contextual data, (3) data submission for the standard pathogen package or Pathogen Data Object Model (DOM) to the public repository, (4) viewing and querying data at NCBI, and (5) data curation for maintaining relevance of public data. The data are available through one of the International Nucleotide Sequence Database Consortium (INSDC) members, with the National Center for Biotechnology Information (NCBI) being the primary focus of this document. NCBI Pathogen Detection is a custom dashboard at NCBI that provides easy access to pathogen data plus results for a standard suite of automated cluster and genotyping analyses important for informing public health and regulatory decision-making.

Indexed as

GenomicsQuality ControlDatabases, GeneticData CurationGenome, BacterialHumansSoftwareFoodborne pathogensGenomeTrakrGenomicsPathogen genomic surveillanceSurveillanceWGS

Identifiers

PMID39235746

What OpenQuestion 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 OpenQuestion graph.