Evidence map›Paper›PMID 39963423›Full record

ArticleComputational and structural biotechnology journal2024

Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.

Julia M Kelliher, Yan Xu, Mark C Flynn, Michal Babinski, Shane Canon, Eric Cavanna, Alicia Clum, Yuri E Corilo, Grant Fujimoto, Cameron Giberson and 20 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

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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

30 authors.

Julia M KelliherBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Yan XuBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Mark C FlynnBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Michal BabinskiBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Shane CanonEnvironmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Eric CavannaEnvironmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Alicia ClumEnvironmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Yuri E CoriloPacific Northwest National Laboratory, Richland, WA, USA.
Grant FujimotoPacific Northwest National Laboratory, Richland, WA, USA.
Cameron GibersonPacific Northwest National Laboratory, Richland, WA, USA.
Leah Y D JohnsonBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Kaitlyn J LiBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Po-E LiBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Valerie LiBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Chien-Chi LoBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Wendi LynchEnvironmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Paul PiehowskiPacific Northwest National Laboratory, Richland, WA, USA.
Kaelan PrimeBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Samuel PurvinePacific Northwest National Laboratory, Richland, WA, USA.
Francisca RodriguezBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Simon RouxEnvironmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Migun ShakyaBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Montana SmithPacific Northwest National Laboratory, Richland, WA, USA.
Setareh SarrafanEnvironmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Shreyas CholiaEnvironmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Lee Ann McCuePacific Northwest National Laboratory, Richland, WA, USA.
Chris MungallEnvironmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Bin HuBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Emiley A Eloe-FadroshEnvironmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Patrick S G ChainBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Accessible and easy-to-use standardized bioinformatics workflows are necessary to advance microbiome research from observational studies to large-scale, data-driven approaches. Standardized multi-omics data enables comparative studies, data reuse, and applications of machine learning to model biological processes. To advance broad accessibility of standardized multi-omics bioinformatics workflows, the National Microbiome Data Collaborative (NMDC) has developed the Empowering the Development of Genomics Expertise (NMDC EDGE) resource, a user-friendly, open-source web application (https://nmdc-edge.org). Here, we describe the design and main functionality of the NMDC EDGE resource for processing metagenome, metatranscriptome, natural organic matter, and metaproteome data. The architecture relies on three main layers (web application, orchestration, and execution) to ensure flexibility and expansion to future workflows. The orchestration and execution layers leverage best practices in software containers and accommodate high-performance computing and cloud computing services. Further, we have adopted a robust user research process to collect feedback for continuous improvement of the resource. NMDC EDGE provides an accessible interface for researchers to process multi-omics microbiome data using production-quality workflows to facilitate improved data standardization and interoperability.

Indexed as

Bioinformatics workflowsMicrobiomeMulti-omicsOpen-sourceSoftwareStandardization

Identifiers

PMID39963423
PMCPMC11832004

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.