Evidence map›Paper›PMID 36303775›Full record

ReviewFrontiers in bioinformatics2021

Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.

Bin Hu, Shane Canon, Emiley A Eloe-Fadrosh, Anubhav, Michal Babinski, Yuri Corilo, Karen Davenport, William D Duncan, Kjiersten Fagnan, Mark Flynn and 18 more

Open access · goldAbstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Frontiers in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
9.7field-weighted citation impact, top 3% of its field
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

13 citing papers in PubMed, 24 citations in OpenAlex.

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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

28 authors at 4 institutions in 1 country.

Bin HuBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Shane CanonLawrence Berkeley National Laboratory, Berkeley, CA, United States.
Emiley A Eloe-FadroshLawrence Berkeley National Laboratory, Berkeley, CA, United States.
AnubhavEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
Michal BabinskiBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Yuri CoriloEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
Karen DavenportBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
William D DuncanLawrence Berkeley National Laboratory, Berkeley, CA, United States.
Kjiersten FagnanLawrence Berkeley National Laboratory, Berkeley, CA, United States.
Mark FlynnBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Brian FosterLawrence Berkeley National Laboratory, Berkeley, CA, United States.
David HaysLawrence Berkeley National Laboratory, Berkeley, CA, United States.
Marcel HuntemannLawrence Berkeley National Laboratory, Berkeley, CA, United States.
Elais K Player JacksonBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Julia KelliherBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Po-E LiBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Chien-Chi LoBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Douglas MansEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
Lee Ann McCueEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
Nigel MounceyLawrence Berkeley National Laboratory, Berkeley, CA, United States.
Christopher J MungallLawrence Berkeley National Laboratory, Berkeley, CA, United States.
Paul D PiehowskiEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
Samuel O PurvineEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
Montana SmithEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
Neha Jacob VargheseLawrence Berkeley National Laboratory, Berkeley, CA, United States.
Donald WinstonPolyneme LLC, New York, NY, United States.
Yan XuBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Patrick S G ChainBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Lawrence Berkeley National Laboratory · USLos Alamos National Laboratory · USPacific Northwest National Laboratory · USEnvironmental Molecular Sciences Laboratory · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.

Indexed as

bioinformaticsinfrastructuremicrobial ecologymicrobiomeomics

Identifiers

PMID36303775
PMCPMC9580927
OpenAlexW4205739714

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.