Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale
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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-01-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2021.826370/full |
| _version_ | 1828137534909054976 |
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| author | Bin Hu Shane Canon Emiley A. Eloe-Fadrosh Anubhav Michal Babinski Yuri Corilo Karen Davenport William D. Duncan Kjiersten Fagnan Mark Flynn Brian Foster David Hays Marcel Huntemann Elais K. Player Jackson Julia Kelliher Po-E. Li Chien-Chi Lo Douglas Mans Lee Ann McCue Nigel Mouncey Christopher J. Mungall Paul D. Piehowski Samuel O. Purvine Montana Smith Neha Jacob Varghese Donald Winston Yan Xu Patrick S. G. Chain |
| author_facet | Bin Hu Shane Canon Emiley A. Eloe-Fadrosh Anubhav Michal Babinski Yuri Corilo Karen Davenport William D. Duncan Kjiersten Fagnan Mark Flynn Brian Foster David Hays Marcel Huntemann Elais K. Player Jackson Julia Kelliher Po-E. Li Chien-Chi Lo Douglas Mans Lee Ann McCue Nigel Mouncey Christopher J. Mungall Paul D. Piehowski Samuel O. Purvine Montana Smith Neha Jacob Varghese Donald Winston Yan Xu Patrick S. G. Chain |
| author_sort | Bin Hu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T18:21:28Z |
| format | Article |
| id | doaj.art-dc6956a6b3c54bc0a65af4d854b974d9 |
| institution | Directory Open Access Journal |
| issn | 2673-7647 |
| language | English |
| last_indexed | 2024-04-11T18:21:28Z |
| publishDate | 2022-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj.art-dc6956a6b3c54bc0a65af4d854b974d92022-12-22T04:09:45ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472022-01-01110.3389/fbinf.2021.826370826370Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at ScaleBin Hu0Shane Canon1Emiley A. Eloe-Fadrosh2 Anubhav3Michal Babinski4Yuri Corilo5Karen Davenport6William D. Duncan7Kjiersten Fagnan8Mark Flynn9Brian Foster10David Hays11Marcel Huntemann12Elais K. Player Jackson13Julia Kelliher14Po-E. Li15Chien-Chi Lo16Douglas Mans17Lee Ann McCue18Nigel Mouncey19Christopher J. Mungall20Paul D. Piehowski21Samuel O. Purvine22Montana Smith23Neha Jacob Varghese24Donald Winston25Yan Xu26Patrick S. G. Chain27Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United StatesEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United StatesEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United StatesEnvironmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United StatesLawrence Berkeley National Laboratory, Berkeley, CA, United StatesPolyneme LLC, New York, NY, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United StatesThe 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.https://www.frontiersin.org/articles/10.3389/fbinf.2021.826370/fullmicrobiomemicrobial ecologyomicsbioinformaticsinfrastructure |
| spellingShingle | Bin Hu Shane Canon Emiley A. Eloe-Fadrosh Anubhav Michal Babinski Yuri Corilo Karen Davenport William D. Duncan Kjiersten Fagnan Mark Flynn Brian Foster David Hays Marcel Huntemann Elais K. Player Jackson Julia Kelliher Po-E. Li Chien-Chi Lo Douglas Mans Lee Ann McCue Nigel Mouncey Christopher J. Mungall Paul D. Piehowski Samuel O. Purvine Montana Smith Neha Jacob Varghese Donald Winston Yan Xu Patrick S. G. Chain Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale Frontiers in Bioinformatics microbiome microbial ecology omics bioinformatics infrastructure |
| title | Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale |
| title_full | Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale |
| title_fullStr | Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale |
| title_full_unstemmed | Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale |
| title_short | Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale |
| title_sort | challenges in bioinformatics workflows for processing microbiome omics data at scale |
| topic | microbiome microbial ecology omics bioinformatics infrastructure |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2021.826370/full |
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