The National Microbiome Data Collaborative Data Portal: An integrated multi-omics microbiome data resource

Emiley A. Eloe-Fadrosh; Faiza Ahmed; Anubhav; Michal Babinski; Jeffrey Baumes; Mark Borkum; Lisa Bramer; Shane Canon; Danielle S. Christianson; Yuri E. Corilo; Karen W. Davenport; Brandon Davis; Meghan Drake; William D. Duncan; Mark C. Flynn; David Hays; Bin Hu; Marcel Huntemann; Julia Kelliher; Sofya Lebedeva; Po E. Li; Mary Lipton; Chien Chi Lo; Stanton Martin; David Millard; Kayd Miller; Mark A. Miller; Paul Piehowski; Elais Player Jackson; Samuel Purvine; T. B.K. Reddy; Rachel Richardson; Marisa Rudolph; Setareh Sarrafan; Migun Shakya; Montana Smith; Kelly Stratton; Jagadish Chandrabose Sundaramurthi; Pajau Vangay; Donald Winston; Elisha M. Wood-Charlson; Yan Xu; Patrick S.G. Chain; Lee Ann McCue; Douglas Mans; Christopher J. Mungall; Nigel J. Mouncey; Kjiersten Fagnan

doi:10.1093/nar/gkab990

The National Microbiome Data Collaborative Data Portal: An integrated multi-omics microbiome data resource

Emiley A. Eloe-Fadrosh, Faiza Ahmed, Anubhav, Michal Babinski, Jeffrey Baumes, Mark Borkum, Lisa Bramer, Shane Canon, Danielle S. Christianson, Yuri E. Corilo, Karen W. Davenport, Brandon Davis, Meghan Drake, William D. Duncan, Mark C. Flynn, David Hays, Bin Hu, Marcel Huntemann, Julia Kelliher, Sofya LebedevaPo E. Li, Mary Lipton, Chien Chi Lo, Stanton Martin, David Millard, Kayd Miller, Mark A. Miller, Paul Piehowski, Elais Player Jackson, Samuel Purvine, T. B.K. Reddy, Rachel Richardson, Marisa Rudolph, Setareh Sarrafan, Migun Shakya, Montana Smith, Kelly Stratton, Jagadish Chandrabose Sundaramurthi, Pajau Vangay, Donald Winston, Elisha M. Wood-Charlson, Yan Xu, Patrick S.G. Chain, Lee Ann McCue, Douglas Mans, Christopher J. Mungall, Nigel J. Mouncey, Kjiersten Fagnan

Computational and Predictive Biology

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

Abstract

The National Microbiome Data Collaborative (NMDC) Data Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed data framework aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles (1). The NMDC Data Portal currently hosts 10.2 terabytes of multi-omics microbiome data, spanning five data types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, and natural organic matter characterizations), generated at two Department of Energy User Facilities, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (LBNL) and the Environmental Molecular Systems Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). A flexible data schema (https://github.com/microbiomedata/nmdc-schema) leveraging community-driven standards underpins how data is managed and integrated. Annotated multi-omic data products are produced by the NMDC workflows and linked through common biosamples to enable search capabilities based on environmental context, instrumentation, and functional attributes. As a pilot system, the NMDC Data Portal offers download capabilities and several search components, including interactive geographic visualization of samples; environmental classification distribution visualized through an interactive Sankey diagram; time-series slider to select longitudinal samples of interest; and an upset plot displaying the number of multi-omics data generated from the same biosample within a study.

Original language	English
Pages (from-to)	D828-D836
Journal	Nucleic Acids Research
Volume	50
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkab990
State	Published - Jan 7 2022

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Eloe-Fadrosh, E. A., Ahmed, F., Anubhav, Babinski, M., Baumes, J., Borkum, M., Bramer, L., Canon, S., Christianson, D. S., Corilo, Y. E., Davenport, K. W., Davis, B., Drake, M., Duncan, W. D., Flynn, M. C., Hays, D., Hu, B., Huntemann, M., Kelliher, J., ... Fagnan, K. (2022). The National Microbiome Data Collaborative Data Portal: An integrated multi-omics microbiome data resource. Nucleic Acids Research, 50(D1), D828-D836. https://doi.org/10.1093/nar/gkab990

@article{54ac6408bc2d45888612835d53206e7a,

title = "The National Microbiome Data Collaborative Data Portal: An integrated multi-omics microbiome data resource",

abstract = "The National Microbiome Data Collaborative (NMDC) Data Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed data framework aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles (1). The NMDC Data Portal currently hosts 10.2 terabytes of multi-omics microbiome data, spanning five data types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, and natural organic matter characterizations), generated at two Department of Energy User Facilities, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (LBNL) and the Environmental Molecular Systems Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). A flexible data schema (https://github.com/microbiomedata/nmdc-schema) leveraging community-driven standards underpins how data is managed and integrated. Annotated multi-omic data products are produced by the NMDC workflows and linked through common biosamples to enable search capabilities based on environmental context, instrumentation, and functional attributes. As a pilot system, the NMDC Data Portal offers download capabilities and several search components, including interactive geographic visualization of samples; environmental classification distribution visualized through an interactive Sankey diagram; time-series slider to select longitudinal samples of interest; and an upset plot displaying the number of multi-omics data generated from the same biosample within a study.",

author = "Eloe-Fadrosh, {Emiley A.} and Faiza Ahmed and Anubhav and Michal Babinski and Jeffrey Baumes and Mark Borkum and Lisa Bramer and Shane Canon and Christianson, {Danielle S.} and Corilo, {Yuri E.} and Davenport, {Karen W.} and Brandon Davis and Meghan Drake and Duncan, {William D.} and Flynn, {Mark C.} and David Hays and Bin Hu and Marcel Huntemann and Julia Kelliher and Sofya Lebedeva and Li, {Po E.} and Mary Lipton and Lo, {Chien Chi} and Stanton Martin and David Millard and Kayd Miller and Miller, {Mark A.} and Paul Piehowski and Jackson, {Elais Player} and Samuel Purvine and Reddy, {T. B.K.} and Rachel Richardson and Marisa Rudolph and Setareh Sarrafan and Migun Shakya and Montana Smith and Kelly Stratton and Sundaramurthi, {Jagadish Chandrabose} and Pajau Vangay and Donald Winston and Wood-Charlson, {Elisha M.} and Yan Xu and Chain, {Patrick S.G.} and McCue, {Lee Ann} and Douglas Mans and Mungall, {Christopher J.} and Mouncey, {Nigel J.} and Kjiersten Fagnan",

note = "Publisher Copyright: {\textcopyright} 2022 Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2022",

month = jan,

day = "7",

doi = "10.1093/nar/gkab990",

language = "English",

volume = "50",

pages = "D828--D836",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

Eloe-Fadrosh, EA, Ahmed, F, Anubhav, Babinski, M, Baumes, J, Borkum, M, Bramer, L, Canon, S, Christianson, DS, Corilo, YE, Davenport, KW, Davis, B, Drake, M, Duncan, WD, Flynn, MC, Hays, D, Hu, B, Huntemann, M, Kelliher, J, Lebedeva, S, Li, PE, Lipton, M, Lo, CC, Martin, S, Millard, D, Miller, K, Miller, MA, Piehowski, P, Jackson, EP, Purvine, S, Reddy, TBK, Richardson, R, Rudolph, M, Sarrafan, S, Shakya, M, Smith, M, Stratton, K, Sundaramurthi, JC, Vangay, P, Winston, D, Wood-Charlson, EM, Xu, Y, Chain, PSG, McCue, LA, Mans, D, Mungall, CJ, Mouncey, NJ & Fagnan, K 2022, 'The National Microbiome Data Collaborative Data Portal: An integrated multi-omics microbiome data resource', Nucleic Acids Research, vol. 50, no. D1, pp. D828-D836. https://doi.org/10.1093/nar/gkab990

TY - JOUR

T1 - The National Microbiome Data Collaborative Data Portal

T2 - An integrated multi-omics microbiome data resource

AU - Eloe-Fadrosh, Emiley A.

AU - Ahmed, Faiza

AU - Anubhav,

AU - Babinski, Michal

AU - Baumes, Jeffrey

AU - Borkum, Mark

AU - Bramer, Lisa

AU - Canon, Shane

AU - Christianson, Danielle S.

AU - Corilo, Yuri E.

AU - Davenport, Karen W.

AU - Davis, Brandon

AU - Drake, Meghan

AU - Duncan, William D.

AU - Flynn, Mark C.

AU - Hays, David

AU - Hu, Bin

AU - Huntemann, Marcel

AU - Kelliher, Julia

AU - Lebedeva, Sofya

AU - Li, Po E.

AU - Lipton, Mary

AU - Lo, Chien Chi

AU - Martin, Stanton

AU - Millard, David

AU - Miller, Kayd

AU - Miller, Mark A.

AU - Piehowski, Paul

AU - Jackson, Elais Player

AU - Purvine, Samuel

AU - Reddy, T. B.K.

AU - Richardson, Rachel

AU - Rudolph, Marisa

AU - Sarrafan, Setareh

AU - Shakya, Migun

AU - Smith, Montana

AU - Stratton, Kelly

AU - Sundaramurthi, Jagadish Chandrabose

AU - Vangay, Pajau

AU - Winston, Donald

AU - Wood-Charlson, Elisha M.

AU - Xu, Yan

AU - Chain, Patrick S.G.

AU - McCue, Lee Ann

AU - Mans, Douglas

AU - Mungall, Christopher J.

AU - Mouncey, Nigel J.

AU - Fagnan, Kjiersten

PY - 2022/1/7

Y1 - 2022/1/7

N2 - The National Microbiome Data Collaborative (NMDC) Data Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed data framework aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles (1). The NMDC Data Portal currently hosts 10.2 terabytes of multi-omics microbiome data, spanning five data types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, and natural organic matter characterizations), generated at two Department of Energy User Facilities, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (LBNL) and the Environmental Molecular Systems Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). A flexible data schema (https://github.com/microbiomedata/nmdc-schema) leveraging community-driven standards underpins how data is managed and integrated. Annotated multi-omic data products are produced by the NMDC workflows and linked through common biosamples to enable search capabilities based on environmental context, instrumentation, and functional attributes. As a pilot system, the NMDC Data Portal offers download capabilities and several search components, including interactive geographic visualization of samples; environmental classification distribution visualized through an interactive Sankey diagram; time-series slider to select longitudinal samples of interest; and an upset plot displaying the number of multi-omics data generated from the same biosample within a study.

AB - The National Microbiome Data Collaborative (NMDC) Data Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed data framework aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles (1). The NMDC Data Portal currently hosts 10.2 terabytes of multi-omics microbiome data, spanning five data types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, and natural organic matter characterizations), generated at two Department of Energy User Facilities, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (LBNL) and the Environmental Molecular Systems Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). A flexible data schema (https://github.com/microbiomedata/nmdc-schema) leveraging community-driven standards underpins how data is managed and integrated. Annotated multi-omic data products are produced by the NMDC workflows and linked through common biosamples to enable search capabilities based on environmental context, instrumentation, and functional attributes. As a pilot system, the NMDC Data Portal offers download capabilities and several search components, including interactive geographic visualization of samples; environmental classification distribution visualized through an interactive Sankey diagram; time-series slider to select longitudinal samples of interest; and an upset plot displaying the number of multi-omics data generated from the same biosample within a study.

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U2 - 10.1093/nar/gkab990

DO - 10.1093/nar/gkab990

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JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

The National Microbiome Data Collaborative Data Portal: An integrated multi-omics microbiome data resource

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