Leveraging Ontologies within the National Microbiome Data Collaborative

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

Leveraging Ontologies within the National Microbiome Data Collaborative

William D. Duncan, Faiza Ahmed, Fnu Anubhav, Jeffrey Baumes, Jonathan Beezley, Mark Borkum, Lisa Bramer, Shane Canon, Patrick Chain, Danielle Christianson, Yuri Corilo, Karen Davenport, Brandon Davis, Meghan Drake, Kjiersten Fagnan, Mark Flynn, David Hays, Bin Hu, Marcel Huntemann, Julia KelliherSofya Lebedeva, Po E. Li, Mary Lipton, Chien Chi Lo, Douglas Mans, Stanton Martin, Lee Ann McCue, David Millard, Kayd Miller, Nigel Mouncey, Paul Piehowski, Elais Player Jackson, Anastasiya Prymolenna, Samuel Purvine, T. B.K. Reddy, Rachel Richardson, Migun Shakya, Montana Smith, Jagadish Chandrabose Sundaramurthi, Mark A. Miller, Deepak Unni, Pajau Vangay, Bruce Wilson, Donald Winston, Elisha Wood-Charlson, Yan Xu, Emiley Eloe-Fadrosh, Christopher J. Mungall

Research output: Contribution to journal › Conference article › peer-review

Abstract

The National Microbiome Data Collaborative (NMDC) is a multi-organizational effort to integrate microbiome data across diverse areas in environmental science. Data provided by the NMDC can then undergo advanced analysis and provide new insights into metagenomics, metatranscriptomics, metaproteomics, and metabolomics. To address these challenges, we have developed our schema using the Linked data Modeling Language (LinkML). This allows us to easily map data to existing standards and ontologies.

Original language	English
Pages (from-to)	141-143
Number of pages	3
Journal	CEUR Workshop Proceedings
Volume	3073
State	Published - 2021
Event	2021 International Conference on Biomedical Ontologies, ICBO 2021 - Bozen-Bolzano, Italy Duration: Sep 16 2021 → Sep 18 2021

Funding

This work is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Bioloicagl and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89C2NA00000133(L2ANL1),DE8-AC05-00OR227(OR2NL),5anDdE-AC05-76RL01830 (PNNL).

Funders	Funder number
Office of Bioloicagl and Environmental Research
U.S. Department of Energy
Office of Science
Biological and Environmental Research	DE-AC02-05CH11231
Lawrence Berkeley National Laboratory	OR2NL, 89C2NA00000133, L2ANL1, DE8-AC05-00OR227
Pacific Northwest National Laboratory

Keywords

Environmental metagenomics
Environmental science
Ontology

Cite this

Duncan, W. D., Ahmed, F., Anubhav, F., Baumes, J., Beezley, J., Borkum, M., Bramer, L., Canon, S., Chain, P., Christianson, D., Corilo, Y., Davenport, K., Davis, B., Drake, M., Fagnan, K., Flynn, M., Hays, D., Hu, B., Huntemann, M., ... Mungall, C. J. (2021). Leveraging Ontologies within the National Microbiome Data Collaborative. CEUR Workshop Proceedings, 3073, 141-143.

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title = "Leveraging Ontologies within the National Microbiome Data Collaborative",

abstract = "The National Microbiome Data Collaborative (NMDC) is a multi-organizational effort to integrate microbiome data across diverse areas in environmental science. Data provided by the NMDC can then undergo advanced analysis and provide new insights into metagenomics, metatranscriptomics, metaproteomics, and metabolomics. To address these challenges, we have developed our schema using the Linked data Modeling Language (LinkML). This allows us to easily map data to existing standards and ontologies.",

keywords = "Environmental metagenomics, Environmental science, Ontology",

author = "Duncan, {William D.} and Faiza Ahmed and Fnu Anubhav and Jeffrey Baumes and Jonathan Beezley and Mark Borkum and Lisa Bramer and Shane Canon and Patrick Chain and Danielle Christianson and Yuri Corilo and Karen Davenport and Brandon Davis and Meghan Drake and Kjiersten Fagnan and Mark Flynn 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 Douglas Mans and Stanton Martin and McCue, {Lee Ann} and David Millard and Kayd Miller and Nigel Mouncey and Paul Piehowski and Jackson, {Elais Player} and Anastasiya Prymolenna and Samuel Purvine and Reddy, {T. B.K.} and Rachel Richardson and Migun Shakya and Montana Smith and Sundaramurthi, {Jagadish Chandrabose} and Miller, {Mark A.} and Deepak Unni and Pajau Vangay and Bruce Wilson and Donald Winston and Elisha Wood-Charlson and Yan Xu and Emiley Eloe-Fadrosh and Mungall, {Christopher J.}",

note = "Publisher Copyright: {\textcopyright} 2021 Copyright for this paper by its authors.; 2021 International Conference on Biomedical Ontologies, ICBO 2021 ; Conference date: 16-09-2021 Through 18-09-2021",

year = "2021",

language = "English",

volume = "3073",

pages = "141--143",

journal = "CEUR Workshop Proceedings",

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Duncan, WD, Ahmed, F, Anubhav, F, Baumes, J, Beezley, J, Borkum, M, Bramer, L, Canon, S, Chain, P, Christianson, D, Corilo, Y, Davenport, K, Davis, B, Drake, M, Fagnan, K, Flynn, M, Hays, D, Hu, B, Huntemann, M, Kelliher, J, Lebedeva, S, Li, PE, Lipton, M, Lo, CC, Mans, D, Martin, S, McCue, LA, Millard, D, Miller, K, Mouncey, N, Piehowski, P, Jackson, EP, Prymolenna, A, Purvine, S, Reddy, TBK, Richardson, R, Shakya, M, Smith, M, Sundaramurthi, JC, Miller, MA, Unni, D, Vangay, P, Wilson, B, Winston, D, Wood-Charlson, E, Xu, Y, Eloe-Fadrosh, E & Mungall, CJ 2021, 'Leveraging Ontologies within the National Microbiome Data Collaborative', CEUR Workshop Proceedings, vol. 3073, pp. 141-143.

TY - JOUR

T1 - Leveraging Ontologies within the National Microbiome Data Collaborative

AU - Duncan, William D.

AU - Ahmed, Faiza

AU - Anubhav, Fnu

AU - Baumes, Jeffrey

AU - Beezley, Jonathan

AU - Borkum, Mark

AU - Bramer, Lisa

AU - Canon, Shane

AU - Chain, Patrick

AU - Christianson, Danielle

AU - Corilo, Yuri

AU - Davenport, Karen

AU - Davis, Brandon

AU - Drake, Meghan

AU - Fagnan, Kjiersten

AU - Flynn, Mark

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 - Mans, Douglas

AU - Martin, Stanton

AU - McCue, Lee Ann

AU - Millard, David

AU - Miller, Kayd

AU - Mouncey, Nigel

AU - Piehowski, Paul

AU - Jackson, Elais Player

AU - Prymolenna, Anastasiya

AU - Purvine, Samuel

AU - Reddy, T. B.K.

AU - Richardson, Rachel

AU - Shakya, Migun

AU - Smith, Montana

AU - Sundaramurthi, Jagadish Chandrabose

AU - Miller, Mark A.

AU - Unni, Deepak

AU - Vangay, Pajau

AU - Wilson, Bruce

AU - Winston, Donald

AU - Wood-Charlson, Elisha

AU - Xu, Yan

AU - Eloe-Fadrosh, Emiley

AU - Mungall, Christopher J.

PY - 2021

Y1 - 2021

N2 - The National Microbiome Data Collaborative (NMDC) is a multi-organizational effort to integrate microbiome data across diverse areas in environmental science. Data provided by the NMDC can then undergo advanced analysis and provide new insights into metagenomics, metatranscriptomics, metaproteomics, and metabolomics. To address these challenges, we have developed our schema using the Linked data Modeling Language (LinkML). This allows us to easily map data to existing standards and ontologies.

AB - The National Microbiome Data Collaborative (NMDC) is a multi-organizational effort to integrate microbiome data across diverse areas in environmental science. Data provided by the NMDC can then undergo advanced analysis and provide new insights into metagenomics, metatranscriptomics, metaproteomics, and metabolomics. To address these challenges, we have developed our schema using the Linked data Modeling Language (LinkML). This allows us to easily map data to existing standards and ontologies.

KW - Environmental metagenomics

KW - Environmental science

KW - Ontology

UR - http://www.scopus.com/inward/record.url?scp=85124417247&partnerID=8YFLogxK

M3 - Conference article

AN - SCOPUS:85124417247

SN - 1613-0073

VL - 3073

SP - 141

EP - 143

JO - CEUR Workshop Proceedings

JF - CEUR Workshop Proceedings

T2 - 2021 International Conference on Biomedical Ontologies, ICBO 2021

Y2 - 16 September 2021 through 18 September 2021

ER -

Leveraging Ontologies within the National Microbiome Data Collaborative

Abstract

Funding

Keywords

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