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 princip...
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| Veröffentlicht in: | Nucleic acids research 2022-01, Vol.50 (D1), p.D828-D836 |
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| creator | Eloe-Fadrosh, Emiley A Ahmed, Faiza Babinski, Michal Baumes, Jeffrey Borkum, Mark Bramer, Lisa Canon, Shane Christianson, Danielle S Corilo, Yuri E Davenport, Karen W Davis, Brandon Drake, Meghan Duncan, William D Flynn, Mark C Hays, David Hu, Bin Huntemann, Marcel Kelliher, Julia Lebedeva, Sofya Li, Po-E Lipton, Mary Lo, Chien-Chi Martin, Stanton Millard, David Miller, Kayd Miller, Mark A Piehowski, Paul Jackson, Elais Player Purvine, Samuel Reddy, T B K Richardson, Rachel Rudolph, Marisa Sarrafan, Setareh Shakya, Migun Smith, Montana Stratton, Kelly Sundaramurthi, Jagadish Chandrabose Vangay, Pajau Winston, Donald Wood-Charlson, Elisha M Xu, Yan Chain, Patrick S G McCue, Lee Ann Mans, Douglas Mungall, Christopher J Mouncey, Nigel J Fagnan, Kjiersten |
| description | 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. |
| doi_str_mv | 10.1093/nar/gkab990 |
| format | Article |
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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.</description><identifier>ISSN: 0305-1048</identifier><identifier>ISSN: 1362-4962</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkab990</identifier><language>eng</language><publisher>United States: Oxford University Press</publisher><subject>BASIC BIOLOGICAL SCIENCES ; Database Issue ; microbial ecology ; microbiome ; ontology</subject><ispartof>Nucleic acids research, 2022-01, Vol.50 (D1), p.D828-D836</ispartof><rights>Published by Oxford University Press on behalf of Nucleic Acids Research 2021. 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c383t-c1ce13e0e614900ae5f3a5fbe72fbe1cbaf26a0c449f57b279082b4a2e2fa6dc3</citedby><orcidid>0000-0001-7969-4823 ; 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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. 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(United States)</creatorcontrib><creatorcontrib>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</creatorcontrib><creatorcontrib>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</creatorcontrib><collection>CrossRef</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Eloe-Fadrosh, Emiley A</au><au>Ahmed, Faiza</au><au>Babinski, Michal</au><au>Baumes, Jeffrey</au><au>Borkum, Mark</au><au>Bramer, Lisa</au><au>Canon, Shane</au><au>Christianson, Danielle S</au><au>Corilo, Yuri E</au><au>Davenport, Karen W</au><au>Davis, Brandon</au><au>Drake, Meghan</au><au>Duncan, William D</au><au>Flynn, Mark C</au><au>Hays, David</au><au>Hu, Bin</au><au>Huntemann, Marcel</au><au>Kelliher, Julia</au><au>Lebedeva, Sofya</au><au>Li, Po-E</au><au>Lipton, Mary</au><au>Lo, Chien-Chi</au><au>Martin, Stanton</au><au>Millard, David</au><au>Miller, Kayd</au><au>Miller, Mark A</au><au>Piehowski, Paul</au><au>Jackson, Elais Player</au><au>Purvine, Samuel</au><au>Reddy, T B K</au><au>Richardson, Rachel</au><au>Rudolph, Marisa</au><au>Sarrafan, Setareh</au><au>Shakya, Migun</au><au>Smith, Montana</au><au>Stratton, Kelly</au><au>Sundaramurthi, Jagadish Chandrabose</au><au>Vangay, Pajau</au><au>Winston, Donald</au><au>Wood-Charlson, Elisha M</au><au>Xu, Yan</au><au>Chain, Patrick S G</au><au>McCue, Lee Ann</au><au>Mans, Douglas</au><au>Mungall, Christopher J</au><au>Mouncey, Nigel J</au><au>Fagnan, Kjiersten</au><aucorp>Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)</aucorp><aucorp>Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)</aucorp><aucorp>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</aucorp><aucorp>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource</atitle><jtitle>Nucleic acids research</jtitle><date>2022-01-07</date><risdate>2022</risdate><volume>50</volume><issue>D1</issue><spage>D828</spage><epage>D836</epage><pages>D828-D836</pages><issn>0305-1048</issn><issn>1362-4962</issn><eissn>1362-4962</eissn><abstract>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.</abstract><cop>United States</cop><pub>Oxford University Press</pub><doi>10.1093/nar/gkab990</doi><orcidid>https://orcid.org/0000-0001-7969-4823</orcidid><orcidid>https://orcid.org/0000-0001-9076-6066</orcidid><orcidid>https://orcid.org/0000-0003-3470-1078</orcidid><orcidid>https://orcid.org/0000-0003-4656-5480</orcidid><orcidid>https://orcid.org/0000-0001-9557-7715</orcidid><orcidid>https://orcid.org/0000-0002-6601-2165</orcidid><orcidid>https://orcid.org/0000-0002-0871-5567</orcidid><orcidid>https://orcid.org/0000-0001-6870-7289</orcidid><orcidid>https://orcid.org/0000-0002-6504-849X</orcidid><orcidid>https://orcid.org/0000-0001-5108-2227</orcidid><orcidid>https://orcid.org/0000-0003-2871-7807</orcidid><orcidid>https://orcid.org/0000-0002-9231-0692</orcidid><orcidid>https://orcid.org/0000-0001-5380-1256</orcidid><orcidid>https://orcid.org/0000-0001-7749-0077</orcidid><orcidid>https://orcid.org/0000-0003-3876-691X</orcidid><orcidid>https://orcid.org/0000-0002-8866-1625</orcidid><orcidid>https://orcid.org/0000-0001-9625-1899</orcidid><orcidid>https://orcid.org/0000-0002-1284-3748</orcidid><orcidid>https://orcid.org/0000-0002-9576-338X</orcidid><orcidid>https://orcid.org/0000-0002-1368-8217</orcidid><orcidid>https://orcid.org/0000-0003-3949-3634</orcidid><orcidid>https://orcid.org/0000-0002-4179-7648</orcidid><orcidid>https://orcid.org/0000-0003-4456-517X</orcidid><orcidid>https://orcid.org/0000-0002-8663-7701</orcidid><orcidid>https://orcid.org/0000-0003-4290-1993</orcidid><orcidid>https://orcid.org/0000-0002-2257-2400</orcidid><orcidid>https://orcid.org/0000-0002-8424-0604</orcidid><orcidid>https://orcid.org/0000-0002-8162-1276</orcidid><orcidid>https://orcid.org/0000-0001-9246-8193</orcidid><orcidid>https://orcid.org/0000-0002-8683-0050</orcidid><orcidid>https://orcid.org/0000-0002-8457-2000</orcidid><orcidid>https://orcid.org/0000-0003-4100-9119</orcidid><orcidid>https://orcid.org/0000-0002-0278-8466</orcidid><orcidid>https://orcid.org/0000-0002-9518-6236</orcidid><orcidid>https://orcid.org/0000-0002-8440-738X</orcidid><orcidid>https://orcid.org/0000-0002-8384-1926</orcidid><orcidid>https://orcid.org/0000-0002-6670-9157</orcidid><orcidid>https://orcid.org/0000-0002-2740-1344</orcidid><orcidid>https://orcid.org/0000-0001-9518-8744</orcidid><orcidid>https://orcid.org/000000029576338X</orcidid><orcidid>https://orcid.org/0000000217219688</orcidid><orcidid>https://orcid.org/0000000222572400</orcidid><orcidid>https://orcid.org/0000000283841926</orcidid><orcidid>https://orcid.org/000000034456517X</orcidid><orcidid>https://orcid.org/0000000286830050</orcidid><orcidid>https://orcid.org/0000000151082227</orcidid><orcidid>https://orcid.org/0000000177490077</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext_linktorsrc |
| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2022-01, Vol.50 (D1), p.D828-D836 |
| issn | 0305-1048 1362-4962 1362-4962 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_8958897 |
| source | Oxford Journals Open Access Collection |
| subjects | BASIC BIOLOGICAL SCIENCES Database Issue microbial ecology microbiome ontology |
| title | The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource |
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