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Title: Towards richer descriptions of our collection of genomes andmetagenomes

Abstract

In this commentary, we advocate building a richer set of descriptions about our invaluable and exponentially growing collection of genomes and metagenomic datasets through the construction of consensus-driven data capture and exchange mechanisms. Standardization activities must proceed within the auspices of open-access and international working bodies, and to tackle the issues surrounding the development of better descriptions of genomic investigations we have formed the Genomic Standards Consortium (GSC). Here, we introduce the 'Minimum Information about a Genome Sequence' specification in the hopes of gaining wider participation in its development and discuss the resources that will be required to support it (standardization of annotations through the use of ontologies and mechanisms of metadata capture, exchange). As part of its wider goals, the GSC also strongly supports improving the 'transparency' of the information contained in existing genomic databases that contain calculated analyses and genomic annotations.

Authors:
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Publication Date:
Research Org.:
COLLABORATION - U. CollegeCork/Ireland
OSTI Identifier:
932679
Report Number(s):
LBNL-60477
Journal ID: ISSN 1087-0156; NABIF9; R&D Project: Y00013; BnR: 600305000; TRN: US200813%%461
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Nature Biotechnology
Additional Journal Information:
Journal Volume: 16; Related Information: Journal Publication Date: 05/01/2008; Journal ID: ISSN 1087-0156
Country of Publication:
United States
Language:
English
Subject:
59; CONSTRUCTION; SPECIFICATIONS; STANDARDIZATION; Genomics standardization open-access Genomics StandardsConsortium ontologies metadata

Citation Formats

Field, D, Garrity, G, Selengut, J, Sterk, P, Tatusova, T, Thomson, N, Ashburner, M, Boore, J L, Cochrane, G, Cole, J, dePamphilus, C, Edwards, R, Faruque, N, Feldman, R, Gray, T, Gurr, S, Haft, D, Hancock, D, Hertz-Fowler, C, Hughes, J, Joint, I, Kane, M, Kennedy, J, Kolker, E, Kyripides, N, Leebens-Mack, J, Lewis, S, Maltsev, N, Markowitz, V, Methe, B, Morrison, N, Nelson, K, Parkhill, J, Sansone, S, Spiers, A, Stevens, R, Swift, P, Taylor, C, Tateno, Y, Tett, T, Turner, S, Ussery, D, Vaughan, B, Whetzel, T, Wilson, G, and Wipat, A. Towards richer descriptions of our collection of genomes andmetagenomes. United States: N. p., 2006. Web.
Field, D, Garrity, G, Selengut, J, Sterk, P, Tatusova, T, Thomson, N, Ashburner, M, Boore, J L, Cochrane, G, Cole, J, dePamphilus, C, Edwards, R, Faruque, N, Feldman, R, Gray, T, Gurr, S, Haft, D, Hancock, D, Hertz-Fowler, C, Hughes, J, Joint, I, Kane, M, Kennedy, J, Kolker, E, Kyripides, N, Leebens-Mack, J, Lewis, S, Maltsev, N, Markowitz, V, Methe, B, Morrison, N, Nelson, K, Parkhill, J, Sansone, S, Spiers, A, Stevens, R, Swift, P, Taylor, C, Tateno, Y, Tett, T, Turner, S, Ussery, D, Vaughan, B, Whetzel, T, Wilson, G, & Wipat, A. Towards richer descriptions of our collection of genomes andmetagenomes. United States.
Field, D, Garrity, G, Selengut, J, Sterk, P, Tatusova, T, Thomson, N, Ashburner, M, Boore, J L, Cochrane, G, Cole, J, dePamphilus, C, Edwards, R, Faruque, N, Feldman, R, Gray, T, Gurr, S, Haft, D, Hancock, D, Hertz-Fowler, C, Hughes, J, Joint, I, Kane, M, Kennedy, J, Kolker, E, Kyripides, N, Leebens-Mack, J, Lewis, S, Maltsev, N, Markowitz, V, Methe, B, Morrison, N, Nelson, K, Parkhill, J, Sansone, S, Spiers, A, Stevens, R, Swift, P, Taylor, C, Tateno, Y, Tett, T, Turner, S, Ussery, D, Vaughan, B, Whetzel, T, Wilson, G, and Wipat, A. 2006. "Towards richer descriptions of our collection of genomes andmetagenomes". United States. https://www.osti.gov/servlets/purl/932679.
@article{osti_932679,
title = {Towards richer descriptions of our collection of genomes andmetagenomes},
author = {Field, D and Garrity, G and Selengut, J and Sterk, P and Tatusova, T and Thomson, N and Ashburner, M and Boore, J L and Cochrane, G and Cole, J and dePamphilus, C and Edwards, R and Faruque, N and Feldman, R and Gray, T and Gurr, S and Haft, D and Hancock, D and Hertz-Fowler, C and Hughes, J and Joint, I and Kane, M and Kennedy, J and Kolker, E and Kyripides, N and Leebens-Mack, J and Lewis, S and Maltsev, N and Markowitz, V and Methe, B and Morrison, N and Nelson, K and Parkhill, J and Sansone, S and Spiers, A and Stevens, R and Swift, P and Taylor, C and Tateno, Y and Tett, T and Turner, S and Ussery, D and Vaughan, B and Whetzel, T and Wilson, G and Wipat, A},
abstractNote = {In this commentary, we advocate building a richer set of descriptions about our invaluable and exponentially growing collection of genomes and metagenomic datasets through the construction of consensus-driven data capture and exchange mechanisms. Standardization activities must proceed within the auspices of open-access and international working bodies, and to tackle the issues surrounding the development of better descriptions of genomic investigations we have formed the Genomic Standards Consortium (GSC). Here, we introduce the 'Minimum Information about a Genome Sequence' specification in the hopes of gaining wider participation in its development and discuss the resources that will be required to support it (standardization of annotations through the use of ontologies and mechanisms of metadata capture, exchange). As part of its wider goals, the GSC also strongly supports improving the 'transparency' of the information contained in existing genomic databases that contain calculated analyses and genomic annotations.},
doi = {},
url = {https://www.osti.gov/biblio/932679}, journal = {Nature Biotechnology},
issn = {1087-0156},
number = ,
volume = 16,
place = {United States},
year = {2006},
month = {6}
}