Publications

The GSC aims to make its activities transparent to the wider community through maintenance of a GSC website and when relevant, publication of GSC led articles. To date several roadmap publications have been published along with reports from all GSC workshops.

GSC Project Publications
GSC Meeting Reports
Other Publications

GSC Project Publications

As an outgrowth of the activities surrounding the creation and implementation of the MIxS standard there are now 18 projects within the GSC. These efforts cover an ever widening range of standardization activities. The following publications are either directly or indirectly related to these projects. Furthermore, two umbrella publications titled Genomic standards consortium projects and The Genomic Standards Consortium detail how these projects are initiated and integrated within GSC.

Minimum Information about a Biosynthetic Gene cluster.  Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I et al. Nat Chem Biol. 2015 ;11(9):625-631. doi:10.1038/nchembio.1890.

The ocean sampling day consortium. Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I et al. Gigascience. 2015 Jun 19;4:27. doi: 10.1186/s13742-015-0066-5.

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Whitman WB, Woyke T, Klenk HP, Zhou Y, Lilburn TG, Beck BJ, De Vos P et al. Stand Genomic Sci. 2015 May 17; 10:26. doi:10.1186/s40793-015-0017-x.

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards. ten Hoopen P, Pesant S, Kottmann R, Kopf A, Bicak M et al. Stand Genomic Sci. 2015 May 8; 10:20. doi:10.1186/s40793-015-0001-5.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M et al. PLoS Biol. 2014 Aug 5;12(8):e1001920. doi: 10.1371/journal.pbio.1001920.

Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R et al. PLoS One. 2014 Mar 3;9(3):e89606. doi: 10.1371/journal.pone.0089606.

The founding charter of the Genomic Observatories Network. Davies N, Field D, Amaral-Zettler L, Clark MS, Deck J et al. Gigascience. 2014 Mar 7;3(1):2. doi: 10.1186/2047-217X-3-2.

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. ISME J. 2014 Jan;8(1):1-3. doi: 10.1038/ismej.2013.176.

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Kyrpides NC, Woyke T, Eisen JA, Garrity G, Lilburn TG, Beck BJ, Whitman WB, Hugenholtz P, Klenk HP. Stand Genomic Sci. 2013 Dec 17;9(3):1278-84. doi: 10.4056/sigs.5068949.

The environment ontology: contextualising biological and biomedical entities. Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE; ENVO Consortium. J Biomed Semantics. 2013 Dec 11;4(1):43. doi: 10.1186/2041-1480-4-43.

Darwin Core: an evolving community-developed biodiversity data standard. Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, Giovanni R, Robertson T, Vieglais D. PLoS One. 2012;7(1):e29715. doi: 10.1371/journal.pone.0029715.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG. Gigascience. 2012 Jul 12;1(1):7. doi: 10.1186/2047-217X-1-7.

A call for an international network of genomic observatories (GOs). Davies N, Meyer C, Gilbert JA, Amaral-Zettler L, Deck J, Bicak M, Rocca-Serra P, Assunta-Sansone S, Willis K, Field D. Gigascience. 2012 Jul 12;1(1):5. doi: 10.1186/2047-217X-1-5.

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, Mavrommatis K, Meyer F. BMC Bioinformatics. 2012 Jun 21;13:141. doi: 10.1186/1471-2105-13-141.

Sequencing data: A genomic network to monitor Earth. Davies N, Field D, Genomic Observatories Network. Nature. 2012 Jan 11;481(7380):145. doi: 10.1038/481145a.

Toward interoperable bioscience data. Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C et al. Nat Genet. 2012 Jan 27;44(2):121-6. doi: 10.1038/ng.1054.

The genomic standards consortium: bringing standards to life for microbial ecology. Yilmaz P, Gilbert JA, Knight R, Amaral-Zettler L, Karsch-Mizrachi I, Cochrane G, Nakamura Y, Sansone SA, Glöckner FO, Field D. ISME J. 2011 Oct;5(10):1565-7. doi: 10.1038/ismej.2011.39.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P et al. Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA. Bioinformatics. 2010 Sep 15;26(18):2354-6. doi: 10.1093/bioinformatics/btq415.

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E et al. Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.

Extending Standards for Genomics and Metagenomics Data: A Research Coordination Network for the Genomic Standards Consortium (RCN4GSC). Wooley JC, Field D, Glöckner FO. Stand Genomic Sci. 2009 Jul 20;1(1):87-90. doi: 10.4056/sigs.26218.

Standards in genomic sciences. Stand Genomic Sci. 2009 Jul 20;1(1):1-2. doi: 10.4056/sigs.34251. 

A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). Kottmann R, Gray T, Murphy S, Kagan L, Kravitz S, Lombardot T, Field D, Glöckner FO. OMICS. 2008 Jun;12(2):115-21. doi: 10.1089/omi.2008.0A10.

Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers. Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D, Dawyndt P. OMICS. 2008 Jun;12(2):123-7. doi: 10.1089/omi.2008.0020.

Toward a standards-compliant genomic and metagenomic publication record. Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O. OMICS. 2008 Jun;12(2):157-60. doi: 10.1089/omi.2008.A2B2.

The minimum information about a genome sequence (MIGS) specification. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P et al. Nat Biotechnol. 2008 May;26(5):541-7. doi: 10.1038/nbt1360.

Meeting Reports

This section includes meeting reports published to date from all GSC and RCN4GSC workshops or GSC-led special interest groups. Additionally, reports from satellite meetings following GSC workshops are included here.

GSC16
Meeting report: advancing practical applications of biodiversity ontologies. Walls RL., Guralnick R, Deck J, Buntzman A, Buttigieg PL, Davies N et al. Stand Genomic Sci. 2014;9(1), 17. doi: 10.1186/1944-3277-9-17

GBWG Hackathon May 2013
Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013). Wieczorek J, Banki O, Blum S, Deck J, Döring M, Dröge G et al. Stand Genomic Sci. 2014;9(3), 585. doi: 10.4056/sigs.4898640.

GSC15
The 15th Genomic Standards Consortium meeting. Schriml L, Mizrachi I, Sterk P, Field D, Hirschman L , Tatusova T et al.  Stand Genomic Sci. 2013;8(1).

GSC14
Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012. Davies N, Field D, Amaral-Zettler L, et al. Stand Genomic Sci. 2014;9(3):1236-1250. doi:10.4056/sigs.4319681.

GSC13
Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012. Gilbert JA, Bao Y, Wang H, Sansone SA, Edmunds SC, Morrison N, Meyer F, Schriml LM, Davies N, Sterk P, Wilkening J, Garrity GM, Field D, Robbins R, Smith DP, Mizrachi I, Moreau C. Stand Genomic Sci. 2012 May 25;6(2):276-86. doi: 10.4056/sigs.2876184.

GBWG Hackathon February 2012
Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012). Tuama EÓ, Deck J, Dröge G, Döring M, Field D, Kottmann R, Ma J, Mori H, Morrison N, Sterk P, Sugawara H, Wieczorek J, Wu L, Yilmaz P. Stand Genomic Sci. 2012 Oct 10;7(1):166-70. doi: 10.4056/sigs.3166513.

GSC12

GBWG May 2011
RCN4GSC Meeting Report: Initiating a Testbed for Managing Data at the Interface of Biodiversity and Genomics/Metagenomics, May 2011. Robbins RJ, Beach J, Blum S, Dawyndt P, Deck J, Kottmann R, Morrison N, Tuama EÓ, San Gil I, Vieglas D, Wieczorek J, Wooley J. Stand Genomic Sci. 2012 Oct 10;7(1):171-4. doi: 10.4056/sigs.3176515.

GSC11
RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011. Robbins RJ, Cochrane G, Davies N, Dawyndt P, Kottmann R, Krishtalka LK, Morrison N, Tuama EÓ, San Gil I, Wooley J. Stand Genomic Sci. 2012 Oct 10;7(1):153-8. doi: 10.4056/sigs.3146509.

GBWG March 2011
RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011. Robbins RJ, Amaral-Zettler L, Bik H, Blum S, Edwards J, Field D, Garrity G, Gilbert JA, Kottmann R, Krishtalka L, Lapp H, Lawrence C, Morrison N, Tuama EÓ, Parr C, San Gil I, Schindel D, Schriml L, Vieglas D, Wooley J. Stand Genomic Sci. 2012 Oct 10;7(1):159-65. doi: 10.4056/sigs.3156511.

GSC 10
Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10. Glass E, Meyer F, Gilbert JA, Field D, Hunter S, Kottmann R, Kyrpides N, Sansone S, Schriml L, Sterk P, White O, Wooley J. Stand Genomic Sci. 2010 Dec 25;3(3):225-31. doi: 10.4056/sigs.1423520.

M5 Roundtable @ ISME13
Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010. Gilbert JA, Meyer F, Knight R, Field D, Kyrpides N, Yilmaz P, Wooley J. Stand Genomic Sci. 2010 Dec 15;3(3):235-9. doi: 10.4056/sigs.1333437.

M3 @ ISMB 2010
Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010. Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O. Stand Genomic Sci. 2010 Dec 4;3(3):232-4. doi: 10.4056/sigs.1383476.

BioSharing @ ISMB 2010
Meeting Report: BioSharing at ISMB 2010. Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Gaudet P, Lewis S, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O, Bramlett B, Gregurick S, Lapp H, Orchard S, Rocca-Serra P, Ruttenberg A, Shah N, Taylor C, Thessen A. Stand Genomic Sci. 2010 Dec 4;3(3):254-8. doi: 10.4056/sigs/1403501.

GSC 9
Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9. Davidsen T, Madupu R, Sterk P, Field D, Garrity G, Gilbert J, Glöckner FO, Hirschman L, Kolker E, Kottmann R, Kyrpides N, Meyer F, Morrison N, Schriml L, Tatusova T, Wooley J. Stand Genomic Sci. 2010 Dec 4;3(3):216-24. doi: 10.4056/sigs.1353455.

GSC 8
Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8. Kyrpides N, Field D, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J. Stand Genomic Sci. 2010 Aug 20;3(1):93-6. doi: 10.4056/sigs.1022942.

M3 @ PSB 2010
Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Hirschman L, Sterk P, Field D, Wooley J, Cochrane G, Gilbert J, Kolker E, Kyrpides N, Meyer F, Mizrachi I, Nakamura Y, Sansone SA, Schriml L, Tatusova T, White O, Yilmaz P. Stand Genomic Sci. 2010 Jun 15;2(3):357-60. doi: 10.4056/sigs.802738.

M3 @ ISMB 2009
Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Special Interest Group at ISMB 2009. Field D, Friedberg I, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J, Gilbert J. Stand Genomic Sci. 2009 Dec 29;1(3):278-82. doi: 10.4056/sigs.641096.

GSC 6 & GSC 7
Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7. Field D, Sterk P, Kyrpides N, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Wooley J, Gilna P. Stand Genomic Sci. 2009 Jul 20;1(1):68-71. doi: 10.4056/sigs.25165.

GSC 5
Meeting report: the fifth Genomic Standards Consortium (GSC) workshop. Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner FO, Kottmann R, Angiuoli S, White O, Dawyndt P, Thomson N, Gil IS, Morrison N, Tatusova T, Mizrachi I, Vaughan R, Cochrane G, Kagan L, Murphy S, Schriml L; Genomic Standards Consortium. OMICS. 2008 Jun;12(2):109-13. doi: 10.1089/omi.2008.A3B3.

GSC 4
Meeting report: the fourth Genomic Standards Consortium (GSC) workshop. Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T. OMICS. 2008 Jun;12(2):101-8. doi: 10.1089/omi.2008.0014.

GSC 3
Meeting Report: eGenomics: Cataloguing Our Complete Genome Collection III. Dawn Field, George Garrity, Tanya Gray, Jeremy Selengut, Peter Sterk, Nick Thomson, Tatiana Tatusova, Guy Cochrane, Frank Oliver Glöckner, Renzo Kottmann, Allyson L. Lister, Yoshio Tateno, and Robert Vaughan. Comp Funct Genomics. 2007; doi:10.1155/2007/47304.

GSC 2
Meeting report: eGenomics: Cataloguing our Complete Genome Collection II. Field D, Morrison N, Selengut J, Sterk P. OMICS. 2006 Summer;10(2):100-4.

GSC 1
eGenomics: Cataloguing our Complete Genome Collection. Field D, Garrity G, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N. Comp Funct Genomics. 2005;6(7-8):363-8. doi: 10.1002/cfg.494.

Other Publications