The Genomic Standards Consortium. by Dawn Field, Linda Amaral-Zettler, Guy Cochrane, James R Cole, Peter Dawyndt, George M Garrity, Jack Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Ilene Karsch-Mizrachi, Hans-Peter Klenk, Rob Knight, Renzo Kottmann, Nikos Kyrpides, Folker Meyer, Inigo San Gil, Susanna-Assunta Sansone, Lynn M Schriml, Peter Sterk, Tatiana Tatusova, David W Ussery, Owen White, John Wooley

“…At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.…”
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COVID-19 pandemic reveals the peril of ignoring metadata standards by Schriml, LM, Chuvochina, M, Davies, N, Eloe-Fadrosh, EA, Finn, RD, Hugenholtz, P, Hunter, CI, Hurwitz, BL, Kyrpides, NC, Meyer, F, Mizrachi, IK, Sansone, S-A, Sutton, G, Tighe, S, Walls, R

“…Here, the Genomic Standards Consortium board highlights the essential need for contextual genomic data FAIRness, for empowering key data-driven biological questions.…”

LIIS: A web-based system for culture collections and sample annotation by Matthew S Forster, Lyn Paterson, Robert J Forster

“…The system supports the import and export of CSV spreadsheets, and stores general metadata designed to complement the environmental packages provided by the Genomic Standards Consortium. The goals of the LIIS are to simplify the storage and archival processes and to provide an easy to access library of laboratory annotations. …”
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The minimum information about a genome sequence (MIGS) specification. by Field, D, Garrity, G, Gray, T, Morrison, N, Selengut, J, Sterk, P, Tatusova, T, Thomson, N, Allen, M, Angiuoli, S, Ashburner, M, Axelrod, N, Baldauf, S, Ballard, S, Boore, J, Cochrane, G, Cole, J, Dawyndt, P, De Vos, P, DePamphilis, C, Edwards, R, Faruque, N, Feldman, R, Gilbert, J, Gilna, P

“…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 (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. …”

A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). by Kottmann, R, Gray, T, Murphy, S, Kagan, L, Kravitz, S, Lombardot, T, Field, D, Glöckner, F

“…The Genomic Contextual Data Markup Language (GCDML) is a core project of the Genomic Standards Consortium (GSC) that implements the "Minimum Information about a Genome Sequence" (MIGS) specification and its extension, the "Minimum Information about a Metagenome Sequence" (MIMS). …”

A standards perspective on genomic data reusability and reproducibility by Ishi Keenum, Scott A. Jackson, Emiley Eloe-Fadrosh, Lynn M. Schriml

“…The International Microbiome and Multi’Omics Standards Alliance (IMMSA, https://www.microbialstandards.org/) and the Genomic Standards Consortium (GSC, https://gensc.org) hosted a 5-part seminar series “A Year of Data Reuse” in 2024 to explore challenges and opportunities of data reuse and reproducibility across disparate domains of the genomic sciences. …”
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The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome by McDonald Daniel, Clemente Jose C, Kuczynski Justin, Rideout Jai, Stombaugh Jesse, Wendel Doug, Wilke Andreas, Huse Susan, Hufnagle John, Meyer Folker, Knight Rob, Caporaso J

“…The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.</p>…”
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CDinFusion--submission-ready, on-line integration of sequence and contextual data. by Wolfgang Hankeln, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Frank Oliver Glöckner

“…To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence data collection and to promote the capturing, exchange and integration of sequence data with contextual data. …”
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Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria by Grote, Jana, Bayindirli, Cansu, Bergauer, Kristin, Carpintero de Moraes, Paula, Chen, Huan, D’Ambrosio, Lindsay, Edwards, Bethanie, Fernandez-Gomez, Beatriz, Hamisi, Mariam, Logares, Ramiro, Nguyen, Dan, Rii, Yoshimi M., Saeck, Emily, Schutte, Charles, Widner, Brittany, Church, Matthew J., Steward, Grieg F., Karl, David M., DeLong, Edward, Eppley, John Marmaduke, Schuster, Stephan C., Kyrpides, Nikos C., Rappe, Michael S.

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MetaBar - a tool for consistent contextual data acquisition and standards compliant submission by Kottmann Renzo, Fink Dennis, Buttigieg Pier, Hankeln Wolfgang, Yilmaz Pelin, Glöckner Frank

“…MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3).…”
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OMeta: an ontology-based, data-driven metadata tracking system by Indresh Singh, Mehmet Kuscuoglu, Derek M. Harkins, Granger Sutton, Derrick E. Fouts, Karen E. Nelson

“…Over the years, many metadata standards developed by various metadata standards initiatives have arisen; the Genomic Standards Consortium’s minimal information standards (MIxS), the GSCID/BRC Project and Sample Application Standard. …”
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Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually sma... by Durham, Bryndan P., Grote, Jana, Whittaker, Kerry A., Bender, Sara J., Luo, Haiwei, Grim, Sharon L., Brown, Julia M., Casey, John R., Dron, Antony, Florez-Leiva, Lennin, Krupke, Andreas, Luria, Catherine M., Mine, Aric H., Nigro, Olivia D., Pather, Santhiska, Talarmin, Agathe, Wear, Emma K., Weber, Thomas S., Wilson, Jesse M., Church, Matthew J., Karl, David M., Steward, Grieg F., Eppley, John M., Kyrpides, Nikos C., Schuster, Stephan, Rappé, Michael S., DeLong, Edward Francis

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Standardized metadata for human pathogen/vector genomic sequences. by Vivien G Dugan, Scott J Emrich, Gloria I Giraldo-Calderón, Omar S Harb, Ruchi M Newman, Brett E Pickett, Lynn M Schriml, Timothy B Stockwell, Christian J Stoeckert, Dan E Sullivan, Indresh Singh, Doyle V Ward, Alison Yao, Jie Zheng, Tanya Barrett, Bruce Birren, Lauren Brinkac, Vincent M Bruno, Elizabet Caler, Sinéad Chapman, Frank H Collins, Christina A Cuomo, Valentina Di Francesco, Scott Durkin, Mark Eppinger, Michael Feldgarden, Claire Fraser, W Florian Fricke, Maria Giovanni, Matthew R Henn, Erin Hine, Julie Dunning Hotopp, Ilene Karsch-Mizrachi, Jessica C Kissinger, Eun Mi Lee, Punam Mathur, Emmanuel F Mongodin, Cheryl I Murphy, Garry Myers, Daniel E Neafsey, Karen E Nelson, William C Nierman, Julia Puzak, David Rasko, David S Roos, Lisa Sadzewicz, Joana C Silva, Bruno Sobral, R Burke Squires, Rick L Stevens, Luke Tallon, Herve Tettelin, David Wentworth, Owen White, Rebecca Will, Jennifer Wortman, Yun Zhang, Richard H Scheuermann

“…It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). …”
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Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability by Raïssa Meyer, Ward Appeltans, William Duncan, Mariya Dimitrova, Yi-Ming Gan, Thomas Stjernegaard Jeppesen, Christopher Mungall, Deborah Paul, Pieter Provoost, Tim Robertson, Lynn Schriml, Saara Suominen, Ramona Walls, Maxime Sweetlove, Visotheary Ung, Anton Van de Putte, Elycia Wallis, John Wieczorek, Pier Buttigieg

“…Convening experts from the Biodiversity Information Standards (TDWG) and the Genomic Standards Consortium (GSC) alongside external stakeholders, the TG aimed to promote sustainable interoperability between the Minimum Information about any (x) Sequence (MIxS) and Darwin Core (DwC) specifications.To achieve this goal, the TG utilized the Simple Standard for Sharing Ontology Mappings (SSSOM) to create a comprehensive mapping of DwC keys to MIxS keys. …”
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Use of low-coverage, large-insert, short-read data for rapid and accurate generation of enhanced-quality draft Pseudomonas genome sequences. by Heath E O'Brien, Yunchen Gong, Pauline Fung, Pauline W Wang, David S Guttman

“…While groups such as the Genomics Standards Consortium have made strong efforts to promote genome standards there is a still a general lack of uniformity among published draft genomes, leading to challenges for downstream comparative analyses. …”
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