Peter Sterk

Publications

• A second special issue of Standards In Genomic Sciences from the Genomic Standards Consortium.

  Dawn Field, Renzo Kottmann, Norman Morrison, Peter Sterk

  Standards in genomic sciences. 11/2011; 5(2):194.
• 12.92

  Impact points

  The Genomic Standards Consortium.

  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, [......], Nikos Kyrpides, Folker Meyer, Inigo San Gil, Susanna-Assunta Sansone, Lynn M Schriml, Peter Sterk, Tatiana Tatusova, David W Ussery, Owen White, John Wooley

  PLoS biology. 06/2011; 9(6):e1001088.

  A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the ... [more] A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. 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.
• 29.50

  Impact points

  Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

  Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James R Cole, Linda Amaral-Zettler, Jack A Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane, [......], James M Tiedje, Doyle V Ward, George M Weinstock, Doug Wendel, Owen White, Andrew Whiteley, Andreas Wilke, Jennifer R Wortman, Tanya Yatsunenko, Frank Oliver Glöckner

  Nature biotechnology. 05/2011; 29(5):415-20.

  Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmen... [more] Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

• Meeting report of the RNA Ontology Consortium January 8-9, 2011.

  Amanda Birmingham, Jose C Clemente, Narayan Desai, Jack Gilbert, Antonio Gonzalez, Nikos Kyrpides, Folker Meyer, Eric Nawrocki, Peter Sterk, Jesse Stombaugh, Zasha Weinberg, Doug Wendel, Neocles B Leontis, Craig Zirbel, Rob Knight, Alain Laederach

  Standards in genomic sciences. 04/2011; 4(2):252-6.

  This report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011. The ROC hosted this workshop to facilitate collaborations among those researchers formalizing concepts in RNA, those developing RNA-r... [more] This report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011. The ROC hosted this workshop to facilitate collaborations among those researchers formalizing concepts in RNA, those developing RNA-related software, and those performing genome annotation and standardization. The workshop included three software presentations, extended round-table discussions, and the constitution of two new working groups, the first to address the need for better software integration and the second to discuss standardization and benchmarking of existing RNA annotation pipelines. These working groups have subsequently pursued concrete implementation of actions suggested during the discussion. Further information about the ROC and its activities can be found at http://roc.bgsu.edu/.

• Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets.

  Norman Morrison, David Hancock, Lynette Hirschman, Peter Dawyndt, Bert Verslyppe, Nikos Kyrpides, Renzo Kottmann, Pelin Yilmaz, Frank Oliver Glöckner, Jeff Grethe, Tim Booth, Peter Sterk, Goran Nenadic, Dawn Field

  Standards in genomic sciences. 04/2011; 4(2):286-92.

  In the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that must be packaged accordingly. Increasingly, eCommerce sellers present heterogeneous product lines to buyer... [more] In the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that must be packaged accordingly. Increasingly, eCommerce sellers present heterogeneous product lines to buyers using faceted browsing. Using this approach we have developed the Ontogrator platform, which allows for rapid retrieval of data in a way that would be familiar to any online shopper. Using Knowledge Organization Systems (KOS), especially ontologies, Ontogrator uses text mining to mark up data and faceted browsing to help users navigate, query and retrieve data. Ontogrator offers the potential to impact scientific research in two major ways: 1) by significantly improving the retrieval of relevant information; and 2) by significantly reducing the time required to compose standard database queries and assemble information for further research. Here we present a pilot implementation developed in collaboration with the Genomic Standards Consortium (GSC) that includes content from the StrainInfo, GOLD, CAMERA, Silva and Pubmed databases. This implementation demonstrates the power of ontogration and highlights that the usefulness of this approach is fully dependent on both the quality of data and the KOS (ontologies) used. Ideally, the use and further expansion of this collaborative system will help to surface issues associated with the underlying quality of annotation and could lead to a systematic means for accessing integrated data resources.

• Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.

  James Rodney Brister, Yiming Bao, Carla Kuiken, Elliot J Lefkowitz, Philippe Le Mercier, Raphael Leplae, Ramana Madupu, Richard H Scheuermann, Seth Schobel, Donald Seto, Susmita Shrivastava, Peter Sterk, Qiandong Zeng, William Klimke, Tatiana Tatusova

  Viruses. 10/2010; 2(10):2258-68.

  Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world's biological databases, it is critically important to recognize that the s... [more] Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world's biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.
• 4.93

  Impact points

  ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.

  Philippe Rocca-Serra, Marco Brandizi, Eamonn Maguire, Nataliya Sklyar, Chris Taylor, Kimberly Begley, Dawn Field, Stephen Harris, Winston Hide, Oliver Hofmann, Steffen Neumann, Peter Sterk, Weida Tong, Susanna-Assunta Sansone

  Bioinformatics (Oxford, England). 09/2010; 26(18):2354-6.

  The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checkli... [more] The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories. Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.org.

• Genomic standards consortium workshop: metagenomics, metadata and metaanalysis (m3).

  Peter Sterk, Lynette Hirschman, Dawn Field, John Wooley

  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 01/2010;

  The M3 workshop has, as its primary focus, the rapidly growing area of metagenomics, including the metadata standards and the meta-analysis approaches needed to organize, process and interpret metagenomics data. The PSB Workshop builds on the first M3 meeting, a Special Interest Group (SIG) meeting ... [more] The M3 workshop has, as its primary focus, the rapidly growing area of metagenomics, including the metadata standards and the meta-analysis approaches needed to organize, process and interpret metagenomics data. The PSB Workshop builds on the first M3 meeting, a Special Interest Group (SIG) meeting at ISMB 2009, organized by the Genomics Standards Consortium.

• Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8.

  Nikos Kyrpides, Dawn Field, Peter Sterk, Renzo Kottmann, Frank Oliver Glöckner, Lynette Hirschman, George M Garrity, Guy Cochrane, John Wooley

  Standards in genomic sciences. 01/2010; 3(1):93-6.

  This report summarizes the proceedings of the 8th meeting of the Genomic Standards Consortium held at the Department of Energy Joint Genome Institute in Walnut Creek, CA, USA on September 9-11, 2009. This three-day workshop marked the maturing of Genomic Standards Consortium from an informal gatheri... [more] This report summarizes the proceedings of the 8th meeting of the Genomic Standards Consortium held at the Department of Energy Joint Genome Institute in Walnut Creek, CA, USA on September 9-11, 2009. This three-day workshop marked the maturing of Genomic Standards Consortium from an informal gathering of researchers interested in developing standards in the field of genomic and metagenomics to an established community with a defined governance mechanism, its own open access journal, and a family of established standards for describing genomes, metagenomes and marker studies (i.e. ribosomal RNA gene surveys). There will be increased efforts within the GSC to reach out to the wider scientific community via a range of new projects. Further information about the GSC and its activities can be found at http://gensc.org/.

• The first special issue of Standards in Genomic Sciences from the Genomic Standards Consortium.

  Dawn Field, Renzo Kottmann, Peter Sterk

  Standards in genomic sciences. 01/2010; 3(3):214-5.

• Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.

  Lynette Hirschman, Peter Sterk, Dawn Field, John Wooley, Guy Cochrane, Jack Gilbert, Eugene Kolker, Nikos Kyrpides, Folker Meyer, Ilene Mizrachi, Yasukazu Nakamura, Susanna-Assunta Sansone, Lynn Schriml, Tatiana Tatusova, Owen White, Pelin Yilmaz

  Standards in genomic sciences. 01/2010; 2(3):357-60.

  This report summarizes the M3 Workshop held at the January 2010 Pacific Symposium on Biocomputing. The workshop, organized by Genomic Standards Consortium members, included five contributed talks, a series of short presentations from stakeholders in the genomics standards community, a poster session... [more] This report summarizes the M3 Workshop held at the January 2010 Pacific Symposium on Biocomputing. The workshop, organized by Genomic Standards Consortium members, included five contributed talks, a series of short presentations from stakeholders in the genomics standards community, a poster session, and, in the evening, an open discussion session to review current projects and examine future directions for the GSC and its stakeholders.

• Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9.

  Tanja Davidsen, Ramana Madupu, Peter Sterk, Dawn Field, George Garrity, Jack Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Eugene Kolker, Renzo Kottmann, Nikos Kyrpides, Folker Meyer, Norman Morrison, Lynn Schriml, Tatiana Tatusova, John Wooley

  Standards in genomic sciences. 01/2010; 3(3):216-24.

  This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided o... [more] This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided overviews of the full range of ongoing GSC projects. It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platform for next-generation collaborative computational infrastructures, building ties with the biodiversity research community and two discussion panels with government and industry participants. Progress was made on all fronts, and major outcomes included the completion of the MIENS specification for publication and the formation of the Biodiversity working group.

• Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10.

  Elizabeth Glass, Folker Meyer, Jack A Gilbert, Dawn Field, Sarah Hunter, Renzo Kottmann, Nikos Kyrpides, Susanna Sansone, Lynn Schriml, Peter Sterk, Owen White, John Wooley

  Standards in genomic sciences. 01/2010; 3(3):225-31.

  This report summarizes the proceedings of the 10th workshop of the Genomic Standards Consortium (GSC), held at Argonne National Laboratory, IL, USA. It was the second GSC workshop to have open registration and attracted over 60 participants who worked together to progress the full range of projects ... [more] This report summarizes the proceedings of the 10th workshop of the Genomic Standards Consortium (GSC), held at Argonne National Laboratory, IL, USA. It was the second GSC workshop to have open registration and attracted over 60 participants who worked together to progress the full range of projects ongoing within the GSC. Overall, the primary focus of the workshop was on advancing the M5 platform for next-generation collaborative computational infrastructures. Other key outcomes included the formation of a GSC working group focused on MIGS/MIMS/MIENS compliance using the ISA software suite and the formal launch of the GSC Developer Working Group. Further information about the GSC and its range of activities can be found at http://gensc.org/.

• Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010.

  Dawn Field, Susanna Sansone, Edward F Delong, Peter Sterk, Iddo Friedberg, Renzo Kottmann, Lynette Hirschman, George Garrity, Guy Cochrane, John Wooley, Folker Meyer, Sarah Hunter, Owen White

  Standards in genomic sciences. 01/2010; 3(3):232-4.

  This report summarizes the proceedings of the first day of the Metagenomics, Metadata and MetaAnalysis (M3) workshop held at the Intelligent Systems for Molecular Biology 2010 conference. The second day, which was dedicated to the inaugural meeting of the BioSharing initiative is presented in a sepa... [more] This report summarizes the proceedings of the first day of the Metagenomics, Metadata and MetaAnalysis (M3) workshop held at the Intelligent Systems for Molecular Biology 2010 conference. The second day, which was dedicated to the inaugural meeting of the BioSharing initiative is presented in a separate report. The Genomic Standards Consortium (GSC) hosted the first day of this Special Interest Group (SIG) at ISMB to continue exploring the bottlenecks and emerging solutions for obtaining biological insights through large-scale comparative analysis of metagenomic datasets. The M3 SIG included invited and selected talks and a panel discussion at the end of the day involving the plenary speakers. Further information about the GSC and its range of activities can be found at http://gensc.org. Information about the newly established BioSharing effort can be found at http://biosharing.org/.

• Meeting Report: BioSharing at ISMB 2010.

  Dawn Field, Susanna Sansone, Edward F Delong, Peter Sterk, Iddo Friedberg, Pascale Gaudet, Susanna Lewis, Renzo Kottmann, Lynette Hirschman, George Garrity, [......], Owen White, Brian Bramlett, Susan Gregurick, Hilmar Lapp, Sandra Orchard, Philippe Rocca-Serra, Alan Ruttenberg, Nigam Shah, Chris Taylor, Anne Thessen

  Standards in genomic sciences. 01/2010; 3(3):254-8.

  This report summarizes the proceedings of the one day BioSharing meeting held at the Intelligent Systems for Molecular Biology (ISMB) 2010 conference in Boston, MA, USA This inaugural BioSharing event was hosted by the Genomic Standards Consortium as part of its M3 & BioSharing special interest ... [more] This report summarizes the proceedings of the one day BioSharing meeting held at the Intelligent Systems for Molecular Biology (ISMB) 2010 conference in Boston, MA, USA This inaugural BioSharing event was hosted by the Genomic Standards Consortium as part of its M3 & BioSharing special interest group (SIG) workshop. The BioSharing event included invited talks from a range of community leaders and a panel discussion at the end of the day. The panel session led to the formal agreement among community leaders to join together to promote cross-community knowledge exchange and collaborations. A key focus of the newly formed Biosharing community will be linking up resources to promote real-world data sharing (virtuous cycle of data) and supporting compliance with data policies through the creation of a one-stop-portal of information. Further information about the newly established BioSharing effort can be found at http://biosharing.org.

• Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

  Carsten Kettner, Dawn Field, Susanna-Assunta Sansone, Chris Taylor, Jan Aerts, Nigel Binns, Andrew Blake, Cedrik M Britten, Ario de Marco, Jennifer Fostel, [......], Sandra Orchard, Helen Parkinson, William Piel, Shoba Ranganathan, Philippe Rocca-Serra, Annapaola Santarsiero, David Shotton, Peter Sterk, Andreas Untergasser, Patricia L Whetzel

  Standards in genomic sciences. 01/2010; 3(3):259-66.

  This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting... [more] This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://mibbi.org/.

• Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

  James Rodney Brister, Bao Yiming, Kuiken Carla, Elliot J Lefkowitz, Philippe Le Mercier, Leplae Raphael, Madupu Ramana, Richard H Scheuermann, Schobel Seth, Seto Donald, Shrivastava Susmita, Sterk Peter, Zeng Qiandong, Klimke William, Tatusova Tatiana

  Viruses. 01/2010;

  Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scien... [more] Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.
• 29.75

  Impact points

  Genomics. Genome project standards in a new era of sequencing.

  P S G Chain, D V Grafham, R S Fulton, M G Fitzgerald, J Hostetler, D Muzny, J Ali, B Birren, D. C. Bruce, C Buhay, [......], J Schmutz, S Sozhamannan, P Sterk, R L Strausberg, G Sutton, N. R. Thomson, J M Tiedje, G Weinstock, A Wollam, J C Detter

  Science (New York, N.Y.). 10/2009; 326(5950):236-7.

• Standards and standard-compliance.

  Peter Sterk

  Standards in genomic sciences. 01/2009; 1(3):216-7.

• Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7.

  Dawn Field, Peter Sterk, Nikos Kyrpides, Renzo Kottmann, Frank Oliver Glöckner, Lynette Hirschman, George M Garrity, John Wooley, Paul Gilna

  Standards in genomic sciences. 01/2009; 1(1):68-71.

  This report summarizes the proceedings of the 6th and 7th workshops of the Genomic Standards Consortium (GSC), held back-to-back in 2008. GSC 6 focused on furthering the activities of GSC working groups, GSC 7 focused on outreach to the wider community. GSC 6 was held October 10-14, 2008 at the Euro... [more] This report summarizes the proceedings of the 6th and 7th workshops of the Genomic Standards Consortium (GSC), held back-to-back in 2008. GSC 6 focused on furthering the activities of GSC working groups, GSC 7 focused on outreach to the wider community. GSC 6 was held October 10-14, 2008 at the European Bioinformatics Institute, Cambridge, United Kingdom and included a two-day workshop focused on the refinement of the Genomic Contextual Data Markup Language (GCDML). GSC 7 was held as the opening day of the International Congress on Metagenomics 2008 in San Diego California. Major achievements of these combined meetings included an agreement from the International Nucleotide Sequence Database Consortium (INSDC) to create a "MIGS" keyword for capturing "Minimum Information about a Genome Sequence" compliant information within INSDC (DDBJ/EMBL /Genbank) records, launch of GCDML 1.0, MIGS compliance of the first set of "Genomic Encyclopedia of Bacteria and Archaea" project genomes, approval of a proposal to extend MIGS to 16S rRNA sequences within a "Minimum Information about an Environmental Sequence", finalization of plans for the GSC eJournal, "Standards in Genomic Sciences" (SIGS), and the formation of a GSC Board. Subsequently, the GSC has been awarded a Research Co-ordination Network (RCN4GSC) grant from the National Science Foundation, held the first SIGS workshop and launched the journal. The GSC will also be hosting outreach workshops at both ISMB 2009 and PSB 2010 focused on "Metagenomics, Metadata and MetaAnalysis" (M(3)). Further information about the GSC and its range of activities can be found at http://gensc.org, including videos of all the presentations at GSC 7.