Software Development by the Genomics Standards Consortium
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The document outlines the efforts of the Genomics Standards Consortium (GSC) to standardize genome descriptions and facilitate the exchange of genomic data. It introduces the Minimum Information about a Genome Sequence (MIGS) and Minimum Information about a Metagenomic Sequence (MIMS) specifications, which include mandatory reporting criteria for genomic data. Additionally, it discusses supporting software and infrastructure, such as the Genome Catalogue and genomic contextual data markup language (GCDML), to enhance data compliance and integration.
Software Development by the Genomics Standards Consortium
- 1. Bringing Standards to Life: Software Development by the Genomics Standards Consortium Renzo Kottmann Microbial Genomics Group Max Planck Institute for Marine Microbiology M3 SIG Stockholm July 2009 1
- 2. Genomic Standards Consortium (GSC) Goal • Promote mechanisms that standardize the description of genomes exchange and integrate genomic data Open-membership, international working body • Established in Sept 2005 • Participants include DDBJ, EMBL, GenBank, Sanger, JCVI, JGI, EBI and a range of US, UK and EU research institutions • Organized a series of workshops 2 2 http://gensc.org and http://gensc.org/gc_wiki/index.php/GSC_Membership
- 3. Minimum Information about a Genome Sequence (MIGS) Specification MIGS extends what DDBJ/EMBL/GenBank request upon submission of a genome sequence • Examples: Description of geographic location of a sample and habitat “Minimum Information about a Metagenomic Sequence” (MIMS) – Temperature – pH Description of sequence generation – Sequencing method – Assembly method 3 3 Field et al. Nat Biotechnol. 2008
- 4. MIGS Checklist 2.0 4 4 Field et al. Nat Biotechnol. 2008
- 5. MIGS Checklist 2.0 M = mandatory 5 5 Field et al. Nat Biotechnol. 2008
- 6. Software Development for MIGS/MIMS Mechanisms for achieving compliance are needed: • Such mechanisms involve an appropriate reporting structure for capturing and exchanging data, software, databases and controlled vocabularies and/or ontologies for defining the terms used in the annotations. 6 Field et al. Nat Biotechnol. 2008
- 7. Software Development for MIGS/MIMS Mechanisms for Supporting Projects: achieving compliance • Habitat-Lite (Ontology are needed: specification) • Such mechanisms involve an appropriate reporting structure for capturing and exchanging data, software, databases and controlled vocabularies and/or ontologies for defining the terms used in the annotations. 7 Field et al. Nat Biotechnol. 2008
- 8. Software Development for MIGS/MIMS Mechanisms for Supporting Projects: achieving compliance • Habitat-Lite (Ontology are needed: specification) • Such mechanisms • Genomic Rosetta Stone involve (Identifier Mapping) an appropriate reporting structure for capturing and exchanging data, software, databases and controlled vocabularies and/or ontologies for defining the terms used in the annotations. 8 Field et al. Nat Biotechnol. 2008
- 9. Software Development for MIGS/MIMS Mechanisms for Supporting Projects: achieving compliance • Habitat-Lite (Ontology are needed: specification) • Such mechanisms • Genomic Rosetta Stone involve (Identifier Mapping) an appropriate reporting • GCDML (MIGS/MIMS structure for capturing and exchanging data, specification in XML) software, databases and controlled vocabularies and/or ontologies for defining the terms used in the annotations. 9 Field et al. Nat Biotechnol. 2008
- 10. Software Development for MIGS/MIMS Mechanisms for Supporting Projects: achieving compliance • Habitat-Lite (Ontology are needed: specification) • Such mechanisms • Genomic Rosetta Stone involve (Identifier Mapping) an appropriate reporting • GCDML (MIGS/MIMS structure for capturing and exchanging data, specification in XML) software, • Genomes Catalogue databases (Database and Web and controlled Server) vocabularies and/or ontologies for defining the terms used in the annotations. 10 Field et al. Nat Biotechnol. 2008
- 11. Aquatic Aquatic: Freshwater Acquatic: Marine Terrestrial Air Fossil Food Organism-Associated Extreme Habitat Other Habitat-Lite (= EnvO-Lite) Easy-to-use (small) set of terms • Captures high-level information about habitat • Derived from the Environment Ontology (EnvO). Meet the needs of multiple users • Annotators, database providers, biologists, and bioinformaticians alike who need to search and employ such data in comparative analyses. Hirschman et al. OMICS. 2008 11 11
- 12. Habitat-Lite 1. Level 2. Level Aquatic soil Aquatic: Freshwater sediment Aquatic: Marine sludge Terrestrial waste water Air hot spring Fossil hydrothermal vent Food biofilm Organism-Associated microbial mat Extreme Habitat Other < 20 terms Hirschman et al. OMICS. 2008 12 12
- 13. Habitat-Lite applied http://www.megx.net/genomes 13 13
- 14. Genomic Rosetta Stone (GRS) Create a unified mapping between different genomic resources Improve navigation across these resources Enable the integration of this information in the near future. Van Brabant et al. OMICS. 2008 14 14
- 15. Genomic Rosetta Stone (GRS) Van Brabant et al. OMICS. 2008 15 15
- 16. Genomic Rosetta Stone (GRS) Enable the integration of this information in the near future Van Brabant et al. OMICS. 2008 16 16
- 17. Genomic Contextual Data Markup Language (GCDML) An Extensible Markup Language (XML) Aim • Implement MIGS/MIMS • Provide even more descriptors • Facilitate exchange and integration of genomic data Kottmann et al. OMICS. 2008 17 17
- 18. GCDML Example (excerpt) <gcdml:originalSample> <gcdml:physicalMaterial> <gcdml:samplingTime><gcdml:notGiven>unknown</gcdml:notGiven></gcdml:samplingTime> <gcdml:samplePointLocation> <gml:LocationKeyWord>Baltic Sea</gml:LocationKeyWord> <gml:LocationString>Kiel Fjord, Baltic Sea, Germany</gml:LocationString> <gcdml:pos2D>54.329 10.149</gcdml:pos2D> <gcdml:determinationMethod>derived from literature</gcdml:determinationMethod> </gcdml:samplePointLocation> <gcdml:marineHabitat> <gcdml:waterBody> <gcdml:depth> <gcdml:measure min="0.00" max="0.05“><gcdml:values uom="m">0.00 0.05</gcdml:values></gcdml:measure> </gcdml:depth> </gcdml:waterBody> </gcdml:marineHabitat> <gcdml:materialType>seawater</gcdml:materialType> <gcdml:amount><gcdml:measure><gcdml:values uom="ml">100</gcdml:values></gcdml:measure></gcdml:amount> </gcdml:physicalMaterial> </gcdml:originalSample> 18 Kottmann et al. OMICS. 2008 18
- 19. GCDML Example (excerpt) <gcdml:originalSample> <gcdml:physicalMaterial> <gcdml:samplingTime><gcdml:notGiven>unknown</gcdml:notGiven></gcdml:samplingTime> <gcdml:samplePointLocation> <gml:LocationKeyWord>Baltic Sea</gml:LocationKeyWord> <gml:LocationString>Kiel Fjord, Baltic Sea, Germany</gml:LocationString> <gcdml:pos2D>54.329 10.149</gcdml:pos2D> <gcdml:determinationMethod>derived from literature</gcdml:determinationMethod> </gcdml:samplePointLocation> <gcdml:marineHabitat> <gcdml:waterBody> <gcdml:depth> <gcdml:measure min="0.00" max="0.05“><gcdml:values uom="m">0.00 0.05</gcdml:values></gcdml:measure> </gcdml:depth> </gcdml:waterBody> </gcdml:marineHabitat> <gcdml:materialType>seawater</gcdml:materialType> <gcdml:amount><gcdml:measure><gcdml:values uom="ml">100</gcdml:values></gcdml:measure></gcdml:amount> </gcdml:physicalMaterial> </gcdml:originalSample> 19 Kottmann et al. OMICS. 2008 19
- 20. GCDML Example (excerpt) <gcdml:originalSample> <gcdml:physicalMaterial> <gcdml:samplingTime><gcdml:notGiven>unknown</gcdml:notGiven></gcdml:samplingTime> <gcdml:samplePointLocation> <gml:LocationKeyWord>Baltic Sea</gml:LocationKeyWord> <gml:LocationString>Kiel Fjord, Baltic Sea, Germany</gml:LocationString> <gcdml:pos2D>54.329 10.149</gcdml:pos2D> <gcdml:determinationMethod>derived from literature</gcdml:determinationMethod> </gcdml:samplePointLocation> <gcdml:marineHabitat> <gcdml:waterBody> <gcdml:depth> <gcdml:measure min="0.00" max="0.05“><gcdml:values uom="m">0.00 0.05</gcdml:values></gcdml:measure> </gcdml:depth> </gcdml:waterBody> </gcdml:marineHabitat> <gcdml:materialType>seawater</gcdml:materialType> <gcdml:amount><gcdml:measure><gcdml:values uom="ml">100</gcdml:values></gcdml:measure></gcdml:amount> </gcdml:physicalMaterial> </gcdml:originalSample> 20 Kottmann et al. OMICS. 2008 20
- 21. Genome Catalogue Online system for capturing MIGS/MIMS compliant reports Field et al. Nature 2008 21 21
- 22. Genome Catalogue Requirements • A Rich toolkit/user-friendly • Designed to give credit to all contributors • XML-based (GCDML) Able to maintain all versions of GCDML schemas • Web services-based Supporting the automated exchange of content • Serve as the international GCAT identifier authority • Comprehensive Containing reports for all taxa and metagenomes • Ontology-supportive • Shared by the GSC 22 22
- 23. Current Status We have specifications: • MIGS/MIMS • Habitat-Lite • Genomic Rosetta Stone Work on supporting software is ongoing: • Genomes Catalogue is in prototype status • Funding This is a long-term endeavour that can not be done on a voluntary basis 23 23
- 24. Disscusion Need of software for: • Creation of MIGS/MIMS data • Storage • Analysis Expand standardization efforts to • Software specification/development • Work on a standardized genomic data management architecture / cyberinfrastructure Data intensive science is successful if it works towards one community with one vision • World Wide Genomics project 24 24
- 25. Acknowledgements All Members of GSC incl. Dawn Field Peter Sterk Saul Kravitz Tanya Gray Megx.net team Frank Oliver Glöckner Ivaylo Kostadinov Melissa Beth Duhaime Pier Luigi Buttigieg Wolfgang Hankeln Pelin Yilmaz 25
- 26. END Looking forward to the discussion Join the GSC http://gensc.org 26 26