Software Development by the Genomics Standards Consortium

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

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

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

MIGS Checklist 2.0 4 4 Field et al. Nat Biotechnol. 2008

MIGS Checklist 2.0 M = mandatory 5 5 Field et al. Nat Biotechnol. 2008

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

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

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

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

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

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

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

Habitat-Lite applied http://www.megx.net/genomes 13 13

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

Genomic Rosetta Stone (GRS) Van Brabant et al. OMICS. 2008 15 15

Genomic Rosetta Stone (GRS) Enable the integration of this information in the near future Van Brabant et al. OMICS. 2008 16 16

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

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

Genome Catalogue Online system for capturing MIGS/MIMS compliant reports Field et al. Nature 2008 21 21

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

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

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

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

END Looking forward to the discussion Join the GSC http://gensc.org 26 26

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Software Development by the Genomics Standards Consortium

by Renzo Kottmann on Jul 18, 2009

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