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Building Communities Around Ontology Development

Building Communities Around Ontology Development. Pankaj Jaiswal Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY pj37@cornell.edu FAO, Rome, Italy September 22, 2007. Gene Ontology Collaborators. Many More Organizations and Numerous Users.

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Building Communities Around Ontology Development

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  1. Building Communities Around Ontology Development Pankaj Jaiswal Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY pj37@cornell.edu FAO, Rome, Italy September 22, 2007

  2. Gene Ontology Collaborators Many More Organizations and Numerous Users Core funding by the National Institute of Health. Several other individual institutional grants from NSF, USDA, MRC, etc.

  3. Plant Ontology Collaborators Many More Organizations and Numerous Users Funded by the National Science Foundation

  4. Starch biosynthesis pathway Chr – 6, Genomic region Gene LOC_Os06g12450.1 LOC_Os06g04200.1 LOC_Os06g51084.1 LOC_Os06g06560.1 QTL AQBN002 -Amylose content, AQCF021 -Grain yield AQGA015 - Amylose content, AQBP002 -Wx AQBN003 Amylose content AQCV039 Chalky endosperm AQCV027 -Chalky endosperm, AQFU016-Amylose content Mutant phenotype wx du9 sbe1 du11

  5. Genetic map-1 Genetic map-2 Physical or Sequence map Inter and Intra Specific Comparative and Translational Genomics and Genetics Polymorphism Candidate gene Gene models Transcripts Peptides Function Expression Pathway Orthologs/homologs Phenotypes/traits/genes identified/ mapped genetically

  6. Starch Biosynthesis From pathway to diversity/germplasm Olsen et al, 2006 – GR_Ref_ID -7050 Germplasm information Nucleotide variation at the Waxy gene

  7. “Infected” Group the relevant genes for Function, location in a cell, role in a process or by phenotypes using Ontologies

  8. is_a (subtype) part_of develops_from plant structure cell tissue sporophyte organ root epidermis root epidermis trichoblast root hair Building the ontology and term-to-term relationships

  9. How does it work? • Some of the ontologies describing the biology. • Gene Ontology (GO) to describe a protein/gene's biochemical property • Molecular Function (e.g. transporter, enzyme) • Role in a Biological Process (e.g. photosynthesis, defense response) • Localization in a Cellular Component (e.g. plastid, cell wall) • Plant Ontology (PO)to describe a protein/gene/phenotype expression • In aPlant Anatomy(e.g. panicle, flower, xylem, phloem) • At aGrowth Stage(e.g. germination, embryo development) • Trait Ontology (TO)to describe the observable feature assayed to determine the phenotype. • Plant traits (e.g. leaf color, plant height, disease resistance) • Environment Ontology (EO) to describe the supplemental treatments and the ecological habitats where a plant sample is subjected to phenotype evaluation (UV light, drought, pests and pathogens)

  10. Ontology collections and registry

  11. Ontologies for use in different formats

  12. Ontology request monitoring via bug tracking tools

  13. Ontology request monitoring via bug tracking tools and open mailing lists

  14. Ontology Management and Standards

  15. Editing and Managing the Ontology Literature OBO-Editor Commit to cvs Database Annotation

  16. Ontology mappings to various other database vocabularies

  17. Ontology Annotations driving the ontology development and uses

  18. Participation in ontology development

  19. Google analytics score for Plant Ontology website traffic tracking

  20. Helpful things • www.geneontology.org • www.plantontology.org • www.gramene.org • www.obofoundry.org • OBOrelations: paper by Chris Mungall and Barry Smith • oboL: paper by Chris Mungall • OBOEdit (ontology editor) download from Sourceforge

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