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Transcript of 1 Building Communities Around Ontology Development Pankaj Jaiswal Dept. of Plant Breeding and...
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Building Communities Around Ontology Development
Pankaj Jaiswal
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY
FAO, Rome, Italy
September 22, 2007
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Gene Ontology Collaborators
Core funding by the National Institute of Health. Several other individual institutional grants from NSF, USDA, MRC, etc.
Many More Organizations and
Numerous Users
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Plant Ontology Collaborators
Funded by the National Science Foundation
Many More Organizations and
Numerous Users
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LOC_Os06g04200.1
LOC_Os06g06560.1
LOC_Os06g12450.1
LOC_Os06g14510.1LOC_Os06g51084.1
AQBN003
Amylose content
AQGA015 - Amylose content, AQBP002 -Wx
AQCV027 -Chalky endosperm, AQFU016-Amylose content
AQBN002 -Amylose content, AQCF021 -Grain yield
AQCV039
Chalky endosperm
Chr – 6, Genomic region
Gene
QTL
Mutant
phenotypewx du11 du9 sbe1
Starch biosynthesis pathway
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Polymorphism
Candidate gene
Gene models
Transcripts
Peptides
Function
Expression
Pathway
Orthologs/homologs
Inter and Intra Specific Comparative and Translational Genomics and Genetics
Phenotypes/traits/genes identified/ mapped genetically
Physical or
Sequence map
Genetic map-2
Genetic map-1
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Nucleotide variation at the Waxy gene
Group Sample size (n)
Nucleotide diversity (π)a
Haplotype diversity
Tajima's D
O. sativa 73 0.0056 0.845 +0.4991
• cv indica 21 0.0059 0.952 +0.3726
• cv trop japonica 18 0.0002 0.739 −1.5037
• cv temp japonica 22 0.00109 0.476 −2.6149
• cv aus 6 0.0028 0.733 +2.0874
• cv aromatic 6 0.0037 0.800 −1.5374
O. rufipogon 9 0.0213 0.972 +1.1864
Olsen et al, 2006 – GR_Ref_ID -7050
Germplasm information
Starch BiosynthesisFrom pathway to
diversity/germplasm
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“Infected”
Group the relevant genes for Function, location in a cell, role in a process or by phenotypes using Ontologies
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plant structure
tissuesporophyte
root
trichoblast
root hair
root epidermis
epidermis
cell organ
is_a (subtype)
part_of
develops_from
Building the ontology and term-to-term relationships
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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 a Plant Anatomy (e.g. panicle, flower, xylem, phloem)
• At a Growth 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)
How does it work?
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Ontology collections and registry
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Ontologies for use in different formats
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Ontology request monitoring via bug tracking tools
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Ontology request monitoring via bug tracking tools and open mailing lists
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Ontology Management and Standards
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Editing and Managing the Ontology
Literature OBO-Editor Commit to cvs Database Annotation
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Ontology mappings to various other database vocabularies
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Ontology Annotations driving the ontology development and uses
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Participation in ontology development
20Google analytics score for Plant Ontology website traffic tracking
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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