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

pj37@cornell.edu

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