Building Communities Around Ontology Development

Building Communities Around Ontology Development Pankaj Jaiswal Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY [email_address] FAO, Rome, Italy September 22, 2007

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

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

LOC_Os06g04200.1 LOC_Os06g06560.1 LOC_Os06g12450.1 LOC_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 phenotype wx du11 du9 sbe1 Starch biosynthesis pathway LOC_Os06g14510.1

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

Nucleotide variation at the Waxy gene Olsen et al, 2006 – GR_Ref_ID -7050 Germplasm information Starch Biosynthesis From pathway to diversity/germplasm +1.1864 0.972 0.0213 9 O. rufipogon − 1.5374 0.800 0.0037 6
cv aromatic
+2.0874 0.733 0.0028 6
cv aus
− 2.6149 0.476 0.00109 22
cv temp japonica
− 1.5037 0.739 0.0002 18
cv trop japonica
+0.3726 0.952 0.0059 21
cv indica
+0.4991 0.845 0.0056 73 O. sativa Tajima's D Haplotype diversity Nucleotide diversity (π) a Sample size ( n ) Group

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

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

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?

Ontology collections and registry

Ontologies for use in different formats

Ontology request monitoring via bug tracking tools

Ontology request monitoring via bug tracking tools and open mailing lists

Ontology Management and Standards

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

Ontology mappings to various other database vocabularies

Ontology Annotations driving the ontology development and uses

Participation in ontology development

Google analytics score for Plant Ontology website traffic tracking

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

Building Communities Around Ontology Development

by AIMS (Agricultural Information Management Standards) FAO of the UN on Feb 22, 2011

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