International Coordination Meeting of Ontology-Based Efforts for Plant Biology

PRO-PO-GO Meeting

Buffalo NYMay 15-16, 2013

Sponsored by

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The genomics and genetics data• More than 30 Reference Plant genomes sequenced

from important and diverse plant species including several crops by various international consortiums.

• Millions of data points representing:o Genetic diversity of crop plants from wild and

cultivated collections.o Arabidopsis 1001 genomes, 3000 rice, 5000

maize lines.o Phenotypes/agronomic traits.o Discovery of novel gene functions.o Climate modeling and impacts on various traits.

• Crop improvement programs by plant breeding .• Data hosted in various international projects and data

archives.

Users:• Researchers, Students, • Farmers, Agriculture extension programs• Policy makers and governments

Ontologies for Plants-1Gene Ontologies to the

Rescue

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity

(FMA, CARO) Phenotypic Quality(PaTO)

Organism-Level Process

(GO)Organ

Function(FMP, CPRO)

CELL AND CELLULAR

COMPONENTCell(CL)

Cellular Component(FMA, GO)

Cellular Function

(GO)Cellular Process

(GO)

MOLECULEMolecule

(ChEBI, SO,RNAO, PRO)

Molecular Function(GO)

Molecular Process

(GO)

GRANULARITY

RELATION TO TIME

Ontologies allowed computational reasoning of questions like:

• What is the function of my favorite gene (product)?

• What role does it play in a biological process?• What is the cellular component location of this

gene product?

All provided by the excellent use of Gene Ontology. However we needed to add more contextual information

to this annotation?

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Banana Soybean

Tomato

Rice Corn

Sorghum

Potato Cassava

Crop productsBunchFruitPodGrainKernelBerryTuberRoot

TraitsColorSizeShapeYieldTextureWeightNutritionCompositionAnatomyStressDiseases

PhenotypesYellowRedGreenElongatedRoughJuicyHardResistantTolerant

Differences in vocabularies & problems in data interpretations

Ontologies allowed computational reasoning of questions like:

• What is the function of my favorite gene (product)? • What role does it play in a biological process?• What is the cellular component location of this gene product?• In what plant part the gene product is expressed or display phenotype?

• At what growth stage of a plant do we see the gene expression or displayed phenotype?

• What anatomical plant structures and growth/developmental stages inherit the function and biological process associated with the above gene product?

• What is the phenotype of this gene?

All provided by the excellent use of Gene Ontology, Plant Ontology and Phenotype and Attribute Ontology (PATO).

However we needed more contextual information for annotation and refine the ontologies as well to cover all plant species?

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Details: Term-Term Relationships (anatomy example)

is_a and part_of are the backbone of all ontologies

develops_from describes shared developmental pathways across all taxons

has_part allows the PO to handle structural variation between taxons

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How Relationships Help In Comparative Genomics?

Bomblies K et al. Development 2003;130:2385-2395

ZM:zfl1

OS:RFL

AT:LFY

Source: Gramene

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO,

PO-Plant Structure)

Plant Trait Ontology

(TO)

Phenotypic Quality(PaTO)

Organism-Level Process

(GO)(PO-growth and

development stages)Organ

Function(FMP, CPRO)

CELL AND CELLULAR

COMPONENTCell(CL)

Cellular Componen

t(FMA, GO)

Cellular Function

(GO)Cellular Process

(GO)

MOLECULEMolecule

(ChEBI, SO,RNAO, PRO)

Molecular Function(GO)

Molecular Process

(GO)

GRANULARITY

Ontologies for Plants-2Plant Ontology to the rescue

RELATION TO TIME

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Crop Varieties, Germplasm and Genetic resources

EnvironmentGeographic locationClimateTreatmentsPestsPathogens

PhysiologyBiochemistry

GenomesGeneticsGenesGenomics

PhenotypesCharactersGene Functions

More Context is Required

Biological Questions

• List all the genes expressed differentially in the leaves of Rice plant varieties IRBB5 and IR24 at the 5-leaf visible growth stage, when the plants were infected with Xanthomonas oryzae pv. oryzae were grown in a growth camber. IRBB5 is resistant and IR24 is susceptible to rice bacterial blight disease.

• Filter the differentially expressed gene set for those with– LRR-domains– Transmembrane domains (e.g. in excess of 1)– Receptor like kinase function– Plasmamembrane cellular location– OR those having Tryptophan decarboxylase function– Tryptophan metabolism– Have known alleles and homologs with disease resistance phenotype

RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

COMPLEX OFORGANISMS

Population and Community Ontology (PCO)

Population Phenotype

Population Process

ORGANISMOrganism

(NCBI Taxonomy)Plant Species

Disease Ontology

(DO)

Phenotypic Quality(PATO)

Plant Trait Ontology

(TO)

Biological Process

(GO)

Plant Growth and

Development State (PO)

ORGANAnatomical Entity

(FMA, CARO, Uberon) Plant Structure Ontology

(PO)

CELL Cell (CL)Plant Cell (PO)

CELLULAR COMPONENT Cellular Component

(FMA, GO)

MOLECULE Molecule(ChEBI, SO, RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

Envi

ronm

ent O

ntol

ogy

(EN

VO

)Pl

ant E

nvir

onm

enta

l Con

ditio

ns (E

O)

Biological Questions• List all the genes expressed differentially in the leaves of Rice plant varieties

IRBB5 and IR24 at the 5-leaf visible growth stage, when the plants were infected/treated with Xanthomonas oryzae pv. oryzae were grown in a growth chamber with 60% humidity. IRBB5 is resistant and IR24 is susceptible to rice bacterial blight disease.

• List all the genes expressed differentially in response to pathogen Xanthomonas oryzae pv. in the leaves of rice IRBB5 and IR29.

• Filter the differentially gene set for those with– LRR-domains– Transmembrane domains (in excess of 5)– Receptor like kinase function– Plasmamembrane cellular location– OR those having Tryptophan decarboxylase function– Tryptophan metabolism– Have known alleles and homologs with disease resistance phenotype

PATO PO

PO

Tax

Tax/EO

OBJ

EO

EO PATOPATO

GO

PRO

GO

Disease

TO

Annotation: Ontology RequirementsObject Object

typeFeature or ontology Feature type Attribute

and scorecontext

XX

Plant/gene/gene-

product/ allele/pop

ulation

Molecular Function GO

PATO

Any of the ontologies including the environment ontology for adding context to the annotation.

E.g. PEP carboxylase activity (GO-MF) in maize is required for C4 carbon assimilation (GO-PB). The process occurs in the plastid (GO-CC) of the leaf mesophyll cell (PO).

Biological Process GO

Cellular component GO

Plant structure PO

Plant growth stage PO

(bio)chemical ChEBI

Disease DO

Protein Domains PROInterPro

Pathway Pathway??

Trait TO

* PRO = Protein Ontology

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Project Partners

Crop Trait Ontology Workshop. Oregon State University12-15 September 2012

OBO

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• Build bridges between diverse set of vocabularies by using reference ontologies.

• Core traits for target are: Yield, Quality, Drought and Disease resistance.

• Develop new and enrich existing field books and guides by integrating ontologies for use in data collection, training and education.

• Develop International partners and collaborations on data collection, annotation and analysis.

• Develop tools for comparative analysis using open data.

• Develop APPs for agriculture extension, genetics and biology researchers.

Project focus areas for crops

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Oregon State University

Cyril Pommier –INRA,BAP; EphesisJacques Legouis –INRAGEDEC, BreedwheatFrancois Tardieu-INRAPhenome, DROPS

Generation Challenge

ProgrammeIntegrated Breeding Platform

BBSRCRuth Bastow-GARnetChris Rawling-Rothamsted Res.

UNITED KINGDOM

Fabio Florani - JulichBjorn Usadel – AacehnUli Schurr – Julich DROPS

GERMANY

NSFCoordinator

Pankaj Jaiswal

J. HuttonLuke RamsayDave Marshall

EBIPaul Kersey

FRANCE

OBO-foundryBarry Smith

RCN PhenotypeNCBO & OBO-Foundry

Cornell, NYBGGramene, SGN, MaizeGDB, UniProt, GO, SoyBase, etc.

USDA - ARS

KBase (DOE)

Focus = Semantic integration framework• Develop Trait ontology for wheat, barley

& brassicaceae• Environment ontology from Phenotyping

platforms• Warehouse, mirroring on server –EBI• Community engagement

Focus = Expansion & Maintenance of the Reference Ontology for Plants and US Outreach• Coordinate the overall project and lead Ontology Development•Use case for the semantic integration framework•Develop data warehouse, visualization and analysis tools•Manage online resource at iPlant

Focus = Crop Ontology, Integrated Breeding Platform services- Breeding for development• Provision of traits and annotations of Wheat, Rice , Maize and

other crops : Cassava, Sorghum, Potato, Yam.• Contribution to the semantic framework• Community engagement

CGIARConsortiumElizabeth Arnaud

ERA-CAPSCoordinators

John Doonan, Aber Univ.Georgios Gkutos, Aber Un.

iPlant

cROP Project Partners

http://crop.cgrb.oregonstate.edu

Orhttp://tinyurl.com/crop-plants

Physical and/or Sequence map

Map-2

Polymorphism

Candidate gene

Gene models

Transcripts

Peptides

Function

Expression

Pathway

Orthologs

Comparative and Translational Genomics

Genetic markers & phenotypes (genes and QTL)

Map-1

Forward

Reverse

Genotype

Phenotype

Genotype

Phenotype

Genome

Map

Marker

Trait

Environment

Data Analysis

Pathway

Germplasm

Genes Ortholog

Are entities connected ?

Host Pathogen InteractionOrganism And Molecular Interactions

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PM

Extra cellular space

Pathogen

Plant HOST CELL

Plant (Disease) Stress Ontology

X

Y

Z

disease: rice bacterial leaf blight disease (IDO)| host species: Oryza sativa (rice) (taxon)| caused by: Xanthomonas oryzae (Taxon)| hassymptom: leaf color pale yellow (TO+PATO) | plant structure: vascular leaf | reported in: Northern Territory (GAZ) |

Ontologies

Spectrum of Controlled Vocabularies

http://www.mkbergman.com/?m=20070516

RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

COMPLEX OFORGANISMS

Population and Community Ontology (PCO)

Population Phenotype

Population Process

ORGANISMOrganism

(NCBI Taxonomy)Plant Species

Disease Ontology

(DO)

Plant Disease

Ontology (PDO)

Plant Infectious Disease

Ontology

Phenotypic Quality(PATO)

Plant Trait Ontology

(TO)

Biological Process

(GO)

Plant Growth and

Development State (PO)

ORGANAnatomical Entity

(FMA, CARO, Uberon) Plant Structure Ontology

(PO)

CELL Cell (CL)Plant Cell (PO)

CELLULAR COMPONENT Cellular Component

(FMA, GO)

MOLECULE Molecule(ChEBI, SO, RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

Envi

ronm

ent O

ntol

ogy

(EN

VO

)Pl

ant E

nvir

onm

enta

l Con

ditio

ns (E

O)

GO: Receptor like Kinase Gene:XA21

Allele-B

Allele-A

has_

func

tion

map

s_to

Oryza genotype

inhe

res_

in

GO: response to pathogen

belongs_to

Disease Ontology Example Building genotype-phenotype associations

cROP Goals A distributed international effort on development of ontologies for plant

specific knowledge domains . Collaborate with existing ontology development efforts for enrichment of

Plant specific terms. Develop standards for annotation of various plant biology data sets. Encourage adoption and integration of cROP ontologies. Invite collaborations on distributed annotation of plant biology data sets. Develop search and analysis tools. Includes integration of on/off-site

datasets and maintain a common information portal for ontology based annotations.

Provide ontologies and annotations via webservices. Collaborate with publishers and NLP projects on integration of cROP

markups, active learning and annotation.

RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

COMPLEX OFORGANISMS

Population and Community Ontology (PCO)

Population Phenotype

Population Process

ORGANISMOrganism

(NCBI Taxonomy)Plant Species

Disease Ontology

(DO)

Plant Disease

Ontology (PDO)

Plant Infectious Disease

Ontology

Phenotypic Quality(PATO)

Plant Trait Ontology

(TO)

Biological Process

(GO)

Plant Growth and

Development State (PO)

ORGANAnatomical Entity

(FMA, CARO, Uberon) Plant Structure Ontology

(PO)

CELL Cell (CL)Plant Cell (PO)

CELLULAR COMPONENT Cellular Component

(FMA, GO)

MOLECULE Molecule(ChEBI, SO, RnaO, PR)

Molecular Function(GO)

Molecular Process

(GO)

Envi

ronm

ent O

ntol

ogy

(EN

VO

)Pl

ant E

nvir

onm

enta

l Con

ditio

ns (E

O)

Open Biomedical and Biological Ontologies

Plant Trait Ontology Workshop

Alumni CenterOregon State University

Corvallis, OR

September 13-15, 2012

Funded by

Several Other Agencies Supporting Travel For Participants

Website: http://tinyurl.com/Trait-Ontology