Download - International Coordination Meeting of Ontology-Based Efforts for Plant Biology PRO-PO-GO Meeting
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