international coordination meeting of ontology based efforts for plant biology pro po go meeting n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
International Coordination Meeting of Ontology-Based Efforts for Plant Biology PRO-PO-GO Meeting PowerPoint Presentation
Download Presentation
International Coordination Meeting of Ontology-Based Efforts for Plant Biology PRO-PO-GO Meeting

Loading in 2 Seconds...

play fullscreen
1 / 28

International Coordination Meeting of Ontology-Based Efforts for Plant Biology PRO-PO-GO Meeting - PowerPoint PPT Presentation


  • 76 Views
  • Uploaded on

International Coordination Meeting of Ontology-Based Efforts for Plant Biology PRO-PO-GO Meeting. Buffalo NY May 15-16, 2013 Sponsored by. The genomics and genetics data.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'International Coordination Meeting of Ontology-Based Efforts for Plant Biology PRO-PO-GO Meeting' - keene


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
international coordination meeting of ontology based efforts for plant biology pro po go meeting

International Coordination Meeting of Ontology-Based Efforts for Plant BiologyPRO-PO-GO Meeting

Buffalo NY

May 15-16, 2013

Sponsored by

slide2

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:
      • Genetic diversity of crop plants from wild and cultivated collections.
        • Arabidopsis 1001 genomes, 3000 rice, 5000 maize lines.
      • Phenotypes/agronomic traits.
      • Discovery of novel gene functions.
      • 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
slide3

RELATION TO TIME

GRANULARITY

Ontologies for Plants-1

Gene Ontologies to the Rescue

ontologies allowed computational reasoning of questions like
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?

slide5

Differences in vocabularies & problems in data interpretations

Rice

Corn

Banana

Soybean

Crop products

Bunch

Fruit

Pod

Grain

Kernel

Berry

Tuber

Root

Tomato

Traits

Color

Size

Shape

Yield

Texture

Weight

Nutrition

Composition

Anatomy

Stress

Diseases

Phenotypes

Yellow

Red

Green

Elongated

Rough

Juicy

Hard

Resistant

Tolerant

Sorghum

Cassava

Potato

ontologies allowed computational reasoning of questions like1
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?

details term term relationships anatomy example
Details: Term-Term Relationships (anatomy example)

is_a andpart_ofare 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

how relationships help in comparative genomics
How Relationships Help In Comparative Genomics?

ZM:zfl1

OS:RFL

AT:LFY

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

Source: Gramene

slide9

RELATION TO TIME

GRANULARITY

Ontologies for Plants-2

Plant Ontology to the rescue

slide10

More Context is Required

Crop Varieties, Germplasm and

Genetic resources

Environment

Geographic location

Climate

Treatments

Pests

Pathogens

Genomes

Genetics

Genes

Genomics

Phenotypes

Characters

Gene Functions

Physiology

Biochemistry

biological questions
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 Xanthomonasoryzaepv. oryzaewere 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
slide12

Environment Ontology (ENVO)

Plant Environmental Conditions (EO)

biological questions1
Biological Questions

PATO

PO

Tax

OBJ

PO

  • 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 Xanthomonasoryzaepv. oryzaewere 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 Xanthomonasoryzaepv. 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

Tax/EO

EO

PATO

PATO

EO

Disease

GO

PRO

GO

TO

annotation ontology requirements
Annotation: Ontology Requirements

* PRO = Protein Ontology

slide15

Project Partners

OBO

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

slide16

Project focus areas for crops

  • 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.
slide17

cROP Project Partners

J. Hutton

Luke Ramsay

Dave Marshall

Cyril Pommier –INRA,BAP; Ephesis

Jacques Legouis –INRAGEDEC, Breedwheat

Francois Tardieu-INRAPhenome, DROPS

BBSRC

Ruth Bastow-GARnet

Chris Rawling-Rothamsted Res.

UNITED KINGDOM

FRANCE

EBI

Paul Kersey

  • ERA-CAPS
  • Coordinators
  • John Doonan, Aber Univ.
  • GeorgiosGkutos, Aber Un.

Fabio Florani - Julich

Bjorn Usadel – Aacehn

UliSchurr – Julich DROPS

  • Focus = Semantic integration framework
  • Develop Trait ontology for wheat, barley & brassicaceae
  • Environment ontology from Phenotyping platforms
  • Warehouse, mirroring on server –EBI
  • Community engagement
  • Generation Challenge Programme
  • Integrated Breeding Platform

GERMANY

Cornell, NYBG

Gramene, SGN, MaizeGDB,

UniProt, GO, SoyBase, etc.

  • CGIAR
  • Consortium
  • Elizabeth Arnaud

iPlant

Oregon State University

KBase (DOE)

USDA - ARS

  • 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

NCBO & OBO-Foundry

RCN Phenotype

  • 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

OBO-foundry

Barry Smith

slide18

http://crop.cgrb.oregonstate.edu

Or

http://tinyurl.com/crop-plants

slide19

Genotype

Polymorphism

Candidate gene

Gene models

Transcripts

Peptides

Function

Expression

Pathway

Orthologs

Genetic markers & phenotypes (genes and QTL)

Map-1

Map-2

Physical and/or

Sequence map

Phenotype

Comparative and Translational Genomics

Forward

Reverse

slide20

Phenotype

Data

Analysis

Genotype

Trait

Germplasm

Marker

Environment

Map

Genome

Pathway

Genes

Ortholog

Are entities connected ?

host pathogen interaction organism and molecular interactions
Host Pathogen InteractionOrganism And Molecular Interactions

Plant

HOST CELL

PM

Extra cellular space

Pathogen

plant disease stress ontology
Plant (Disease) Stress Ontology

disease: rice bacterial leaf blight disease (IDO)

| host species: Oryza sativa (rice) (taxon)

| caused by: Xanthomonasoryzae (Taxon)| has

symptom: leaf color pale yellow (TO+PATO) | plant structure: vascular leaf | reported in: Northern Territory (GAZ) |

slide23

Ontologies

Spectrum of Controlled Vocabularies

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

slide24

Key:

Purple stars: New Ontologies to be developed

Cyan stars: work with the existing collaborator ontologies for desired plant enrichment

Yellow stars: ongoing in-house efforts

Environment Ontology (ENVO)

Plant Environmental Conditions (EO)

disease ontology example building genotype phenotype associations

GO: response to pathogen

Disease Ontology Example Building genotype-phenotype associations

Allele-B

GO: Receptor like Kinase

Gene:XA21

maps_to

Allele-A

has_function

inheres_in

belongs_to

Oryza genotype

crop goals
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.
slide27

Open Biomedical and Biological Ontologies

Environment Ontology (ENVO)

Plant Environmental Conditions (EO)

slide28

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

Plant Trait Ontology Workshop

Alumni Center

Oregon State University

Corvallis, OR

September 13-15, 2012

Funded by

Several Other Agencies Supporting Travel For Participants