A Comparative mapping resource

http://www.gramene.org

ONTOLOGY DEVELOPMENT AND INTEGRATION IN GRAMENE

Pankaj JaiswalCornell University

AcknowledgementsLeonore Reiser

Sue Rhee

Tanya Berardini

Leszek Vincent

Mary Polacco

Toby Kellogg

Peter Stevens

Yukiko Yamazaki

Nori Kurata

Michael Ashburner

Midori Harris

Dom Paolillo Jr.

Richard Bruskiewich

Graham McLaren

An Ontology is a glossary of keywords arranged in a structured order or a network, and the organization is based on biological concepts.

This structure is a type of hierarchy that reflects biological concepts and relationships.

The nodes at the top (“root”) of the tree are more general cases, and the more specific terms are at the bottom (“leaves”) of the structure.

What is an Ontology ?

In Gramene we have ontologies that are organized around three different types of biological concepts.

•Gene Ontology (GO) describes a protein/gene's biochemical properties

• 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) describes where and when a protein, gene or phenotype is expressed

• In a Plant Anatomy (e.g. panicle, flower, xylem, phloem)

• At a Growth Stage (e.g. germination, embryo development)

•Trait Ontology (TO) describes the observable features that are assayed to determine the phenotype.

• Plant traits (e.g. leaf color, plant height, disease resistance)

Ontology Types

Anatomy concept

Instance of (is a type of):

Used to describe the relationship between a child term and a more general parent term. For example: a caryopsis is a type of fruit; a panicle is a type of inflorescence.

Part of:

Used to indicate the relationship between a child term that is a part of the parent term. For example: the ectocarp is a part of the pericarp, which in turn is part of the fruit.

Develops from:

Used to describe the relationship between a child term that develops from its parent term. For example: a seed coat (testa) develops from the integuments; a leaf develops from a leaf primordium.

Each 'child term' has a unique relationship to its 'parent term'.

termPlant structure

inflorescence

flower

tissue

organ

tapetum

stamen

anther

pollen

shoot

floral organ

sepal petaldl1stl1cpsDu8

Cpsstl1Du8

Du8

Fl1dl1stl1cpsDu8

genes

Part ofInstance of

Ontology concept

How to build associations?

How to build associations?

Ontology Uses

• The vocabularies/keywords (ontology) are used to annotate:

•Molecular characteristics of a protein and/or gene.

•Tissue specific expression profile of a gene or phenotype

•Observable feature (trait) assayed to determine a phenotype

• These annotations (associations) are recorded in databases such as Gramene.

• These keywords help in searching your favorite gene/protein/phenotype

• Can help find your favorite gene/phenotype and also discover other functional or phenotypic homologs

How to find your favorite gene product (protein) ?

Click “Ontology” on the Gramene navigation bar

Select “Gene Ontology” Type your query e.g. search for function alpha-amylase in Gene Ontology

Click here for more help on Ontology

Suggests the type of experiments carried out to ascertain its function.IEP: Inferred from Expression PatternISS: Inferred from sequence or structural similarity

Ontology Annotation includes various experimental evidence codes

ISSISS Inferred from Sequence/Structural SimilarityInferred from Sequence/Structural Similarity

IDAIDA Inferred from Direct AssayInferred from Direct Assay

IPIIPI Inferred from Physical InteractionInferred from Physical Interaction

TASTAS Traceable Author StatementTraceable Author Statement

NASNAS Non-traceable Author StatementNon-traceable Author Statement

IMPIMP Inferred from Mutant PhenotypeInferred from Mutant Phenotype

IGIIGI Inferred from Genetic InteractionInferred from Genetic Interaction

IEPIEP Inferred from Expression PatternInferred from Expression Pattern

ICIC Inferred by CuratorInferred by Curator

IEAIEA Inferred from electronic annotationInferred from electronic annotation

NDND No Data availableNo Data available

Ontology Annotation includes various experimental evidence codes

ISS Inferred from Sequence/Structural SimilarityIDA Inferred from Direct AssayIPI Inferred from Physical InteractionTAS Traceable Author StatementNAS Non-traceable Author StatementIMP Inferred from Mutant PhenotypeIGI Inferred from Genetic InteractionIEP Inferred from Expression PatternIC Inferred by CuratorND No Data available

IEA Inferred from electronic annotation

Select “Plant Ontology”Type your query e.g. search for plant part stem in Plant Ontology

How to find your favorite phenotype ?

Stem is a PART OF “vegetative Shoot” and also a PART Of “secondary axillary shoot”

# Number of mutants associated with this plant part

Download/Display all the phenotypes associated

with “stem”

Features of a PO term

Suggests the type of experiments carried out to ascertain its function.TAS: Traceable Author StatementIAGP: Inferred from association between genotype and phenotype

Mutant gene symbol(allows alphabetical sorting)

Mutant gene name. Links to the Gramene mutant entry page

Children terms in the tree following the Primary vocabulary term for which the protein function was annotated

PO Associations

Select “Plant Ontology”

Type your query e.g. search for plant growth stage germination in Plant Ontology

How to find your favorite phenotype expressed at a given growth stage ?

Follow the search results by selecting the term e.g.“germination” in rice (GRO:0007051). Display / download all associations to view associated phenotypes.

B. Select “Trait Ontology”A. Type your query e.g. search for plant trait plant height

C. Hit Search button

How to find your favorite phenotype by trait association ?

The assayed traitWhen was it assayed ?

Where was it assayed ?

What else can YOU do?

• Send us your review of the terms, definitions and relationships to ensure accuracy.

• Suggest new terms, definitions, or improvements to the structures.

• Use the terms in describing data in publications and databases.

• If your project on cereal plants is generating data sets that may require these kinds of annotations and associations, please feel free to reach us at gramene@gramene.org. We will be happy to help you guide through the annotation process.