Transcript Ontologies (Susan McCouch) ()

A Comparative mapping resource
ONTOLOGY DEVELOPMENT AND
INTEGRATION IN GRAMENE
http://www.gramene.org
Pankaj Jaiswal
Cornell University
Acknowledgements
Leonore 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
What is an Ontology ?
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.
Ontology Types
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)
Anatomy concept
Each 'child term' has a unique relationship to its 'parent term'.
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.
Ontology concept
organ
shoot
inflorescence
term
Part of
Instance of
Plant structure
Fl1
dl1
stl1
cps
Du8
genes
tissue
flower
floral organ
sepal
petal
Cps
stl1
Du8
Du8
stamen
dl1
stl1
cps
Du8
anther
pollen
tapetum
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
Pattern
ISS: Inferred from sequence or
structural similarity
Ontology Annotation includes various experimental
evidence codes
ISS
IDA
IPI
TAS
NAS
IMP
IGI
IEP
IC
IEA
ND
Inferred from Sequence/Structural Similarity
Inferred from Direct Assay
Inferred from Physical Interaction
Traceable Author Statement
Non-traceable Author Statement
Inferred from Mutant Phenotype
Inferred from Genetic Interaction
Inferred from Expression Pattern
Inferred by Curator
Inferred from electronic annotation
No Data available
Ontology Annotation includes various experimental
evidence codes
ISS
IDA
IPI
TAS
NAS
IMP
IGI
IEP
IC
ND
Inferred from Sequence/Structural Similarity
Inferred from Direct Assay
Inferred from Physical Interaction
Traceable Author Statement
Non-traceable Author Statement
Inferred from Mutant Phenotype
Inferred from Genetic Interaction
Inferred from Expression Pattern
Inferred by Curator
No Data available
IEA
Inferred from electronic annotation
How to find your favorite phenotype ?
Type your query
e.g. search for plant part stem
in Plant Ontology
Select “Plant Ontology”
Features of a PO term
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”
PO Associations
Mutant gene symbol
(allows alphabetical sorting)
Children terms in the
tree following the
Primary vocabulary
term for which the
protein function was
annotated
Mutant gene name.
Links to the
Gramene mutant
entry page
Suggests the type of experiments
carried out to ascertain its function.
TAS: Traceable Author Statement
IAGP: Inferred from association
between genotype and phenotype
How to find your favorite phenotype expressed at
a given growth stage ?
Type your query
e.g. search for plant growth
stage germination in Plant
Ontology
Select “Plant Ontology”
Follow the search results by selecting the term e.g.“germination” in rice
(GRO:0007051). Display / download all associations to view associated phenotypes.
How to find your favorite phenotype by trait association ?
C. Hit Search button
A. Type your query
e.g. search for plant
trait plant height
B. Select “Trait Ontology”
The assayed trait
When 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
[email protected]. We will be happy to help you
guide through the annotation process.