Transcript OBO-PO Cooper (LC 7 - ICBO

The Plant Ontology:
Development of a Reference
Ontology for all Plants
Plant Ontology Consortium Members and Curators*:
Laurel D. Cooper*, Justin Elser, Justin Preece and Pankaj Jaiswal*:
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
Ramona L. Walls* and Dennis W. Stevenson: The New York Botanical Garden, Bronx, NY
Maria A. Gandolfo: Department of Plant Biology, Cornell University, Ithaca, NY
Ontology Consultants:
Chris Mungall: Gene Ontology, Lawrence Berkeley National Lab, Berkeley, CA
Barry Smith: OBO Foundry, Department of Philosophy, University at Buffalo, NY
www.plantontology.org
Vision and Goals of the Plant
Ontology:
• Develop PO as a reference ontology for plants:
-describe anatomy and development of all plants
• Conform to OBO Foundry Principles of openness,
collaborative development and interoperability, etc *
• Facilitate annotation of comparative plant genomics
data
• Interact with other ontologies such as GO, TO, CARO, PATO,
etc
Challenges in expanding the Plant Ontology to cover
all plants:
Diversity in anatomy, morphology, life cycles, growth
patterns
Seed plants
(Angiosperms and Gymnosperms)
Pteridophytes
(Ferns and Lycopods)
Bryophytes
(Mosses, Hornworts and Liverworts)
Algae
Bowman et al, Cell, 2007
Phylogenetic diversity can result in inconsistency
in nomenclature:
Instances of leaf: (PO:0025034)
maple leaf pine needle
palm frond
Different names are used for the
same structure
Asteraceae
Poaceae
Different structures can have the same
name e.g. ‘floret’
The PO provides consistent terminology for
annotation of plant structures and growth and
developmental stages across taxa
Recent changes to the PO:
Two branches or subdomains of the PO are now merged:
Plant Anatomy Ontology (PAO)
Plant Growth and Development Stage Ontology (PGDSO)
Top level of PAO from CARO
plant anatomical entity
portion of plant substance
plant cell
plant structure
plant organ
H
portion of
plant tissue
cardinal organ
part
H
P
part_of
H
has_part
whole plant
vascular
system
P
collective plant
structure
is_a
plant anatomical space
collective organ part
structure
rhizoid
ovary
trichome
in vitro plant
structure
embryo plant
structure
Relations in the PO allow for an accurate
expression of biology
is_a and part_of are
the backbone of all
anatomical
ontologies
shoot system
has_part allows the PO to
handle structural variation
among taxa
is_a
reproductive
shoot system
is_a
flower
is_a
develops_from
describes shared
developmental
pathways across all
taxa
has_part
inflorescence
develops_from
infructescence
part_of
perianth
part_of
gynoecium
The participates_in relation links an anatomical
entity to a plant growth or development stage
whole plant
growth stage
plant structure
Example:
sporophyte
phase
plant
organ
participates_in
sporangium
Describes plant structures that only
occur during a specific growth and
development stages
is_a
A sporangium is_a plant organ
that produces spores which
participates_in a sporophyte phase
Ontology structure covers plant domain through
general and specific terms
General terms for all plants, or
homosporous plants
Specialized child terms for
heterosporous plants, like angiosperms
How the PO meets the OBO Foundry criteria:
1. Opennes- web browser, SVN, wiki
2. Common shared syntax- OBO and OWL
3. Unique identifier space: PO:xxxxxxx
4. Versioning system; #15, May 2011; etc
5. Orthogonality –yes, improving; e.g. PO-Cell
Ontology
6. Textual definitions- complete
OBO Foundry criteria, Cont.
7. Relations from the OBO Relation Ontology- yes
8. Documentation- on web and publications
9. Term request tracker on SourceForge- well utilized
10. Collaborative Development- recent examples
11. Plurality of user base – wide adoption, outreach
Documentation- on web and publications
* Cooper and Walls, et al. The Plant Ontology: A Comparative Plant Sciences Tool for All Plant Taxa, (In
preparation)
*Ilic et al, 2008. Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering
plants. In Anatomy Ontologies for Bioinformatics, Springer, 2008, p 27-42.
* Avraham et al, 2008. The Plant Ontology Database: a community resource for plant structure and
development stages controlled vocabulary and annotations. Nucleic Acid Research, 36(Database issue):D449D454
* Ilic et al, 2007. The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a
flowering plant.
Plant Physiology, 2007, 143: 587-599
* Jaiswal et al, 2005. Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages.
Comparative and Functional Genomics, 2005, Volume 6(7-8), 388 - 397
Collaborative development of the
PO:
Recent examples:
•Addition of terms for Musa (bananas), Solanaceae (potatos,etc)
• Added ~80 new terms in the recent release for the Physcomitrella
(Moss) Genome Annotation group
Wide range of Users and Collaborators:
Cell Ontology
Your logo could be here too!
The Plant Ontology facilitates comparative
plant genomics
Cross-taxa
comparisons:
AtMEE58
MEE58?
plant cell
I
fusiform
initial
I
D MEE58?
AtMEE58
axial cell
AtMEE58
>500,000+ associations for >1300 terms
I
xylem
element
I
MEE58?
hydroid
Annotations allow for data analysis:
Annotations may be created based on microarray, EST, QTL, protein, germplasm,
phenotype or other data sets, or whole genome sequencing projects.
Example microarray data set with PO and GO annotations:
PO terms corresponding to synonyms
used in the study:
* inflorescence (PO:0009049)
** shoot axis (PO:0025029)
*** whole plant in the seedling stage (PO:0000003)
Contact us if you are interested in providing and maintaining
annotations files for your project
Data Image From: Wang, et al. (2010). The Plant Journal, 61.
Tool Development:
PO web services being
developed for the
Semantic web:
Phenote annotation tool
being developed for use
by plant scientists
Future directions:
• Need to expand development of tools to link to other
ontologies, e.g. GO, CL
• Shortage of plant-specific phenotypic descriptors in
PATO
• Expanding genomics coverage of PO; e.g. TAIR, SGN,
Physcomitrella, MaizeGDB and ….?
Thanks!