The Plant Ontology: Development of a Reference Ontology for all Plants
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Transcript of The Plant Ontology: Development of a Reference Ontology for all Plants
The Plant Ontology: Development of a Reference
Ontology for all Plants
www.plantontology.org
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, CABarry Smith: OBO Foundry, Department of Philosophy, University at Buffalo, NY
Vision and Goals of the Plant Ontology:
• Develop PO as a reference ontology for plants:-describe anatomy and development of all plants
• Facilitate annotation of comparative plant genomics data
• Interact with other ontologies such as GO, TO, CARO, PATO, etc
• Conform to OBO Foundry Principles of openness, collaborative development and interoperability, 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 palm frond pine needle
Different names are used for the same structure
The PO provides consistent terminology for annotation of plant structures and growth and
developmental stages across taxa
Different structures can have the same name e.g. ‘floret’
Asteraceae Poaceae
Two branches or subdomains of the PO are now merged:
Plant Growth and Development Stage Ontology (PGDSO)
Plant Anatomy Ontology (PAO)
Recent changes to the PO:
Top level of PAO from CARO
is_apart_ofhas_partH
P
plant anatomical entity
plant anatomical spaceplant structureportion of plant substance
plant organ portion of plant tissue
whole plantplant cell
cardinal organ part
collective plant structure
collective organ part structure
trichome embryo plant structure
in vitro plant structure
rhizoid
H P
vascular system
ovaryH
Relations in the PO allow for an accurate expression of biology
is_a and part_of are the backbone of all anatomical ontologies
has_part allows the PO to handle structural variation among taxa
develops_from describes shared developmental pathways across all taxa
reproductive shoot system
inflorescence
flower
part_of
infructescence
has_partis_a
gynoeciumperianth
shoot system
is_a
is_a
develops_from part_of
The participates_in relation links an anatomical entity to a plant growth or development stage
is_a
plant structurewhole plant
growth stage
sporophyte phase
plant organ
sporangium
participates_in
Describes plant structures that only occur during a specific growth and development stages
Example: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):D449-D454
* 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:
• Added ~80 new terms in the recent release for the Physcomitrella (Moss) Genome Annotation group
Recent examples:• Addition of terms for Musa (bananas), Solanaceae (potatos,etc)
Wide range of Users and Collaborators:
Your logo could be here too!
Cell Ontology
The Plant Ontology facilitates comparative plant genomics
>500,000+ associations for >1300 termsMEE58?AtMEE58
AtMEE58
hydroidxylem element
I I
plant cell
axial cell
fusiform initial
MEE58?
MEE58?D
I
AtMEE58
I
Cross-taxa comparisons:
Annotations allow for data analysis:
Data Image From: Wang, et al. (2010). The Plant Journal, 61.
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:
Contact us if you are interested in providing and maintaining annotations files for your project
PO terms corresponding to synonyms used in the study:* inflorescence (PO:0009049)** shoot axis (PO:0025029)*** whole plant in the seedling stage (PO:0000003)
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!