1 The Plant Ontology TM Consortium (POC) and an Ontology for Maize/Corn (Zea mays) Plant Structure Leszek Vincent, Maize Mapping Project, Univ. of Missouri-

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The Plant OntologyThe Plant OntologyTMTM Consortium Consortium (POC) and an Ontology for (POC) and an Ontology for

Maize/Corn (Maize/Corn (Zea maysZea mays) Plant ) Plant StructureStructure

Leszek Vincent, Maize Mapping Project, Univ. of Missouri-Columbia, MO, USA

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gene structures, products, functions, locations

phenotypes;

traits;

developmental stages, anatomical parts, morphology & other information.

Plant biology databases are expanding in number, size & complexity (e.g. Gramene, MaizeDB, Solanaceae Genome Network, TAIR).

These information-rich databases face the challenge of accurately & consistently documenting features such as:

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Increasingly desirable for inter-database queries to be performed between plant-based databases to exploit comparative genomic strategies to elucidate plant functions.

However, terms used to describe comparable objects in each database are quite variable and limit the ability to accurately and successfully query information in and across different databases.

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One solution to this problem involves the development and application of structured controlled vocabularies arranged in ontologies.

In the world of structured information, controlled vocabularies, arranged in ontologies, play a very important role in facilitating information retrieval.

Furthermore, the definitions that accompany the controlled vocabulary terms facilitate the consistent use of the controlled vocabulary terms in database curation.

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understanding the biological relationships between plant parts (cells, tissues, organs);

correctly representing these relationships via ontologies which comprise biologically correct & internationally acceptable controlled vocabularies. [Garbage in … garbage out!]

Controlled vocabulary terms in biological ontologies should be arranged in such a way that their placement reflects the known or putative biological relationships / associations between the objects represented by the controlled vocabulary terms.

Considerable effort must be invested in:

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Plant OntologyPlant OntologyTMTM Consortium Consortium

These ontologies will provide Open-Source, Controlled Vocabularies of Defined Terms for specific plant-based databases.

developing various controlled vocabularies (CV’s)

CV’s arranged in ontologies representing important knowledge domains of plant biology - both current and future knowledge.

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First meeting at the PAMG X meeting - further exposure at PAGM XI meeting (2003) at Bioinformatic Interfaces, Ontologies and Interoperability workshop

Contributed to refinement of DAG-Edit software & User Guide.

Considerable ‘synteny’ between PO Consortium and GO Consortium.

Developed a ‘White Paper’ on Proposed Plant OntologyTM Consortium.

The Plant OntologyPlant OntologyTMTM Consortium Consortium - applying and extending the Gene Ontologyapplying and extending the Gene OntologyTMTM paradigmparadigm to knowledge domains pertinent to monocot, dicot and other plant taxa - initially Zea mays, Oryza sativa & Arabidopsis thaliana.

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Facilitate the communications, productivity & collaborations amongst the collaborators / associates of the POC;

Network with research groups working on other plant taxa to facilitate the provision of appropriate controlled vocabularies & ontologies;

Extend collaboration with the GO Consortium;

To be an open-source of controlled vocabulary;

Develop standards for plant ontologies;

Aims of the Plant OntologyAims of the Plant OntologyTM TM Consortium:Consortium:

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Ontogenetic & phylogenetic concepts & data to be used in development of ontological relationships & testing of these relationships via the True Path RuleTrue Path Rule - more on this later.

Exploring possible additional relationship types - e.g. primary root

Derived-From lateral root

Interface/synergy with plant genomics & plant phylogenetics - Phylo-GenomicsPhylo-Genomics. Workshop at PAGM XI (2003) - NSF-RCN "Deep Gene" Phylogenetics and Plant Genomics Discussion Workshop.

Contributed ideas towards a possible framework of ontologies for biology.

Evidence codes - additional?

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Gramene - Comparative Mapping Resource for Grains

TAIR - The Arabidopsis Information Resource

MaizeDB - The Maize Database

IRIS - International Rice Information System

Anticipated that the Plant OntologyPlant OntologyTMTM Consortium Consortium will impact the bioinformatics research of national & international plant-based researchers e.g. soybean, sugarcane, cassava, Medicago, grains, Solanaceae, trees…

Current collaborators/associates of thePlant OntologyTM Consortium:

Number space allocated to each PO developer group.

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Besides the development of taxon-specific data repositories (e.g. Gramene, MaizeDB, TAIR) the SPRIG site at bioinformatics.org is also to be devoloped as a public repository for PO data.

[SPRIG= Specialized Plant Resources for Informatics & Genomics]

A website for the Plant OntologyTM Consortium is being developed -

www.plantontology.org

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Incorporating a phylogenetic perspective in the development and use of Plant Ontologies

Phylogenetic systematics is the way that biologists reconstruct the pattern of putative evolutionary events that have led to the distribution and diversity of life.

Phylogenetic tools have been used to understand extant genome-related processes.

These tools have been powerfully used to advance the understanding of family and ordinal classification proposed by The Angiosperm Phylogeny Group (1998).

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Explicit phylogenetics can inform inference of function and change in function in special ways that cannot be achieved with other current approaches (e.g. BLAST-based).

Phylogenetic approach to genomics (involving

cladistics) includes explicit inference of putative

ancestral & derived characteristics at multiple,

nested levels of comparison - unlike similarity-based

comparative analyses (often pairwise comparisons)

e.g. phenetics.

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which genes are orthologous or paralogous;

how the function of gene families has changed through history;

what are the conserved and variable components that define genes with known functions;

how close gene relatives may often have different functions.

All these issues are of great interest.

In the area of molecular biology it can be argued that explicitly phylogenetic approaches do lead to deeper insights, such as:

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Almost all gene families are deeply branching but shallowly sampled due to the preponderance of Arabidopsis and rice (Oryza) providing the main source of evidence for much of the plant genome.

It is likely that ongoing ontology research will continue to use BLAST-based approaches as a practical and rapid substitute for phylogenetic inferences. Why?

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Extensive sampling of genomes will enable tests for orthologous vs paralogous genes to be performed - for subsequent inclusion / synthesis in the True Path Rule test.

Such resources will facilitate phylogenetically driven analysis of genome-wide expression data.

Needless to say work on global alignments and putative phylogenies of many gene families is needed.

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plant structure (anatomy & morphology) ?

traits (characters) ?

phenotypes (character-states) ?

gene products ?

development ?

For Consideration:

Is there a role for the appropriate use of phylogenetic information in the development of phylogenetically grounded ontologies for:

The integration of genomics and phylogenetics provides powerful analytical tools for elucidation of natural experiments - Phylo-Genomics.

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This paradigm is being tested in the development of the Plant Structure Ontology for Zea mays.

The incorporation of a phylogenetic perspective should render these ontologies even more useful.

Some of the current research on ontologies for gene products is based on ‘function’ (analogy).

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Zea mays L. Plant Structure Ontology

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The Zea mays Plant Structure Ontology was

“Anatomy (incl. morphology) ontology”

- new name is less ‘territorial’

The structural and functional specialization of

plant anatomy, expressed in the plant’s

phenotype as morphology and

micromorphology, is being included within the

Plant Structure Ontology.

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The Zea mays Plant Structure Ontology covers:

cell types;

tissue types;

organ types:

- roots

- stems

- leaves

- inflorescences (ears, tassels)

- fruits (ear)

- seeds (caryopses)

A more expanded territory of the GO paradigm

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The principal plant tissues are being grouped on the basis of topographic continuity, as in other vascular plants:

- the dermal;

- the vascular ;

- the fundamental (or ground) system.

Building the Zea mays Plant Structure Ontology requires a comprehensive list of unique characters (traits) that encompass the entire plant structure - down to each individual component of each floret etc.

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The character list being developed for the Plant Structure Ontology is also being used to upgrade the Body Parts table of the Maize Data Base (MaizeDB) - much interchange between the Controlled Vocabulary and MaizeDB.

Each unique character (trait) in the character list is a Controlled Vocabulary term which is an internationally recognized botanical term.

A comprehensive definition and dbx ref. and any synonym(s) is being developed for each CV term.

24DAG-Edit Demos possible

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DAG-Edit Demos possible

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Term Name: liguleSynonym: noneDefinition: The ligule in Zea mays is a protruding line of tissue on the inner/upper (adaxial) surface of the leaf at the boundary between the leaf-sheath and the leaf blade (lamina) - the ligular region of the leaf. This unique line of epidermal tissue appears to be composed of 'fused hairs'. The ligule is oriented almost perpendicular to the adjacent leaf surface.Reference: M. Freeling & B. Lane:1994. The Maize Leaf. In: M. Freeling & V. Walbot (eds.) (1994). The Maize Handbook. Springer-Verlag, New York, ISBN: 3-540-97826-7; A. Fahn:(1982). Plant Anatomy, p.244-245, ISBN: 0-08-028029-3; Gibbs Russell et al.:(1990). Grasses of Southern Africa, ISBN: 0-620-14846-2.PO ID#: PO:0015009MaizeDB ID# 64473Link to Interactive Maize PlantZea mays Plant Structure Ontology ; PO:0015036

- [i] anatomy & morphology ; PO:0015038- [i] whole organism; PO:0015037

+ [p] cell type ; PO:0015014- [p] organ ; PO:0015050

+ [i] culm ; PO:0015072 ; + [i] lateral branch ; PO:0015073- [i] leaf ; PO:0015031

- [i] adult leaf ; PO:0015060 + [p] leaf blade ; PO:0015027+ [p] leaf sheath ; PO:0015024- [p] ligule ; PO:0015009

• [p] ligule appearance ; PO:0015007• [p] ligule consistency ; PO:0015058+ [p] ligule indumentum ; PO:0015057• [p] ligule projections ; PO:0015003

- [i] juvenile leaf ; PO:0015059+ [p] leaf blade ; PO:0015027+ [p] leaf sheath ; PO:0015024

+ [i] root ; PO:0015034+ [i] tassel (functionally male inflorescence) ; PO:0015085

Ontology for ligule

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Ontology for ligule

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Ontology for ligule

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Ontology for ligule

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Partially supported by

Acknowledgements:

Colleagues of the Plant OntologyTM Consortium:

- Leonore Reiser - TAIR

- Pankaj Jaiswal - Gramene

- Ed Coe - MMP/MaizeDB

- Mary Polacco - MMP/MaizeDB

Also: Various colleagues associated with the Gene OntologyTM Consortium.

Documents

1 The Plant Ontology TM Consortium (POC) and an Ontology for Maize/Corn (Zea mays) Plant Structure Leszek Vincent, Maize Mapping Project, Univ. of Missouri-