gene structures, products, functions, locations

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

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: • gene structures, products, functions, locations • phenotypes; • traits; • developmental stages, anatomical parts, morphology & other information.

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.

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.

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: • 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!]

Plant OntologyTM 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 currentand future knowledge.

The Plant OntologyTM Consortium - applying and extending the Gene OntologyTM paradigmto knowledge domains pertinent to monocot, dicotand other plant taxa - initially Zea mays, Oryza sativa & Arabidopsis thaliana. • Considerable ‘synteny’ between PO Consortium and GO Consortium. • First meeting at the PAMG X meeting - further exposure at PAGM XI meeting (2003) at Bioinformatic Interfaces, Ontologies and Interoperability workshop • Developed a ‘White Paper’ on Proposed Plant OntologyTM Consortium. • Contributed to refinement of DAG-Edit software & User Guide.

Aims of the Plant OntologyTM Consortium: • Facilitate the communications, productivity & collaborations amongst the collaborators / associates of the POC; • To be an open-source of controlled vocabulary; • Network with research groups working on other plant taxa to facilitate the provision of appropriate controlled vocabularies & ontologies; • Develop standards for plant ontologies; • Extend collaboration with the GO Consortium;

Exploring possible additional relationship types - • e.g. primary root • Derived-From lateral root • Evidence codes - additional? • Contributed ideas towards a possible framework of ontologies for biology. • Ontogenetic & phylogenetic concepts & data to be used in development of ontological relationships & testing of these relationships via the True Path Rule - more on this later. • Interface/synergy with plant genomics & plant phylogenetics - Phylo-Genomics. Workshop at PAGM XI (2003) - NSF-RCN "Deep Gene" Phylogenetics and Plant Genomics Discussion Workshop.

Anticipated that the Plant OntologyTM 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 the Plant OntologyTM Consortium: Number space allocated to each PO developer group. • Gramene - Comparative Mapping Resource for Grains • IRIS - International Rice Information System • MaizeDB - The Maize Database • TAIR - The Arabidopsis Information Resource

A website for the Plant OntologyTM Consortium is being developed - www.plantontology.org 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]

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

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. 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).

In the area of molecular biology it can be argued that explicitly phylogenetic approaches do lead to deeper insights, such as: All these issues are of great interest. • 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.

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

Needless to say work on global alignments and putative phylogenies of many gene families is needed. Such resources will facilitate phylogenetically driven analysis of genome-wide expression data. 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.

The integration of genomics and phylogenetics provides powerful analytical tools for elucidation of natural experiments - Phylo-Genomics. For Consideration: Is there a role for the appropriate use of phylogenetic information in the development of phylogenetically grounded ontologies for: • plant structure (anatomy & morphology) ? • traits (characters) ? • phenotypes (character-states) ? • gene products ? • development ?

Some of the current research on ontologies for gene products is based on ‘function’ (analogy). The incorporation of a phylogenetic perspective should render these ontologies even more useful. This paradigm is being tested in the development of the Plant Structure Ontology for Zea mays.

Zea mays L. Plant Structure Ontology

The Zea maysPlant 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.

The Zea maysPlant Structure Ontology covers: A more expanded territory of the GO paradigm • cell types; • tissue types; • organ types: - roots • - stems • - leaves • - inflorescences (ears, tassels) • - fruits (ear) • - seeds (caryopses)

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 maysPlant 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.

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.

DAG-Edit Demos possible

Term Name: ligule Synonym: none Definition: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:0015009 MaizeDB ID# 64473 Link to Interactive Maize Plant Zea 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

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.

gene structures, products, functions, locations