Botanists building ontologies to cope with information overload

ORIGINAL: KurzweilAI
August 22, 2012

A few of the 20 to 100 million plant species in the world (credit: Eleassar/Wikimedia Commons)

Botanists are building ontologies such as the Plant Ontology (PO) to transform plant science by facilitating new ways of gathering and exploring data, Ramona Walls (New York Botanical Garden) and colleagues explain in an open-access article in the American Journal of Botany.

An ontology (in the information science meanng) is a description of the types of entities within a given domain and the relationships among them. When data from many divergent sources, such as data about some specific plant organ, are associated or “tagged” with particular terms from a single ontology or set of interrelated ontologies, the data become easier to find.

Computers can also use the logical relationships in the ontologies to correctly combine the information from the different databases and to aggregate data associated with the different subclasses or parts of entities.

For example, suppose a researcher is searching online for all examples of gene expression in a leaf. Any botanist performing this search would include experiments that described gene expression in petioles and midribs or in a frond.

However, a search engine would not know that it needs to include these terms in its search — unless it was told that a frond is a type of leaf, and that every petiole and every midrib are parts of some leaf. It is this information that ontologies provide.

Ontology showing how two leaf structures relate to “vascular leaf” (credit: Plant Ontology Consortium)

Four keys areas of plant science could benefit from the use of ontologies, the authors say: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education.

REFERENCES:

R. L. Walls, B. Athreya, L. Cooper, J. Elser, M. A. Gandolfo, P. Jaiswal, C. J. Mungall, J. Preece, S. Rensing, B. Smith, D. W. Stevenson, Ontologies as integrative tools for plant science, American Journal of Botany, 2012, DOI: 10.3732/ajb.1200222 (open access)

Topics: Biotech | Computers/Infotech/UI | Environment/Climate