About the SoyBase ontologies

These ontologies were developed to suggest a controlled vocabulary for soybean field growth stages (SoyWGR), indivdual plant development (SoyGRO) and traits (SoyTO). These are only a suggestion. Input from the community will be necessary to update and extend the ontologies. Because of this, these ontologies should also be considered a "work in progress".

Where applicable, soybean specific terms have been associated with their Plant Ontology (PO) and Gramene Plant Trait Ontology (TO) synonyms to facilitate cross species comparisons.

Please feel free to contact us for corrections, additions, and questions.

SoyBase Soybean Whole Plant Growth Stage Ontology

This ontology was developed to describe soybean field growth stages as published in "Soybean Growth and Development" Iowa State University Extension publication PM 1945 by Palle Pedersen. It describes soybean growth and development from the stand point of determining the growth of a field of soybeans. Some terms relate to a single plant, but others are applicable to a field as a whole. Where possible, these terms are linked to their Plant Ontology Whole Plant Growth or Structure synonyms to facilitate cross-species comparisons.

The SoyBase Soybean Whole Plant Growth ontology can be found HERE

A tutorial for the Whole Plant Growth Ontology can be accessed HERE

SoyBase Soybean Developmental Ontology

This ontology was developed to enumerate the parts of a soybean plant in order to follow the temporal development of individual plants. The ontology was modeled after the system described in Bucciarelli et al. (2006) Plant Phys 142:207-219. In this ontology, plant development is described in terms of metamers. Metamers consist of a plant internode and node. Each Metamer is numbered squentially starting at 1 for the cotoledonary node on up. Lateral branches are numbered for the metamer on the main stem from which they are derived along with the number of their lateral metamer. This system allows the user to describe the temporal and spatial development of individual soybean plant structures.

The SoyBase Soybean Development Ontology can be found HERE

A tutorial for the Developmental Ontology can be accessed HERE

SoyBase Soybean Trait Ontology

This ontology was developed as a guide to describing soybean growth taits. These terms were developed from GRIN Soybean Descriptors. and soybean QTLs described in SoyBase as well as other publications. These terms include yeild, biotic and abiotic stress resistance, and growth and developmental traits. Traits for biotic stresses such as bacterial, fungal and viral resistance have been listed by the binomial of the causitive organism. Where applicable, the common name of the pathogen has been included as a synonym. This is necessary because diseases caused by an organism are called different things in different parts of the globe. In the case of the fungi the teleomorph (sexual stage) name of the organism is used as the main identifier with the anamorph (asexual stage) name supplied as a synonym where it is known. In cases where the causitive organism has been described under numerous binomials such as the case with some insects, the organism is listed under one binomial with the other binomials included as synonyms. Synonyms to terms in the Plant Trait Ontology are also included where applicable to facilitate cross-species comparisons.

The SoyBase Soybean Trait Ontology can be found HERE

A tutorial for the Trait Ontology can be accessed HERE