Tools

SoyBase Soybean Ontologies

The ontologies below were developed to provide a controlled vocabulary for
  • field growth stages (Soybean Whole Plant Growth Ontology),
  • plant structure (Soybean Structure Ontology),
  • development (Soybean Development Ontology), and
  • plant traits (Soybean Trait Ontology).
Where applicable, soybean specific terms have been associated with their Plant Ontology (PO) synonyms to facilitate cross species comparisons. Since the original release of the SoyBase Ontologies, they have been re-factored at the request of the Plant Ontology Consortium. This change resulted in the elimination of a separate accession system for SoyTO and SoyGRO. These terms were re-accessioned into the SoyWGR namespace and the SoyWGR prefix was changed to SOY. Input from the community is welcomed. Please contact us for corrections, additions, and questions.

Browse and Search Soybean Whole Plant Growth Terms

This ontology was developed to unite three different ontologies for soybean development: the BBCH scale, the more generic Plant Ontology Consortium's Whole Plant Growth Ontology, and the Soybean Growth and Development 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. This ontology has also been linked where possible to synonymous stages in the BBCH scale to allow researchers to more easily translate research data compiled using the BBCH scale to data compiled using the familiar V and R stages.

For convienience, see a conversion table linking the V and R stages to their respective Plant Ontology Whole Plant Growth terms and the BBCH scale.

Browse and Search Soybean Structure Terms

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.

Browse and Search Developmental Terms

This ontology was developed to describe the growth and maturation of individual soybean tissues or organ systems. The structure was modeled on that of the greater Plant Ontology with modifications to accommodate soybean development.

Browse and Search Soybean Trait Terms

This ontology was developed as a guide to describing soybean growth taits. These terms were developed from GRIN Soybean Descriptors and soybean triats and 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.