Relations in the Plant Ontology
The relations describe on this page are used in the current version of the Plant Ontology.
Relations are formally (logically) defined in the OBO Relation Ontology (RO).
A current version of the OBO Relation Ontology is hosted by the OBO Foundry and can be viewed or download from Source Forge.
Relations
is_a
ID: OBO_REL:is_a
alt_id: OBO_REL:0000001
Properties: transitive, reflexive, anti-symmetric
Definition: For continuants: C is_a C' if and only if: given any c that instantiates C at a time t, c instantiates C' at t. For processes: P is_a P' if and only if: that given any p that instantiates P, then p instantiates P'.
A is_a B Should be read to mean: Every instance of A is an instance of B.
This relation is used to indicate the relationship between a specific class and a more general one (subsumption rather than instantiation). For example, megasprophyll is_a sporophyll and sporophyll is_a phyllome. This means that every instance of megasporophyll is a sporophyll. Since the is_a relation is transitive, every megasporophyll is also a phyllome.
The is_a relation is the fundamental relation of the PO, and all classes in the PO should have an is_a relationship to another class.
part_of
ID: OBO_REL:part_of
alt_id: OBO_REL:0000002
Properties: transitive, reflexive, anti-symmetric
Definition: For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
A part_of B Should be read to mean: Every A instance of A is part of some B. This does not imply that every B is has some A as a part.
This relation is used to indicate that one class is part of another class. For example, ectocarp is part_of pericarp, which in turn is part_of fruit. The part_of relation should only be applied when every instance of the child is part of some instance of the parent. In this example, every instance of ectocarp is part of some pericarp. However, this does not mean that every pericarp has some ectocarp as a part. The part_of relation is transitive, so every instance of ectocarp is also part of some fruit.
has_part
ID: OBO_REL:has_part
alt_id: OBO_REL:0000003
Properties: transitive, reflexive, anti-symmetric
Definition: This relation does not yet have a formal definition in the RO
This relation is used to indicate that one class always has an instance of another class as a part. For example, inflorescence has_part flower. This means that every instance of inflorescence has a flower as a part, but it does not imply that every flower is part of an inflorescence.
derives_from
This relation is used to indicate that one plant structure succeeds another across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier structure is inherited by the later. For example, leaf-derived cultured plant cell is derives_from leaf indicates that a significant portion of the matter (in fact, all of it) of a leaf-derived cultured plant cell is inherited from some cell in a leaf.
develops_from
This relation is used to indicate that a plant structure develops from its parent term. For example, root hair cell develops_ from trichoblast. The develops_from relation is a more specific case of the derives_from relation in the OBO relation ontology, and a formal definition is under development. The develops_from relation is not transitive.
adjacent_to
This relation is used when one plant structure is in permanent contact with another plant structure. For example, anther wall endothecium adjacent_to anther wall exothecium. In this example, every instance of anther wall endothecium should be in permanent contact (adjacent_to) some instance of anther wall exothecium. This does not imply that every anther wall exothecium is adjacent to some anther wall endothecium. If the latter were also true, that relation would have to be asserted separately. The adjacent_to relation is not transitive.
participates_in
The participates_in relation provides a link between an independent occurant in the PAO and a continuant in the PGDSO. It is used to indicate that an anatomical entity only occurs during a particular plant growth or development stage. Participates_in is a specific case of the more general inheres_in relation; occurrants (i.e., things) generally inhere in continuants (i.e., processes). In the PO, the participates_in relation provides a way of more clearly defining structures that occur only in a particular growth stage or phase, such as archegonium participates_in gametophytic phase or vascular tissue participates_in sporophytic phase. The participates_in relation can also be used post-compositionally to describe structures such as gametophyte, sporophyte, or seedling. For example, a user wishing to annotate to sporophyte should describe it as a whole plant that participats_in the sporophyte phase.
