Relations in the Plant Ontology

The relations described 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. 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 most fundamental relation of the PO, and all classes in the PO should have an is_a relationship to another class.

examples

• megasprophyll is_a sporophyll

• 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.

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 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 each specific instance of one class is part of an instance 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.

examples

• ectocarp part_of pericarp

The former means that every instance of ectocarp is part of some instance of pericarp.

The part_of relation is transitive. Thus, since we know also that

• pericarp part_of fruit.

then it follows that every instance of ectocarp is also part of some instance of 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.

A has_part B should be read to mean: Every instance of A has some instance of B as a part. This does not imply that every B is part of someA.

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.

examples

• inflorescence has_part flower

means that every instance of inflorescence has some instance of flower as part. Note that this does not imply that every instance of flower is part of some inflorescence. The has_part relation is transitive.

part_of or has_part?

There are many examples of plant structures, where both A has_part B and B part_of A. For example, every stomatal complex has_part guard cell, and every guard cell is part_of a stomatal complex. In principle, both of these relations could be specified. However, due to limitations in computerized reasoning, having reciprocal part_of and has_part relations in the PO causes loading errors with most software. Therefore, the PO does not specify these mutual relationship. If both relations are possible, we choose to use only the part_of relation, because most reasoners are better able to make correct inferences over part_of than over has_part. We use the has_part relation only when the reciprocal part_of relation cannot be use (see the example above with inflorescence and flower).

derives_from

ID: OBO_REL:derives_from

alt_id: OBO_REL:0000015

Properties: transitive

Definition: Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.

A derives_from B should be read to mean: Every instance of A exists at a point in time later than some instance of B from which it was derived, and every instance of A inherited a biologically significant portion of its matter from the instance of B from which it was derived.

This relation is used to indicate that one plant structure succeeds another in time 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 of a leaf-derived cultured plant cell is inherited from some cell in a leaf.

There are currently only two uses of derives_from in the PO: root-derived cultured plant cell (PO:0000008) derives_from root (PO:0009005) and leaf-derived cultured plant cell (PO:0000007) derives_from leaf (PO:0025034)

examples

• leaf-derived cultured plant cell derives_from leaf

indicates that a significant portion of the matter of a leaf-derived cultured plant cell is inherited from some leaf.

develops_from

ID: develops_from is not in the OBO Relation Ontology

Properties: not specified

Definition: A formal definition is under development.

A develops_from B should be read to mean: Every instance of A develops from some B.

The develops_from relation is a more specific case of the derives_from or transformation_of? relation. Develops_from is used to indicate that a plant structure develops from its parent term. For example, root hair cell develops_ from trichoblast and tetrad of microspores develops_from microsporocyte.

Nearly every plant structure could have at least one develops_from relation to another, such that eventually every term would have its origin to an embryo or spore (for in vivo plant structures). However, the PO restricts the use of develops_from to a limited number of PAO classes towards the bottom of the tree. Developmental patterns for many structures vary across taxa, so that specifying develops_from relations for all structures for all plants would require the creation of separate hierarchies for each taxon, leading to term inflation and unnecessary confusion. Future uses of the PO may require a more complete develops_from hierarchy, but for its current uses, proliferation of develops_from relations would add unnecessary complexity to the PO. Furthermore, the development of many structures has not been studied, particularly in non-model species, so it is too early to assert many of the develops_from relations in an ontology that must apply to all plants.

examples

• root hair cell develops_ from trichoblast

signifies that each root hair cell develops from some trichoblast.

adjacent_to: The adjacent_to 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

signifying that every instance of anther wall endothecium should be in permanent contact (adjacent_to) some instance of anther wall exothecium. Note that adjacent_to is not symmetric. Thus not 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 also not transitive.

adjacent_to

ID: OBO_REL:adjacent_to

alt_id: OBO_REL:0000012

Definition: C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity

A adjacent_to B should be read to mean: Every instance of A is adjacent to (in contact with or in spatial proximity to) some B.

This relation is used when one plant structure is disjoint from but 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 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

ID: OBO_REL:participates_in

alt_id: OBO_REL:0000020

Definition: This relation does not yet have a formal definition in the RO.

A participates_in B should be read to mean: Every instance of A occurs during that part of a plant life cycle described by B. It does not mean that every plant life cycle phase or growth stage B will have A as a participant.

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 sporophyte phase.

examples

• archegonium participates_in gametophytic phase

• 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'.

has_participant

ID: OBO_REL:has_participant

Axioms

disjoint_from

(from OboEdit users guide)

disjoint_from - This symmetric relation indicates that two classes are disjoint. If two classes A and B are marked disjoint, no subclass of A may be a subclass of B, and no subclass of B may be a subclass of A. disjoint_from is similar to the owl relation owl:disjointWith