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).

Download a current version of the OBO Relation Ontology:

• http://purl.obolibrary.org/obo/ro.owl
• http://purl.obolibrary.org/obo/ro.obo

Note that OBO_REL is deprecated and has been replaced by RO, which is under development and may be subsumed by the BFO.

Icons

Icons for PO relations can be downloaded from our SVN site

Relations

Note: The RO is currently under development, so the definitions and xrefs for these relations may change.

  is_a

This relation is similar to the OWL relations owl:subClassOf (for classes) and owl:subPropertyOf (for relations).

is transitive: true

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 the instances of a specific class and the instances of a more general one. For example, megasprophyll is_a sporophyll and sporophyll is_a phyllome. This means that every instance of megasporophyll is an instance of sporophyll. Since the is_a relation is transitive, every instance of megasporophyll is also an instance of 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

  part_of

id: part_of

name: part_of

is_transitive: true

xref: BFO:0000050

A part_of B should be read to mean: Every instance of A is part of some instance of B. For example, ectocarp is part_of pericarp, and pericarp is part_of fruit mean that every instance of ectocarp is part of some instance of pericarp and every instance of pericarp is part_of some instance of fruit. Because the part_of relation is transitive, we can also infer that every ectocarp is part_of some fruit.

A part_of B does not imply that every instance of B has some instance of A as a part, so we cannot infer that every pericarp has some ectocarp as a part.

Examples:

• ectocarp part_of pericarp
• pericarp part_of fruit

  has_part

id: has_part

name: has_part

is_transitive: true

xref: BFO:0000051

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 an instance of a flower as a part, but it does not imply that every flower is part of some inflorescence.

Examples:

• inflorescence has_part flower
• cambial zone has_part cambium

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_by_manipulation_from

id: derives_by_manipulation_from

name: derives_by_manipulation_from

domain: in vitro plant structure

This is a more specific case of the derives_from relation in RO.

A derives_by_manipulation_from B is true if (1) A is an in vitro plant structure, and (2) A exists at a point in time later than B from which it was created through human manipulation, and (3) A inherited a biologically significant portion of its matter from B.

This relation is used in the Plant Ontology only for in vitro plant structures. For example, leaf-derived cultured plant cell derives_by_manipulation_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.

Examples:

There are currently only two uses of derives_by_manipulation_from in the PO:

• root-derived cultured plant cell (PO:0000008) derives_by_manipulation_from root (PO:0009005)
• leaf-derived cultured plant cell (PO:0000007) derives_by_manipulation_from leaf (PO:0025034)

  develops_from

id: develops_from

name: develops_from

xref: RO:0002202

is_transitive: true

The definition of this relation is currently being worked on by the PO and metazoan anatomy ontology developers. We present an informal description here: if A develops_from B, then either A and B are cells, and the lineage of B can be traced back to A, or A and B are structures made of cells, and the majority of cells in B develop from cells in A.

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 plant structures toward 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

  adjacent_to

id: adjacent_to

name: adjacent_to

xref: RO:0002220

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.

Examples:

• anther wall endothecium adjacent_to anther wall exothecium
• plant cuticle adjacent_to epidermis

  participates_in

id: participates_in

name: participates_in

holds_over_chain: part_of participates_in

domain: continuant

range: occurent

A participates_in B should be read to mean: Every instance of plant anatomical entity A participates in some instance of plant structure development stage B.

In the Plant Ontology, the participates_in relation is used to indicate that an anatomical entity (an independent continuant) occurs only during a specific plant structure development stage (an occurent).

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 participates_in sporophyte phase.

A more specific subtype of the participates_in relation is being considered for the Plant Ontology.

Examples:

• archegonium participates_in gametophytic phase
• vascular tissue participates_in sporophytic phase

  has_participant

id: has_participant

name: has_participant

domain: occurent

range: continuant

A has_participant B should be read to mean: Every instance of occurent A has some instance of continuant B as a participant.

In the Plant Ontology, the has_participant relation is used to indicate that a plant structure development stage (an occurent) has as its primary participant a plant anatomical entity (an independent continuant).

A more specific subtype of the has_participant relation, such as "has_primary_participant" is being considered for the Plant Ontology.

Examples:

• trichome development stage has_participant trichome
• plant tissue development stage has-participant portion of plant tissue

  located_in

id: located_in

name: located_in

xref: BFO_0000171

domain: independent continuant

range: independent continuant

A located_in B should be read to mean: The region at which any instance of A is located at time T is a continuant part of the region at which some instance of B is located.

The "located in at some time" relation in the BFO is defined such that A may or may not be part of B. However, the PO uses located_in more specifically, that is, only when A is part of a different organism than B (and therefore not part of B).

If A is part of the same organism as B, then the more specific relation "part_of" is used.

In the Plant Ontology, "A located_in B" is used to specify that A is a plant anatomical entity that is part of one organism, B is a plant anatomical entity that is part of another organism, and A is located in B, for example, "embryo sac located in plant ovary ovule".

As of 7/2012, only a few located in relations have been added to the PO, and many relations that should use located_in use part_of instead. This will gradually be replaced by the more accurate located in relation.

Example: see embryo sac (PO:0025074)

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