Difference between revisions of "Relations in the Plant Ontology"
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The relations described on this page are used in the current version of 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 [http:// | + | Relations are formally (logically) defined in the [http://code.google.com/p/obo-relations/ 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| + | Note that OBO_REL is deprecated and has been replaced by RO. | ||
=Relations= | =Relations= | ||
| + | The RO is currently under development, so the definitions and xrefs for these relations may change. | ||
==is_a== | ==is_a== | ||
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| − | |||
| − | |||
| − | + | is transitive: true | |
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'. | 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'. | ||
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'''A''' is_a '''B''' should be read to mean: Every instance of '''A''' is an instance of '''B'''. | '''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 | + | 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 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. | 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. | ||
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===examples=== | ===examples=== | ||
*megasprophyll is_a sporophyll | *megasprophyll is_a sporophyll | ||
| − | |||
*sporophyll is_a phyllome | *sporophyll is_a phyllome | ||
| − | + | ==part_of== | |
| + | id: part_of | ||
| + | name: part_of | ||
| − | + | is_transitive: true | |
| − | |||
| − | + | xref: BFO:0000050 | |
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| − | |||
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.) | 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.) | ||
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===examples=== | ===examples=== | ||
*ectocarp part_of pericarp | *ectocarp part_of pericarp | ||
| + | *pericarp part_of fruit | ||
| − | + | ==has_part== | |
| + | id: has_part | ||
| − | + | name: has_part | |
| − | + | is_transitive: true | |
| − | + | xref: BFO:0000051 | |
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'''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 some'''A'''. | '''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 some'''A'''. | ||
| − | 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 | + | 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=== | ===examples=== | ||
*inflorescence has_part flower | *inflorescence has_part flower | ||
| − | + | *cambial zone has_part cambium | |
| − | |||
==part_of or has_part?== | ==part_of or has_part?== | ||
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==derives_from== | ==derives_from== | ||
| − | + | id: derives_by_manipulations_from | |
| − | + | name: derives_by_manipulations_from | |
| − | |||
| − | + | '''A''' derives_by_manipulations_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_manipulations_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. | |
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| − | This relation is used | ||
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===examples=== | ===examples=== | ||
| − | *leaf-derived cultured plant cell | + | There are currently only two uses of derives_by_manipulations_from in the PO: |
| + | *root-derived cultured plant cell (PO:0000008) derives_by_manipulations_from root (PO:0009005) | ||
| + | *leaf-derived cultured plant cell (PO:0000007) derives_by_manipulations_from leaf (PO:0025034) | ||
| + | ==develops_from== | ||
| + | id: develops_from | ||
| − | + | name: develops_from | |
| − | + | xref: RO:0002202 | |
| − | |||
| − | + | is_transitive: true | |
| − | |||
| − | '''A''' develops_from '''B''' should be read to mean: Every instance of '''A''' develops from some '''B'''. | + | '''A''' develops_from '''B''' should be read to mean: Every instance of '''A''' develops from some instance of '''B'''. |
| − | The | + | 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 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. | 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. | ||
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===examples=== | ===examples=== | ||
*root hair cell develops_ from trichoblast | *root hair cell develops_ from trichoblast | ||
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==adjacent_to== | ==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'''. | '''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. | 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 | ||
==participates_in== | ==participates_in== | ||
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===examples=== | ===examples=== | ||
*archegonium participates_in gametophytic phase | *archegonium participates_in gametophytic phase | ||
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*vascular tissue participates_in sporophytic phase | *vascular tissue participates_in sporophytic phase | ||
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===examples=== | ===examples=== | ||
| + | *trichome development stage has_participant trichome | ||
| + | *plant tissue development stage has-participant portion of plant tissue | ||
=Axioms= | =Axioms= | ||
Revision as of 14:21, 20 March 2012
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:
Note that OBO_REL is deprecated and has been replaced by RO.
Relations
The RO is currently under development, so the definitions and xrefs for these relations may change.
is_a
is transitive: true
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 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
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
- 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_from
id: derives_by_manipulations_from
name: derives_by_manipulations_from
A derives_by_manipulations_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_manipulations_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_manipulations_from in the PO:
- root-derived cultured plant cell (PO:0000008) derives_by_manipulations_from root (PO:0009005)
- leaf-derived cultured plant cell (PO:0000007) derives_by_manipulations_from leaf (PO:0025034)
develops_from
id: develops_from
name: develops_from
xref: RO:0002202
is_transitive: true
A develops_from B should be read to mean: Every instance of A develops from some instance of B.
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 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
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
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
examples
- trichome development stage has_participant trichome
- plant tissue development stage has-participant portion of plant tissue
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
