Difference between revisions of "Relations in the Plant Ontology"

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(Created page with '''This page is under construction.'' Under the standard Plant Ontology data structure, terms are allowed to have a limited number of relations. Relations are formally defined in…')
 
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''This page is under construction.''
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The relations describe on this page are used in the current version of the Plant Ontology.
  
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Under the standard Plant Ontology data structure, terms are allowed to have a limited number of relations. Relations are formally defined in the [http://www.obofoundry.org/ro/ OBO relation ontology].
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Relations are formally (logically) defined in the [http://www.obofoundry.org/ro/ OBO Relation Ontology] (RO).
  
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For more details about relations, including formal defintions, see [[Relations in the Plant Ontology]].
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A current version of the OBO Relation Ontology is hosted by [http://www.obofoundry.org/ the OBO Foundry] and can be viewed or download from [http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/OBO_REL/ro.obo Source Forge].
  
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The PO currently has following term-to-term relation types:
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=Relations=
  
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'''is_a:''' 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.
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==is_a==
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ID: OBO_REL:is_a
  
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'''part_of:''' 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.
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alt_id: OBO_REL:0000001
  
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'''has_part:''' 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.  The has_part relation is transitive.
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Properties: transitive, reflexive, anti-symmetric
  
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'''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.
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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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'''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 [http://www.obofoundry.org/ro/ OBO relation ontology], and a formal definition is under development. The develops_from relation is not transitive.
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'''A''' is_a '''B''' Should be read to mean: Every instance of '''A''' is an instance of '''B'''.  
  
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'''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.  
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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.  
  
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'''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.
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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.
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==part_of==
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ID: OBO_REL:part_of
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alt_id: OBO_REL:0000002
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Properties: transitive, reflexive, anti-symmetric
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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.)
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'''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.
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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.
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==has_part==
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ID: OBO_REL:has_part
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alt_id: OBO_REL:0000003
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Properties: transitive, reflexive, anti-symmetric
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Definition: This relation does not yet have a formal definition in the RO
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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.
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==derives_from==
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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.
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==develops_from==
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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 [http://www.obofoundry.org/ro/ OBO relation ontology], and a formal definition is under development. The develops_from relation is not transitive.
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==adjacent_to==
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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.
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==participates_in==
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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.

Revision as of 16:39, 26 May 2011

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.

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