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://www.obofoundry.org/ro/ OBO Relation Ontology] (RO).
+
Relations are formally (logically) defined in the [http://code.google.com/p/obo-relations/ OBO Relation Ontology] (RO).
  
−
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].
+
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Note that OBO_REL is deprecated and has been replaced by RO, which is under development and may be subsumed by the BFO.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 [https://github.com/Planteome/common-files-for-ref-ontologies/tree/master/icons GitHub Repository]
  
 
=Relations=
 
=Relations=
 +
Note: The RO is being incorporated into the new [http://code.google.com/p/bfo/ Basic Formal Ontology] (BFO2), which is under development. The definitions and xrefs for these relations may change with the release of the BFO2.
  
−
==is_a==
+
* Relation stanzas should contain an xref to BFO or RO in the Xref field (not in the dbxref field)
−
ID: OBO_REL:is_a
 
  
−
alt_id: OBO_REL:0000001
+
e.g. BFO:0000062  ''preceded_by''
  
−
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'.
+
==http://plantontology.org/amigo/docs/images/is_a.gif   is_a==
 +
This relation is identical to SubClassOf from the OWL specification. Please refer to the OBO Format specification (http://oboformat.org) for more details.
 +
 
 +
is transitive: true
  
 
'''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 a sporophyll. Since the is_a relation is transitive, every megasporophyll is also a phyllome.  
+
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.
 +
 
 +
Furthermore, every instance of A has some distinguishing characteristics that none of the other instances of B have, that is, they should have some additional quality that distinguishes them from the more general type.  
  
 
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.
  
−
==part_of==
+
Examples:
−
ID: OBO_REL:part_of
+
* megasprophyll is_a sporophyll
 +
* sporophyll is_a phyllome
 +
 
 +
==http://plantontology.org/amigo/docs/images/part_of.gif   part_of==
 +
id: part_of
 +
 
 +
name: part_of
  
−
alt_id: OBO_REL:0000002
+
is_transitive: true
  
−
Properties: transitive, reflexive, anti-symmetric
+
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 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''' 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.
+
'''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.
  
−
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.
 
  
−
==has_part==
+
Among anatomical entities, this is a spatial relationship, implying that A exists within the space occupied by B. Among development stages, it is means that processes in stage A occurs as part of processes in stage B (e.g., embryo development stage part_of seed development stage in seed plants)
−
ID: OBO_REL:has_part
 
  
−
alt_id: OBO_REL:0000003
+
Examples:
 +
* ectocarp part_of pericarp
 +
* pericarp part_of fruit
  
−
Properties: transitive, reflexive, anti-symmetric
+
==http://plantontology.org/amigo/docs/images/has_part.gif   has_part==
 +
id: has_part
  
−
Definition: This relation does not yet have a formal definition in the RO.
+
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 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 an inflorescence.  
+
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.  
  
−
==part_of or has_part?==
+
Note that part_of and has_part are logically independent. Two terms may have one or the other or both relationships between each other.
 +
 
 +
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).
 
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==
+
==http://plantontology.org/amigo/docs/images/derives_by_manipulation_from.gif   derives_by_manipulation_from==
−
ID: OBO_REL:derives_from
+
id: derives_by_manipulation_from
  
−
alt_id: OBO_REL:0000015
+
name: derives_by_manipulation_from
  
−
Properties: transitive
+
domain: in vitro plant structure
  
−
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'.
+
is_transitive: false????
  
−
'''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 is a more specific case of the derives_from (RO:0001000) relation in RO.
  
−
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.
+
'''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'''.
  
−
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)
+
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.
  
−
==develops_from==
+
Examples:
−
ID: develops_from is not in the OBO Relation Ontology
 
  
−
Properties: not specified
+
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)
  
−
Definition: A formal definition is under development.
+
==http://plantontology.org/amigo/docs/images/develops_from.gif   develops_from==
 +
id: develops_from
  
−
'''A''' develops_from '''B''' should be read to mean: Every instance of '''A''' develops from some '''B'''.
+
name: develops_from
  
−
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.
+
xref: RO:0002202
  
−
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.
+
is_transitive: true
  
−
==adjacent_to==
+
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'''.
−
ID: OBO_REL:adjacent_to
 
  
−
alt_id: OBO_REL:0000012
+
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.
  
−
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
+
Every instance of A either was once an instance of B (it is a transformation_of B) or inherited a significant portion of its matter from B (it derives_from B).  The develops_from relation is more familiar to biologists than the transformation_of or derives_from relations and allows for situations in which it is uncertain if two entities are related by transformation or derivation.
 +
 
 +
Examples:
 +
*root hair cell develops_ from trichoblast
 +
 
 +
==http://plantontology.org/amigo/docs/images/adjacent_to.gif   adjacent_to==
 +
id: adjacent_to
 +
 
 +
name: adjacent_to
 +
 
 +
xref: RO:0002220
 +
 
 +
is_transitive: false
  
 
'''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'''.
Line 91: Line 132:
 
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.
  
−
==participates_in==
+
''Every instance of A is spatially disjoint from but in permanent contact with some instance of B. Note that this is not a reciprocal relationship, so A adjacent_to B does not imply B adjacent_to A.''
−
ID: OBO_REL:participates_in
 
  
−
alt_id: OBO_REL:0000020
+
Examples:
 +
* anther wall endothecium adjacent_to anther wall exothecium
 +
* plant cuticle adjacent_to epidermis
  
−
Definition: This relation does not yet have a formal definition in the RO.
+
==http://plantontology.org/amigo/docs/images/participates_in.gif   participates_in==
 +
id: participates_in
  
−
'''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.
+
name: 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).
+
holds_over_chain: part_of participates_in
  
−
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.
+
domain: continuant
  
 +
range: occurent
 +
 +
is_transitive: false?
 +
 +
'''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
 +
 +
==http://plantontology.org/amigo/docs/images/has_participant.gif   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
 +
 +
''(1) Every instance of A is a plant structure development stage and every instance of B is a plant anatomical entity and (2) Every instance of occurent A has some instance of continuant B as a participant.''
 +
 +
==http://plantontology.org/amigo/docs/images/located_in.gif   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. These will gradually be replaced by the more accurate located_in relation.
 +
 +
 +
Example:
 +
see [http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0025074&session_id=1191b1341869507 embryo sac] (PO:0025074)
 +
 +
 +
==[[File:Preceded_by.gif]] preceded_by==
 +
[http://www.ontobee.org/browser/rdf.php?o=RO&iri=http://purl.obolibrary.org/obo/BFO_0000062 preceded_by OntoBee page]
 +
 +
id: preceded_by
 +
 +
name: preceded_by
 +
 +
xref: BFO_0000062
 +
 +
domain: occurrent
 +
 +
range: occurrent
 +
 +
time: atemporal
 +
 +
transitive: yes
 +
 +
 +
The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P.
 +
 +
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C.   
 +
 +
Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.source:
 +
 +
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
 +
 +
Link to discussion on [https://github.com/Planteome/plant-ontology/issues/552 GitHub]
 +
 +
==[[File:precedes.gif]] precedes==
 +
[http://www.ontobee.org/browser/rdf.php?o=RO&iri=http://purl.obolibrary.org/obo/BFO_0000063 precedes OntoBee page]
 +
 +
id: precedes
 +
 +
name: precedes
 +
 +
xref: BFO_0000063
 +
 +
domain: occurrent
 +
 +
range: occurrent
 +
 +
time: atemporal
 +
 +
transitive: yes
 +
 +
Note: precedes is the inverse of preceded_by
 +
 +
Example:
 +
* Each of the three later stages of plant embryo development: plant embryo true leaf formation stage (PO:0001095), plant embryo coleoptilar stage (PO:0001094), and  plant embryo cotyledonary stage (PO:0001078) ''precedes'' mature plant embryo stage (PO:0001081), depending upon the taxa
 +
 +
 +
[[file:precedes_example.png]]
 +
 +
see discussion on [https://github.com/Planteome/plant-ontology/issues/552 GitHub]
 +
 +
=Axioms=
 
==disjoint_from==
 
==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

Latest revision as of 17:24, 8 October 2015

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, which is under development and may be subsumed by the BFO.

Icons

Icons for PO relations can be downloaded from our GitHub Repository

Relations

Note: The RO is being incorporated into the new Basic Formal Ontology (BFO2), which is under development. The definitions and xrefs for these relations may change with the release of the BFO2.

  • Relation stanzas should contain an xref to BFO or RO in the Xref field (not in the dbxref field)

e.g. BFO:0000062 preceded_by


is_a.gif   is_a

This relation is identical to SubClassOf from the OWL specification. Please refer to the OBO Format specification (http://oboformat.org) for more details.

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.

Furthermore, every instance of A has some distinguishing characteristics that none of the other instances of B have, that is, they should have some additional quality that distinguishes them from the more general type.

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.gif   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.


Among anatomical entities, this is a spatial relationship, implying that A exists within the space occupied by B. Among development stages, it is means that processes in stage A occurs as part of processes in stage B (e.g., embryo development stage part_of seed development stage in seed plants)

Examples:

  • ectocarp part_of pericarp
  • pericarp part_of fruit

has_part.gif   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.

Note that part_of and has_part are logically independent. Two terms may have one or the other or both relationships between each other.

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.gif   derives_by_manipulation_from

id: derives_by_manipulation_from

name: derives_by_manipulation_from

domain: in vitro plant structure

is_transitive: false????

This is a more specific case of the derives_from (RO:0001000) 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.gif   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.

Every instance of A either was once an instance of B (it is a transformation_of B) or inherited a significant portion of its matter from B (it derives_from B). The develops_from relation is more familiar to biologists than the transformation_of or derives_from relations and allows for situations in which it is uncertain if two entities are related by transformation or derivation.

Examples:

  • root hair cell develops_ from trichoblast

adjacent_to.gif   adjacent_to

id: adjacent_to

name: adjacent_to

xref: RO:0002220

is_transitive: false

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.

Every instance of A is spatially disjoint from but in permanent contact with some instance of B. Note that this is not a reciprocal relationship, so A adjacent_to B does not imply B adjacent_to A.

Examples:

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

participates_in.gif   participates_in

id: participates_in

name: participates_in

holds_over_chain: part_of participates_in

domain: continuant

range: occurent

is_transitive: false?

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.gif   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

(1) Every instance of A is a plant structure development stage and every instance of B is a plant anatomical entity and (2) Every instance of occurent A has some instance of continuant B as a participant.

located_in.gif   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. These will gradually be replaced by the more accurate located_in relation.


Example: see embryo sac (PO:0025074)


Preceded by.gif preceded_by

preceded_by OntoBee page

id: preceded_by

name: preceded_by

xref: BFO_0000062

domain: occurrent

range: occurrent

time: atemporal

transitive: yes


The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P.

An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C.

Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.source:

http://www.obofoundry.org/ro/#OBO_REL:preceded_by

Link to discussion on GitHub

Precedes.gif precedes

precedes OntoBee page

id: precedes

name: precedes

xref: BFO_0000063

domain: occurrent

range: occurrent

time: atemporal

transitive: yes

Note: precedes is the inverse of preceded_by

Example:

  • Each of the three later stages of plant embryo development: plant embryo true leaf formation stage (PO:0001095), plant embryo coleoptilar stage (PO:0001094), and plant embryo cotyledonary stage (PO:0001078) precedes mature plant embryo stage (PO:0001081), depending upon the taxa


Precedes example.png

see discussion on GitHub

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

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