format-version: 1.2
date: 02:07:2008 11:23
saved-by: wablo
auto-generated-by: OBO-Edit 1.002
remark: Biometarel is a meta-ontology that gives a logical classification of relations in biomedical ontologies, not considering the semantics of the relations. The OBO ontology format is assumed for these onoloties. In genereal, the ontology format should consist of labeled nodes and labeled arrows between the nodes. These nodes can represent either classes or instances. The collection of all the arrows from a certain source-node to a certain target-node, is called a multi-arrow. The classification of the multi-arrows results in a role hierarchy, of which the classes are relation types. This classification is under 'is related to'. A meta-classification of relation types results in the relation type classification. This classification is under 'relation type'. Under 'composite' are constructs for the annotation of relation type compositions.

[Term]
id: METAREL:0000001
name: is related to
def: "'Is related to' is the root term in the relation multi-arrow classification. This classification corresponds with a role hierarchy in Description Logics. A relation multi-arrow is the collection of all the relation arrows that start in the same source-term and end in the same target-term. Hence, between two terms, there can be at most two relation multi-arrows, one per direction. \nA class of multi-arrows is a relation type. 'Is related to' is the name of such a class. A multi-arrow can be an instance of different relation types. Every instanciation of a relation type by the multi-arrow corresponds with a relation arrow. \nThe relation arrows are the asserted and visualised elements in ontologies. They are arrows that bear a label with the name of their corresponding relation type. In good ontologies often only one relation arrow, or none at all, are asserted per multi-arrow. 'Is related to' would not be asserted in a good ontology, although much multi-arrows can contain an arrow with the name of the relation type 'is related to'." [METAREL:wb]

[Term]
id: METAREL:0000002
name: relation type
def: "A relation type is a class of relation multi-arrows. Such a class can have properties like transitivity, symmetry, reflexivity, invertibility, compositionality with other relation types, and more. The relation types are instances in the relation type classification, and are classified on such properties. Hence, the class named 'relation type' is a meta-class, being a class of classes. All the subclasses of 'relation type' are also meta-classes." [METAREL:wb]

[Term]
id: METAREL:0000003
name: composite
def: "Three relation types r1, r2 and r3 (not necessarily all different) form a composite r1_r2_r3 if for all the triples of nodes a, b, c (all different) for which there is an arrow from a to b with the name of r1 and an arrow from b to c with the name of r2, there is also an arrow from a to c with the name of r3." [METAREL:wb]
is_a: METAREL:0000019 ! composite construct

[Term]
id: METAREL:0000004
name: is class related to
def: "A relation multi-arrow between two classes is an 'is class related to', if the multi-arrow is an instance of any class relation type.\n" [METAREL:wb]
xref: OBO_REL:relationship
is_a: METAREL:0000001 ! is related to
disjoint_from: METAREL:0000005 ! is instance-class related to
disjoint_from: METAREL:0000006 ! is instance related to

[Term]
id: METAREL:0000005
name: is instance-class related to
def: "A relation multi-arrow from an instance to a class is an 'is instance-class related to', if the multi-arrow is an instance of any instance-class relation type." [METAREL:wb]
is_a: METAREL:0000001 ! is related to
disjoint_from: METAREL:0000004 ! is class related to
disjoint_from: METAREL:0000006 ! is instance related to

[Term]
id: METAREL:0000006
name: is instance related to
def: "A relation multi-arrow between two instances is an 'is instance related to', if the multi-arrow is an instance of any instance relation type." [METAREL:wb]
is_a: METAREL:0000001 ! is related to
disjoint_from: METAREL:0000004 ! is class related to
disjoint_from: METAREL:0000005 ! is instance-class related to

[Term]
id: METAREL:0000007
name: class relation type
def: "Any relation type of which all the multi-arrows are between two classes is a class relation type." [METAREL:wb]
is_a: METAREL:0000002 ! relation type

[Term]
id: METAREL:0000008
name: instance-class relation type
def: "Any relation type of which all the multi-arrows are from an instance to a class is an instance-class relation type." [METAREL:wb]
is_a: METAREL:0000002 ! relation type

[Term]
id: METAREL:0000009
name: instance relation type
def: "Any relation type of which all the multi-arrows are between two instances is an instance relation type." [METAREL:wb]
is_a: METAREL:0000002 ! relation type

[Term]
id: METAREL:0000010
name: interchangeable complex composite
def: "The first, the second and the resulting relation type are all different. If the first and the second relation type change their positions, it still gives the same resulting relation type. E.g. 'is father of' + 'is grandfather of' results in 'is great-grandfather of'. In DL notation: R o S < T or S o R < T." [METAREL:wb]
is_a: METAREL:0000003 ! composite

[Term]
id: METAREL:0000011
name: interchangeable priority composite
def: "The resulting relation type is the same as the first or the second relation type, but the first and the second are different. If the first and the second relation type change their positions, it still gives the same resulting relation type. E.g. 'is part of' + 'is a' results in 'is part of' In DL notation: R o S < R or S o R < R." [METAREL:wb]
is_a: METAREL:0000003 ! composite

[Term]
id: METAREL:0000012
name: fixed complex composite
def: "The first, the second and the resulting relation type are all different.\nIf the first and the second relation type change their positions, then it does not give the same resulting relation type any longer. E.g. 'is brother of' + 'is father of' results in 'is uncle of'. In DL notation: R o S < T." [METAREL:wb]
is_a: METAREL:0000003 ! composite

[Term]
id: METAREL:0000013
name: fixed priority composite
def: "The resulting relation type is the same as the second relation type, but different from the first relation type. If the first and the second relation type change their positions, then it\ndoes not give the same resulting relation type any longer. E.g. 'is sibling of' + 'is child of' results in 'is child of'. In DL notation: R o S < S." [METAREL:wb]
is_a: METAREL:0000003 ! composite

[Term]
id: METAREL:0000014
name: transitivity composite
def: "The first, the second and the resulting relation type are all the same for a transitive composite, so this relation type is transitive. E.g. 'is ancestor of' + 'is ancestor of' results in 'is ancestor of'. In DL notation: R o R < R." [METAREL:wb]
is_a: METAREL:0000003 ! composite

[Term]
id: METAREL:0000015
name: twin composite
def: "The first and the second relation type are the same for a twin composite, but they differ from the resulting relation type E.g. 'is father of' + 'is father of' results in 'is grandfather of'. In DL notation: R o R < S." [METAREL:wb]
is_a: METAREL:0000003 ! composite

[Term]
id: METAREL:0000016
name: is instance of
def: "'Is instance of' is an instance-class relation type. For an instance i and a class A holds: 'i is instance of A' if i is an instance of the class A. In an ontology, classes are used to classify instances on the basis of properties the instances have. If an instance has the properties as defined by a class, than the instance is an instance of the class." [METAREL:wb]
synonym: "instance of" EXACT []
xref: OBO_REL:instance_of
is_a: METAREL:0000005 ! is instance-class related to
relationship: type_instance_of METAREL:0000008 ! instance-class relation type

[Term]
id: METAREL:0000017
name: is a
def: "'Is a' is a class relation type. A class A is a class B if and only if every instance of class A is also an instance of class B." [METAREL:wb]
synonym: "Is a" EXACT []
synonym: "is_a" EXACT []
xref: OBO_REL:is_a
xref: owl:subClassOf
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0000037 ! is same as
relationship: type_instance_of METAREL:0000021 ! pure class relation type
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type

[Term]
id: METAREL:0000018
name: is disjoint from
def: "'Is disjoint from' is a class relation type holding between any two disjoint classes. Two classes are disjoint if and only if they do not have any instance in common." [METAREL:wb]
synonym: "disjoint from" EXACT []
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0000038 ! is different from
relationship: type_instance_of METAREL:0000021 ! pure class relation type

[Term]
id: METAREL:0000019
name: composite construct
def: "A composite construct is used to build role inclusion axioms (RIA). E.g. the first relation 'is brother of' and the second relation 'is father of' result in 'is uncle of'." [METAREL:wb]

[Term]
id: METAREL:0000020
name: role based class relation type
def: "A role based class relation type is a class relation type of which the relation arrows represent one synthesized statement derived from the instance relation arrows of the corresponding instance relation type. E.g. if all the instances of the class 'leg' are part of one (or more) instances of the class 'body', we can derive the role based class relation arrow 'leg is part of body'. " [METAREL:wb]
is_a: METAREL:0000007 ! class relation type

[Term]
id: METAREL:0000021
name: pure class relation type
def: "A pure class relation type is a class relation type of which the relation arrows are not a synthesis of corresponding instance relation arrows. The relation arrows of a pure class relation type express statements about properties of the two involved classes, that are not inherited by the instances of the classes. E.g disjointness and union are properties of classes, not of instances. If something like has_more_instances_than would be a relation type, it would be a pure class relation type too." [METAREL:wb]
is_a: METAREL:0000007 ! class relation type

[Term]
id: METAREL:0000022
name: composite entailing construct
def: "A composite entailing construct entails many composites of the same type, being one of the seven composite types, from 'fixed complex composite' to 'twin composite'. It does so by relating three metaclasses of relation type, which can also be singleton metaclasses with only one relation type. It relates to the metaclasses with 'has first relation', 'has second relation' and 'has resulting relation', which deliver respectively the first relation types, the second relation types and the resulting relation types. It relates to the composite type with 'entails', which restricts the possible combinations of relation types by the definition of the composite type. " []
is_a: METAREL:0000019 ! composite construct

[Term]
id: METAREL:0000023
name: reflexive relation type
is_a: METAREL:0000002 ! relation type

[Term]
id: METAREL:0000024
name: transitive relation type
is_a: METAREL:0000002 ! relation type

[Term]
id: METAREL:0000025
name: transitivity construct
def: "Every transitive relation type  forms a transitivity_composite by occuring as the first relation type, the second relation type and the resulting relation type of the composite." []
is_a: METAREL:0000022 ! composite entailing construct
relationship: entails METAREL:0000014 ! transitivity composite
relationship: first_relation METAREL:0000024 ! transitive relation type
relationship: resulting_relation METAREL:0000024 ! transitive relation type
relationship: second_relation METAREL:0000024 ! transitive relation type

[Term]
id: METAREL:0000026
name: all-some relation type
def: "An all-some relation type is a role-based class relation type of which all the relation arrows should be total and are allowed to be not surjective.  A class relation arrow is total if all the instances of the source class have at least one corresponding instance relation arrow to the target class. It is surjective if all the instances from the target class recieve at least one corresponding instance relation arrow from the source class. E.g. 'tusk is part of animal' is a total arrow as every tusk is part of an animal. 'Animal has part tusk' is not total and therefore not allowed for an all-some relation type." [METAREL:wb]
is_a: METAREL:0000020 ! role based class relation type

[Term]
id: METAREL:0000027
name: invertible relation type
def: "An invertible relation type is a role-based class relation type of which all the class relation arrows should be total and surjective. A class relation arrow is total and surjective if there starts at least one corresponding instance relation arrow for every instance in the source class and if there arrives at least one corresponding instance relation arrow for every instance in the target class. E.g. 'tusk is integral part of elephant' is a total and surjective class relation arrow as every tusk is part of an elephant and for every elephant there is a tusk which is a part of the elephant. " [METAREL:wb]
comment: A consequent name for 'invertible relation type' could be 'all-all relation type'.
is_a: METAREL:0000020 ! role based class relation type

[Term]
id: METAREL:0000028
name: some-some relation type
def: "A some-some relation type is a role-based class relation type of which all the relation arrows are allowed to be not total and are allowed to be not surjective.  A class relation arrow is total if all the instances of the source class have at least one corresponding instance relation arrow to the target class. It is surjective if all the instances from the target class recieve at least one corresponding instance relation arrow from the source class. E.g. 'human eats pig' is a some-some relation arrow as some people do not eat pork, and not all pigs are cattle." [METAREL:wb]
comment: The some-some relation type should be avoided in a good ontology design.
is_a: METAREL:0000020 ! role based class relation type

[Term]
id: METAREL:0000029
name: all-some is-a construct
def: "Every all-some relation type has priority over the 'is a' relation type. 'Is part of' + 'is a' results in 'is part of'. 'Is a' + 'is part of' also results in 'is pa'Is related to'rt of'. E.g. beard 'is part of' man 'is a' human ==> beard 'is part of' human." [METAREL:wb]
is_a: METAREL:0000022 ! composite entailing construct
relationship: entails METAREL:0000011 ! interchangeable priority composite
relationship: first_relation METAREL:0000017 ! is a
relationship: resulting_relation METAREL:0000026 ! all-some relation type
relationship: second_relation METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0000030
name: role
def: "A role is an instance relation type that can only be asserted and validated by someone who has real world knowledge. It does not follow from logical definitions that relate to the knowledge base itself, but it models the reality with its exceptions." [METAREL:wb]
is_a: METAREL:0000009 ! instance relation type

[Term]
id: METAREL:0000031
name: instance domain relation type
def: "An instance domain relation type is an derivable instance relation type that is fully defined for an automatic reasoner by a domain and a range. E.g. if the instance domain relation type continuant_occurrent_instance_related_to is defined by the domain continuant and the range occurrent, than every continuant is continuant_occurrent_class_related_to every occurrent." [METAREL:wb]
is_a: METAREL:0000033 ! derivable instance relation type

[Term]
id: METAREL:0000032
name: class domain relation type
def: "A class domain relation type is a class relation type that is fully defined for an automatic reasoner by a domain and a range. E.g. if the class domain relation type 'is continuant-occurrent class related to' is defined by the domain continuant and the range occurrent, than every subclass of continuant 'is continuant-occurrent class related to' every subclass of occurrent." [METAREL:wb]
is_a: METAREL:0000007 ! class relation type

[Term]
id: METAREL:0000033
name: derivable instance relation type
def: "A derivable instance relation type is an instance relation type that is fully defined for an automatic reasoner. You do not need any real world knowledge to derive or validate the relation arrows." [METAREL:wb]
is_a: METAREL:0000009 ! instance relation type

[Term]
id: METAREL:0000034
name: reflex relation type
def: "A reflex relation type is a derivable instance relation type that is derivable by an automatic reasoner if it knows only whether the source and the target instance are the same or not." [METAREL:wb]
is_a: METAREL:0000033 ! derivable instance relation type

[Term]
id: METAREL:0000037
name: is same as
def: "'Is same as' is an instance relation type which holds between any instance and itself, but not between two different instances." [METAREL:wb]
synonym: "same as" EXACT []
is_a: METAREL:0000006 ! is instance related to
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000034 ! reflex relation type

[Term]
id: METAREL:0000038
name: is different from
def: "'Is different from' is an instance relation type holding between any two instances, but not between an instance and itself." [METAREL:wb]
is_a: METAREL:0000006 ! is instance related to
relationship: type_instance_of METAREL:0000034 ! reflex relation type

[Term]
id: METAREL:0000039
name: transitive-over composite
def: "The resulting relation type is the same as the first relation type, but different from the second relation type. If the first and the second relation type change their positions, then it\ndoes not give the same resulting relation type any longer. E.g. 'is brohter of' + 'is sister of' results in 'is brother of'. In DL notation: R o S < R." [METAREL:wb]
is_a: METAREL:0000003 ! composite

[Term]
id: METAREL:0010001
name: is adjacent to
def: "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" [PMID:15892874]
xref: OBO_REL:adjacent_to
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0010015 ! is adjacent to
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010002
name: is agent in
xref: OBO_REL:agent_in
is_a: METAREL:0010042 ! participates in
relationship: class_level_constructed_from METAREL:0010016 ! is agent in
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010003
name: is contained in
def: "C contained_in 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 located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)" [PMID:15892874]
comment: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation.    If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows:    c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t.    The containment relation on the instance level can then be defined (see definition):
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0010017 ! is contained in
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010004
name: contains
xref: OBO_REL:contains
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0010018 ! contains
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010005
name: is continuant-continuant related to
def: "'Is continuant-continuant related to' is a class domain relation type with continuant as domain and as range. It is the supertype of any possible class relation type that has continuant as domain and as range." [METAREL:wb]
is_a: METAREL:0000004 ! is class related to
disjoint_from: METAREL:0010006 ! is continuant-occurent related to
disjoint_from: METAREL:0010040 ! is occurent-continuant related to
relationship: class_level_constructed_from METAREL:0010019 ! is continuant-continuant related to
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000032 ! class domain relation type

[Term]
id: METAREL:0010006
name: is continuant-occurent related to
def: "'Is continuant-occurent related to' is a class domain relation type with continuant as domain and occurent as range. It is the supertype of any possible class relation type that has continuant as domain and occurent as range." [METAREL:wb]
is_a: METAREL:0000004 ! is class related to
disjoint_from: METAREL:0010005 ! is continuant-continuant related to
disjoint_from: METAREL:0010040 ! is occurent-continuant related to
relationship: class_level_constructed_from METAREL:0010020 ! is continuant-occurent related to
relationship: type_instance_of METAREL:0000032 ! class domain relation type

[Term]
id: METAREL:0010007
name: is derived into
xref: OBO_REL:derived_into
is_a: METAREL:0010005 ! is continuant-continuant related to
relationship: class_level_constructed_from METAREL:0010021 ! is derived into
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010008
name: derives from
def: "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'." [PMID:15892874]
comment: Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it 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. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
synonym: "derived_from" EXACT []
xref: OBO_REL:derives_from
is_a: METAREL:0010005 ! is continuant-continuant related to
relationship: class_level_constructed_from METAREL:0010022 ! derives from
relationship: type_instance_of METAREL:0000024 ! transitive relation type

[Term]
id: METAREL:0010009
name: derives immediately from
def: "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'." [PMID:15892874]
xref: PMID:15892874
is_a: METAREL:0010008 ! derives from
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010010
name: has agent
def: "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process" [PMID:15892874]
xref: OBO_REL:has_agent
is_a: METAREL:0010013 ! has participant
relationship: class_level_constructed_from METAREL:0010024 ! has agent
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010011
name: has integral part
xref: OBO_REL:has_integral_part
is_a: METAREL:0010012 ! has part
relationship: class_level_constructed_from METAREL:0010025 ! has part
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000027 ! invertible relation type

[Term]
id: METAREL:0010012
name: has part
xref: OBO_REL:has_part
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0010025 ! has part
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010013
name: has participant
def: "P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t" [PMID:15892874]
comment: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
xref: OBO_REL:has_participant
is_a: METAREL:0010040 ! is occurent-continuant related to
relationship: class_level_constructed_from METAREL:0010026 ! has participant
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010014
name: has proper part
xref: OBO_REL:has_proper_part
is_a: METAREL:0010012 ! has part
relationship: class_level_constructed_from METAREL:0010027 ! has proper part
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010015
name: is adjacent to
is_a: METAREL:0000006 ! is instance related to
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010016
name: is agent in
is_a: METAREL:0010032 ! participates in
relationship: METAREL:inverse_of METAREL:0010024 ! has agent
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010017
name: is contained in
is_a: METAREL:0000006 ! is instance related to
relationship: METAREL:inverse_of METAREL:0010018 ! contains
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010018
name: contains
is_a: METAREL:0000006 ! is instance related to
relationship: METAREL:inverse_of METAREL:0010017 ! is contained in
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010019
name: is continuant-continuant related to
def: "'Is continuant-continuant related to' is an instance domain relation type with continuant as domain and as range. It is the supertype of any possible instance relation type that has continuant as domain and as range." [METAREL:wb]
is_a: METAREL:0000006 ! is instance related to
disjoint_from: METAREL:0010020 ! is continuant-occurent related to
disjoint_from: METAREL:0010030 ! is occurent-continuant related to
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000031 ! instance domain relation type

[Term]
id: METAREL:0010020
name: is continuant-occurent related to
def: "'Is continuant-occurent related to' is an instance domain relation type with continuant as domain and occurent as range. It is the supertype of any possible instance relation type that has continuant as domain and occurent as range." [METAREL:wb]
is_a: METAREL:0000006 ! is instance related to
disjoint_from: METAREL:0010019 ! is continuant-continuant related to
disjoint_from: METAREL:0010030 ! is occurent-continuant related to
relationship: type_instance_of METAREL:0000031 ! instance domain relation type

[Term]
id: METAREL:0010021
name: is derived into
is_a: METAREL:0010019 ! is continuant-continuant related to
relationship: METAREL:inverse_of METAREL:0010022 ! derives from
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010022
name: derives from
is_a: METAREL:0010019 ! is continuant-continuant related to
relationship: METAREL:inverse_of METAREL:0010021 ! is derived into
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010023
name: derives immediately from
is_a: METAREL:0010022 ! derives from
relationship: has_transitive_closure METAREL:0010022 ! derives from
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010024
name: has agent
is_a: METAREL:0010026 ! has participant
relationship: METAREL:inverse_of METAREL:0010016 ! is agent in
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010025
name: has part
is_a: METAREL:0000006 ! is instance related to
relationship: METAREL:inverse_of METAREL:0010031 ! is part of
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010026
name: has participant
is_a: METAREL:0010030 ! is occurent-continuant related to
relationship: METAREL:inverse_of METAREL:0010032 ! participates in
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010027
name: has proper part
is_a: METAREL:0010025 ! has part
relationship: METAREL:inverse_of METAREL:0010035 ! is proper part of
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010028
name: is located in
is_a: METAREL:0010019 ! is continuant-continuant related to
relationship: METAREL:inverse_of METAREL:0010029 ! is location of
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010029
name: is location of
is_a: METAREL:0010019 ! is continuant-continuant related to
relationship: METAREL:inverse_of METAREL:0010028 ! is located in
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010030
name: is occurent-continuant related to
def: "'Is occurent-continuant related to' is an instance domain relation type with occurent as domain and continuant as range. It is the supertype of any possible instance relation type that has occurent as domain and continuant as range." [METAREL:wb]
is_a: METAREL:0000006 ! is instance related to
disjoint_from: METAREL:0010019 ! is continuant-continuant related to
disjoint_from: METAREL:0010020 ! is continuant-occurent related to
relationship: type_instance_of METAREL:0000031 ! instance domain relation type

[Term]
id: METAREL:0010031
name: is part of
is_a: METAREL:0000006 ! is instance related to
relationship: METAREL:inverse_of METAREL:0010025 ! has part
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010032
name: participates in
is_a: METAREL:0010020 ! is continuant-occurent related to
relationship: METAREL:inverse_of METAREL:0010026 ! has participant
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010033
name: is preceded by
is_a: METAREL:0000006 ! is instance related to
relationship: METAREL:inverse_of METAREL:0010034 ! precedes
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010034
name: precedes
is_a: METAREL:0000006 ! is instance related to
relationship: METAREL:inverse_of METAREL:0010033 ! is preceded by
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010035
name: is proper part of
is_a: METAREL:0010031 ! is part of
relationship: METAREL:inverse_of METAREL:0010027 ! has proper part
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010036
name: is transformation of
is_a: METAREL:0010019 ! is continuant-continuant related to
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010037
name: is integral part of
def: "C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [PMID:15892874]
xref: OBO_REL:integral_part_of
is_a: METAREL:0010041 ! is part of
relationship: class_level_constructed_from METAREL:0010031 ! is part of
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000027 ! invertible relation type

[Term]
id: METAREL:0010038
name: is located in
def: "C located_in 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 *located_in* c'. (Here *located_in* is the instance-level location relation.)" [PMID:15892874]
xref: OBO_REL:located_in
is_a: METAREL:0010005 ! is continuant-continuant related to
relationship: class_level_constructed_from METAREL:0010028 ! is located in
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010039
name: is location of
xref: OBO_REL:location_of
is_a: METAREL:0010005 ! is continuant-continuant related to
relationship: class_level_constructed_from METAREL:0010029 ! is location of
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010040
name: is occurent-continuant related to
def: "'Is occurent-continuant related to' is a class domain relation type with occurent as domain and continuant as range. It is the supertype of any possible class relation type that has occurent as domain and continuant as range." [METAREL:wb]
is_a: METAREL:0000004 ! is class related to
disjoint_from: METAREL:0010005 ! is continuant-continuant related to
disjoint_from: METAREL:0010006 ! is continuant-occurent related to
relationship: class_level_constructed_from METAREL:0010030 ! is occurent-continuant related to
relationship: type_instance_of METAREL:0000032 ! class domain relation type

[Term]
id: METAREL:0010041
name: is part of
def: "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.)" [PMID:15892874]
comment: Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception.    This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions.    For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t.    Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
synonym: "Part of" EXACT []
synonym: "part of" EXACT []
synonym: "part_of" EXACT []
xref: OBO_REL:part_of
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0010031 ! is part of
relationship: type_instance_of METAREL:0000023 ! reflexive relation type
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010042
name: participates in
xref: OBO_REL:participates_in
is_a: METAREL:0010006 ! is continuant-occurent related to
relationship: class_level_constructed_from METAREL:0010032 ! participates in
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010043
name: is preceded by
def: "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. " [PMID:15892874]
comment: 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.    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. 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.
xref: OBO_REL:preceded_by
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0010033 ! is preceded by
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010044
name: precedes
xref: OBO_REL:precedes
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0010034 ! precedes
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010045
name: is proper part of
def: "As for part_of, with the additional constraint that subject and object are distinct" [PMID:15892874]
xref: OBO_REL:proper_part_of
is_a: METAREL:0010041 ! is part of
relationship: class_level_constructed_from METAREL:0010035 ! is proper part of
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010046
name: is transformation of
def: "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2." [PMID:15892874]
comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
xref: OBO_REL:transformation_of
is_a: METAREL:0010005 ! is continuant-continuant related to
relationship: class_level_constructed_from METAREL:0010036 ! is transformation of
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010047
name: develops from
is_a: METAREL:0000006 ! is instance related to
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010048
name: develops from
synonym: "Develops from" EXACT []
synonym: "develops from" EXACT []
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0010047 ! develops from
relationship: type_instance_of METAREL:0000024 ! transitive relation type
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010049
name: negatively regulates
is_a: METAREL:0010053 ! regulates
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010050
name: negatively_regulates
is_a: METAREL:0010054 ! regulates
relationship: class_level_constructed_from METAREL:0010049 ! negatively regulates
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010051
name: positively regulates
is_a: METAREL:0010053 ! regulates
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010052
name: positively regulates
is_a: METAREL:0010054 ! regulates
relationship: class_level_constructed_from METAREL:0010051 ! positively regulates
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010053
name: regulates
is_a: METAREL:0000006 ! is instance related to
relationship: type_instance_of METAREL:0000030 ! role

[Term]
id: METAREL:0010054
name: regulates
is_a: METAREL:0000004 ! is class related to
relationship: class_level_constructed_from METAREL:0010053 ! regulates
relationship: type_instance_of METAREL:0000026 ! all-some relation type

[Term]
id: METAREL:0010055
name: located-in part-of construct
def: "Located_in has priority over part_of. A is located in C whenever A is located in B and B is part of C or A is part of B and B is located in C." [METAREL:wb]
is_a: METAREL:0000011 ! interchangeable priority composite
relationship: first_relation METAREL:0010038 ! is located in
relationship: resulting_relation METAREL:0010038 ! is located in
relationship: second_relation METAREL:0010041 ! is part of

[Typedef]
id: adjacent_to
name: is adjacent to
def: "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" [PMID:15892874]
comment: Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum
is_a: class_related_to ! is class related to

[Typedef]
id: agent_in
name: is agent in
xref: OBO_REL:agent_in
is_transitive: true
is_a: participates_in ! participates in
inverse_of: has_agent ! has agent

[Typedef]
id: associated_with
name: is associated with
comment: This relationship is vague and up for discussion.
is_symmetric: true
is_a: class_related_to ! is class related to

[Typedef]
id: association
name: is in association with
def: "C in association with C' produces C'' if and only if for all c belonging to C and c' belonging to C', exists a c'' (belonging to C'') which is the result of the reversible union between c and c'." [CCO:ea]
comment: Ternary relationship. See http://www.w3.org/TR/swbp-n-aryRelations/ for the OWL equivalent. The dissociation is a reversible splitting into simpler entities.
xref: CCO_REL:association
is_a: class_related_to ! is class related to

[Typedef]
id: BSPO:0000095
name: is anatomical related to
xref: FBql:00005860
is_a: class_related_to ! is class related to

[Typedef]
id: BSPO:0000096
name: is anterior to
synonym: "is rostral to" EXACT []
synonym: "rostral_to" EXACT []
xref: FBql:00005863
is_transitive: true
is_a: BSPO:0000095 ! is anatomical related to
inverse_of: BSPO:0000099 ! is posterior to

[Typedef]
id: BSPO:0000097
name: is distal to
xref: FBql:00005867
is_transitive: true
is_a: BSPO:0000095 ! is anatomical related to
inverse_of: BSPO:0000100 ! is proximal to

[Typedef]
id: BSPO:0000098
name: is dorsal to
synonym: "is superior to" EXACT []
synonym: "superior_to" EXACT []
xref: FBql:00005865
is_transitive: true
is_a: BSPO:0000095 ! is anatomical related to
inverse_of: BSPO:0000102 ! is ventral to

[Typedef]
id: BSPO:0000099
name: is posterior to
synonym: "caudal_to" EXACT []
synonym: "is caudal to" EXACT []
xref: FBql:00005864
is_transitive: true
is_a: BSPO:0000095 ! is anatomical related to
inverse_of: BSPO:0000096 ! is anterior to

[Typedef]
id: BSPO:0000100
name: is proximal to
xref: FBql:00005868
is_transitive: true
is_a: BSPO:0000095 ! is anatomical related to
inverse_of: BSPO:0000097 ! is distal to

[Typedef]
id: BSPO:0000101
name: surrounds
xref: FBql:00005861
is_transitive: true
is_a: BSPO:0000095 ! is anatomical related to

[Typedef]
id: BSPO:0000102
name: is ventral to
synonym: "inferior_to" EXACT []
synonym: "is inferior to" EXACT []
xref: FBql:00005866
is_transitive: true
is_a: BSPO:0000095 ! is anatomical related to
inverse_of: BSPO:0000098 ! is dorsal to

[Typedef]
id: BSPO:0000103
name: is in the vicinity of
xref: FBql:00005862
is_transitive: true
is_a: BSPO:0000095 ! is anatomical related to

[Typedef]
id: catalyses
name: catalyses
def: "C catalyses P if and only if for all c (catalyst) belonging to C, exists a p (belonging to P) which chemical reaction rate is increased by c." [CCO:ea]
comment: C inhibits P if and only if for all c (inhibitor) belonging to C, exists a p (belonging to P) which chemical reaction rate is reduced or prevented by c.
synonym: "activates" EXACT []
xref: CCO_REL:catalyses
is_a: class_related_to ! is class related to

[Typedef]
id: class_level_constructed_from
name: is class level constructed from
def: "A role-based class relation type is class level constructed from the corresponding instance relation type on which it is based. E.g. 'is part of' (like in 'leg is part of body') is class level constructed from the instance-'is part of' (like in 'Belgium is part of Europe')." [METAREL:wb]
is_a: metarelated_to ! is metarelated to

[Typedef]
id: class_related_to
name: is class related to
is_a: related_to ! is related to

[Typedef]
id: codes_for
name: codes for
def: "g encodes for p where g a Gene and p is a Protein." [CCO:ea]
synonym: "encodes" EXACT [CCO:ea]
xref: CCO_REL:codes_for
is_a: class_related_to ! is class related to

[Typedef]
id: contained_in
name: is contained in
def: "C contained_in 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 located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)" [PMID:15892874]
comment: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation.    If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows:    c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t.    The containment relation on the instance level can then be defined (see definition):
xref: OBO_REL:contained_in
is_a: class_related_to ! is class related to
inverse_of: contains ! contains

[Typedef]
id: contains
name: contains
def: "'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'." [PSI-MOD:ref]
comment: The inverse relationship to "part of".
is_transitive: true
is_a: class_related_to ! is class related to

[Typedef]
id: degradates
name: degradates into
def: "C degradates (into NIL) if and only if for all c belonging to C, exists c', c'', ... (belonging to C', C'', ...) which are the result of any undesired breakdown of c with impairment or loss of its characteristic properties." [CCO:ea]
comment: NIL entity must be created.
synonym: "catabolises into" EXACT []
synonym: "decomposes into" EXACT []
xref: CCO_REL:degradates
is_a: class_related_to ! is class related to

[Typedef]
id: derived_into
name: is derived into
xref: OBO_REL:derived_into
is_transitive: true
is_a: class_related_to ! is class related to
inverse_of: derives_from ! derives from

[Typedef]
id: derives_from
name: derives from
def: "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'." [PMID:15892874]
comment: Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it 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. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
is_transitive: true
is_a: class_related_to ! is class related to
inverse_of: derived_into ! is derived into

[Typedef]
id: develops_from
name: develops from
is_transitive: true
is_a: class_related_to ! is class related to

[Typedef]
id: encoded_by
name: is encoded by
def: "p is encoded by g where p is a Protein and g a Gene." [CCO:ea]
synonym: "is coded by" EXACT [CCO:ea]
synonym: "is produced by" EXACT [CCO:ea]
xref: CCO_REL:encoded_by
is_a: class_related_to ! is class related to

[Typedef]
id: entails
name: entails
def: "A composite entailing construct entails composites of a certain type." [METAREL:wb]
is_a: metarelated_to ! is metarelated to

[Typedef]
id: first_relation
name: has first relation
def: "'Has first relation' is a metarelation that relates a composite with a relation type. Consider the composite R_S_T, and the relation types R, S and T imply: if A is R-related to B and B is S-related to C, than A is T-related to C. Than R_S_T has first relation R." [METAREL:wb]
is_a: metarelated_to ! is metarelated to

[Typedef]
id: has_agent
name: has agent
def: "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process" [PMID:15892874]
xref: OBO_REL:has_agent
is_a: has_participant ! has participant
inverse_of: agent_in ! is agent in

[Typedef]
id: has_axis
name: has axis
is_a: class_related_to ! is class related to

[Typedef]
id: has_function
name: has function
def: "P has_function F where P is a protein and F a molecular function" [CCO:ea]
xref: CCO_REL:has_function
is_a: class_related_to ! is class related to

[Typedef]
id: has_functional_parent
name: has functional parent
def: "'Entity A' has_functional_parent 'Entity B' implies that 'Entity B' has at least one chacteristic group from which 'Entity A' can be derived by functional modification." [PSI-MOD:ref]
comment: This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent.
is_transitive: true
is_a: class_related_to ! is class related to

[Typedef]
id: has_integral_part
name: has integral part
xref: OBO_REL:has_integral_part
is_transitive: true
is_a: has_part ! has part

[Typedef]
id: has_origin
name: has origin
is_a: class_related_to ! is class related to

[Typedef]
id: has_parent_hydride
name: has parent hydride
is_a: class_related_to ! is class related to

[Typedef]
id: has_part
name: has part
xref: OBO_REL:has_part
is_transitive: true
is_a: class_related_to ! is class related to
inverse_of: part_of ! is part of

[Typedef]
id: has_participant
name: has participant
def: "P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t" [PMID:15892874]
comment: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
is_a: class_related_to ! is class related to
inverse_of: participates_in ! participates in

[Typedef]
id: has_position
name: has position
is_a: class_related_to ! is class related to

[Typedef]
id: has_proper_part
name: has proper part
xref: OBO_REL:has_proper_part
is_transitive: true
is_a: has_part ! has part
inverse_of: proper_part_of ! is proper part of

[Typedef]
id: has_quality
name: has quality
is_a: class_related_to ! is class related to

[Typedef]
id: has_rank
name: has taxonomic rank
is_a: class_related_to ! is class related to

[Typedef]
id: has_role
name: has role
is_a: class_related_to ! is class related to

[Typedef]
id: has_source
name: has source
def: "o has_source O where o is a gene or gene product and O an organism." [CCO:ea]
xref: CCO_REL:has_source
is_a: class_related_to ! is class related to

[Typedef]
id: has_transitive_closure
name: has transitive closure
def: "'Has transitive closure' is a metarelation between two relation types. A relation type R is the transitive closure of a relation type S if and only if \nR is transitive, \nS is a R, \nthere is no transitive relation type T, other than R, for which S is a T is a R. \nThen we have S has transitive closure R." [METAREL:wb]
is_a: metarelated_to ! is metarelated to

[Typedef]
id: homologous_to
name: is homologous to
def: "Instance 3-ary relation; continuant x in taxon A is homologous to continuant y in taxon B when both are genealogical descended from [the same entity] in their most common ancestor taxon C." [TAO:Curator]
is_symmetric: true
is_a: similar_to ! is similar to

[Typedef]
id: instance_of
name: is instance of
def: "A relation between an instance and a class. For components: a primitive relation between a component instance and a class which it instantiates at a specific time. For processes: a primitive relation, between a process instance and a class which it instantiates, holding independently of time" [PMID:15892874]
comment: The instance_of relationship is considered axiomatic by the obo file format specification; ie it is taken for granted. The is_a relation is still included in this ontology for completeness
xref: OBO_REL:instance_of
is_a: related_to ! is related to

[Typedef]
id: integral_part_of
name: is integral part of
def: "C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [PMID:15892874]
xref: OBO_REL:integral_part_of
is_transitive: true
is_a: part_of ! is part of

[Typedef]
id: interacts_with
name: interacts with
def: "C interacts_with C' if and only if for all c belonging to C, exists a c' (belonging to C') which plays a role with c'." [CCO:ea]
xref: CCO_REL:interacts_with
is_symmetric: true
is_transitive: true
is_a: class_related_to ! is class related to

[Typedef]
id: is_a
name: is a
def: "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'." [PMID:15892874]
comment: The is_a relationship is considered axiomatic by the obo file format specification, and by OWL
synonym: "is subtype of" EXACT []
xref: OBO_REL:is_a
xref: owl:subClassOf
is_transitive: true
is_a: class_related_to ! is class related to

[Typedef]
id: is_conjugate_acid_of
name: is conjugate acid of
is_cyclic: true
is_a: class_related_to ! is class related to

[Typedef]
id: is_conjugate_base_of
name: is conjugate base of
is_cyclic: true
is_a: class_related_to ! is class related to

[Typedef]
id: is_enantiomer_of
name: is enantiomer of
is_cyclic: true
is_a: class_related_to ! is class related to

[Typedef]
id: is_part_of
name: is part of
is_a: class_related_to ! is class related to

[Typedef]
id: is_substituent_group_from
name: is substituent group from
is_a: class_related_to ! is class related to

[Typedef]
id: is_tautomer_of
name: is tautomer of
is_cyclic: true
is_a: class_related_to ! is class related to

[Typedef]
id: located_in
name: is located in
is_transitive: true
is_a: class_related_to ! is class related to

[Typedef]
id: location_of
name: is the location of
xref: OBO_REL:location_of
is_transitive: true
is_a: class_related_to ! is class related to
inverse_of: located_in ! is located in

[Typedef]
id: made_of
name: is made of
is_a: class_related_to ! is class related to

[Typedef]
id: member_of
name: is member of
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
is_transitive: true
is_a: class_related_to ! is class related to

[Typedef]
id: METAREL:inverse_of
name: is inverse of
def: "Relation type A is the inverse of relation type B if for every relation multi-arrow that is an instance of A, the relation multi-arrow in the opposite direction is an instance of B." [METAREL:wb]
synonym: "inverse of" EXACT []
is_a: metarelated_to ! is metarelated to

[Typedef]
id: metarelated_to
name: is metarelated to
def: "An 'is metarelated to' is a construct that relates relation types (the instances of the relation type classification), that have logic connections with each other." [METAREL:wb]

[Typedef]
id: negatively_regulates
name: negatively regulates
is_a: regulates ! regulates

[Typedef]
id: non_functional_homolog_of
name: is non-functional homolog of
def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
is_a: homologous_to ! is homologous to

[Typedef]
id: opposite_to
name: is opposite to
is_a: class_related_to ! is class related to

[Typedef]
id: orthogonal_to
name: is orthogonal to
def: "crossing at right angles" [BSPO:cjm]
is_a: class_related_to ! is class related to

[Typedef]
id: orthologous_to
name: is orthologous to
is_symmetric: true
is_a: homologous_to ! is homologous to

[Typedef]
id: paralogous_to
name: is paralogous to
is_symmetric: true
is_a: homologous_to ! is homologous to

[Typedef]
id: part_of
name: is part of
def: "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.)" [PMID:15892874]
xref: OBO_REL:part_of
is_transitive: true
is_a: class_related_to ! is class related to
inverse_of: has_part ! has part

[Typedef]
id: participates_in
name: participates in
xref: OBO_REL:participates_in
is_a: class_related_to ! is class related to
inverse_of: has_participant ! has participant

[Typedef]
id: position_of
name: is position of
is_a: class_related_to ! is class related to

[Typedef]
id: positively_regulates
name: positively regulates
is_a: regulates ! regulates

[Typedef]
id: preceded_by
name: is preceded by
def: "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. " [PMID:15892874]
comment: 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.    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. 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.
is_transitive: true
is_a: class_related_to ! is class related to
inverse_of: precedes ! precedes

[Typedef]
id: precedes
name: precedes
xref: OBO_REL:precedes
is_transitive: true
is_a: class_related_to ! is class related to
inverse_of: preceded_by ! is preceded by

[Typedef]
id: proper_part_of
name: is proper part of
def: "As for part_of, with the additional constraint that subject and object are distinct" [PMID:15892874]
xref: OBO_REL:proper_part_of
is_transitive: true
is_a: part_of ! is part of
inverse_of: has_proper_part ! has proper part

[Typedef]
id: regulates
name: regulates
is_a: class_related_to ! is class related to

[Typedef]
id: related_to
name: is related to

[Typedef]
id: relational_disjoint_from
name: is disjoint from
def: "Relation type A is disjoint from relation type B if for every relation multi-arrow that is an instance of A, the relation multi-arrow is not an instance of B." [METAREL:wb]
synonym: "disjoint from" BROAD [METAREL:0000018]
is_a: metarelated_to ! is metarelated to

[Typedef]
id: relational_is_a
name: is a
def: "Relation type A relational is a relation type B if for every relation multi-arrow that is an instance of A, the relation multi-arrow is also an instance of B." [METAREL:wb]
synonym: "is_a" BROAD [METAREL:0000017]
is_a: metarelated_to ! is metarelated to

[Typedef]
id: resulting_relation
name: has resulting relation
def: "'Has resulting relation' is a metarelation that relates a composite with a relation type. Consider the composite R_S_T, and the relation types R, S and T imply: if A is R-related to B and B is S-related to C, than A is T-related to C. Than R_S_T has resulting relation T." [METAREL:wb]
is_a: metarelated_to ! is metarelated to

[Typedef]
id: second_relation
name: has second relation
def: "'Has second relation' is a metarelation that relates a composite with a relation type. Consider the composite R_S_T, and the relation types R, S and T imply: if A is R-related to B and B is S-related to C, than A is T-related to C. Than R_S_T has second relation S." [METAREL:wb]
is_a: metarelated_to ! is metarelated to

[Typedef]
id: sequence_of
name: is sequence of
is_a: class_related_to ! is class related to

[Typedef]
id: similar_to
name: is similar to
is_symmetric: true
is_a: class_related_to ! is class related to

[Typedef]
id: source_of
name: is source of
def: "O is source_of o where O is an organism and o a gene or gene product." [CCO:ea]
xref: CCO_REL:source_of
is_a: class_related_to ! is class related to

[Typedef]
id: transformation_of
name: is transformation of
def: "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2." [PMID:15892874]
comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
xref: OBO_REL:transformation_of
is_transitive: true
is_a: class_related_to ! is class related to

[Typedef]
id: transforms_into
name: transforms into
xref: CCO_REL:transforms_into
is_a: class_related_to ! is class related to

[Typedef]
id: type_instance_of
name: is type-instance of
def: "'Is type-instance of' is a metarelation to indicate that a relation type is an instance of a metaclass in the relation type classification. E.g. 'is part of' 'is type-instance of' all-some relation type." [METAREL:wb]
is_a: metarelated_to ! is metarelated to

[Typedef]
id: unit_of
name: is unit of
is_a: class_related_to ! is class related to

[Typedef]
id: variant_of
name: is a variant of
def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop]
is_a: class_related_to ! is class related to