twin composite
is related to
is conjugate base of
A relevant relation type is a relation type that users of a knowledge base might need in their queries or in answers on queries. E.g. 'is related to' is not a relevant relation type.
'Is different from' is an instance relation type holding between any two instances, but not between an instance and itself.
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'.
is part of
is in the vicinity of
For continuants%3A C is_a C' if and only if%3A given any c that instantiates C at a time t, c instantiates C' at t. For processes%3A P is_a P' if and only if%3A that given any p that instantiates P, then p instantiates P'.
has second relation
is posterior to
is disjoint from
transitivity construct
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.
is homologous to
is similar to
p is encoded by g where p is a Protein and g a Gene.
reflexive relation type
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.
composite entailing construct
participates in
o has_source O where o is a gene or gene product and O an organism.
relevant relation type
precedes
is distal to
composite
is metarelated to
has function
has origin
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.
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.
'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%3A 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.
instance relation type
Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally%3A 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.
P has_function F where P is a protein and F a molecular function
is position of
is associated with
invertible relation type
is transformation of
This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent.
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%3A nuclear membrane adjacent_to cytoplasm%3B seminal vesicle adjacent_to urinary bladder%3B ovary adjacent_to parietal pelvic peritoneum
has source
is substituent group from
is made of
is a
C adjacent to C' if and only if%3A given any instance c that instantiates C at a time t, there is some c' such that%3A c' instantiates C' at time t and c and c' are in spatial proximity
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%3A R o S %3C R or S o R %3C R.
all-some is-a construct
is opposite to
The some-some relation type should be avoided in a good ontology design.
'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.
all-some relation type
'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'.
has part
Any relation type of which all the multi-arrows are from an instance to a class is an instance-class relation type.
catalyses
surrounds
is enantiomer of
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
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%3A R o S %3C T or S o R %3C T.
A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann%3A A taxonomy of part-whole relations. Cognitive Science 1987, 11%3A417-444.
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.
is conjugate acid of
is source of
negatively regulates
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.
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.
interchangeable priority composite
is class related to
A' is a variant (mutation) of A %3D 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.
is different from
instance domain relation type
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%3A R o S %3C R.
fixed priority composite
This relationship is vague and up for discussion.
has quality
is a variant of
'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%3A 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.
A relationship between a pseudogenic feature and its functional ancestor.
transitive-over composite
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\ndoes 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%3A R o S %3C T.
'Is instance of' is an instance-class relation type. For an instance i and a class A holds%3A '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.
derives from
entails
A consequent name for 'invertible relation type' could be 'all-all relation type'.
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'.
has position
P preceded_by P' if and only if%3A 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.
has integral part
Ternary relationship. See http%3A%2F%2Fwww.w3.org%2FTR%2Fswbp-n-aryRelations%2F for the OWL equivalent. The dissociation is a reversible splitting into simpler entities.
has resulting relation
Containment obtains in each case between material and immaterial continuants, for instance%3A lung contained_in thoracic cavity%3B 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%3A c1 overlap c2 at t %3Ddef 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)%3A
has parent hydride
O is source_of o where O is an organism and o a gene or gene product.
regulates
A relation type R is a reflexive relation type when A R A applies for all A in the domain of R.
is preceded by
is instance of
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.
is proximal to
relation type
is non-functional homolog of
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.
instance-class relation type
is paralogous to
'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.
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.
has first relation
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.
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.
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%3A R o R %3C R.
P has_participant C if and only if%3A given any process p that instantiates P there is some continuant c, and some time t, such that%3A c instantiates C at t and c participates in p at t
composite construct
A relation type R is a transitive relation type when A R B and B R C implies A R C, for all A,B and C in the domain of R.
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').
class relation type
has transitive closure
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%3A R o S %3C S.
The instance_of relationship is considered axiomatic by the obo file format specification%3B ie it is taken for granted. The is_a relation is still included in this ontology for completeness
is located in
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.
'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'.
is ventral to
codes for
is derived into
is orthogonal to
pure class relation type
transforms into
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.
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%3A osteocyte derives_from osteoblast. Formally%3A C derives_immediately_from C' if and only if%3A 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%3A there is an chain of immediate derivation relations connecting C to C'.
has taxonomic rank
'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%3A 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.
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.
is sequence of
class domain relation type
is in association with
has functional parent
is integral part of
is tautomer of
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.
'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.
C contained_in C' if and only if%3A given any instance c that instantiates C at a time t, there is some c' such that%3A 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.)
A relation between an instance and a class. For components%3A a primitive relation between a component instance and a class which it instantiates at a specific time. For processes%3A a primitive relation, between a process instance and a class which it instantiates, holding independently of time
is contained in
is dorsal to
degradates into
has agent
is adjacent to
is member of
'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.
'Is same as' is an instance relation type which holds between any instance and itself, but not between two different instances.
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.
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.
is class level constructed from
interchangeable complex composite
role based class relation type
has proper part
role
is the location of
transitivity composite
is anatomically related to
is orthologous to
The is_a relationship is considered axiomatic by the obo file format specification, and by OWL
develops from
g encodes for p where g a Gene and p is a Protein.
transitive relation type
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'.
'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.
contains
Any relation type of which all the multi-arrows are between two classes is a class relation type.
reflex relation type
is instance-class related to
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.
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'.
is type-instance of
is encoded by
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.
has role
derivable instance relation type
For continuants%3A C part_of C' if and only if%3A 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%3A P part_of P' if and only if%3A 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.)
As for part_of, with the additional constraint that subject and object are distinct
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.
A composite entailing construct entails composites of a certain type.
The inverse relationship to "part of".
is unit of
C integral_part_of C' if and only if%3A C part_of C' AND C' has_part C
is anterior to
has participant
is proper part of
Instance 3-ary relation%3B 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.
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.
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%3A 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.
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.
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.
is instance related to
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
has axis
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%3A R o R %3C S.
interacts with
An example is%3A translation preceded_by transcription%3B 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%3A 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%3B 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%3B 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.
some-some relation type
Any relation type of which all the multi-arrows are between two instances is an instance relation type.
positively regulates
NIL entity must be created.
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 %3D%3D%3E beard 'is part of' human.
is inverse of
fixed complex composite
is agent in