twin composite
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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%3A R o R %3C S.
type: METAREL
is a: composite
name: twin composite

derives from
is a: is class related to
type: rel type
is type-instance of: transitive relation type
is type-instance of: all-some relation type
is transitive: true
name: derives from
definition:
  db xref:
    dbname: PMID
    acc: 15892874
  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%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'.
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%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.

is related to
name: is related to
type: rel type

is conjugate base of
is type-instance of: all-some relation type
type: rel type
is cyclic: true
is a: is class related to
name: is conjugate base of

has role
is a: is class related to
type: rel type
is type-instance of: all-some relation type
name: has role

is located in
type: rel type
is transitive: true
is a: is class related to
name: is located in
is type-instance of: all-some relation type
is type-instance of: transitive relation type

is part of
name: is part of
is type-instance of: all-some relation type
is type-instance of: reflexive relation type
is type-instance of: transitive relation type
type: rel type
is transitive: true
definition:
  db xref:
    dbname: PMID
    acc: 15892874
  def: 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.)
xref:
  acc: part_of
  dbname: OBO_REL
is a: is class related to
is reflexive: true

is in the vicinity of
name: is in the vicinity of
is type-instance of: transitive relation type
is type-instance of: all-some relation type
type: rel type
is a: is anatomically related to
xref:
  dbname: FBql
  acc: 00005862
is a: is class related to
is transitive: true

has second relation
name: has second relation
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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%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.
type: rel type
is a: is metarelated to

is posterior to
name: is posterior to
type: rel type
is type-instance of: transitive relation type
is type-instance of: all-some relation type
is transitive: true
is a: is anatomically related to
xref:
  acc: 00005864
  dbname: FBql
synonym:
  syn: caudal_to
  scope: EXACT
synonym:
  syn: is caudal to
  scope: EXACT
is a: is class related to

is disjoint from
name: is disjoint from
is a: is metarelated to
synonym:
  scope: BROAD
  db xref:
    acc: 0000018
    dbname: METAREL
  syn: disjoint from
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
type: rel type

is disjoint from
name: is disjoint from
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
synonym:
  scope: EXACT
  syn: disjoint from
is class level constructed from: is different from
is type-instance of: pure class relation type
type: METAREL
is a: is class related to

is related to
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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'.
name: is related to
type: METAREL

transitivity construct
name: transitivity construct
definition:
  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.
has second relation: transitive relation type
entails: transitivity composite
type: METAREL
is a: composite entailing construct

relation type
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
type: METAREL
name: relation type

db xref:
  dbname: METAREL
  acc: wb
def: 'Is same as' is an instance relation type which holds between any instance and itself, but not between two different instances.

is homologous to
name: is homologous to
is type-instance of: all-some relation type
type: rel type
is a: is similar to
is symmetric: true
definition:
  db xref:
    dbname: TAO
    acc: Curator
  def: 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.
is a: is class related to

is similar to
name: is similar to
type: rel type
is type-instance of: all-some relation type
is symmetric: true
is a: is class related to

reflexive relation type
name: reflexive relation type
definition:
  def: A relation type R is a reflexive relation type when A R A applies for all A in the domain of R.
  db xref:
    dbname: METAREL
    acc: wb
type: METAREL
is a: relation type

composite entailing construct
name: composite entailing construct
definition:
  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.
type: METAREL
is a: composite construct

participates in
name: participates in
is type-instance of: all-some relation type
is a: is class related to
type: rel type
xref:
  acc: participates_in
  dbname: OBO_REL

relevant relation type
name: relevant relation type
definition:
  def: 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.
  db xref:
    dbname: METAREL
    acc: wb
is a: relation type
type: METAREL

precedes
name: precedes
is type-instance of: transitive relation type
is type-instance of: all-some relation type
type: rel type
is transitive: true
xref:
  acc: precedes
  dbname: OBO_REL
is a: is class related to

is distal to
name: is distal to
type: rel type
is type-instance of: all-some relation type
is type-instance of: transitive relation type
is a: is anatomically related to
is transitive: true
xref:
  acc: 00005867
  dbname: FBql
is a: is class related to

composite
name: composite
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
type: METAREL
is a: composite construct

is paralogous to
is type-instance of: all-some relation type
is a: is homologous to
type: rel type
name: is paralogous to
is symmetric: true
is a: is class related to

negatively regulates
is type-instance of: all-some relation type
name: negatively regulates
type: rel type
is a: regulates
is a: is class related to

interacts with
is type-instance of: all-some relation type
type: rel type
xref:
  dbname: CCO_REL
  acc: interacts_with
is symmetric: true
definition:
  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'.
  db xref:
    dbname: CCO
    acc: ea
is a: is class related to
name: interacts with

surrounds
type: rel type
name: surrounds
is type-instance of: transitive relation type
is type-instance of: all-some relation type
is transitive: true
is a: is anatomically related to
xref:
  acc: 00005861
  dbname: FBql
is a: is class related to

is source of
is type-instance of: all-some relation type
name: is source of
type: rel type
xref:
  dbname: CCO_REL
  acc: source_of
definition:
  def: O is source_of o where O is an organism and o a gene or gene product.
  db xref:
    dbname: CCO
    acc: ea
is a: is class related to

composite construct
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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'.
type: METAREL
name: composite construct

is metarelated to
name: is metarelated to
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
type: rel type

is member of
type: rel type
comment: 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.
is type-instance of: transitive relation type
is type-instance of: all-some relation type
is transitive: true
name: is member of
is a: is class related to

develops from
is type-instance of: transitive relation type
is type-instance of: all-some relation type
type: rel type
is transitive: true
is a: is class related to
name: develops from

is anatomically related to
is type-instance of: all-some relation type
type: rel type
xref:
  dbname: FBql
  acc: 00005860
is a: is class related to
name: is anatomically related to

is associated with
type: rel type
name: is associated with
comment: This relationship is vague and up for discussion.
is type-instance of: all-some relation type
is symmetric: true
is a: is class related to

has quality
is type-instance of: all-some relation type
name: has quality
type: rel type
is a: is class related to

is type-instance of
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
type: rel type
name: is type-instance of
is a: is metarelated to

has position
type: rel type
is type-instance of: all-some relation type
name: has position
is a: is class related to

instance domain relation type
type: METAREL
is a: derivable instance relation type
name: instance domain relation type
definition:
  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.
  db xref:
    dbname: METAREL
    acc: wb

is orthogonal to
is type-instance of: all-some relation type
type: rel type
name: is orthogonal to
definition:
  db xref:
    dbname: BSPO
    acc: cjm
  def: crossing at right angles
is a: is class related to

has function
name: has function
is type-instance of: all-some relation type
is a: is class related to
type: rel type
definition:
  def: P has_function F where P is a protein and F a molecular function
  db xref:
    acc: ea
    dbname: CCO
xref:
  acc: has_function
  dbname: CCO_REL

role
type: METAREL
is a: instance relation type
definition:
  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.
  db xref:
    dbname: METAREL
    acc: wb
name: role

is dorsal to
synonym:
  syn: is superior to
  scope: EXACT
synonym:
  syn: superior_to
  scope: EXACT
xref:
  acc: 00005865
  dbname: FBql
is type-instance of: all-some relation type
is type-instance of: transitive relation type
is a: is anatomically related to
type: rel type
is a: is class related to
name: is dorsal to
is transitive: true

regulates
type: rel type
is type-instance of: all-some relation type
name: regulates
is a: is class related to

has part
is type-instance of: all-some relation type
is type-instance of: transitive relation type
name: has part
type: rel type
is transitive: true
xref:
  dbname: OBO_REL
  acc: has_part
is a: is class related to

all-some is-a construct
type: METAREL
name: all-some is-a construct
is a: composite entailing construct
definition:
  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 %3D%3D%3E beard 'is part of' human.
  db xref:
    dbname: METAREL
    acc: wb
has second relation: all-some relation type
entails: interchangeable priority composite

has origin
name: has origin
is type-instance of: all-some relation type
type: rel type
is a: is class related to

transitive-over composite
type: METAREL
name: transitive-over composite
is a: composite
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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%3A R o S %3C R.

has taxonomic rank
is type-instance of: all-some relation type
type: rel type
name: has taxonomic rank
is a: is class related to

is orthologous to
type: rel type
is type-instance of: all-some relation type
is symmetric: true
is a: is homologous to
name: is orthologous to
is a: is class related to

reflex relation type
type: METAREL
is a: derivable instance relation type
definition:
  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.
  db xref:
    dbname: METAREL
    acc: wb
name: reflex relation type

is proximal to
is type-instance of: transitive relation type
is type-instance of: all-some relation type
type: rel type
is a: is anatomically related to
name: is proximal to
is transitive: true
xref:
  acc: 00005868
  dbname: FBql
is a: is class related to

is anterior to
is type-instance of: all-some relation type
is type-instance of: transitive relation type
type: rel type
is a: is anatomically related to
synonym:
  syn: is rostral to
  scope: EXACT
synonym:
  syn: rostral_to
  scope: EXACT
is transitive: true
xref:
  dbname: FBql
  acc: 00005863
is a: is class related to
name: is anterior to

class domain relation type
type: METAREL
is a: class relation type
definition:
  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.
  db xref:
    dbname: METAREL
    acc: wb
name: class domain relation type

degradates into
is type-instance of: all-some relation type
type: rel type
synonym:
  syn: catabolises into
  scope: EXACT
synonym:
  syn: decomposes into
  scope: EXACT
xref:
  dbname: CCO_REL
  acc: degradates
definition:
  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.
  db xref:
    dbname: CCO
    acc: ea
name: degradates into
is a: is class related to
comment: NIL entity must be created.

is preceded by
is type-instance of: transitive relation type
is type-instance of: all-some relation type
type: rel type
name: is preceded by
is transitive: true
definition:
  def: 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.
  db xref:
    dbname: PMID
    acc: 15892874
is a: is class related to
comment: 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.

derivable instance relation type
type: METAREL
is a: instance relation type
definition:
  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.
  db xref:
    dbname: METAREL
    acc: wb
name: derivable instance relation type

is instance of
is type-instance of: instance-class relation type
xref:
  acc: instance_of
  dbname: OBO_REL
definition:
  db xref:
    dbname: METAREL
    acc: wb
  def: '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.
synonym:
  syn: instance of
  scope: EXACT
type: METAREL
name: is instance of
is a: is instance-class related to

is in association with
type: rel type
is type-instance of: all-some relation type
comment: 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.
name: is in association with
definition:
  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'.
  db xref:
    dbname: CCO
    acc: ea
xref:
  acc: association
  dbname: CCO_REL
is a: is class related to

is a variant of
type: rel type
is type-instance of: all-some relation type
name: is a variant of
definition:
  def: 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.
  db xref:
    dbname: SO
    acc: immuno_workshop
is a: is class related to

is substituent group from
is type-instance of: all-some relation type
name: is substituent group from
type: rel type
is a: is class related to

is a
type: rel type
synonym:
  syn: is subtype of
  scope: EXACT
xref:
  acc: is_a
  dbname: OBO_REL
xref:
  dbname: owl
  acc: subClassOf
definition:
  def: 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'.
  db xref:
    dbname: PMID
    acc: 15892874
is type-instance of: all-some relation type
is type-instance of: reflexive relation type
is type-instance of: transitive relation type
is transitive: true
name: is a
comment: The is_a relationship is considered axiomatic by the obo file format specification, and by OWL
is a: is class related to
is reflexive: true

has source
is type-instance of: all-some relation type
name: has source
is a: is class related to
xref:
  dbname: CCO_REL
  acc: has_source
definition:
  def: o has_source O where o is a gene or gene product and O an organism.
  db xref:
    acc: ea
    dbname: CCO
type: rel type

contains
is type-instance of: all-some relation type
is type-instance of: transitive relation type
type: rel type
is transitive: true
definition:
  db xref:
    dbname: PSI-MOD
    acc: ref
  def: 'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'.
name: contains
is a: is class related to
comment: The inverse relationship to "part of".

is contained in
xref:
  dbname: OBO_REL
  acc: contained_in
is type-instance of: all-some relation type
type: rel type
comment: 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
definition:
  db xref:
    acc: 15892874
    dbname: PMID
  def: 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.)
is a: is class related to
name: is contained in

has axis
type: rel type
is type-instance of: all-some relation type
is a: is class related to
name: has axis

is encoded by
is type-instance of: all-some relation type
type: rel type
synonym:
  syn: is coded by
  db xref:
    acc: ea
    dbname: CCO
  scope: EXACT
synonym:
  db xref:
    dbname: CCO
    acc: ea
  scope: EXACT
  syn: is produced by
definition:
  def: p is encoded by g where p is a Protein and g a Gene.
  db xref:
    acc: ea
    dbname: CCO
xref:
  dbname: CCO_REL
  acc: encoded_by
is a: is class related to
name: is encoded by

transitivity composite
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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%3A R o R %3C R.
type: METAREL
name: transitivity composite
is a: composite

entails
definition:
  db xref:
    dbname: METAREL
    acc: wb
  def: A composite entailing construct entails composites of a certain type.
name: entails
type: rel type
is a: is metarelated to

fixed complex composite
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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\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.
type: METAREL
is a: composite
name: fixed complex composite

interchangeable priority composite
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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%3A R o S %3C R or S o R %3C R.
type: METAREL
name: interchangeable priority composite
is a: composite

is adjacent to
is type-instance of: all-some relation type
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%3A nuclear membrane adjacent_to cytoplasm%3B seminal vesicle adjacent_to urinary bladder%3B ovary adjacent_to parietal pelvic peritoneum
type: rel type
definition:
  def: 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
  db xref:
    acc: 15892874
    dbname: PMID
name: is adjacent to
is a: is class related to

interchangeable complex composite
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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%3A R o S %3C T or S o R %3C T.
type: METAREL
name: interchangeable complex composite
is a: composite

is integral part of
is type-instance of: invertible relation type
is type-instance of: reflexive relation type
is type-instance of: transitive relation type
type: rel type
is a: is part of
is transitive: true
xref:
  acc: integral_part_of
  dbname: OBO_REL
definition:
  db xref:
    dbname: PMID
    acc: 15892874
  def: C integral_part_of C' if and only if%3A C part_of C' AND C' has_part C
name: is integral part of
is a: is class related to
is reflexive: true

pure class relation type
definition:
  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.
  db xref:
    dbname: METAREL
    acc: wb
type: METAREL
name: pure class relation type
is a: class relation type

instance relation type
name: instance relation type
definition:
  db xref:
    dbname: METAREL
    acc: wb
  def: Any relation type of which all the multi-arrows are between two instances is an instance relation type.
type: METAREL
is a: relation type

is conjugate acid of
is type-instance of: all-some relation type
name: is conjugate acid of
type: rel type
is cyclic: true
is a: is class related to

dbname: owl
acc: subClassOf

is class related to
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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
xref:
  dbname: OBO_REL
  acc: relationship
type: METAREL
name: is class related to
disjoint from: is instance related to
disjoint from: is instance-class related to
is a: is related to

is transformation of
type: rel type
name: is transformation of
is type-instance of: transitive relation type
is type-instance of: all-some relation type
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.
is transitive: true
definition:
  def: 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.
  db xref:
    dbname: PMID
    acc: 15892874
xref:
  acc: transformation_of
  dbname: OBO_REL
is a: is class related to

transitive relation type
definition:
  def: 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.
  db xref:
    dbname: METAREL
    acc: wb
type: METAREL
name: transitive relation type
is a: relation type

has agent
is type-instance of: all-some relation type
type: rel type
is a: has participant
xref:
  acc: has_agent
  dbname: OBO_REL
definition:
  db xref:
    dbname: PMID
    acc: 15892874
  def: As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
name: has agent
is a: is class related to

is position of
type: rel type
name: is position of
is type-instance of: all-some relation type
is a: is class related to

fixed priority composite
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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%3A R o S %3C S.
type: METAREL
name: fixed priority composite
is a: composite

catalyses
is type-instance of: all-some relation type
name: catalyses
type: rel type
definition:
  db xref:
    acc: ea
    dbname: CCO
  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.
xref:
  acc: catalyses
  dbname: CCO_REL
synonym:
  syn: activates
  scope: EXACT
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.
is a: is class related to

is agent in
type: rel type
is type-instance of: all-some relation type
is type-instance of: transitive relation type
is transitive: true
is a: participates in
xref:
  dbname: OBO_REL
  acc: agent_in
is a: is class related to
name: is agent in

positively regulates
is type-instance of: all-some relation type
type: rel type
is a: regulates
is a: is class related to
name: positively regulates

is opposite to
type: rel type
name: is opposite to
is type-instance of: all-some relation type
is a: is class related to

role based class relation type
definition:
  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'.
  db xref:
    dbname: METAREL
    acc: wb
type: METAREL
name: role based class relation type
is a: class relation type

is unit of
is type-instance of: all-some relation type
type: rel type
is a: is class related to
name: is unit of

is the location of
type: rel type
is type-instance of: transitive relation type
is type-instance of: all-some relation type
is transitive: true
xref:
  acc: location_of
  dbname: OBO_REL
name: is the location of
is a: is class related to

is class level constructed from
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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').
type: rel type
name: is class level constructed from
is a: is metarelated to

invertible relation type
definition:
  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.
  db xref:
    dbname: METAREL
    acc: wb
name: invertible relation type
type: METAREL
comment: A consequent name for 'invertible relation type' could be 'all-all relation type'.
is a: role based class relation type

is sequence of
is type-instance of: all-some relation type
type: rel type
name: is sequence of
is a: is class related to

transforms into
type: rel type
is type-instance of: all-some relation type
name: transforms into
xref:
  dbname: CCO_REL
  acc: transforms_into
is a: is class related to

is instance-class related to
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
type: METAREL
disjoint from: is class related to
disjoint from: is instance related to
name: is instance-class related to
is a: is related to

is derived into
is type-instance of: all-some relation type
is type-instance of: transitive relation type
type: rel type
is transitive: true
name: is derived into
xref:
  acc: derived_into
  dbname: OBO_REL
is a: is class related to

some-some relation type
definition:
  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.
  db xref:
    dbname: METAREL
    acc: wb
comment: The some-some relation type should be avoided in a good ontology design.
type: METAREL
name: some-some relation type
is a: role based class relation type

class relation type
definition:
  db xref:
    dbname: METAREL
    acc: wb
  def: Any relation type of which all the multi-arrows are between two classes is a class relation type.
type: METAREL
name: class relation type
is a: relation type

codes for
is type-instance of: all-some relation type
type: rel type
name: codes for
definition:
  db xref:
    acc: ea
    dbname: CCO
  def: g encodes for p where g a Gene and p is a Protein.
xref:
  dbname: CCO_REL
  acc: codes_for
synonym:
  syn: encodes
  db xref:
    acc: ea
    dbname: CCO
  scope: EXACT
is a: is class related to

is instance related to
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
type: METAREL
disjoint from: is class related to
disjoint from: is instance-class related to
is a: is related to
name: is instance related to

is non-functional homolog of
type: rel type
is type-instance of: all-some relation type
is a: is homologous to
name: is non-functional homolog of
definition:
  def: A relationship between a pseudogenic feature and its functional ancestor.
  db xref:
    acc: ke
    dbname: SO
is a: is class related to

is made of
is type-instance of: all-some relation type
name: is made of
type: rel type
is a: is class related to

has participant
type: rel type
is type-instance of: all-some relation type
definition:
  def: 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
  db xref:
    dbname: PMID
    acc: 15892874
is a: is class related to
name: has participant
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 different from
definition:
  def: 'Is different from' is an instance relation type holding between any two instances, but not between an instance and itself.
  db xref:
    dbname: METAREL
    acc: wb
is type-instance of: reflex relation type
type: METAREL
name: is different from
is a: is instance related to

all-some relation type
definition:
  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.
  db xref:
    dbname: METAREL
    acc: wb
name: all-some relation type
type: METAREL
is a: role based class relation type

has parent hydride
type: rel type
is type-instance of: all-some relation type
name: has parent hydride
is a: is class related to

is proper part of
is type-instance of: all-some relation type
is type-instance of: transitive relation type
type: rel type
is a: is part of
definition:
  db xref:
    acc: 15892874
    dbname: PMID
  def: As for part_of, with the additional constraint that subject and object are distinct
xref:
  acc: proper_part_of
  dbname: OBO_REL
is a: is class related to
is transitive: true
name: is proper part of

instance-class relation type
definition:
  db xref:
    dbname: METAREL
    acc: wb
  def: Any relation type of which all the multi-arrows are from an instance to a class is an instance-class relation type.
type: METAREL
name: instance-class relation type
is a: relation type

has functional parent
type: rel type
comment: This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent.
is type-instance of: all-some relation type
is type-instance of: transitive relation type
is transitive: true
name: has functional parent
definition:
  db xref:
    dbname: PSI-MOD
    acc: ref
  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.
is a: is class related to

is ventral to
is type-instance of: all-some relation type
is type-instance of: transitive relation type
type: rel type
is a: is anatomically related to
xref:
  acc: 00005866
  dbname: FBql
synonym:
  scope: EXACT
  syn: inferior_to
synonym:
  syn: is inferior to
  scope: EXACT
name: is ventral to
is a: is class related to
is transitive: true

has proper part
is type-instance of: transitive relation type
is type-instance of: all-some relation type
type: rel type
is a: has part
xref:
  acc: has_proper_part
  dbname: OBO_REL
is a: is class related to
is transitive: true
name: has proper part

is part of
is type-instance of: all-some relation type
type: rel type
is a: is class related to
name: is part of

is enantiomer of
is type-instance of: all-some relation type
name: is enantiomer of
type: rel type
is cyclic: true
is a: is class related to

has integral part
is type-instance of: invertible relation type
is type-instance of: transitive relation type
type: rel type
is a: has part
name: has integral part
xref:
  dbname: OBO_REL
  acc: has_integral_part
is a: is class related to
is transitive: true

is tautomer of
is type-instance of: all-some relation type
type: rel type
is cyclic: true
is a: is class related to
name: is tautomer of

is instance of
is type-instance of: all-some relation type
type: rel type
name: is instance of
definition:
  db xref:
    acc: 15892874
    dbname: PMID
  def: 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
xref:
  acc: instance_of
  dbname: OBO_REL
comment: 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 a: is class related to

is a
name: is a
is a: is metarelated to
synonym:
  scope: BROAD
  db xref:
    dbname: METAREL
    acc: 0000017
  syn: is_a
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
type: rel type

scope: EXACT
syn: same as

is class related to
is a: is related to
name: is class related to
type: rel type

db xref:
  dbname: METAREL
  acc: wb
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.

has resulting relation
is a: is metarelated to
name: has resulting relation
definition:
  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%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.
  db xref:
    dbname: METAREL
    acc: wb
type: rel type

syn: is_a
scope: EXACT

has first relation
is a: is metarelated to
type: rel type
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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%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.
name: has first relation

dbname: OBO_REL
acc: is_a

is inverse of
type: rel type
is a: is metarelated to
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.
synonym:
  scope: EXACT
  syn: inverse of
name: is inverse of

has transitive closure
type: rel type
is a: is metarelated to
name: has transitive closure
definition:
  db xref:
    dbname: METAREL
    acc: wb
  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.

scope: EXACT
syn: Is a