This ontology contains logical relations to be shared across the different OBO ontologies. Each OBO ontology is free to extend this set with relations specific to the biology within that ontology

In the definitions, variables c, d, ..., p, q, ... range over instances of continuants and processes respectively. C, D, ..., P, Q, ... range over the corresponding classes

For a discussion of instance-level relations and also of additional axioms needed to infer transitivity and other properties of the relations listed above see http://genomebiology.com/2005/6/5/R46 or the OBO relations page hosted at http://obo.sourceforge.net/relationship

")
(instance OBO_REL-has_part Sowl-TransitiveProperty)
(instance OBO_REL-precedes Sowl-TransitiveProperty)
(instance OBO_REL-has_integral_part Sowl-TransitiveProperty)
(termFormat EnglishLanguage OBO_REL-has_part "has_part")
(documentation OBO_REL-preceded_by EnglishLanguage "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.")
(documentation EnglishLanguage "Version of OBO format.")
(termFormat EnglishLanguage OBO_REL-preceded_by "preceded_by")
(instance located Sowl-TransitiveProperty)
(termFormat EnglishLanguage location "location_of")
(termFormat EnglishLanguage "has_improper_part")
(mo-definition OBO_REL-contained_in ""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]")
(termFormat EnglishLanguage properPart "proper_part_of")
(documentation EnglishLanguage "General comments on the ontology.")
(mo-definition OBO_REL-derives_from ""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]")
(documentation EnglishLanguage "A namespace defined for use in the
ontology.")
(termFormat EnglishLanguage Smo-definedSubset "definedSubset")
(termFormat EnglishLanguage agent "agent_in")
(mo-savedBy "cjm")
(instance OBO_REL-derives_from Sowl-TransitiveProperty)
(termFormat EnglishLanguage Smo-Subset "Subset")
(termFormat EnglishLanguage OBO_REL-adjacent_to "adjacent_to")
(documentation OBO_REL-contained_in EnglishLanguage "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):")
(instance OBO_REL-participates_in BinaryRelation)
(domain Smo-inSubset 2 Smo-Subset)
(instance Smo-definedSubset BinaryRelation)
(instance location Sowl-TransitiveProperty)
(documentation Smo-inSubset EnglishLanguage "Declares a term/typedef
to be in a subset.")
(instance OBO_REL-has_part BinaryRelation)
(documentation EnglishLanguage "OBSOLETE. The definition is "As
for part_of, with the additional constraint that subject and object
may be identical". However, part_of is already reflexive,
therefore improper_part_of is identical to part_of. If read
differently, as "improper_part_of is part_of but not
proper_part_of",improper_part_of becomes identity. So,
improper_part_of is either identical to part_of or to identity, and
not an intuitive synonym for either of them. [Robert Hoehndorf]")
(mo-exactSynonym OBO_REL-is_a ""is_subtype_of" []")
(mo-definition OBO_REL-has_participant ""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]")
(mo-definition OBO_REL-integral_part_of ""C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [PMID:15892874]")
(instance OBO_REL-transformation_of Sowl-TransitiveProperty)
(instance properPart Sowl-TransitiveProperty)
(termFormat EnglishLanguage OBO_REL-is_a "is_a")
(documentation EnglishLanguage "Obsoleted")
(documentation EnglishLanguage "Date/time of last edit and save.")
(instance OBO_REL-has_agent BinaryRelation)
(termFormat EnglishLanguage OBO_REL-relationship "relationship")
(mo-defaultNamespace "relationship")
(mo-definition OBO_REL-relationship ""A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances." []")
(mo-definition instance ""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]")
(instance located BinaryRelation)
(owl-AnnotationProperty "null")
(termFormat EnglishLanguage located "located_in")