ro.obo file ro.obo ro.obo 17395b687a65719902e39e2920a598a2 1210988704 1210988707

1.2 cjm cjm relationship <p>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</p><div class="notes"><p>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</p><p> 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 <a href="http://genomebiology.com/2005/6/5/R46">http://genomebiology.com/2005/6/5/R46</a> or the OBO relations page hosted at <a href="http://obo.sourceforge.net/relationship">http://obo.sourceforge.net/relationship</a></div> cvs version $Revision: 1.1 $ release version 1.01

OBO_REL:is_a OBO_REL:0000001 is_a 1 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'. 15892874 PMID The is_a relationship is considered axiomatic by the obo file format specification. In the representation of obo in OWL, where obo terms are represented as OWL classes, is_a is mapped on to the subClassOf axiom is_subtype_of subClassOf owl 1 1 1 relationship OBO_REL:part_of OBO_REL:0000002 part_of 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.) 15892874 PMID 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. OBO_REL:has_part 1 1 1 relationship OBO_REL:has_part OBO_REL:0000003 has_part OBO_REL:part_of 1 1 1 relationship OBO_REL:integral_part_of OBO_REL:0000004 integral_part_of OBO_REL:part_of C integral_part_of C' if and only if: C part_of C' AND C' has_part C 15892874 PMID 1 1 1 relationship OBO_REL:has_integral_part OBO_REL:0000005 has_integral_part OBO_REL:has_part 1 1 1 relationship OBO_REL:proper_part_of OBO_REL:0000006 proper_part_of OBO_REL:part_of As for part_of, with the additional constraint that subject and object are distinct 15892874 PMID OBO_REL:has_proper_part 1 relationship OBO_REL:has_proper_part OBO_REL:0000007 has_proper_part OBO_REL:has_part OBO_REL:proper_part_of 1 relationship OBO_REL:located_in OBO_REL:0000008 located_in 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.) 15892874 PMID Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus OBO_REL:location_of 1 1 relationship OBO_REL:location_of OBO_REL:0000009 location_of OBO_REL:located_in 1 1 relationship OBO_REL:contained_in OBO_REL:0000010 contained_in OBO_REL:contains 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.) 15892874 PMID 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): relationship OBO_REL:contains OBO_REL:0000011 contains OBO_REL:contained_in relationship OBO_REL:adjacent_to OBO_REL:0000012 adjacent_to 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 15892874 PMID 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 1 relationship OBO_REL:transformation_of OBO_REL:0000013 transformation_of 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. 15892874 PMID 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. OBO_REL:develops_from 1 relationship OBO_REL:transformed_into OBO_REL:0000014 transformed_into Obsoleted 1 relationship OBO_REL:derives_from OBO_REL:0000015 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'. 15892874 PMID 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. derived_from OBO_REL:derived_into OBO_REL:develops_from 1 relationship OBO_REL:derived_into OBO_REL:0000016 derived_into OBO_REL:derives_from 1 relationship OBO_REL:preceded_by OBO_REL:0000017 preceded_by 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. 15892874 PMID 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. OBO_REL:precedes 1 relationship OBO_REL:precedes OBO_REL:0000018 precedes OBO_REL:preceded_by 1 relationship OBO_REL:has_participant OBO_REL:0000019 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 15892874 PMID 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. OBO_REL:participates_in relationship OBO_REL:participates_in OBO_REL:0000020 participates_in OBO_REL:has_participant relationship OBO_REL:has_agent OBO_REL:0000021 has_agent OBO_REL:has_participant As for has_participant, but with the additional condition that the component instance is causally active in the relevant process 15892874 PMID OBO_REL:agent_in relationship OBO_REL:agent_in OBO_REL:0000022 agent_in OBO_REL:participates_in OBO_REL:has_agent relationship OBO_REL:instance_of OBO_REL:0000023 instance_of 1 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 15892874 PMID 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 relationship OBO_REL:has_improper_part OBO_REL:0000024 has_improper_part OBSOLETE: See reasons for obsoletion of improper_part_of 1 1 1 relationship OBO_REL:improper_part_of OBO_REL:0000025 improper_part_of OBO_REL:part_of As for part_of, with the additional constraint that subject and object may be identical 15892874 PMID 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] OBO_REL:has_improper_part 1 1 1 relationship OBO_REL:inheres_in OBO_REL:0000026 inheres_in has_bearer A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation. cjm GOC 1 This relation links qualities, functions, dispositions and other dependent continuants to their bearers. Examples: A particular shape that inheres in a lung; The redness that ineres in a Drosophila eye; Catalytic activity function inheres_in catalytic molecule. Note that inherence is a functional relation: if x inheres_in y at t and x inheres_in z at t, then y=z. We leave open the possibility of a relation multiply_inheres_in, such as between a gene sequence and the multiple chromosomes it multiply inheres in. The super-relation of both inheres_in and multiply_inheres_in would be depends_on OBO_REL:bearer_of 1-01 change to specifically_inheres_in name of inverse relation? can dependent continuants inhere in occurrents? is inherence a functional relation? Do we need to distinguish between specific inherence (functional) and generic/multiple inherence (non-functional) relationship OBO_REL:bearer_of OBO_REL:0000027 bearer_of has_inherent has_inherer A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in cjm GOC Examples: red eye bearer_of redness OBO_REL:inheres_in relationship OBO_REL:quality_of OBO_REL:0000028 quality_of is_quality_of A relation between a quality Q and an entity E. Q quality_of E iff: Q inheres_in E and Q is a quality cjm GOC OBO_REL:inheres_in OBO_REL:has_quality 1-01 relationship OBO_REL:has_quality OBO_REL:0000029 has_quality A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality cjm GOC OBO_REL:bearer_of can occurrents have qualities? OBO_REL:quality_of 1-01 relationship OBO_REL:function_of OBO_REL:0000030 function_of A relation between a function F and an entity E. F function_of E iff: Q inheres_in E and Q is a function cjm GOC OBO_REL:inheres_in Example: 'to blood pump' function_of 'heart' OBO_REL:has_function relationship OBO_REL:has_function OBO_REL:0000031 has_function Relation between an independent continuant and a function. cjm GOC OBO_REL:bearer_of heart has_function to-pump-blood OBO_REL:function_of relationship OBO_REL:role_of OBO_REL:0000032 role_of A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role cjm GOC OBO_REL:inheres_in Example: 'to blood pump' function_of 'heart' OBO_REL:has_function relationship OBO_REL:has_role OBO_REL:0000033 has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. cjm GOC OBO_REL:bearer_of relationship OBO_REL:realizes OBO_REL:0000034 realizes Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation cjm GOC executes is_realization_of has_function_part OBO_REL:realized_by The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes 1-01 relationship OBO_REL:realized_by OBO_REL:0000035 realized_by Relation between a function and a process. Reciprocal relation of realizes cjm GOC executed_during has_realization OBO_REL:realizes 1-01 relationship OBO_REL:towards OBO_REL:0000036 towards A relation between a relational quality and an entity type. Q towards E iff: for any qQt, q towards E at t. cjm GOC with respect to directed to to depends_on in-use does this belong in an application ontology? In logical frameworks that support n-ary relations, this is an extra argument on the inherence relation (see Neuhaus paper, SQU). For frameworks with binary relations we need a way to indicate a linkage between the relational quality and the entity type it is directed 'towards' Examples: sensitivity towards chlorine; the PATO:concentration of a liquid with respect to some chemical entity type relationship OBO_REL:develops_from OBO_REL:0000038 develops_from A relation between two continuants, C and D. C develops_from D if C derived_from D or C transformation_of D. On the class level: C develops from D if and only if, for any x and any time t, the following holds: if x instantiates C at time t, then 1. either for some time t1, x instantiates D at t1 and t1 precedes t, and there is no time interval t2 such that x instantiates C at t2 and x instantiates D at t2 ; 2. or for some time t1 , there is some y such that y instantiates D at t1 and x derived_from y. On the instance level: x develops_from y is indistinguishable from x derives_from y cjm GOC Examples: eye develops_from eye disc; erythrocyte develops_from reticulocyte. Note that ontologies should use either derives_from or transformation_of where appropriate, but the develops_from relation can be used where one does not want to differentiate between these 2 cases 1 relationship OBO_REL:relationship relationship A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances. cjm GOC 1 this relation was superfluous, so it has been obsoleted relationship