format-version: 1.2
date: 23:12:2008 15:31
saved-by: wablo
remark: Biorel consists of the Typedefs in Biometarel that correspond with biomedical relation types that are actually used in the OBO Foundry.

[Typedef]
id: adjacent_to
name: is adjacent to
def: "C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity" [PMID:15892874]
comment: Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum

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

[Typedef]
id: associated_with
name: is associated with
comment: This relationship is vague and up for discussion.
is_symmetric: true

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

[Typedef]
id: BSPO:0000095
name: is anatomically related to
xref: FBql:00005860

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

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

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

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

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

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

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

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

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

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

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

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

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

[Typedef]
id: derived_into
name: is derived into
xref: OBO_REL:derived_into
is_transitive: true
inverse_of: derives_from ! derives from

[Typedef]
id: derives_from
name: derives from
def: "Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'." [PMID:15892874]
comment: Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
is_transitive: true
inverse_of: derived_into ! is derived into

[Typedef]
id: develops_from
name: develops from
is_transitive: true

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

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

[Typedef]
id: has_axis
name: has axis

[Typedef]
id: has_function
name: has function
def: "P has_function F where P is a protein and F a molecular function" [CCO:ea]
xref: CCO_REL:has_function

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

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

[Typedef]
id: has_origin
name: has origin

[Typedef]
id: has_parent_hydride
name: has parent hydride

[Typedef]
id: has_part
name: has part
xref: OBO_REL:has_part
is_transitive: true
inverse_of: part_of ! is part of

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

[Typedef]
id: has_position
name: has position

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

[Typedef]
id: has_quality
name: has quality

[Typedef]
id: has_rank
name: has taxonomic rank

[Typedef]
id: has_role
name: has role

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

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

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

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

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

[Typedef]
id: is_a
name: is a
def: "For continuants: C is_a C' if and only if: given any c that instantiates C at a time t, c instantiates C' at t. For processes: P is_a P' if and only if: that given any p that instantiates P, then p instantiates P'." [PMID:15892874]
comment: The is_a relationship is considered axiomatic by the obo file format specification, and by OWL
synonym: "is subtype of" EXACT []
xref: OBO_REL:is_a
xref: owl:subClassOf
is_reflexive: true
is_transitive: true

[Typedef]
id: is_conjugate_acid_of
name: is conjugate acid of
is_cyclic: true

[Typedef]
id: is_conjugate_base_of
name: is conjugate base of
is_cyclic: true

[Typedef]
id: is_enantiomer_of
name: is enantiomer of
is_cyclic: true

[Typedef]
id: is_part_of
name: is part of

[Typedef]
id: is_substituent_group_from
name: is substituent group from

[Typedef]
id: is_tautomer_of
name: is tautomer of
is_cyclic: true

[Typedef]
id: located_in
name: is located in
is_transitive: true

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

[Typedef]
id: made_of
name: is made of

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

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

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

[Typedef]
id: opposite_to
name: is opposite to

[Typedef]
id: orthogonal_to
name: is orthogonal to
def: "crossing at right angles" [BSPO:cjm]

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

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

[Typedef]
id: part_of
name: is part of
def: "For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)" [PMID:15892874]
xref: OBO_REL:part_of
is_reflexive: true
is_transitive: true
inverse_of: has_part ! has part

[Typedef]
id: participates_in
name: participates in
xref: OBO_REL:participates_in
inverse_of: has_participant ! has participant

[Typedef]
id: position_of
name: is position of

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

[Typedef]
id: preceded_by
name: is preceded by
def: "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. " [PMID:15892874]
comment: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C.    The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is_transitive: true
inverse_of: precedes ! precedes

[Typedef]
id: precedes
name: precedes
xref: OBO_REL:precedes
is_transitive: true
inverse_of: preceded_by ! is preceded by

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

[Typedef]
id: regulates
name: regulates

[Typedef]
id: sequence_of
name: is sequence of

[Typedef]
id: similar_to
name: is similar to
is_symmetric: true

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

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

[Typedef]
id: transforms_into
name: transforms into
xref: CCO_REL:transforms_into

[Typedef]
id: unit_of
name: is unit of

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