annotate test-data/relationship_id_vs_relationship_def.tab @ 0:b2471db454a0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6

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
association	C in association with C' produces C'' if and only if for all c belonging to C and c' belongin to C', exists a c'' (belonging to C'') which is the result of the reversible union between c and c'.
catalyses	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.
codes_for	g encodes for p where g a Gene and p is a Protein.
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.)
degradates	C is degradated (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.
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'.
encoded_by	p is encoded by g where p is a Protein and g a Gene.
has_agent	As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
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
has_source	o originates from O where o is a gene or gene product and O an organism.
improper_part_of	As for part_of, with the additional constraint that subject and object may be identical
integral_part_of	C integral_part_of C' if and only if: C part_of C' AND C' has_part C
interacts_with	C interacts_with C' if and only if for all c belonging to C, exists a c' (belonging to C') which plays a role with c'.
is_a	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'.
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.)
participates_in	C participates_in P if and only if: given any continuant c that instantiates C there is some process p, and some time t, such that: p has part c at t
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.)
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. 
proper_part_of	As for part_of, with the additional constraint that subject and object are distinct
relationship	A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances.
source_of	O source of o where O is an organism and o a gene or gene product.
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.