SWI-Prolog 5.8.1
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Show allShow sourcepathway_db.pro -- represents biological pathways

Synopsis

:- use_module(bio(pathway_db)).

%
demo:-
  nl.

Details

See exploring_pathways.txt

Additional Information

snapshot_continuant(E, Ref)
maps a state-specific snapshot of an entity (e.g. Hydron in the cytosol) to the endurant/continuant (e.g. Hydron)
snapshot_db_id(E, DB, ID)
composes snapshot_continuant/2 and entity_db_id/3
Example: (=)'|'snapshot_db_id(cdk2_nucleoplasm, 'UniProt', 'P12345')'|'=
Example: (=)'|'snapshot_db_id(H_cytosol, 'CHEBI', '12345')'|'=
entity_db_id(Ref, DB, ID)
deprecated
- ?
event(?E)
true if E is an event
atomic_event(?E)
true if E has no sub-events
preceded_by(P2, P1)
true if P2 is causally preceded_by P1
pathway_initiated_by(?P, ?E, ?E1)
E1 preceded_by E, E1 is in the P but E is not
event_catalyst(E, C, CI, Type)
should be renamed event_controller/4?
event_catalyst(E, C, CI)
as event_catalyst/4
event_catalyst(E, C)
as event_catalyst/4
event_input(E, M, Num:integer)
true if event E takes Num copies of M as input
event_input(E, C)
as event_input/2, without cardinality
event_input_molecule(?E, ?M)
composition of event_input/2 and has_leaf_part/2.

if E takes a complex as input, then this is true if M is a molecule snapshot and part_of that complex

event_output(E, C, Num:integer)
true if event E takes Num copies of M as output
event_output(E, C)
see event
event_output_molecule(?E, ?M)
composition of event_output/2 and has_leaf_part/2
event_participant_role(E, C, Role)
event_participating_continuant_roleT(?E, ?Cont, ?Role)
Cont participates in E (or a super-event of E) with role Role
subpathway_of(P, W)
includes reactions to pathways
pathway_overlaps(A, B)
pathways overlap if they have events in common. this includes as a degenerate case subpwathway_ofRT/2. note this predicate is reflexive
pathway_partial_overlaps(A, B)
as pathway_overlaps/2, with the additional constraint that neither pathway is part of the other
located_in(C, L)
corresponds to cellularLocation/2 relation between a snapshot and a continuant. The container is typically a cellular component.
molecule_modification(?Mol, ?Mod)
true if snapshot of molecule Mol is distinguished by modification Mod
modification_type(?Mod, ?Type)
Type will typically be a CHEBI class ID

Some typical types (and their labels):

Also: PubChem Compound:65396, GLYCAN:G12373

target_type(?Target, ?Type)
type will typically be a class ID from CHEBI. e.g. an amino acid
has_part(W, P, Num)
has_part(W, P)
has_partT(W, P)
transitive closure of has_partT/2
has_partRT(W, P)
reflexive transitive closure of has_partT/2
has_leaf_part(+W, ?Parts:set) is det
set of all leaf-nodes in the partonomy for W. this is locally reflexive for all leaf parts
part_of(?P, ?W)
inverse of has_part/2
part_ofT(?P, ?W)
transitive closure of part_of/2
transport(?Event, ?Slice1, ?Loc1, ?Slice2, ?Loc2, ?Continuant)
true if Event is a transportation reaction with Continuant as cargo. @param Event typically a reaction @param Slice1 4D instance of Continuant at beginning of process @param Loc1 start location @param Slice2 4D instance of Continuant at end of process @param Loc2 end location @param Continuant cargo (typically a reference entity such as CHEBI or GO)
transport(P, L1, L2, C)
as transport/6
transport_destination(?Event, ?Location)
see transport/6
transport_source(?Event, ?Location)
see transport/6
transport_cargo(?Event, ?Continuant)
see transport/6
transport_chain(?C, ?PL:list, ?LL:list)
true if C is a continuant which is passed along sequentially along the locations in LL via the events in PL

can take a long time to enumerate all solutions as there are many transport chains

Example: 

freeze(C,C\='http://www.reactome.org/biopax#H___ChEBI_15378_'),
  transport_chain(C,PL,L),length(L,Len),Len>4.

Undocumented predicates

The following predicates are exported, but not or incorrectly documented.

pathway_adjacent_to(Arg1, Arg2)
transformation(Arg1, Arg2, Arg3)
pathway_initiated_by(Arg1, Arg2)
autophosphorylation(Arg1)
self_catalyzing(Arg1, Arg2)
has_subeventRT(Arg1, Arg2)
has_leaf_parts(Arg1, Arg2)
has_subeventT(Arg1, Arg2)
subpathway_ofRT(Arg1, Arg2)
reaction_inputs_outputs(Arg1, Arg2, Arg3)
is_dna_region(Arg1)
is_rna_region(Arg1)
is_protein(Arg1)
is_small_molecule(Arg1)
pathway_adjacent_to(Arg1, Arg2, Arg3, Arg4)
results_in_binding_of(Arg1, Arg2)
event_participant_roleT(Arg1, Arg2, Arg3)
modification_target(Arg1, Arg2)
pathway_overlaps(Arg1, Arg2, Arg3)
pathway_partial_overlaps(Arg1, Arg2, Arg3)
pathway_starts_with(Arg1, Arg2)
dephosphorylation(Arg1, Arg2, Arg3)
self_catalyzing(Arg1)
has_subevent(Arg1, Arg2)
phosphorylation(Arg1, Arg2, Arg3)
subpathway_ofT(Arg1, Arg2)
event_chain(Arg1)
event_xref(Arg1, Arg2)
is_rna(Arg1)
is_complex(Arg1)
is_dna(Arg1)